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Animal models of ischemic stroke are procedures inducing cerebral ischemia. The aim is the study of basic processes or potential therapeutic interventions in this disease, and the extension of the pathophysiological knowledge on and/or the improvement of medical treatment of human ischemic stroke.
Ischemic stroke has a complex pathophysiology involving the interplay of many different cells and tissues such as neurons, glia, endothelium, and the immune system. These events cannot be mimicked satisfactorily in vitro yet. Thus a large portion of stroke research is conducted on animals.
== Overview ==
Several models in different species are currently known to produce cerebral ischemia[1]. Global ischemia models, both complete and incomplete, tend to be easier to perform. However, they are less immediately relevant to human stroke than the focal stroke models, because global ischemia is not a common feature of human stroke. However, in various settings global ischemia is also relevant, e.g. in global anoxic brain damage due to cardiac arrest. Different species also vary in their susceptibility to the various types of ischemic insults. An example is gerbils. They do not have a Circle of Willis and stroke can be induced by common carotid artery occlusion alone.
== Mechanisms of inducing ischemic stroke ==
Some of the mechanisms which have been used are:
Complete global ischemia
Decapitation
Aorta/vena cava occlusion
External neck tourniquet or cuff
Cardiac arrest
Incomplete global ischemia
Hemorrhage or hypotension
Hypoxic ischemia
Intracranial hypertension and common carotid artery occlusion
Two-vessel occlusion and hypotension
Four-vessel occlusion
Unilateral common carotid artery occlusion (in some species only)
Focal cerebral ischemia
Endothelin-1-induced constriction of arteries and veins
Middle cerebral artery occlusion
Spontaneous brain infarction (in spontaneously hypertensive rats)
Macrosphere embolization
Multifocal cerebral ischemia
Blood clot embolization
Microsphere embolization
Photothrombosis
== Hypoxic Ischemia models ==
One of the most commonly used animal models of hypoxic ischemia was originally described by Levine in 1960 and later refined by Rice et al., in 1981. This approach is useful to study hypoxic ischemia in the developing brain, since newborn rat pups are utilized in this model. Briefly, 7 day old rat pups undergo a permanent unilateral carotid artery ligation with a subsequent 3 hour exposure to a hypoxic environment (8% oxygen). This model creates a unilateral infarct in the hemisphere ipsilateral to the ligation, since the hypoxia alone is subthreshold for injury at this age. The area of injury is typically concentrated in periventricular regions of the brain, especially cortical and hippocampal areas.
== Focal ischemia models ==
They are divided into techniques including reperfusion of the ischemic tissue (transient focal cerebral ischemia) and those without reperfusion (permanent focal cerebral ischemia). The following models are established [2]:
Endothelin-1 -induced constriction of arteries and veins
Middle cerebral artery occlusion (MCAO)
MCAO avoiding craniotomy
Embolic middle cerebral artery occlusion
Endovascular filament middle cerebral artery occlusion (transient or permanent)
MCAO involving craniotomy
Permanent transcranial middle cerebral artery occlusion
Transient transcranial middle cerebral artery occlusion
Direct tissue damage
Cerebrocortical photothrombosis
=== Endothelin-1 -induced constriction of arteries and veins ===
Endothelin-1 is a potent vasoconstrictor which is produced endogenously during ischemic stroke and which contributes to overall loss of cells and disability. Exogenous endothelin-1 can also be used to induce stroke and cell death after sustained vasoconstriction with reperfusion. It can be microinjected to induce focal stroke in small tissue volumes (e.g., cortical grey matter, white matter or subcortical tissue) or after injection near the Middle cerebral artery. It is often used as a model of focal stroke to evaluate candidate pro-regenerative therapies. One advantage of this model of stroke is that it causes highly reproducible infarcts. Another benefit is that it can be used in elderly rats with only very low resulting mortality.
=== Embolic middle cerebral artery occlusion ===
Middle cerebral artery (MCA) occlusion is achieved in this model by injecting particles like blood clots (thrombembolic MCAO) or artificial spheres into the carotid artery of animals as an animal model of ischemic stroke. Thrombembolic MCAO is achieved either by injecting clots that were formed in vitro [3]or by endovascular instillation of thrombin for in situ clotting [4]. The thrombembolic model is closest to the pathophysiology of human cardioembolic stroke. When injecting spheres into the cerebral circulation, their size determines the pattern of brain infarction: Macrospheres (300–400 μm) induce infarcts similar to those achieved by occlusion of the proximal MCA [5], whereas microsphere (~ 50 μm) injection results in distal, diffuse embolism [6]. However, the quality of MCAO – and thus the volume of brain infarcts – is very variable, a fact which is further aggravated by a certain rate of spontaneous lysis of injected blood clots.
=== Endovascular filament middle cerebral artery occlusion ===
The technique of endovascular filament (intraluminal suture) MCAO as an animal model of ischemic stroke was described first by Koizumi [7]. It is applied to rats and mice. A piece of surgical filament is introduced into the internal carotid artery and forwarded until the tip occludes the origin of the middle cerebral artery, resulting in a cessation of blood flow and subsequent brain infarction in its area of supply. If the suture is removed after a certain interval, reperfusion is achieved (transient MCAO); if the filament is left in place the procedure is suitable as model of permanent MCAO, too. The most common modification is based on Longa (1989) [8] who described filament introduction via the external carotid artery, allowing closure of the access point with preserved blood supply via the common and internal carotid artery to the brain after the removal of the filament. Known pitfalls of this method are insufficient occlusion, subarachnoid hemorrhage [9], hyperthermia [10], and necrosis of the ipsilateral extracranial tissue [11]. Filament MCAO is not applicable to all rat strains [12].
=== Permanent transcranial middle cerebral artery occlusion ===
In this animal model of ischemic stroke the middle cerebral artery (MCA) is surgically dissected and subsequently permanently occluded, e.g. by electrocautery or ligation. Occlusion can be performed on the proximal [13] or distal [14] part of the MCA. In the latter, ischemic damage is restricted to the cerebral cortex. MCAO can be combined with temporal or permanent common carotid artery occlusion. These models require a small craniotomy.
=== Transient transcranial middle cerebral artery occlusion ===
The technique of modeling ischemic stroke by transient transcranial MCAO is similar to that of permanent transcranial MCAO, with the MCA being reperfused after a defined period of focal cerebral ischemia [15]. Like permanent MCAO, craniotomy is required and common carotid artery (CCA) occlusion can be combined. Occluding one MCA and both CCAs is referred to as the three vessel occlusion model of focal cerebral ischemia.
=== Cerebrocortical photothrombosis ===
Photothrombotic models of ischemic stroke use local intravascular photocoagulation of circumscribed cortical areas. After intravenous injection of photosensitive dyes like rose-bengal, the brain is irradiated through the skull via a small hole or a thinned cranial window, leading to photochemical occlusion of the irradiated vessels with secondary tissue ischemia [16]. This approach was initially proposed by Rosenblum and El-Sabban in 1977, and improved by Watson in 1985 in the rat brain. This method has also been adapted for use in mice.
== See also ==
animal models of stroke
== References ==
^ Beech, J. S.; S. C. Williams; C. A. Campbell; P. M. Bath; A. A. Parsons; A. J. Hunter; D. K. Menon (2001). "Further characterisation of a thromboembolic model of stroke in the rat". Brain Res. 895 (1–2): 18–24. doi:10.1016/S0006-8993(00)03331-X. PMID 11259755. S2CID 23949622.
^ Buchan, A. M.; D. Xue; A. Slivka (February 1, 1992). "A new model of temporary focal neocortical ischemia in the rat". Stroke. 23 (2): 273–9. CiteSeerX 10.1.1.328.5256. doi:10.1161/01.str.23.2.273. PMID 1561658.
^ Carmichael, S. T. (2005). "Rodent models of focal stroke: size, mechanism, and purpose". NeuroRx. 2 (3): 396–409. doi:10.1602/neurorx.2.3.396. PMC 1144484. PMID 16389304.
^ Chen, S. T.; C. Y. Hsu; E. L. Hogan; H. Maricq; J. D. Balentine (July 1, 1986). "A model of focal ischemic stroke in the rat: reproducible extensive cortical infarction". Stroke. 17 (4): 738–43. doi:10.1161/01.str.17.4.738. PMID 2943059.
^ Dittmar, M.; T. Spruss; G. Schuierer; M. Horn (2003). "External carotid artery territory ischemia impairs outcome in the endovascular filament model of middle cerebral artery occlusion in rats". Stroke. 34 (9): 2252–7. doi:10.1161/01.STR.0000083625.54851.9A. PMID 12893948.
^ Dittmar, M. S.; B. Vatankhah; N. P. Fehm; G. Schuierer; U. Bogdahn; M. Horn; F. Schlachetzki (2006). "Fischer-344 rats are unsuitable for the MCAO filament model due to their cerebrovascular anatomy". J Neurosci Methods. 156 (1–2): 50–4. doi:10.1016/j.jneumeth.2006.02.003. PMID 16530845. S2CID 25920789.
^ Gerriets, T.; F. Li; M. D. Silva; X. Meng; M. Brevard; C. H. Sotak; M. Fisher (2003). "The macrosphere model: evaluation of a new stroke model for permanent middle cerebral artery occlusion in rats". J Neurosci Methods. 122 (2): 201–11. doi:10.1016/S0165-0270(02)00322-9. PMID 12573479. S2CID 16433975.
^ Gerriets, T.; E. Stolz; M. Walberer; C. Muller; C. Rottger; A. Kluge; M. Kaps; M. Fisher; G. Bachmann (2004). "Complications and Pitfalls in Rat Stroke Models for Middle Cerebral Artery Occlusion: A Comparison Between the Suture and the Macrosphere Model Using Magnetic Resonance Angiography". Stroke. 35 (10): 2372–2377. doi:10.1161/01.STR.0000142134.37512.a7. PMID 15345802.
^ Graham, S.M; McCullough, L.D; Murphy, S.J (2004). "Animal Models of Ischemic Stroke: Balancing Experimental Aims and Animal Care" (PDF). Comp Med. 54 (5): 486–496. PMID 15575362. Archived from the original (PDF) on 2007-10-09.
^ Koizumi, J.; Y. Yoshida; T. Nakazawa; G. Ooneda (1986). "Experimental studies of ischemic brain edema. I: a new experimental model of cerebral embolism in rats in which recirculation can be introduced in the ischemic area". Jpn J Stroke. 8: 1–8. doi:10.3995/jstroke.8.1.
^ Longa, E. Z.; P. R. Weinstein; S. Carlson; R. Cummins (January 1, 1989). "Reversible middle cerebral artery occlusion without craniectomy in rats". Stroke. 20 (1): 84–91. doi:10.1161/01.str.20.1.84. PMID 2643202.
^ Mayzel-Oreg, O.; T. Omae; M. Kazemi; F. Li; M. Fisher; Y. Cohen; C. H. Sotak (2004). "Microsphere-induced embolic stroke: an MRI study". Magn Reson Med. 51 (6): 1232–8. doi:10.1002/mrm.20100. PMID 15170844.
^ Schmid-Elsaesser, R.; S. Zausinger; E. Hungerhuber; A. Baethmann; H. J. Reulen (October 1, 1989). "A critical reevaluation of the intraluminal thread model of focal cerebral ischemia: evidence of inadvertent premature reperfusion and subarachnoid hemorrhage in rats by laser-Doppler flowmetry". Stroke. 29 (10): 2162–70. doi:10.1161/01.str.29.10.2162. PMID 9756599.
^ Tamura, A.; D. I. Graham; J. McCulloch; G. M. Teasdale (1981). "Focal cerebral ischaemia in the rat: 1. Description of technique and early neuropathological consequences following middle cerebral artery occlusion". J Cereb Blood Flow Metab. 1 (1): 53–60. doi:10.1038/jcbfm.1981.6. PMID 7328138.
^ Watson, B. D.; W. D. Dietrich; R. Busto; M. S. Wachtel; M. D. Ginsberg (1985). "Induction of reproducible brain infarction by photochemically initiated thrombosis". Ann Neurol. 17 (5): 497–504. doi:10.1002/ana.410170513. PMID 4004172. S2CID 37827695.
^ Zhang, Z.; R. L. Zhang; Q. Jiang; S. B. Raman; L. Cantwell; M. Chopp (1997). "A new rat model of thrombotic focal cerebral ischemia". J Cereb Blood Flow Metab. 17 (2): 123–35. doi:10.1097/00004647-199702000-00001. PMID 9040491.
== References == | Wikipedia/Animal_models_of_ischemic_stroke |
Animal models of depression are research tools used to investigate depression and action of antidepressants. They are used as a simulation to investigate the symptomatology and pathophysiology of depressive illness and to screen novel antidepressants. These models provide insights into molecular, genetic, and epigenetic factors associated with depression. Criteria for valid animal models include face, construct, and predictive validity. Endophenotypes, such as anhedonia, behavioral despair, changes in appetite, neuroanatomical alterations, neuroendocrine disturbances, alterations in sleep architecture, and anxiety-related behaviors, are evaluated in these models. Antidepressant screening tests are employed to assess the effects of genetic, pharmacological, or environmental manipulations. Stress models including learned helplessness, chronic mild stress, and social defeat stress simulate the impact of stressors on depression. Early life stress models, psychostimulant withdrawal models, olfactory bulbectomy, and genetically engineered mice contribute to a comprehensive understanding of depression's etiology and potential therapeutic interventions.
== Introduction ==
=== Depression ===
Major depressive disorder is commonly called "clinical depression" or "depression." It is a common, long-lasting and diverse psychiatric syndrome that significantly affects a person's thoughts, behavior, feelings and sense of well-being. According to the DSM-5, someone diagnosed with depression should be showing at least five symptoms and they should last two weeks. Depression can include a variety of different symptoms and does not always look the same for everyone. Some of these symptoms may include sadness, anxiousness, emptiness, hopelessness, worry, helplessness, worthlessness, guilt, irritableness, hurt, or restlessness. People experiencing depression may also lose interest in activities that once were pleasurable, experience loss of appetite, overeat, have problems concentrating, remembering details, making decisions, and may contemplate or attempt suicide. Insomnia, excessive sleeping, fatigue, loss of energy, aches, pains, or digestive problems that are resistant to treatment may also be present.
=== Modeling depression in animals ===
It is difficult to develop an animal model that perfectly reproduces the symptoms of depression in patients. It is generic that 3 standards may be used to evaluate the reliability of an animal version of depression: the phenomenological or morphological appearances (face validity), a comparable etiology (assemble validity), and healing similarities (predictive validity). Many animals lack self-consciousness, self-reflection, and consideration; moreover, hallmarks of the disorder such as depressed mood, low self-esteem or suicidality are hardly accessible in non-humans. However, depression, as other mental disorders, consists of endophenotypes that can be reproduced independently and evaluated in animals. An ideal animal model offers an opportunity to understand molecular, genetic, and epigenetic factors that may lead to depression. By using animal models, the underlying molecular alterations and the causal relationship between genetic, or environmental, alterations and depression can be examined. This would afford a better insight into pathology of depression because animal models are indispensable for identifying novel therapies for depression.
=== Endophenotypes in animal model of depression ===
The following endophenotypes have been described:
Anhedonia: The loss of interest is a core symptom of depression. Anhedonia in rodents can be assessed by sucrose preference or by intracranial self-stimulation.
Behavioral despair: Behavioral despair might be assessed with tests such as the forced-swimming test or the tail suspension test.
Changes in appetite or weight gain: Depression is often associated with changes in appetite or weight gain, which is easily measured in rodents. There was a study done where the experimental group of mice had a suppressed feeding schedule; this resulted in the mice showing depressive-like symptoms.
Neuroanatomy: Depressed subjects display decreased hippocampal volume. Rodents exposed to chronic stress or excess glucocorticoids exhibit similar signs of hippocampal loss of neurons and dendritic atrophy.
Neuroendocrine disturbances: Disturbances of the hypothalamic–pituitary–adrenal axis (HPA) are one of the most consistent symptoms in major depression. The functionality of the HPA can be assessed by dexamethasone suppression test .
Alterations in sleep architecture: Disturbances in the circadian rhythm and especially in the sleep architecture are often observed in depression. In rodents, it is accessible via electroencephalography (EEG).
Anxiety-related behavior: Anxiety is a symptom with high prevalence in depression. Animal models of depression often display altered anxiety-related behavior.
=== Criteria for valid animal models of depression ===
An appropriate animal model of human depression should fulfill the following criteria as much as possible: strong phenomenological similarities and similar pathophysiology (face validity), comparable etiology (construct validity), and common treatment (predictive validity). Depression is a heterogeneous disorder and its many symptoms are hard to produce in laboratory animals. When studying depression used in animals originally, symptoms equivalent to odd social behavior and emotion were used to determine if the animal had depression. The question therefore remains whether we can know if the animal is "depressed". They are unable to have the emotions that are associated specifically with humans, like sadness. Few models of depression fully fit these validating criteria, and most models currently used rely on either actions of known antidepressants or responses to stress. It is not necessary for an "ideal" animal model of depression to exhibit all the abnormalities of depression-relevant behaviors, just as not all patients manifest every possible symptom of depression.
== Creating models ==
Research use a number of standardized ways to induce depression-like symptoms in lab animals. The most commonly used type of models are based on stress.
=== Stress models ===
Certain types of human depression are precipitated by stressful life events, and vulnerable individuals experiencing these stressors. Consequently, the majority of animal models of depression are based on the exposure to various types of acute or chronic stressors.
==== Adult stress models ====
Learned helplessness: The learned helplessness model (LH), one of the well validated animal models, is the best replicated one. The rationale is that exposure to uncontrollable and stressful life events makes people feel like they are losing control, and this sometimes leads to depressive like behaviors. The model is based on the observation that animals also develop deficits in escape, cognitive and rewarded behaviors when they have been subjected to repeated unavoidable and uncontrollable shocks. LH is induced in one day or over several days of repeated inescapable stress by the treating of tail shock or foot shock in shuttle boxes. Helpless behavior is evaluated by analyzing the performance in an active escape test, such as the latency to press a lever or cross a door. An advantage of LH is that the cognitive and other behavioral outcomes seem to be correlated, thus helping to understand the depressive symptomatology in humans. This model can also be generally used to measure the escape performance of mice with different mutations in which target genes of depression may affect the vulnerability to develop a depressive-like state. These excellent face and predictive validities make LH an interesting model to explore the pathophysiology of depression. The biggest disadvantage of LH is it requires very strong stressors to induce the behavioral phenotypes which does raise ethical problems. Also, most of the symptoms do not persist long enough following cessation of the uncontrollable shock.
Chronic mild stress: The chronic mild stress (CMS) model is probably the most valid animal model of depression. It aims to model a chronic depressive-like state that develops gradually over time in response to stress, and they can provide more natural induction. CMS involves the exposure of animals to a series of mild and unpredictable stressors (periods of food and water deprivation, small temperature reductions, changes of cage mates, and other similar individually innocuous manipulations) during at least 2 weeks. The model has been reported to result in long lasting changes of behavioral, neurochemical, neuroimmune, and neuroendocrinological variables. This resembles reward functions, that include decreased intracranial self-stimulation, and reflects anhedonia that is reversed by chronic, but not acute, antidepressant treatment. This CMS model can be used to screen and test potential antidepressant compounds and to develop new treatment strategies.The advantages of this model are its good predictive validity (behavioral changes are reversed by chronic treatment with a wide variety of antidepressants), face validity (almost all demonstrable symptoms of depression have been reproduced), and construct validity (CMS causes a generalized decrease in responsiveness to rewards). However, there is a common practical difficulty in carrying out CMS experiments, which are labor-intensive, demanding of space, and of long duration. The procedure can be difficult to be established and data can be hardly replicated.
Social defeat stress: Social defeat stress (SDS) is a chronic and recurring factor in the lives of virtually all higher animal species. Humans experiencing social defeat show increased symptoms of depression, loneliness, anxiety, social withdrawal and a loss of self-esteem. Since the majority of stress stimuli in humans that lead to psychopathological changes are of social nature, SDS model have gained increasing attention since they might render useful to study certain endophenotypes of depression. During the stress period, the male rodent will be introduced into a different territory of other males for each day as an intruder. This causes it to be investigated, attacked and defeated by the residents. The consequent behavior changes in the subject caused by SDS, like decreased social interaction or lack of interest, are similar to some parts of human depression. Behavioral treatment and antidepressants can reverse these changes in an SDS model.Like CMS, SDS has good predictive validity (behavioral changes are reversed by chronic treatment with a wide variety of antidepressants), face validity (many symptoms of depression have been reproduced), and construct validity (causing a generalized decrease in responsiveness to rewards). SDS gives another validity that only chronic, but not acute, antidepressant administration can reverse the social aversion. One disadvantage of SDS model is the long duration. To apply an SDS model for studying human depression, the period of it should last at least 20 days or only anxiety symptoms could be induced. Only male rodents can be used for this model, since female rodents do not fight each other in a resident–intruder confrontation.
==== Early life stress models ====
Early adverse experiences such as traumatic life events in childhood result in an increased sensitivity to the effects of stress later in life and influence the vulnerability to depression. Suitable animal models could provide a basis for understanding potential mechanisms of environmental and developmental factors of individual differences in stress reactivity and vulnerability to disorders. Models of early life stress involve prenatal stress, early postnatal handling and maternal separation. All these treatments have been demonstrated to produce significant effects that last until adulthood.
Maternal deprivation: The maternal deprivation model is the most widely used early life stress model. This model manipulates the maternal separation of early life deprivation, in which pups are separated from the dam for 1–24 h per day during the first two postnatal weeks. Maternal separation results in increased anxiety- and depression-like behaviors and increased HPA response in adulthood.
=== Other models ===
Olfactory bulbectomy: Removal of the olfactory bulb in rodents results in a disruption of the limbic-hypothalamic axis with the consequence of behavioral, neurochemical, neuroendocrine and neuroimmune changes. Many of these resemble changes seen in depressed patients. It is still not clear how bulbectomy in animals actually relates to depression in humans; it might simply result from a high intensity of chronic stressor caused by chronic sensory deprivation. This model shows high predictive validity as it mimics the slow onset of antidepressant action reported in clinical studies. It responds chronic, but not sub-chronic, antidepressant treatment and does not response to other drugs.
Psychostimulant withdrawal (amphetamine, cocaine): In humans, withdrawal from chronic psychostimulants generates symptoms that have strong behavioral and physiological parallels to depression. Therefore, the examination of the behavioral effects of drug withdrawal in rodents may provide insights into the underlying neurobiological mechanisms and aid in the development of animal models of depression that are sensitive to antidepressant agents. Following withdrawal from drugs such as amphetamine or cocaine, rodents display behavioral changes that are highly similar to some aspects of depression in humans, such as anhedonia, and behaviors opposite to those seen after treatment with antidepressant drugs.
Genetically engineered mice: Only few generated mutant lines can be regarded as depression models, for example, α2A adrenergic receptor knockout mice, glucocorticoid receptor heterozygous mice, and cAMP response element-binding protein overexpressing mice.
Forward genetics: Forward genetics allows identifying relevant genes without any prior knowledge of genetic to the phenotype. Large scale random mutagenesis screens, like ENU, have resulted in a great number of mutants displaying depression or antidepressant-like behavior.
== Evaluating symptoms ==
The degree of depression-like symptoms in an animal is evaluated using a number of tests. Tests provide a measure of an animal's response to inescapable stress (lack of attempt to escape is seen as despair/hopelessness) and to reward (lack of response indicates anhedonia), or to measure its degree of anxiety.
=== Despair-based ===
Forced-swimming test: The forced-swimming test (FST) is based on the observation that animals develop an immobile posture in an inescapable cylinder filled with water. In this test, immobility is interpreted as a passive stress-coping strategy or depression-like behavior (behavioral despair). After antidepressant administration, the animals will actively perform escape-directed behaviors with longer duration than animals with control saline treatment. FST is the most widely used tool in depression research, more specifically as a screen for acute antidepressants.The advantages of FST are that it is low-cost and a fast, reliable tool. It is also easy to handle and has proven its reliability across laboratories for testing potential antidepressant activities with a strong predictive validity and it allows rapid screening of large numbers of drugs. The major disadvantages of FST are that it has poor face and construct validities. The test is sensitive to acute treatment only, and its validity for non-monoamine antidepressants is uncertain
Tail suspension test: The TST, also known as tail suspension test, shares a common theoretical basis and behavioral measure with the FST. In the TST, mice are suspended by their tails using adhesive tape to a horizontal bar for a certain couple of minutes, and the time of immobility is recorded. Typically, the suspended rodents perform immediately escape-like behaviors, followed by developing an immobile posture. If antidepressants are given prior to the test, the subjects will be engaged in escape-directed behaviors for longer periods of time than after saline treatment, exhibiting a decrease in duration of immobility.A major advantage of the TST is that it is simple and inexpensive. A major disadvantage of the TST is that it is restricted to mice. Like FST, TST is sensitive to acute treatment only, and its validity for non-monoamine antidepressants is uncertain.
=== Reward-based ===
Sucrose preference: Rodents are born with an interest in sweet foods or solutions. Reduced preference for sweet solution in sucrose preference test represents anhedonia. This reduction can be reversed by treatment with chronic antidepressants. This test may measure the affective state and motivation of subject rodents; however, the face and construct validity of the sucrose preference test to measure depression-related behavior appears low.
Intracranial self-stimulation: Intracranial self-stimulation (ICSS) can be utilized in rodents to understand how drugs affect the function of brain reward system. In this paradigm, the animal is trained to spin a wheel to receive a current through electrodes implanted in its own brain for rewarding the hypothalamic stimulation. ICSS shares a common theoretical basis with the sucrose preference. Reduced preference for self-stimulating reward cognition represents a loss of interest, fatigue and a loss of energy. This usually occurs during depressive episodes, but, this reduction can be reversed by treatment with antidepressants. Like sucrose preference test, ICSS can measure the affective state and motivation of subject rodents, and again, further validation is needed for working as a model of depression.
=== Anxiety-based ===
Novelty-induced hypophagia: Hypophagia, one of the anxiety symptoms in rodents, is defined as the reduction in feeding in response to novelty, and it can be evoked by various novel features of the environment, including novel food, novel testing environment and novel food containers. Novelty-induced hypophagia (NIH) is a recently developed test which measures the latency and consumption of food in a novel unfamiliar environment. The test rather reflects the anxiolytic effects of antidepressants and the response is seen only after chronic treatment with antidepressants.
Open field: Rodents tend to avoid brightly illuminated areas, and this avoidance is interpreted as a symptom of anxiety. Open field is a bright enclosure and during the test rodents are placed in this arena thus forcing them to interact with a bright environment. The movement of the experimental subject will be recorded in distance and pathway.
Elevated plus maze: For the elevated plus maze test, the rodents are placed at the intersection of the four arms of the maze (two open, two closed), facing an open arm. The number of entries and time spent in each arm is recorded and valid results are obtained in a single 5-minute testing session. An increase in the open-arm time is an index of anti-anxiety behavior of rodents.
Dark/light box: The dark/light box test is also based on the rodents' innate aversion to brightly illuminated areas and on the spontaneous exploratory behavior of the animals. A natural conflict situation occurs when an animal is exposed to an unfamiliar environment or novel objects. The conflict is between the tendency to explore and the initial tendency to avoid the unfamiliar. The exploratory activity reflects the combined result of these tendencies in novel situations. The test apparatus of dark/light box consists of a dark compartment and an illuminated compartment. Drug-induced increases in behaviors in the white part of a two-compartment box are suggested as an index of anxiolytic activity.
Open field test, elevated plus maze test, and dark/light box test can work as an antidepressant screen by measuring anxiety-related behavior as an accompanying endophenotype of depression. It is known that some antidepressants will cause a decrease in behavior in these tests just like anxiolytics. However, the response to some antidepressants couldn't be detected. These tests each have their own problems and it is difficult to discriminate decreased anxiety-related avoidance from increased novelty-seeking in these tests.
== Benefits of animal models ==
A benefit to this model of research is the production of antidepressants. While antidepressants are helpful, the effects of current antidepressant drugs are often significantly delayed, with improvements beginning around 3–6 weeks after treatment is started. Antidepressant screening tests provide only an end-point behavioral or physiological measure designed to assess the effect of the genetic, pharmacological, or environmental manipulation. This is unlike models which can be defined as an organism or a particular state of an organism that reproduces aspects of human pathology. Despite the clinical success of many antidepressant drugs, such as tricyclic antidepressants (TCAs), monoamine oxidase inhibitors (MAOIs), and serotonin reuptake inhibitors (SRIs), many individuals' symptoms are not adequately alleviated by medication alone, and other methods of treatment may be recommended.
Antidepressant and depression research is ongoing. There is a lot more knowledge now and people struggling have access to the tools they need when seeking help. Animal research has been a successful way for experts to gain this knowledge and it continues to have positive impacts in the medical field and beyond.
== See also ==
Animal testing
Institutional Animal Care and Use Committees
Pit of despair, an apparatus used for animal models of clinical depression
Conditioned avoidance response test § Test of other drug effects
== References == | Wikipedia/Animal_models_of_depression |
An infection is the invasion of tissues by pathogens, their multiplication, and the reaction of host tissues to the infectious agent and the toxins they produce. An infectious disease, also known as a transmissible disease or communicable disease, is an illness resulting from an infection.
Infections can be caused by a wide range of pathogens, most prominently bacteria and viruses. Hosts can fight infections using their immune systems. Mammalian hosts react to infections with an innate response, often involving inflammation, followed by an adaptive response.
Treatment for infections depends on the type of pathogen involved. Common medications include:
Antibiotics for bacterial infections.
Antivirals for viral infections.
Antifungals for fungal infections.
Antiprotozoals for protozoan infections.
Antihelminthics for infections caused by parasitic worms.
Infectious diseases remain a significant global health concern, causing approximately 9.2 million deaths in 2013 (17% of all deaths). The branch of medicine that focuses on infections is referred to as infectious diseases.
== Types ==
Infections are caused by infectious agents (pathogens) including:
Bacteria (e.g. Mycobacterium tuberculosis, Staphylococcus aureus, Escherichia coli, Clostridium botulinum, and Salmonella spp.)
Viruses and subviral agents such as viroids and prions. (E.g. HIV, Rhinovirus, Lyssaviruses such as Rabies virus, Ebolavirus and Severe acute respiratory syndrome coronavirus 2)
Fungi, further subclassified into:
Ascomycota, including yeasts such as Candida (the most common fungal infection); filamentous fungi such as Aspergillus; Pneumocystis species; and dermatophytes, a group of organisms causing infection of skin and other superficial structures in humans.
Basidiomycota, including the human-pathogenic genus Cryptococcus.
Parasites, which are usually divided into:
Unicellular organisms (e.g. malaria, Toxoplasma, Babesia)
Macroparasites (worms or helminths) including nematodes such as parasitic roundworms and pinworms, tapeworms (cestodes), and flukes (trematodes, such as schistosomes). Diseases caused by helminths are sometimes termed infestations, but are sometimes called infections.
Arthropods such as ticks, mites, fleas, and lice, can also cause human disease, which conceptually are similar to infections, but invasion of a human or animal body by these macroparasites is usually termed infestation.
== Signs and symptoms ==
The signs and symptoms of an infection depend on the type of disease. Some signs of infection affect the whole body generally, such as fatigue, loss of appetite, weight loss, fevers, night sweats, chills, aches and pains. Others are specific to individual body parts, such as skin rashes, coughing, or a runny nose.
In certain cases, infectious diseases may be asymptomatic for much or even all of their course in a given host. In the latter case, the disease may only be defined as a "disease" (which by definition means an illness) in hosts who secondarily become ill after contact with an asymptomatic carrier. An infection is not synonymous with an infectious disease, as some infections do not cause illness in a host.
=== Bacterial or viral ===
As bacterial and viral infections can both cause the same kinds of symptoms, it can be difficult to distinguish which is the cause of a specific infection. Distinguishing the two is important, since viral infections cannot be cured by antibiotics whereas bacterial infections can.
== Pathophysiology ==
There is a general chain of events that applies to infections, sometimes called the chain of infection or transmission chain. The chain of events involves several steps – which include the infectious agent, reservoir, entering a susceptible host, exit and transmission to new hosts. Each of the links must be present in a chronological order for an infection to develop. Understanding these steps helps health care workers target the infection and prevent it from occurring in the first place.
=== Colonization ===
Infection begins when an organism successfully enters the body, grows and multiplies. This is referred to as colonization. Most humans are not easily infected. Those with compromised or weakened immune systems have an increased susceptibility to chronic or persistent infections. Individuals who have a suppressed immune system are particularly susceptible to opportunistic infections. Entrance to the host at host–pathogen interface, generally occurs through the mucosa in orifices like the oral cavity, nose, eyes, genitalia, anus, or the microbe can enter through open wounds. While a few organisms can grow at the initial site of entry, many migrate and cause systemic infection in different organs. Some pathogens grow within the host cells (intracellular) whereas others grow freely in bodily fluids.
Wound colonization refers to non-replicating microorganisms within the wound, while in infected wounds, replicating organisms exist and tissue is injured. All multicellular organisms are colonized to some degree by extrinsic organisms, and the vast majority of these exist in either a mutualistic or commensal relationship with the host. An example of the former is the anaerobic bacteria species, which colonizes the mammalian colon, and an example of the latter are the various species of staphylococcus that exist on human skin. Neither of these colonizations are considered infections. The difference between an infection and a colonization is often only a matter of circumstance. Non-pathogenic organisms can become pathogenic given specific conditions, and even the most virulent organism requires certain circumstances to cause a compromising infection. Some colonizing bacteria, such as Corynebacteria sp. and Viridans streptococci, prevent the adhesion and colonization of pathogenic bacteria and thus have a symbiotic relationship with the host, preventing infection and speeding wound healing.
The variables involved in the outcome of a host becoming inoculated by a pathogen and the ultimate outcome include:
the route of entry of the pathogen and the access to host regions that it gains
the intrinsic virulence of the particular organism
the quantity or load of the initial inoculant
the immune status of the host being colonized
As an example, several staphylococcal species remain harmless on the skin, but, when present in a normally sterile space, such as in the capsule of a joint or the peritoneum, multiply without resistance and cause harm.
An interesting fact that gas chromatography–mass spectrometry, 16S ribosomal RNA analysis, omics, and other advanced technologies have made more apparent to humans in recent decades is that microbial colonization is very common even in environments that humans think of as being nearly sterile. Because it is normal to have bacterial colonization, it is difficult to know which chronic wounds can be classified as infected and how much risk of progression exists. Despite the huge number of wounds seen in clinical practice, there are limited quality data for evaluated symptoms and signs. A review of chronic wounds in the Journal of the American Medical Association's "Rational Clinical Examination Series" quantified the importance of increased pain as an indicator of infection. The review showed that the most useful finding is an increase in the level of pain [likelihood ratio (LR) range, 11–20] makes infection much more likely, but the absence of pain (negative likelihood ratio range, 0.64–0.88) does not rule out infection (summary LR 0.64–0.88).
=== Disease ===
Disease can arise if the host's protective immune mechanisms are compromised and the organism inflicts damage on the host. Microorganisms can cause tissue damage by releasing a variety of toxins or destructive enzymes. For example, Clostridium tetani releases a toxin that paralyzes muscles, and staphylococcus releases toxins that produce shock and sepsis. Not all infectious agents cause disease in all hosts. For example, less than 5% of individuals infected with polio develop disease. On the other hand, some infectious agents are highly virulent. The prion causing mad cow disease and Creutzfeldt–Jakob disease invariably kills all animals and people that are infected.
Persistent infections occur because the body is unable to clear the organism after the initial infection. Persistent infections are characterized by the continual presence of the infectious organism, often as latent infection with occasional recurrent relapses of active infection. There are some viruses that can maintain a persistent infection by infecting different cells of the body. Some viruses once acquired never leave the body. A typical example is the herpes virus, which tends to hide in nerves and become reactivated when specific circumstances arise.
Persistent infections cause millions of deaths globally each year. Chronic infections by parasites account for a high morbidity and mortality in many underdeveloped countries.
=== Transmission ===
For infecting organisms to survive and repeat the infection cycle in other hosts, they (or their progeny) must leave an existing reservoir and cause infection elsewhere. Infection transmission can take place via many potential routes:
Droplet contact, also known as the respiratory route, and the resultant infection can be termed airborne disease. If an infected person coughs or sneezes on another person the microorganisms, suspended in warm, moist droplets, may enter the body through the nose, mouth or eye surfaces.
Fecal-oral transmission, wherein foodstuffs or water become contaminated (by people not washing their hands before preparing food, or untreated sewage being released into a drinking water supply) and the people who eat and drink them become infected. Common fecal-oral transmitted pathogens include Vibrio cholerae, Giardia species, rotaviruses, Entamoeba histolytica, Escherichia coli, and tape worms. Most of these pathogens cause gastroenteritis.
Sexual transmission, with the result being called sexually transmitted infection.
Oral transmission, diseases that are transmitted primarily by oral means may be caught through direct oral contact such as kissing, or by indirect contact such as by sharing a drinking glass or a cigarette.
Transmission by direct contact, Some diseases that are transmissible by direct contact include athlete's foot, impetigo and warts.
Vehicle transmission, transmission by an inanimate reservoir (food, water, soil).
Vertical transmission, directly from the mother to an embryo, fetus or baby during pregnancy or childbirth. It can occur as a result of a pre-existing infection or one acquired during pregnancy.
Iatrogenic transmission, due to medical procedures such as injection or transplantation of infected material.
Vector-borne transmission, transmitted by a vector, which is an organism that does not cause disease itself but that transmits infection by conveying pathogens from one host to another.
The relationship between virulence versus transmissibility is complex; with studies have shown that there were no clear relationship between the two. There is still a small number of evidence that partially suggests a link between virulence and transmissibility.
== Diagnosis ==
Diagnosis of infectious disease sometimes involves identifying an infectious agent either directly or indirectly. In practice most minor infectious diseases such as warts, cutaneous abscesses, respiratory system infections and diarrheal diseases are diagnosed by their clinical presentation and treated without knowledge of the specific causative agent. Conclusions about the cause of the disease are based upon the likelihood that a patient came in contact with a particular agent, the presence of a microbe in a community, and other epidemiological considerations. Given sufficient effort, all known infectious agents can be specifically identified.
Diagnosis of infectious disease is nearly always initiated by medical history and physical examination. More detailed identification techniques involve the culture of infectious agents isolated from a patient. Culture allows identification of infectious organisms by examining their microscopic features, by detecting the presence of substances produced by pathogens, and by directly identifying an organism by its genotype.
Many infectious organisms are identified without culture and microscopy. This is especially true for viruses, which cannot grow in culture. For some suspected pathogens, doctors may conduct tests that examine a patient's blood or other body fluids for antigens or antibodies that indicate presence of a specific pathogen that the doctor suspects.
Other techniques (such as X-rays, CAT scans, PET scans or NMR) are used to produce images of internal abnormalities resulting from the growth of an infectious agent. The images are useful in detection of, for example, a bone abscess or a spongiform encephalopathy produced by a prion.
The benefits of identification, however, are often greatly outweighed by the cost, as often there is no specific treatment, the cause is obvious, or the outcome of an infection is likely to be benign.
=== Symptomatic diagnostics ===
The diagnosis is aided by the presenting symptoms in any individual with an infectious disease, yet it usually needs additional diagnostic techniques to confirm the suspicion. Some signs are specifically characteristic and indicative of a disease and are called pathognomonic signs; but these are rare. Not all infections are symptomatic.
In children the presence of cyanosis, rapid breathing, poor peripheral perfusion, or a petechial rash increases the risk of a serious infection by greater than 5 fold. Other important indicators include parental concern, clinical instinct, and temperature greater than 40 °C.
=== Microbial culture ===
Many diagnostic approaches depend on microbiological culture to isolate a pathogen from the appropriate clinical specimen. In a microbial culture, a growth medium is provided for a specific agent. A sample taken from potentially diseased tissue or fluid is then tested for the presence of an infectious agent able to grow within that medium. Many pathogenic bacteria are easily grown on nutrient agar, a form of solid medium that supplies carbohydrates and proteins necessary for growth, along with copious amounts of water. A single bacterium will grow into a visible mound on the surface of the plate called a colony, which may be separated from other colonies or melded together into a "lawn". The size, color, shape and form of a colony is characteristic of the bacterial species, its specific genetic makeup (its strain), and the environment that supports its growth. Other ingredients are often added to the plate to aid in identification. Plates may contain substances that permit the growth of some bacteria and not others, or that change color in response to certain bacteria and not others. Bacteriological plates such as these are commonly used in the clinical identification of infectious bacterium. Microbial culture may also be used in the identification of viruses: the medium, in this case, being cells grown in culture that the virus can infect, and then alter or kill. In the case of viral identification, a region of dead cells results from viral growth, and is called a "plaque". Eukaryotic parasites may also be grown in culture as a means of identifying a particular agent.
In the absence of suitable plate culture techniques, some microbes require culture within live animals. Bacteria such as Mycobacterium leprae and Treponema pallidum can be grown in animals, although serological and microscopic techniques make the use of live animals unnecessary. Viruses are also usually identified using alternatives to growth in culture or animals. Some viruses may be grown in embryonated eggs. Another useful identification method is Xenodiagnosis, or the use of a vector to support the growth of an infectious agent. Chagas disease is the most significant example, because it is difficult to directly demonstrate the presence of the causative agent, Trypanosoma cruzi in a patient, which therefore makes it difficult to definitively make a diagnosis. In this case, xenodiagnosis involves the use of the vector of the Chagas agent T. cruzi, an uninfected triatomine bug, which takes a blood meal from a person suspected of having been infected. The bug is later inspected for growth of T. cruzi within its gut.
=== Microscopy ===
Another principal tool in the diagnosis of infectious disease is microscopy. Virtually all of the culture techniques discussed above rely, at some point, on microscopic examination for definitive identification of the infectious agent. Microscopy may be carried out with simple instruments, such as the compound light microscope, or with instruments as complex as an electron microscope. Samples obtained from patients may be viewed directly under the light microscope, and can often rapidly lead to identification. Microscopy is often also used in conjunction with biochemical staining techniques, and can be made exquisitely specific when used in combination with antibody based techniques. For example, the use of antibodies made artificially fluorescent (fluorescently labeled antibodies) can be directed to bind to and identify a specific antigens present on a pathogen. A fluorescence microscope is then used to detect fluorescently labeled antibodies bound to internalized antigens within clinical samples or cultured cells. This technique is especially useful in the diagnosis of viral diseases, where the light microscope is incapable of identifying a virus directly.
Other microscopic procedures may also aid in identifying infectious agents. Almost all cells readily stain with a number of basic dyes due to the electrostatic attraction between negatively charged cellular molecules and the positive charge on the dye. A cell is normally transparent under a microscope, and using a stain increases the contrast of a cell with its background. Staining a cell with a dye such as Giemsa stain or crystal violet allows a microscopist to describe its size, shape, internal and external components and its associations with other cells. The response of bacteria to different staining procedures is used in the taxonomic classification of microbes as well. Two methods, the Gram stain and the acid-fast stain, are the standard approaches used to classify bacteria and to diagnosis of disease. The Gram stain identifies the bacterial groups Bacillota and Actinomycetota, both of which contain many significant human pathogens. The acid-fast staining procedure identifies the Actinomycetota genera Mycobacterium and Nocardia.
=== Biochemical tests ===
Biochemical tests used in the identification of infectious agents include the detection of metabolic or enzymatic products characteristic of a particular infectious agent. Since bacteria ferment carbohydrates in patterns characteristic of their genus and species, the detection of fermentation products is commonly used in bacterial identification. Acids, alcohols and gases are usually detected in these tests when bacteria are grown in selective liquid or solid media.
The isolation of enzymes from infected tissue can also provide the basis of a biochemical diagnosis of an infectious disease. For example, humans can make neither RNA replicases nor reverse transcriptase, and the presence of these enzymes are characteristic., of specific types of viral infections. The ability of the viral protein hemagglutinin to bind red blood cells together into a detectable matrix may also be characterized as a biochemical test for viral infection, although strictly speaking hemagglutinin is not an enzyme and has no metabolic function.
Serological methods are highly sensitive, specific and often extremely rapid tests used to identify microorganisms. These tests are based upon the ability of an antibody to bind specifically to an antigen. The antigen, usually a protein or carbohydrate made by an infectious agent, is bound by the antibody. This binding then sets off a chain of events that can be visibly obvious in various ways, dependent upon the test. For example, "Strep throat" is often diagnosed within minutes, and is based on the appearance of antigens made by the causative agent, S. pyogenes, that is retrieved from a patient's throat with a cotton swab. Serological tests, if available, are usually the preferred route of identification, however the tests are costly to develop and the reagents used in the test often require refrigeration. Some serological methods are extremely costly, although when commonly used, such as with the "strep test", they can be inexpensive.
Complex serological techniques have been developed into what are known as immunoassays. Immunoassays can use the basic antibody – antigen binding as the basis to produce an electro-magnetic or particle radiation signal, which can be detected by some form of instrumentation. Signal of unknowns can be compared to that of standards allowing quantitation of the target antigen. To aid in the diagnosis of infectious diseases, immunoassays can detect or measure antigens from either infectious agents or proteins generated by an infected organism in response to a foreign agent. For example, immunoassay A may detect the presence of a surface protein from a virus particle. Immunoassay B on the other hand may detect or measure antibodies produced by an organism's immune system that are made to neutralize and allow the destruction of the virus.
Instrumentation can be used to read extremely small signals created by secondary reactions linked to the antibody – antigen binding. Instrumentation can control sampling, reagent use, reaction times, signal detection, calculation of results, and data management to yield a cost-effective automated process for diagnosis of infectious disease.
=== PCR-based diagnostics ===
Technologies based upon the polymerase chain reaction (PCR) method will become nearly ubiquitous gold standards of diagnostics of the near future, for several reasons. First, the catalog of infectious agents has grown to the point that virtually all of the significant infectious agents of the human population have been identified. Second, an infectious agent must grow within the human body to cause disease; essentially it must amplify its own nucleic acids to cause a disease. This amplification of nucleic acid in infected tissue offers an opportunity to detect the infectious agent by using PCR. Third, the essential tools for directing PCR, primers, are derived from the genomes of infectious agents, and with time those genomes will be known if they are not already.
Thus, the technological ability to detect any infectious agent rapidly and specifically is currently available. The only remaining blockades to the use of PCR as a standard tool of diagnosis are in its cost and application, neither of which is insurmountable. The diagnosis of a few diseases will not benefit from the development of PCR methods, such as some of the clostridial diseases (tetanus and botulism). These diseases are fundamentally biological poisonings by relatively small numbers of infectious bacteria that produce extremely potent neurotoxins. A significant proliferation of the infectious agent does not occur, this limits the ability of PCR to detect the presence of any bacteria.
=== Metagenomic sequencing ===
Given the wide range of bacterial, viral, fungal, protozoal, and helminthic pathogens that cause debilitating and life-threatening illnesses, the ability to quickly identify the cause of infection is important yet often challenging. For example, more than half of cases of encephalitis, a severe illness affecting the brain, remain undiagnosed, despite extensive testing using the standard of care (microbiological culture) and state-of-the-art clinical laboratory methods. Metagenomic sequencing-based diagnostic tests are currently being developed for clinical use and show promise as a sensitive, specific, and rapid way to diagnose infection using a single all-encompassing test. This test is similar to current PCR tests; however, an untargeted whole genome amplification is used rather than primers for a specific infectious agent. This amplification step is followed by next-generation sequencing or third-generation sequencing, alignment comparisons, and taxonomic classification using large databases of thousands of pathogen and commensal reference genomes. Simultaneously, antimicrobial resistance genes within pathogen and plasmid genomes are sequenced and aligned to the taxonomically classified pathogen genomes to generate an antimicrobial resistance profile – analogous to antibiotic sensitivity testing – to facilitate antimicrobial stewardship and allow for the optimization of treatment using the most effective drugs for a patient's infection.
Metagenomic sequencing could prove especially useful for diagnosis when the patient is immunocompromised. An ever-wider array of infectious agents can cause serious harm to individuals with immunosuppression, so clinical screening must often be broader. Additionally, the expression of symptoms is often atypical, making a clinical diagnosis based on presentation more difficult. Thirdly, diagnostic methods that rely on the detection of antibodies are more likely to fail. A rapid, sensitive, specific, and untargeted test for all known human pathogens that detects the presence of the organism's DNA rather than antibodies is therefore highly desirable.
=== Indication of tests ===
There is usually an indication for a specific identification of an infectious agent only when such identification can aid in the treatment or prevention of the disease, or to advance knowledge of the course of an illness prior to the development of effective therapeutic or preventative measures. For example, in the early 1980s, prior to the appearance of AZT for the treatment of AIDS, the course of the disease was closely followed by monitoring the composition of patient blood samples, even though the outcome would not offer the patient any further treatment options. In part, these studies on the appearance of HIV in specific communities permitted the advancement of hypotheses as to the route of transmission of the virus. By understanding how the disease was transmitted, resources could be targeted to the communities at greatest risk in campaigns aimed at reducing the number of new infections. The specific serological diagnostic identification, and later genotypic or molecular identification, of HIV also enabled the development of hypotheses as to the temporal and geographical origins of the virus, as well as a myriad of other hypothesis. The development of molecular diagnostic tools have enabled physicians and researchers to monitor the efficacy of treatment with anti-retroviral drugs. Molecular diagnostics are now commonly used to identify HIV in healthy people long before the onset of illness and have been used to demonstrate the existence of people who are genetically resistant to HIV infection. Thus, while there still is no cure for AIDS, there is great therapeutic and predictive benefit to identifying the virus and monitoring the virus levels within the blood of infected individuals, both for the patient and for the community at large.
=== Classification ===
==== Subclinical versus clinical (latent versus apparent) ====
Symptomatic infections are apparent and clinical, whereas an infection that is active but does not produce noticeable symptoms may be called inapparent, silent, subclinical, or occult. An infection that is inactive or dormant is called a latent infection. An example of a latent bacterial infection is latent tuberculosis. Some viral infections can also be latent, examples of latent viral infections are any of those from the Herpesviridae family.
The word infection can denote any presence of a particular pathogen at all (no matter how little) but also is often used in a sense implying a clinically apparent infection (in other words, a case of infectious disease). This fact occasionally creates some ambiguity or prompts some usage discussion; to get around this it is common for health professionals to speak of colonization (rather than infection) when they mean that some of the pathogens are present but that no clinically apparent infection (no disease) is present.
==== Course of infection ====
Different terms are used to describe how and where infections present over time. In an acute infection, symptoms develop rapidly; its course can either be rapid or protracted. In chronic infection, symptoms usually develop gradually over weeks or months and are slow to resolve. In subacute infections, symptoms take longer to develop than in acute infections but arise more quickly than those of chronic infections. A focal infection is an initial site of infection from which organisms travel via the bloodstream to another area of the body.
==== Primary versus opportunistic ====
Among the many varieties of microorganisms, relatively few cause disease in otherwise healthy individuals. Infectious disease results from the interplay between those few pathogens and the defenses of the hosts they infect. The appearance and severity of disease resulting from any pathogen depend upon the ability of that pathogen to damage the host as well as the ability of the host to resist the pathogen. However, a host's immune system can also cause damage to the host itself in an attempt to control the infection. Clinicians, therefore, classify infectious microorganisms or microbes according to the status of host defenses – either as primary pathogens or as opportunistic pathogens.
===== Primary pathogens =====
Primary pathogens cause disease as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence (the severity of the disease they cause) is, in part, a necessary consequence of their need to reproduce and spread. Many of the most common primary pathogens of humans only infect humans, however, many serious diseases are caused by organisms acquired from the environment or that infect non-human hosts.
===== Opportunistic pathogens =====
Opportunistic pathogens can cause an infectious disease in a host with depressed resistance (immunodeficiency) or if they have unusual access to the inside of the body (for example, via trauma). Opportunistic infection may be caused by microbes ordinarily in contact with the host, such as pathogenic bacteria or fungi in the gastrointestinal or the upper respiratory tract, and they may also result from (otherwise innocuous) microbes acquired from other hosts (as in Clostridioides difficile colitis) or from the environment as a result of traumatic introduction (as in surgical wound infections or compound fractures). An opportunistic disease requires impairment of host defenses, which may occur as a result of genetic defects (such as chronic granulomatous disease), exposure to antimicrobial drugs or immunosuppressive chemicals (as might occur following poisoning or cancer chemotherapy), exposure to ionizing radiation, or as a result of an infectious disease with immunosuppressive activity (such as with measles, malaria or HIV disease). Primary pathogens may also cause more severe disease in a host with depressed resistance than would normally occur in an immunosufficient host.
===== Secondary infection =====
While a primary infection can practically be viewed as the root cause of an individual's current health problem, a secondary infection is a sequela or complication of that root cause. For example, an infection due to a burn or penetrating trauma (the root cause) is a secondary infection. Primary pathogens often cause primary infection and often cause secondary infection. Usually, opportunistic infections are viewed as secondary infections (because immunodeficiency or injury was the predisposing factor).
===== Other types of infection =====
Other types of infection consist of mixed, iatrogenic, nosocomial, and community-acquired infection. A mixed infection is an infection that is caused by two or more pathogens. An example of this is appendicitis, which is caused by Bacteroides fragilis and Escherichia coli. The second is an iatrogenic infection. This type of infection is one that is transmitted from a health care worker to a patient. A nosocomial infection is also one that occurs in a health care setting. Nosocomial infections are those that are acquired during a hospital stay. Lastly, a community-acquired infection is one in which the infection is acquired from a whole community.
==== Infectious or not ====
One manner of proving that a given disease is infectious, is to satisfy Koch's postulates (first proposed by Robert Koch), which require that first, the infectious agent be identifiable only in patients who have the disease, and not in healthy controls, and second, that patients who contract the infectious agent also develop the disease. These postulates were first used in the discovery that Mycobacteria species cause tuberculosis.
However, Koch's postulates cannot usually be tested in modern practice for ethical reasons. Proving them would require experimental infection of a healthy individual with a pathogen produced as a pure culture. Conversely, even clearly infectious diseases do not always meet the infectious criteria; for example, Treponema pallidum, the causative spirochete of syphilis, cannot be cultured in vitro – however the organism can be cultured in rabbit testes. It is less clear that a pure culture comes from an animal source serving as host than it is when derived from microbes derived from plate culture.
Epidemiology, or the study and analysis of who, why and where disease occurs, and what determines whether various populations have a disease, is another important tool used to understand infectious disease. Epidemiologists may determine differences among groups within a population, such as whether certain age groups have a greater or lesser rate of infection; whether groups living in different neighborhoods are more likely to be infected; and by other factors, such as gender and race. Researchers also may assess whether a disease outbreak is sporadic, or just an occasional occurrence; endemic, with a steady level of regular cases occurring in a region; epidemic, with a fast arising, and unusually high number of cases in a region; or pandemic, which is a global epidemic. If the cause of the infectious disease is unknown, epidemiology can be used to assist with tracking down the sources of infection.
==== Contagiousness ====
Infectious diseases are sometimes called contagious diseases when they are easily transmitted by contact with an ill person or their secretions (e.g., influenza). Thus, a contagious disease is a subset of infectious disease that is especially infective or easily transmitted. All contagious diseases are infectious, but not vice versa. Other types of infectious, transmissible, or communicable diseases with more specialized routes of infection, such as vector transmission or sexual transmission, are usually not regarded as "contagious", and often do not require medical isolation (sometimes loosely called quarantine) of those affected. However, this specialized connotation of the word "contagious" and "contagious disease" (easy transmissibility) is not always respected in popular use.
Infectious diseases are commonly transmitted from person to person through direct contact. The types of direct contact are through person to person and droplet spread. Indirect contact such as airborne transmission, contaminated objects, food and drinking water, animal person contact, animal reservoirs, insect bites, and environmental reservoirs are another way infectious diseases are transmitted. The basic reproduction number of an infectious disease measures how easily it spreads through direct or indirect contact.
==== By anatomic location ====
Infections can be classified by the anatomic location or organ system infected, including:
Urinary tract infection
Skin infection
Respiratory tract infection
Odontogenic infection (an infection that originates within a tooth or in the closely surrounding tissues)
Vaginal infections
Intra-amniotic infection
In addition, locations of inflammation where infection is the most common cause include pneumonia, meningitis and salpingitis.
== Prevention ==
Techniques like hand washing, wearing gowns, and wearing face masks can help prevent infections from being passed from one person to another. Aseptic technique was introduced in medicine and surgery in the late 19th century and greatly reduced the incidence of infections caused by surgery. Frequent hand washing remains the most important defense against the spread of unwanted organisms. There are other forms of prevention such as avoiding the use of illicit drugs, using a condom, wearing gloves, and having a healthy lifestyle with a balanced diet and regular exercise. Cooking foods well and avoiding foods that have been left outside for a long time is also important.
Antimicrobial substances used to prevent transmission of infections include:
antiseptics, which are applied to living tissue/skin
disinfectants, which destroy microorganisms found on non-living objects.
antibiotics, called prophylactic when given as prevention rather as treatment of infection. However, long term use of antibiotics leads to resistance of bacteria. While humans do not become immune to antibiotics, the bacteria does. Thus, avoiding using antibiotics longer than necessary helps preventing bacteria from forming mutations that aide in antibiotic resistance.
One of the ways to prevent or slow down the transmission of infectious diseases is to recognize the different characteristics of various diseases. Some critical disease characteristics that should be evaluated include virulence, distance traveled by those affected, and level of contagiousness. The human strains of Ebola virus, for example, incapacitate those infected extremely quickly and kill them soon after. As a result, those affected by this disease do not have the opportunity to travel very far from the initial infection zone. Also, this virus must spread through skin lesions or permeable membranes such as the eye. Thus, the initial stage of Ebola is not very contagious since its victims experience only internal hemorrhaging. As a result of the above features, the spread of Ebola is very rapid and usually stays within a relatively confined geographical area. In contrast, the human immunodeficiency virus (HIV) kills its victims very slowly by attacking their immune system. As a result, many of its victims transmit the virus to other individuals before even realizing that they are carrying the disease. Also, the relatively low virulence allows its victims to travel long distances, increasing the likelihood of an epidemic.
Another effective way to decrease the transmission rate of infectious diseases is to recognize the effects of small-world networks. In epidemics, there are often extensive interactions within hubs or groups of infected individuals and other interactions within discrete hubs of susceptible individuals. Despite the low interaction between discrete hubs, the disease can jump and spread in a susceptible hub via a single or few interactions with an infected hub. Thus, infection rates in small-world networks can be reduced somewhat if interactions between individuals within infected hubs are eliminated (Figure 1). However, infection rates can be drastically reduced if the main focus is on the prevention of transmission jumps between hubs. The use of needle exchange programs in areas with a high density of drug users with HIV is an example of the successful implementation of this treatment method. Another example is the use of ring culling or vaccination of potentially susceptible livestock in adjacent farms to prevent the spread of the foot-and-mouth virus in 2001.
A general method to prevent transmission of vector-borne pathogens is pest control.
In cases where infection is merely suspected, individuals may be quarantined until the incubation period has passed and the disease manifests itself or the person remains healthy. Groups may undergo quarantine, or in the case of communities, a cordon sanitaire may be imposed to prevent infection from spreading beyond the community, or in the case of protective sequestration, into a community. Public health authorities may implement other forms of social distancing, such as school closings, lockdowns or temporary restrictions (e.g. circuit breakers) to control an epidemic.
=== Immunity ===
Infection with most pathogens does not result in death of the host and the offending organism is ultimately cleared after the symptoms of the disease have waned. This process requires immune mechanisms to kill or inactivate the inoculum of the pathogen. Specific acquired immunity against infectious diseases may be mediated by antibodies and/or T lymphocytes. Immunity mediated by these two factors may be manifested by:
a direct effect upon a pathogen, such as antibody-initiated complement-dependent bacteriolysis, opsonoization, phagocytosis and killing, as occurs for some bacteria,
neutralization of viruses so that these organisms cannot enter cells,
or by T lymphocytes, which will kill a cell parasitized by a microorganism.
The immune system response to a microorganism often causes symptoms such as a high fever and inflammation, and has the potential to be more devastating than direct damage caused by a microbe.
Resistance to infection (immunity) may be acquired following a disease, by asymptomatic carriage of the pathogen, by harboring an organism with a similar structure (crossreacting), or by vaccination. Knowledge of the protective antigens and specific acquired host immune factors is more complete for primary pathogens than for opportunistic pathogens. There is also the phenomenon of herd immunity which offers a measure of protection to those otherwise vulnerable people when a large enough proportion of the population has acquired immunity from certain infections.
Immune resistance to an infectious disease requires a critical level of either antigen-specific antibodies and/or T cells when the host encounters the pathogen. Some individuals develop natural serum antibodies to the surface polysaccharides of some agents although they have had little or no contact with the agent, these natural antibodies confer specific protection to adults and are passively transmitted to newborns.
==== Host genetic factors ====
The organism that is the target of an infecting action of a specific infectious agent is called the host. The host harbouring an agent that is in a mature or sexually active stage phase is called the definitive host. The intermediate host comes in contact during the larvae stage. A host can be anything living and can attain to asexual and sexual reproduction.
The clearance of the pathogens, either treatment-induced or spontaneous, it can be influenced by the genetic variants carried by the individual patients. For instance, for genotype 1 hepatitis C treated with Pegylated interferon-alpha-2a or Pegylated interferon-alpha-2b (brand names Pegasys or PEG-Intron) combined with ribavirin, it has been shown that genetic polymorphisms near the human IL28B gene, encoding interferon lambda 3, are associated with significant differences in the treatment-induced clearance of the virus. This finding, originally reported in Nature, showed that genotype 1 hepatitis C patients carrying certain genetic variant alleles near the IL28B gene are more possibly to achieve sustained virological response after the treatment than others. Later report from Nature demonstrated that the same genetic variants are also associated with the natural clearance of the genotype 1 hepatitis C virus.
== Treatments ==
When infection attacks the body, anti-infective drugs can suppress the infection. Several broad types of anti-infective drugs exist, depending on the type of organism targeted; they include antibacterial (antibiotic; including antitubercular), antiviral, antifungal and antiparasitic (including antiprotozoal and antihelminthic) agents. Depending on the severity and the type of infection, the antibiotic may be given by mouth or by injection, or may be applied topically. Severe infections of the brain are usually treated with intravenous antibiotics. Sometimes, multiple antibiotics are used in case there is resistance to one antibiotic. Antibiotics only work for bacteria and do not affect viruses. Antibiotics work by slowing down the multiplication of bacteria or killing the bacteria. The most common classes of antibiotics used in medicine include penicillin, cephalosporins, aminoglycosides, macrolides, quinolones and tetracyclines.
Not all infections require treatment, and for many self-limiting infections the treatment may cause more side-effects than benefits. Antimicrobial stewardship is the concept that healthcare providers should treat an infection with an antimicrobial that specifically works well for the target pathogen for the shortest amount of time and to only treat when there is a known or highly suspected pathogen that will respond to the medication.
== Susceptibility to infection ==
Pandemics such as COVID-19 show that people dramatically differ in their susceptibility to infection. This may be because of general health, age, or their immune status, e.g. when they have been infected previously. However, it also has become clear that there are genetic factor which determine susceptibility to infection. For instance, up to 40% of SARS-CoV-2 infections may be asymptomatic, suggesting that many people are naturally protected from disease. Large genetic studies have defined risk factors for severe SARS-CoV-2 infections, and genome sequences from 659 patients with severe COVID-19 revealed genetic variants that appear to be associated with life-threatening disease. One gene identified in these studies is type I interferon (IFN). Autoantibodies against type I IFNs were found in up to 13.7% of patients with life-threatening COVID-19, indicating that a complex interaction between genetics and the immune system is important for natural resistance to Covid.
Similarly, mutations in the ERAP2 gene, encoding endoplasmic reticulum aminopeptidase 2, seem to increase the susceptibility to the plague, the disease caused by an infection with the bacteria Yersinia pestis. People who inherited two copies of a complete variant of the gene were twice as likely to have survived the plague as those who inherited two copies of a truncated variant.
Susceptibility also determined the epidemiology of infection, given that different populations have different genetic and environmental conditions that affect infections.
== Epidemiology ==
An estimated 1,680 million people died of infectious diseases in the 20th century and about 10 million in 2010.
The World Health Organization collects information on global deaths by International Classification of Disease (ICD) code categories. The following table lists the top infectious disease by number of deaths in 2002. 1993 data is included for comparison.
The top three single agent/disease killers are HIV/AIDS, TB and malaria. While the number of deaths due to nearly every disease have decreased, deaths due to HIV/AIDS have increased fourfold. Childhood diseases include pertussis, poliomyelitis, diphtheria, measles and tetanus. Children also make up a large percentage of lower respiratory and diarrheal deaths. In 2012, approximately 3.1 million people have died due to lower respiratory infections, making it the number 4 leading cause of death in the world.
=== Historic pandemics ===
With their potential for unpredictable and explosive impacts, infectious diseases have been major actors in human history. A pandemic (or global epidemic) is a disease that affects people over an extensive geographical area. For example:
Plague of Justinian, from 541 to 542, killed between 50% and 60% of Europe's population.
The Black Death of 1347 to 1352 killed 25 million in Europe over five years. The plague reduced the old world population from an estimated 450 million to between 350 and 375 million in the 14th century.
The introduction of smallpox, measles, and typhus to the areas of Central and South America by European explorers during the 15th and 16th centuries caused pandemics among the native inhabitants. Between 1518 and 1568 disease pandemics are said to have caused the population of Mexico to fall from 20 million to 3 million.
The first European influenza epidemic occurred between 1556 and 1560, with an estimated mortality rate of 20%.
Smallpox killed an estimated 60 million Europeans during the 18th century (approximately 400,000 per year). Up to 30% of those infected, including 80% of the children under 5 years of age, died from the disease, and one-third of the survivors went blind.
In the 19th century, tuberculosis killed an estimated one-quarter of the adult population of Europe; by 1918 one in six deaths in France were still caused by TB.
The Influenza Pandemic of 1918 (or the Spanish flu) killed 25–50 million people (about 2% of world population of 1.7 billion). Today Influenza kills about 250,000 to 500,000 worldwide each year.
In 2021, COVID-19 emerged as a major global health crisis, directly causing 8.7 million deaths, making it one of the leading causes of mortality worldwide.
=== Emerging diseases ===
In most cases, microorganisms live in harmony with their hosts via mutual or commensal interactions. Diseases can emerge when existing parasites become pathogenic or when new pathogenic parasites enter a new host.
Coevolution between parasite and host can lead to hosts becoming resistant to the parasites or the parasites may evolve greater virulence, leading to immunopathological disease.
Human activity is involved with many emerging infectious diseases, such as environmental change enabling a parasite to occupy new niches. When that happens, a pathogen that had been confined to a remote habitat has a wider distribution and possibly a new host organism. Parasites jumping from nonhuman to human hosts are known as zoonoses. Under disease invasion, when a parasite invades a new host species, it may become pathogenic in the new host.
Several human activities have led to the emergence of zoonotic human pathogens, including viruses, bacteria, protozoa, and rickettsia, and spread of vector-borne diseases, see also globalization and disease and wildlife disease:
Encroachment on wildlife habitats. The construction of new villages and housing developments in rural areas force animals to live in dense populations, creating opportunities for microbes to mutate and emerge.
Changes in agriculture. The introduction of new crops attracts new crop pests and the microbes they carry to farming communities, exposing people to unfamiliar diseases.
The destruction of rain forests. As countries make use of their rain forests, by building roads through forests and clearing areas for settlement or commercial ventures, people encounter insects and other animals harboring previously unknown microorganisms.
Uncontrolled urbanization. The rapid growth of cities in many developing countries tends to concentrate large numbers of people into crowded areas with poor sanitation. These conditions foster transmission of contagious diseases.
Modern transport. Ships and other cargo carriers often harbor unintended "passengers", that can spread diseases to faraway destinations. While with international jet-airplane travel, people infected with a disease can carry it to distant lands, or home to their families, before their first symptoms appear.
== Germ theory of disease ==
In Antiquity, the Greek historian Thucydides (c. 460 – c. 400 BCE) was the first person to write, in his account of the plague of Athens, that diseases could spread from an infected person to others. In his On the Different Types of Fever (c. 175 AD), the Greco-Roman physician Galen speculated that plagues were spread by "certain seeds of plague", which were present in the air. In the Sushruta Samhita, the ancient Indian physician Sushruta theorized: "Leprosy, fever, consumption, diseases of the eye, and other infectious diseases spread from one person to another by sexual union, physical contact, eating together, sleeping together, sitting together, and the use of same clothes, garlands and pastes." This book has been dated to about the sixth century BC.
A basic form of contagion theory was proposed by Persian physician Ibn Sina (known as Avicenna in Europe) in The Canon of Medicine (1025), which later became the most authoritative medical textbook in Europe up until the 16th century. In Book IV of the Canon, Ibn Sina discussed epidemics, outlining the classical miasma theory and attempting to blend it with his own early contagion theory. He mentioned that people can transmit disease to others by breath, noted contagion with tuberculosis, and discussed the transmission of disease through water and dirt. The concept of invisible contagion was later discussed by several Islamic scholars in the Ayyubid Sultanate who referred to them as najasat ("impure substances"). The fiqh scholar Ibn al-Haj al-Abdari (c. 1250–1336), while discussing Islamic diet and hygiene, gave warnings about how contagion can contaminate water, food, and garments, and could spread through the water supply, and may have implied contagion to be unseen particles.
When the Black Death bubonic plague reached Al-Andalus in the 14th century, the Arab physicians Ibn Khatima (c. 1369) and Ibn al-Khatib (1313–1374) hypothesised that infectious diseases were caused by "minute bodies" and described how they can be transmitted through garments, vessels and earrings. Ideas of contagion became more popular in Europe during the Renaissance, particularly through the writing of the Italian physician Girolamo Fracastoro. Anton van Leeuwenhoek (1632–1723) advanced the science of microscopy by being the first to observe microorganisms, allowing for easy visualization of bacteria.
In the mid-19th century John Snow and William Budd did important work demonstrating the contagiousness of typhoid and cholera through contaminated water. Both are credited with decreasing epidemics of cholera in their towns by implementing measures to prevent contamination of water. Louis Pasteur proved beyond doubt that certain diseases are caused by infectious agents, and developed a vaccine for rabies. Robert Koch provided the study of infectious diseases with a scientific basis known as Koch's postulates. Edward Jenner, Jonas Salk and Albert Sabin developed effective vaccines for smallpox and polio, which would later result in the eradication and near-eradication of these diseases, respectively. Alexander Fleming discovered the world's first antibiotic, penicillin, which Florey and Chain then developed. Gerhard Domagk developed sulphonamides, the first broad spectrum synthetic antibacterial drugs.
=== Medical specialists ===
The medical treatment of infectious diseases falls into the medical field of Infectious Disease and in some cases the study of propagation pertains to the field of Epidemiology. Generally, infections are initially diagnosed by primary care physicians or internal medicine specialists. For example, an "uncomplicated" pneumonia will generally be treated by the internist or the pulmonologist (lung physician). The work of the infectious diseases specialist therefore entails working with both patients and general practitioners, as well as laboratory scientists, immunologists, bacteriologists and other specialists.
An infectious disease team may be alerted when:
The disease has not been definitively diagnosed after an initial workup
The patient is immunocompromised (for example, in AIDS or after chemotherapy);
The infectious agent is of an uncommon nature (e.g. tropical diseases);
The disease has not responded to first line antibiotics;
The disease might be dangerous to other patients, and the patient might have to be isolated
== Society and culture ==
Several studies have reported associations between pathogen load in an area and human behavior. Higher pathogen load is associated with decreased size of ethnic and religious groups in an area. This may be due high pathogen load favoring avoidance of other groups, which may reduce pathogen transmission, or a high pathogen load preventing the creation of large settlements and armies that enforce a common culture. Higher pathogen load is also associated with more restricted sexual behavior, which may reduce pathogen transmission. It also associated with higher preferences for health and attractiveness in mates. Higher fertility rates and shorter or less parental care per child is another association that may be a compensation for the higher mortality rate. There is also an association with polygyny which may be due to higher pathogen load, making selecting males with a high genetic resistance increasingly important. Higher pathogen load is also associated with more collectivism and less individualism, which may limit contacts with outside groups and infections. There are alternative explanations for at least some of the associations although some of these explanations may in turn ultimately be due to pathogen load. Thus, polygyny may also be due to a lower male: female ratio in these areas but this may ultimately be due to male infants having increased mortality from infectious diseases. Another example is that poor socioeconomic factors may ultimately in part be due to high pathogen load preventing economic development.
== Fossil record ==
Evidence of infection in fossil remains is a subject of interest for paleopathologists, scientists who study occurrences of injuries and illness in extinct life forms. Signs of infection have been discovered in the bones of carnivorous dinosaurs. When present, however, these infections seem to tend to be confined to only small regions of the body. A skull attributed to the early carnivorous dinosaur Herrerasaurus ischigualastensis exhibits pit-like wounds surrounded by swollen and porous bone. The unusual texture of the bone around the wounds suggests they were affected by a short-lived, non-lethal infection. Scientists who studied the skull speculated that the bite marks were received in a fight with another Herrerasaurus. Other carnivorous dinosaurs with documented evidence of infection include Acrocanthosaurus, Allosaurus, Tyrannosaurus and a tyrannosaur from the Kirtland Formation. The infections from both tyrannosaurs were received by being bitten during a fight, like the Herrerasaurus specimen.
== Outer space ==
A 2006 Space Shuttle experiment found that Salmonella typhimurium, a bacterium that can cause food poisoning, became more virulent when cultivated in space. On April 29, 2013, scientists in Rensselaer Polytechnic Institute, funded by NASA, reported that, during spaceflight on the International Space Station, microbes seem to adapt to the space environment in ways "not observed on Earth" and in ways that "can lead to increases in growth and virulence". More recently, in 2017, bacteria were found to be more resistant to antibiotics and to thrive in the near-weightlessness of space. Microorganisms have been observed to survive the vacuum of outer space.
== See also ==
== References ==
== External links ==
European Center for Disease Prevention and Control
U.S. Centers for Disease Control and Prevention,
Infectious Disease Society of America (IDSA)
Vaccine Research Center Information concerning vaccine research clinical trials for Emerging and re-Emerging Infectious Diseases.
Microbes & Infection (journal) | Wikipedia/Infectious_diseases |
Most animal testing involves invertebrates, especially Drosophila melanogaster, a fruit fly, and Caenorhabditis elegans, a nematode. These animals offer scientists many advantages over vertebrates, including their short life cycle, simple anatomy and the ease with which large numbers of individuals may be studied. Invertebrates are often cost-effective, as thousands of flies or nematodes can be housed in a single room.
With the exception of some cephalopods in the European Union, invertebrate species are not protected under most animal research legislation, and therefore the total number of invertebrates used remains unknown.
== Main uses ==
Research on invertebrates is the foundation for current understanding of the genetics of animal development. C. elegans is especially valuable as the precise lineage of all the organism's 959 somatic cells is known, giving a complete picture of how this organism goes from a single cell in a fertilized egg, to an adult animal. The genome of this nematode has also been fully sequenced and any one of these genes can easily be inactivated through RNA interference, by feeding the worms antisense RNA. A major success in the work on C. elegans was the discovery that particular cells are programmed to die during development, leading to the discovery that programmed cell death is an active process under genetic control. The simple nervous system of this nematode allows the effects of genetics on the development of nerves to be studied in detail. However, the lack of an adaptive immune system and the simplicity of its organs prevent C. elegans from being used in medical research such as vaccine development.
The fly D. melanogaster is the most widely used animal in genetic studies. This comes from the simplicity of breeding and housing the flies, which allows large numbers to be used in experiments. Molecular biology is relatively simple in these organisms and a huge variety of mutant and genetically modified flies have been developed. Fly genetics has been vital in the study of development, the cell cycle, behavior, and neuroscience. The similarities in the basic biochemistry of all animals allows flies to be used as simple systems to investigate the genetics of conditions such as heart disease and neurodegenerative disease. However, like nematodes, D. melanogaster is not widely used in applied medical research, as the fly immune system differs greatly from that found in humans, and diseases in flies can be very different from diseases in humans.
Other uses of invertebrates include studies on social behavior.
== See also ==
Animal testing on non-human primates
Animal testing on rodents
Testing cosmetics on animals
Pain in invertebrates
== References ==
== Further reading ==
General
Lawrence PA. "The Making of a Fly: The Genetics of Animal Design." Blackwell Publishing Limited (March 1, 1992) ISBN 0-632-03048-8
Demerec M. "Biology of Drosophila" Macmillan Pub Co. (January 2000) ISBN 0-02-843870-1
Hall, DH. "C. Elegans Atlas" Cold Spring Harbor Laboratory Press (November 30, 2007) ISBN 0-87969-715-6
Practical
Goldstein LSB, (Ed) Fryberg EA. "Methods in Cell Biology: Drosophila Melanogaster : Practical Uses in Cell and Molecular Biology" Academic Press (January 1995) ISBN 0-12-564145-1
Epstein HF, (Ed), Shakes DC. "Methods in Cell Biology: Caenorhabditis Elegans : Modern Biological Analysis of an Organism" Academic Press (October 1995) ISBN 0-12-240545-5
== External links ==
FlyBase Main Drosophila research database.
WormBase Main C. elegans research database. | Wikipedia/Animal_testing_on_invertebrates |
A cellular model is a mathematical model of aspects of a biological cell, for the purposes of in silico research.
Developing such models has been a task of systems biology and mathematical biology. It involves developing efficient algorithms, data structures, visualization and communication tools to orchestrate the integration of large quantities of biological data with the goal of computer modeling. It involves the use of computer simulations of cellular subsystems, such as the networks of metabolites and enzymes which comprise metabolism, signal transduction pathways and gene regulatory networks.
== Overview ==
The eukaryotic cell cycle is very complex and is one of the most studied topics, since its misregulation leads to cancers.
It is possibly a good example of a mathematical model as it deals with simple calculus but gives valid results. Two research groups have produced several models of the cell cycle simulating several organisms. They have recently produced a generic eukaryotic cell cycle model which can represent a particular eukaryote depending on the values of the parameters, demonstrating that the idiosyncrasies of the individual cell cycles are due to different protein concentrations and affinities, while the underlying mechanisms are conserved (Csikasz-Nagy et al., 2006).
By means of a system of ordinary differential equations these models show the change in time (dynamical system) of the protein inside a single typical cell; this type of model is called a deterministic process (whereas a model describing a statistical distribution of protein concentrations in a population of cells is called a stochastic process).
To obtain these equations an iterative series of steps must be done: first the several models and observations are combined to form a consensus diagram and the appropriate kinetic laws are chosen to write the differential equations, such as rate kinetics for stoichiometric reactions, Michaelis-Menten kinetics for enzyme substrate reactions and Goldbeter–Koshland kinetics for ultrasensitive transcription factors, afterwards the parameters of the equations (rate constants, enzyme efficiency coefficients and Michaelis constants) must be fitted to match observations; when they cannot be fitted the kinetic equation is revised and when that is not possible the wiring diagram is modified. The parameters are fitted and validated using observations of both wild type and mutants, such as protein half-life and cell size.
In order to fit the parameters the differential equations need to be studied. This can be done either by simulation or by analysis.
In a simulation, given a starting vector (list of the values of the variables), the progression of the system is calculated by solving the equations at each time-frame in small increments.
In analysis, the properties of the equations are used to investigate the behavior of the system depending on the values of the parameters and variables. A system of differential equations can be represented as a vector field, where each vector described the change (in concentration of two or more protein) determining where and how fast the trajectory (simulation) is heading. Vector fields can have several special points: a stable point, called a sink, that attracts in all directions (forcing the concentrations to be at a certain value), an unstable point, either a source or a saddle point which repels (forcing the concentrations to change away from a certain value), and a limit cycle, a closed trajectory towards which several trajectories spiral towards (making the concentrations oscillate).
A better representation which can handle the large number of variables and parameters is called a bifurcation diagram (bifurcation theory): the presence of these special steady-state points at certain values of a parameter (e.g. mass) is represented by a point and once the parameter passes a certain value, a qualitative change occurs, called a bifurcation, in which the nature of the space changes, with profound consequences for the protein concentrations: the cell cycle has phases (partially corresponding to G1 and G2) in which mass, via a stable point, controls cyclin levels, and phases (S and M phases) in which the concentrations change independently, but once the phase has changed at a bifurcation event (cell cycle checkpoint), the system cannot go back to the previous levels since at the current mass the vector field is profoundly different and the mass cannot be reversed back through the bifurcation event, making a checkpoint irreversible. In particular the S and M checkpoints are regulated by means of special bifurcations called a Hopf bifurcation and an infinite period bifurcation.
== Molecular level simulations ==
Cell Collective is a modeling software that enables one to house dynamical biological data, build computational models, stimulate, break and recreate models. The development is led by Tomas Helikar, a researcher within the field of computational biology. It is designed for biologists, students learning about computational biology, teachers focused on teaching life sciences, and researchers within the field of life science. The complexities of math and computer science are built into the backend and one can learn about the methods used for modeling biological species, but complex math equations, algorithms, programming are not required and hence won't impede model building.
The mathematical framework behind Cell Collective is based on a common qualitative (discrete) modeling technique where the regulatory mechanism of each node is described with a logical function [for more comprehensive information on logical modeling, see ].
In the July 2012 issue of Cell, a team led by Markus Covert at Stanford published the most complete computational model of a cell to date. The model of the roughly 500-gene Mycoplasma genitalium contains 28 algorithmically-independent components incorporating work from over 900 sources. It accounts for interactions of the complete genome, transcriptome, proteome, and metabolome of the organism, marking a significant advancement for the field.
Most attempts at modeling cell cycle processes have focused on the broad, complicated molecular interactions of many different chemicals, including several cyclin and cyclin-dependent kinase molecules as they correspond to the S, M, G1 and G2 phases of the cell cycle. In a 2014 published article in PLOS computational biology, collaborators at University of Oxford, Virginia Tech and Institut de Génétique et Développement de Rennes produced a simplified model of the cell cycle using only one cyclin/CDK interaction. This model showed the ability to control totally functional cell division through regulation and manipulation only the one interaction, and even allowed researchers to skip phases through varying the concentration of CDK. This model could help understand how the relatively simple interactions of one chemical translate to a cellular level model of cell division.
== Projects ==
Multiple projects are in progress.
CytoSolve - Commercial platform, possibly using MATLAB
Synthecell - Experimental group
Karyote - Indiana University - No longer active
E-Cell Project - Last updated 2020
Virtual Cell - University of Connecticut Health Center - Simulation platform rather than a build a cell project
Silicon Cell - No longer active
WholeCell - Stanford University - No longer active
MCell - National Center for Multiscale Modeling of Biological Systems (MMBioS) - Active as of 2023
== See also ==
Biological data visualization
Biological Applications of Bifurcation Theory
Molecular modeling software
Membrane computing is the task of modeling specifically a cell membrane.
Biochemical Switches in the Cell Cycle
Masaru Tomita
== References == | Wikipedia/Cellular_model |
Breast cancer metastatic mouse models are experimental approaches in which mice are genetically manipulated to develop a mammary tumor leading to distant focal lesions of mammary epithelium created by metastasis. Mammary cancers in mice can be caused by genetic mutations that have been identified in human cancer. This means models can be generated based upon molecular lesions consistent with the human disease.
== Breast cancer metastasis ==
Metastasis is a process of migration of tumour cells from the primary cancer site to a distant location where the cancer cells form secondary tumors. Metastatic breast cancer represents the most devastating attribute of cancer and it is considered an advanced-stage event. Human breast cancer metastasizes to multiple distant organs such as the brain, lungs, bones and liver.
=== Genetic diversity between primary and metastatic tumor ===
The classical theory developed in the early 70's anticipated that metastasis is due to genetically determined subpopulations in primary tumours. The genetic variance between metastatic foci is significant for only particular locus and within specific cell populations or only one-cell population shows differences and some loci are divergent only in one cell subpopulation. This explains the concept of tumour heterogeneity and the order of genetic events during tumor evolution. Many of the genes driving the growth at primary site can determine the dissemination and colonization at the ectopic site. Breast cancer is consensually considered genetically and clinically as a heterogeneous disease, in that it reflects the heterogeneity of the normal breast tissue at its origin17873350. A number of discrete genetic events have to occur in order to enable individual tumor cells that have the capacity to grow at an ectopic site. The metastatic progression depends on the regulation of developmental programs and environmental events. The metastatic potential of sub populations within mouse mammary cells is now considered as relatively an early event and dissemination occurs at the same time of pre invasive or micro-invasive lesions. The genetic profiles of primary and metastatic lesions in breast carcinomas show a large extent of clonal pertinence between lesions. There are various patterns of prevalence of genetic mutations in the genomes of primary breast tumour and its metastases. It also confirms the genetic heterogeneity between the primary neoplasm of breast cancer patients and their respective metastases.
=== Genes involved in organ specific metastasis ===
Breast cancer phenotypes periodically express genes in metastasis that are indispensable for the metastatic process. Metastatic diversity is mediated by the activation of genes that act as coupling to organ-specific growth. The growth of lesions at the ectopic site depends on multiple complex interactions between metastatic cells and host homeostatic mechanisms. Lethal protein-protein interactions at the metastatic site aid the survival of adapted cells.
== Generating mouse models of breast cancer ==
Targeted expression of oncogenes in mouse mammary epithelial cells is a way of modeling human breast cancer. Mutation or over expression of oncogenes can be kept under controlled expression in a very specific cellular context rather than throughout the organism. Another way to model human breast cancer is done through the targeted inhibition of a tumor suppressor gene.
=== Mice in genetic research ===
In 1909, Clarence C. Little developed the first inbred strain, the DBA (Dilute, brown non-Agouti) mouse.
In 1915, N.M Haldane identified first linkage in mouse between Albino mice and pink eye dilution on chromosome seven.
In 1921, C57BL became one of the most widely used mice in genetics and was the first strain to have its genome sequenced.
In 1982, Palmiter and Brinster implanted a foreign gene into fertilized egg, finally generating the first transgenic mice genetically engineered to express dominant oncogenes.
In 1982, the stimulation of expression from the MMTV-LTR (Mouse mammary tumor virus-Long terminal repeat) was done by multiple rounds of pregnancy and lactation to evaluate the relevance of a cellular proto-oncogene, c-myc.
=== Human and mouse: a genomic comparison ===
Genetic studies of common diseases in humans suffer significant limitations for practical and ethical reasons. Human cell lines can be used to model disease but it is difficult to study processes at the tissue level, within an organ or across the entire body. Mice can be a good representation of diseases in humans because:.
There are close similarities of physiology, development and cell biology between mice and humans.
Humans and mice both have around 30,000 protein-coding genes. The number of mouse genes without a corresponding human homologue is less than 1%.
90% of the human and mouse genomes are syntenic.
40% of both human and mouse genomes can be aligned at the nucleotide level.
Mice have relatively short gestation periods.
Mice take a brief time to reach sexual maturity.
Mice have large litter sizes.
The availability of hundreds of mutations affecting almost every tissue and aspect of development.
Mice may not be an ideal model for breast cancer. This is mainly due to the lack of precision in many of the models. When looking at metastasis, it is difficult to determine the precise location as well as its frequency. Another issue revolves around the epithelial sub types and the inability to specifically target them when targeting a mutation. An example of this would be determining the development of tumors in K14-Cre BRCA2 mice. In a standard case, the excision of BRCA2 resulted in no tumorgenesis, but if p53 was mutated and inactivated, tumorgenesis would occur. Therefore, there is not a definitive answer in terms of the origin of the tumor, due to the extra mutation in p53.
=== Metastatic mouse mammary carcinoma cell lines ===
Various mouse mammary carcinoma cell lines, like 4T1 and TS/A, are metastatic in syngeneic immunocompetent mice and can be used to identify genes and pathways involved in the metastatic process.
=== Simple tumor transplantation models ===
Transplantation of tumor cells into immunodeficient mice is a tool to study breast cancer and its metastatic effects. The transplantation occurs as either allotransplants or xenographic transplants. Commonly, human cells are inoculated in an immunocompromised murine recipient. Inoculating cells through intra ductal transplantations, by cleared mammary fat pad injections or by transplantations into the tail vein. Different organs can be seeded with breast cancer cells depending on the route of injection
Cardiac injection: Bone
Tail vein injection: Lung
Splenic injection: Liver
Carotid artery Injection: Brain
=== Tumor tissue transplant models ===
The specific immunodeficient mice that were used were the NOD/SCID mouse (non-obese diabetic/severe conditional immunodeficient). These mutations allow for the integration of new xenograft tissue. The mouse must first have their mammary fat pads humanized by injecting human telemorase-immortalized human mammary stromal fibroblasts(RMF/EG fibroblasts) into the mammary fat pads. Without this injection, the human mammary epithelial cells en-grafted onto the pad are unable to colonize and grow. The RMF/EG fibroblast must then be irradiated to allow the expression of key proteins and growth factors. After 4 weeks of development, the newly en-grafted human mammary epithelial cells expanded within the fat pad.
=== Genetically engineered mice to study metastasis ===
Genetically engineered mice are constructed to model human phenotypes and pathologies. Mutant mice may include transgenes using different delivery methods:
The use of bacteria-derived tetracycline-inducible system permitting the switching on or off (Tet-On/Tet-Off system)
Targeted mutations by knock in gene and knock out sequence by using Cre-Lox recombination system
Introduction of retro viral mutations
Introduction of chemically induced mutations
==== Transgenic mouse models of breast cancer ====
The mice undergoing the process of transgenesis are known as transgenic mice. A basic transgene has a promoter region, Protein coding sequence, Intron and a stop codon. Mouse mammary tumor virus (MMTV), is a retro virus that has been a known promoter to cause breast tumors once activated. MMTV is a heritable somatic mutagen whose target range is limited. It harbors a regulatory DNA sequence called the long terminal repeat (LTR), which promotes steroid-hormone-inducible transcription. Tumorgenesis that was induced by the mouse mammary tumor virus can also be done by integration of the viral genome. The sites of integration have been known to be critical genes for cellular regulation.
Whey acidic protein (WAP), is another common promoter used to generate mouse mammary cancer models. For a list of other mammary gland specific promoters and mouse models see.
==== MMTV-PyMT ====
MMTV-PyMT is the model of breast cancer metastasis, in which MMTV-LTR is used to drive the expression of mammary gland specific polyomavirus middle T-antigen, leading to a rapid development of highly metastatic tumors. MMTV-PyMT is the most commonly used model for the study of mammary tumor progression and metastasis. MMTV-PyMT mice are then crossed bred with other genetically modified mice to generate various types of breast cancer models, including:
PI3K/Akt signalling in metastasis can be demonstrated in MMTV-PyMT; Akt1−/− mice.
Chemoattractive paracrine loop of colony-stimulating factor-1 (CSF-1) and EGF ligands between tumor-associated macrophages (TAMs) and tumor cells, and the lung metastasis can be studied by crossing MMTV-PyMT mice with Csf-1−/− mice.
The role of an innate and adaptive immune response to assist metastasis can be studied in MMTV-PyMT; Rag1−/− mice in which CD4+ T cells are selectively lost. Interleukin-4 (IL4) lacking model of MMTV-PyMT; IL4−/− mice.
Role of the adhesion molecule CD44 in lung metastasis.
Conditional ablation in MMTV-PyMT breast cancer cells has been done to reveal pro-metastatic actions of the angiogenic factors, Vascular endothelial growth factor A (VEGF-A).
The role of autocrine transforming growth factor beta 1(TGF-β1) signaling on motility and survival in PymT cells derived from an MMTV-PymT mouse mammary cancer.
Others are MMTV-PyMT; uPA-/- and MMTV-PyMT; MEKK1-/-.
==== MMTV-HER2/neu ====
The MMTV-LTR can also be used to promote receptor tyrosine-protein kinase ErbB2 to transform the mouse mammary epithelium. ErbB2 is an oncogene amplified and overexpressed in around 20% of human breast cancers. The mice harbouring this oncogene develop multifocal adenocarcinomas with lung metastases at about 15 weeks after pregnancy.
To create a more accurate representation of HER2 gene mutations, researchers have fused the mouse gene containing neu and a rat gene containing neu. This addresses the issue in terms of modeling the amplification of HER2 in mice development. In the non-fused mouse, the mammary gland would revert to a near virgin, but with this addition the mammary gland maintained the developed function.
==== Bi-transgenic models ====
Mouse models having two transgenes are called bi transgenic. To check the cooperation of two oncogenes, Tim Stewert and group made the first bi-transgenic mouse models in 1987, MMTV-Myc and MMTV- Ras mice were crossed with a resulting acceleration in tumorigenesis. Expression of TGFβ in the breast cancer cells of MMTV-ErbB2; MMTV-TGFβ double-transgenic mice can induce higher levels of circulating tumor cells and lung metastasis. Ras gene can be combined with rtTA (reverse tetracycline transactivator) to generate bi-transgenic inducible mouse model through tetracycline-controlled transcriptional activation e.g. mice carrying TetO-KrasG12D (TOR) and MMTV-rtTA (MTB), comes with the transgene expressing the reverse tetracycline transactivator (rtTA) in mammary epithelial cells.
==== Tri-transgenic models ====
Tri-transgenic mouse models constitute of more than two genes. Multiple combinations and genetic modifications are made in such a way that either one or all the genes are put into a continuously expressed status, or in a controlled fashion to activate them at different time points. For example, TOM( TetO-myc); TOR; MTB mice, where both the myc (M) and ras (R) genes are under the control of tetracycline operators. They can also both be activated or deactivated by adding doxycycline. Other combinations in this respect are TOM; Kras; MTB, where myc can be induced and uninduced at various time points while Kras is in continuous expressed state, and myc; TOR; MTB model is vice versa.
== Applications of genetically modified mice to study metastasis ==
Metastatic cascade can be studied by keeping the gene activation under control or by adding a reporter gene e.g. Beta actin GFP (Green fluorescent protein) or RFP (Red fluorescent protein).
=== Identification of genes that regulate metastasis ===
By knocking in/knocking out specific genes by homologous recombination, the extent of metastasis can be measured and new target genes identification can be achieved e.g. a gene that consistently regulates metastatic behavior of cancer cells is TGF-β1. Acute ablation of TGF-β signaling in MMTV-PyMT mammary tumor cells leads to a five-fold increase in lung metastasis.
Certain enhancer regions can also be analyzed and can be determined to be a crucial part of cell proliferation e.g. an enhancing region that is associated with a cancer critical gene p53 which was determined via CRISPR-Cas9.
=== Lineage tracing in metastasis models ===
The quantitative lineage-tracing strategies have proven to be successful in resolving cell fates in normal epithelial tissues either using tissue –specific or stem-cell-specific transgenes. To conduct an inducible lineage-tracing experiment two components must be engineered into the mouse genome: a switch and a reporter. The switch is commonly a drug-regulated form of the bacterial enzyme Cre-recombinase. This enzyme recognizes specific sequences, called LoxP sites. Proteins that are capable of enhancing the identification of labeled cells or a specific population in unlabelled cells are encoded by the reporter transgenes. After harvesting all the ten mouse mammary glands from the transgenic mice, single cell suspension is usually made and transplanted either in tail vein of non transgenic recipient mice or in cleared fat pad of non-transgenic mice repopulating the mammary fat pad. These cells are then followed in the blood stream, lungs, bone marrow and liver to look for the favorable site of metastasis.these transgenic cells can be traced according to their special features of either fluorescence or induced by placing the recipients on doxycycline food.
=== Circulating tumor cells ===
Another tool to study breast cancer metastasis is to look for circulating tumor cells in transgenic mice e.g. MMTV-PyMT mice can respond to various therapies in shedding tumor cells in the blood leading to lung metastasis. Not only in blood but cells can be detected in bone marrow e.g. cytokeratin-positive cells in the bone marrow of MMTV-pyMT and MMTV-Neu transgenic mice were identified but not in the wild type controls.
=== Limitations ===
In the absence of specific markers for mammary cells, models with genetic marking of tumor cells gives the best experimental advantage, however the low volume of peripheral blood that can be obtained from live animals limits the application of this technique.
== In vivo imaging of metastatic mouse models ==
Transgenic mouse models can be imaged by various non-invasive techniques.
=== Bioluminescence imaging ===
Bioluminescence imaging relies on the detection of light produced by the enzymatic oxidation of an exogenous substrate. The substrate luciferin, is oxidized to oxyluciferin in the presence of luciferase and emits light, which can be detected using an IVIS system such as a Xenogen machine. Dissociated mammary cells from MMTV-PyMT: IRES: Luc; MTB (Internal ribosome entry site: Luciferin) animals (which were not exposed to doxycycline) can be injected into the lateral tail veins of immunodeficient mice on a doxycycline-free diet. No bioluminescence signal will be observed in the lungs of recipient mice until they are given doxycycline food. Bioluminescence can then be detected in the chest within 2 weeks of the start of doxycycline exposure. Luciferase is injected just before taking the images.
=== Fluorescent imaging ===
Intravital microscopy with multi photon excitation is a technique to visualize genetically engineered cells directly in vivo. Multi step metastatic cascades can be visualized by labelling with unique fluorescent colour under fluorescence microscope.
=== Radioisotopic imaging ===
Positron emission tomography (PET), single photon emission computed tomography (SPECT) and computed tomography (CT) have been used to compare the efficiency of these in vivo imaging for detecting lesions at an early stage and to evaluate the response to chemotherapy.
=== MRI Imaging ===
Magnetic resonance imaging requires the use of nano-particles(liposomes) and an MRI contrast agent called gadolinium. The particles were then placed in vesicles via a polycarbonate membrane filter. The nano-particles are injected into the metastases evolved mice, and left there for twenty-four hours. These mice are then scanned, and in the imaging software there are accumulations of these particles in certain areas where cells have metastasized.
== See also ==
Ensembl genome database of model organisms
Fate mapping
Firefly luciferin
Gene targeting
Gene trapping
Genetic recombination
History of model organisms
Homologous recombination
Recombinase-mediated cassette exchange
Site-specific recombinase technology
== References ==
== External links ==
http://www.la-press.com/tetracycline-regulated-systems-in-functional-oncogenomics-article-a200 A detailed overview of Tet-systems in functional oncogenomics | Wikipedia/Mouse_models_of_breast_cancer_metastasis |
The Generic Model Organism Database (GMOD) project provides biological research communities with a toolkit of open-source software components for visualizing, annotating, managing, and storing biological data. The GMOD project is funded by the United States National Institutes of Health, National Science Foundation and the USDA Agricultural Research Service.
== History ==
The GMOD project was started in the early 2000s as a collaboration between several model organism databases (MODs) who shared a need to create similar software tools for processing data from sequencing projects. MODs, or organism-specific databases, describe genome and other information about important experimental organisms in the life sciences and capture the large volumes of data and information being generated by modern biology. Rather than each group designing their own software, four major MODs--FlyBase, Saccharomyces Genome Database, Mouse Genome Database, and at or run off a Chado schema database.
== Chado database schema ==
The Chado schema aims to cover many of the classes of data frequently used by modern biologists, from genetic data to phylogenetic trees to publications to organisms to microarray data to IDs to RNA/protein expression. Chado makes extensive use of controlled vocabularies to type all entities in the database; for example: genes, transcripts, exons, transposable elements, etc., are stored in a feature table, with the type provided by Sequence Ontology. When a new type is added to the Sequence Ontology, the feature table requires no modification, only an update of the data in the database. The same is largely true of analysis data that can be stored in Chado as well.
The existing core modules of Chado are:
sequence - for sequences/features
cv - for controlled-vocabs/ontologies
general - currently just dbxrefs
organism - taxonomic data
pub - publication and references
companalysis - augments sequence module with computational analysis data
map - non-sequence maps
genetic - genetic and phenotypic data
expression - gene expression
natural diversity - population data
== Software ==
The full list of GMOD software components is found on the GMOD Components page. These components include:
== Participating databases ==
The following organism databases are contributing to and/or adopting GMOD components for model organism databases.
== Related projects ==
Bioperl, BioJava, Biopython, BioRuby, etc.
Ensembl
Gene Ontology
DAS
Genomics Unified Schema
Manatee: Manual Annotation Tool
Biocurator.org
Open Biomedical Ontologies
Sequence Ontology Project
== See also ==
Biological database
Genome project
Genomics
Genome
== References ==
== External links ==
GMOD website | Wikipedia/Generic_Model_Organism_Database |
An animal model (short for animal disease model) is a living, non-human, often genetic-engineered animal used during the research and investigation of human disease, for the purpose of better understanding the disease process without the risk of harming a human. Although biological activity in an animal model does not ensure an effect in humans, many drugs, treatments and cures for human diseases are developed in part with the guidance of animal models. Animal models representing specific taxonomic groups in the research and study of developmental processes are also referred to as model organisms. There are three main types of animal models: Homologous, Isomorphic and Predictive.
Homologous animals have the same causes, symptoms and treatment options as would humans who have the same disease.
Isomorphic animals share the same symptoms and treatments, only.
Predictive models are similar to a particular human disease in only a couple of aspects. However, these are useful in isolating and making predictions about mechanisms of a set of disease features.
== Phylogeny and genetic similarity ==
Although scientific study of animals predates Charles Darwin by several hundred years, the primary justification for the use of animals in research is based on the evolutionary principle that all organisms share some degree of relatedness and genetic similarity due to common ancestry. The study of taxonomic human relatives, then, can provide a great deal of information about mechanism and disease within the human body that can be useful in medicine.
Various phylogenetic trees for vertebrates have been constructed using comparative proteomics, genetics, genomics as well as the geochemical and fossil record. These estimations tell us that humans and chimpanzees last shared a common ancestor about 6 million years ago (mya). As our closest relatives, chimpanzees have a lot of potential to tell us about mechanisms of disease (and what genes may be responsible for human intelligence). However, chimpanzees are rarely used in research and are protected from highly invasive procedures. The most common animal model is the rodent. Phylogenic trees estimate that humans and rodents last shared a common ancestor ~80-100mya. Despite this distant split, humans and rodents have far more similarities than they do differences. This is due to the relative stability of large portions of the genome; making the use of vertebrate animals particularly productive.
Recently, genomic data has been added to techniques to make close comparisons between species and determine relatedness. Humans share about 99% of our genome with chimpanzees (98.7% with bonobos) and over 90% with the mouse. With so much of the genome conserved across species, it is relatively impressive that the differences between humans and mice can be accounted for in approximately six thousand genes (of ~30,000 total). Scientists have been able to take advantage of these similarities in generating experimental and predictive models of human disease.
== Disease models ==
Animal models serving in research may have an existing, inbred or induced disease or injury that is similar to a human condition. These test conditions are often termed as animal models of disease. The use of animal models allows researchers to investigate disease states in ways which would be inaccessible in a human patient, performing procedures on the non-human animal that imply a level of harm that would not be considered ethical to inflict on a human.
As in noted the introduction, animal models can be classified as homologous, isomorphic or predictive. Animal models can also be more broadly classified into four categories:
experimental,
spontaneous,
negative,
orphan.
Experimental models are most common. These refer to models of disease that resemble human conditions in phenotype or response to treatment but are induced artificially in the laboratory. Some examples include:
The use of metrazol (pentylenetetrazol) as an animal model of epilepsy
Immunisation with an auto-antigen to induce an immune response to model autoimmune diseases such as Experimental autoimmune encephalomyelitis
Occlusion of the middle cerebral artery as an animal model of ischemic stroke
Injection of blood in the basal ganglia of mice as a model for hemorrhagic stroke
Sepsis and septic shock induction by impairing the integrity of barrier tissues, administering live pathogens or toxins
Infecting animals with pathogens to reproduce human infectious diseases
Injecting animals with agonists or antagonists of various neurotransmitters to reproduce human mental disorders
Using ionizing radiation to cause tumors
Using gene transfer to cause tumors
Implanting animals with tumors to test and develop treatments using ionizing radiation
Genetically selected (such as in diabetic mice also known as NOD mice)
Various animal models for screening of drugs for the treatment of glaucoma
The use of the ovariectomized rat in osteoporosis research
Use of Plasmodium yoelii as a model of human malaria
Spontaneous models refer to diseases that are analogous to human conditions that occur naturally in the animal being studied. These models are rare, but informative.
Negative models essentially refer to control animals, which are useful for validating an experimental result.
Orphan models refer to diseases for which there is no human analog and occur exclusively in the species studied.
The increase in knowledge of the genomes of non-human primates and other mammals that are genetically close to humans is allowing the production of genetically engineered animal tissues, organs and even animal species which express human diseases, providing a more robust model of human diseases in an animal model.
The best models of disease are similar in etiology (mechanism of cause) and phenotype (signs and symptoms) to the human equivalent. However complex human diseases can often be better understood in a simplified system in which individual parts of the disease process are isolated and examined. For instance, behavioral analogues of anxiety or pain in laboratory animals can be used to screen and test new drugs for the treatment of these conditions in humans. A 2000 study found that animal models concorded (coincided on true positives and false negatives) with human toxicity in 71% of cases, with 63% for nonrodents alone and 43% for rodents alone.
In 1987, Davidson et al. suggested that selection of an animal model for research be based on nine considerations. These include
"1) appropriateness as an analog, 2) transferability of information, 3) genetic uniformity of organisms, where applicable, 4) background knowledge of biological properties, 5) cost and availability, 6) generalizability of the results, 7) ease of and adaptability to experimental manipulation, 8) ecological consequences, and 9) ethical implications."
== Behavioral sciences ==
Animal models observed in the sciences of psychology and sociology are often termed animal models of behavior. It is difficult to build an animal model that perfectly reproduces the symptoms of depression in patients. Animals lack self-consciousness, self-reflection and consideration; moreover, hallmarks of the disorder such as depressed mood, low self-esteem or suicidality are hardly accessible in non-humans. However, depression, as other mental disorders, consists of endophenotypes that can be reproduced independently and evaluated in animals. An ideal animal model offers an opportunity to understand molecular, genetic and epigenetic factors that may lead to depression. By using animal models, the underlying molecular alterations and the causal relationship between genetic or environmental alterations and depression can be examined, which would afford a better insight into pathology of depression. In addition, animal models of depression are indispensable for identifying novel therapies for depression.
== Challenges and criticisms ==
Many animal models serving as test subjects in biomedical research, such as rats and mice, may be selectively sedentary, obese and glucose intolerant. This may confound their use to model human metabolic processes and diseases as these can be affected by dietary energy intake and exercise.
Animal models of psychiatric illness give rise to other concerns. Qualitative assessments of behavior are too often subjective. This would lead the investigator to observe what they want to observe in subjects, and to render conclusions in line with their expectations. Also, the imprecise diagnostic criteria for psychiatric illnesses inevitably lead to problems modeling the condition; e.g., since a person with major depressive disorder may experience weight loss or weight gain, insomnia or hypersomnia, we cannot with any certainty say that a rat with insomnia and weight loss is depressed. Furthermore, the complex nature of psychiatric conditions makes it difficult/impossible to translate human behaviors and deficits; e.g., language deficit plays a major role in autistic spectrum disorders, but – since rodents do not have language – it is not possible to develop a language-impaired "autistic" mouse.
== Ethics ==
Debate about the ethical use of animals in research dates at least as far back as 1822 when the British Parliament enacted the first law for animal protection preventing cruelty to cattle, the Cruel Treatment of Cattle Act 1822. This was followed by the Cruelty to Animals Act 1835 and the Cruelty to Animals Act 1849, which criminalized ill-treating, over-driving, and torturing animals. In 1876, under pressure from the National Anti-Vivisection Society, the Cruelty to Animals Act 1849 was amended by the Cruelty to Animals Act 1876 to include regulations governing the use of animals in research. This new act stipulated that 1) experiments must be proven absolutely necessary for instruction, or to save or prolong human life; 2) animals must be properly anesthetized; and 3) animals must be killed as soon as the experiment is over. Today, these three principles are central to the laws and guidelines governing the use of animals and research. In the U.S., the Animal Welfare Act of 1970 (see also Laboratory Animal Welfare Act) set standards for animal use and care in research. This law is enforced by APHIS's Animal Care program see AWA policies.
In academic settings in which NIH funding is used for animal research, institutions are governed by the NIH Office of Laboratory Animal Welfare (OLAW). At each site, OLAW guidelines and standards are upheld by a local review board called the Institutional Animal Care and Use Committee (IACUC). All laboratory experiments involving living animals are reviewed and approved by this committee. In addition to proving the potential for benefit to human health, minimization of pain and distress, and timely and humane euthanasia, experimenters must justify their protocols based on the principles of Replacement, Reduction and Refinement.
Replacement refers to efforts to engage alternatives to animal use. This includes the use of computer models, non-living tissues and cells, and replacement of "higher-order" animals (primates and mammals) with "lower" order animals (e.g. cold-blooded animals, invertebrates, bacteria) wherever possible (list of common model organisms approved for use by the NIH).
Reduction refers to efforts to minimize number of animals used during the course of an experiment, as well as prevention of unnecessary replication of previous experiments. To satisfy this requirement, mathematical calculations of statistical power are employed to determine the minimum number of animals that can be used to get a statistically significant experimental result. Reduction involves methods to maximize information provided while minimizing the number of animals applied.
Refinement refers to efforts to make experimental design as painless and efficient as possible in order to minimize the suffering of each animal subject.
While significant advances have been made in the care and treatment of animals, this is an ever-evolving debate. Animal rights and protection groups such as the ASPCA, PETA and BUAV continue to advocate for the best laboratory conditions, and experimental protocols possible for animals in research. Pressure from these groups has also led to novel modes of experimentation, which does not involve the sacrifice of live animals.
One aspect of this debate; however, continues to be difficult to resolve: the classification of animals according to a hierarchy, which protects some species more than others. Next to humans, primates are the most protected species in experimentation. The rationale for this has both evolutionary and philosophical underpinnings. Because chimpanzees and other non-human primates can demonstrate intelligence, and social structure that they have a life experiences that is more cognitively complex than lower species. Conversely, this kind of moralizing of complexity of interaction and thought could be considered speciesism. Ultimately, this is an argument not likely to be resolved, however most people are more comfortable with the idea of experimentation that involves worms or flies than mice, dogs, or monkeys.
== Alternatives ==
Ethical concerns, as well as the cost, maintenance and relative inefficiency of animal research has encouraged development of alternative methods for the study of disease. Cell culture and in vitro studies provide an alternative that preserves the physiology of the living cell, but does not require the sacrifice of an animal for mechanistic studies. Human induced pluripotent stem cells can also elucidate new mechanisms for understanding cancer and cell regeneration. Imaging studies (such as MRI or PET scans) enable non-invasive study of human subjects. Recent advances in genetics and genomics can identify disease-associated genes, which can be targeted for therapies.
== See also ==
Animal models of autism
Animal models of schizophrenia
Animal testing on invertebrates
Animal testing on rodents
Animal testing
Britches (monkey)
Ensembl genome database
History of animal testing
History of model organisms
In vivo
Knockout rat
Mouse models of colorectal and intestinal cancer
== References ==
== External links ==
Transgenic Animal Models – Biomedcode
Knock Out Rat Consortium – KORC
Emice – National Cancer Institute | Wikipedia/Animal_disease_model |
In geography, the temperate climates of Earth occur in the middle latitudes (approximately 23.5° to 66.5° N/S of the Equator), which span between the tropics and the polar regions of Earth. These zones generally have wider temperature ranges throughout the year and more distinct seasonal changes compared to tropical climates, where such variations are often small; they usually differ only in the amount of precipitation.
In temperate climates, not only do latitudinal positions influence temperature changes, but various sea currents, prevailing wind direction, continentality (how large a landmass is) and altitude also shape temperate climates.
The Köppen climate classification defines a climate as "temperate" C, when the mean temperature is above −3 °C (26.6 °F) but below 18 °C (64.4 °F) in the coldest month to account for the persistence of frost. However, some adaptations of Köppen set the minimum at 0 °C (32.0 °F). Continental climates are classified as D and considered to be varieties of temperate climates, having more extreme temperatures, with mean temperatures in the coldest month usually being below −3 °C (26.6 °F).
== Zones and climates ==
The north temperate zone extends from the Tropic of Cancer (approximately 23.5° north latitude) to the Arctic Circle (approximately 66.5° north latitude). The south temperate zone extends from the Tropic of Capricorn (approximately 23.5° south latitude) to the Antarctic Circle (at approximately 66.5° south latitude).
In some climate classifications, the temperate zone may be divided into several smaller climate zones, based on monthly temperatures, the coldest month, and rainfall. These can include the subtropical zone (humid subtropical and Mediterranean climate), and the cool temperate zone (oceanic and continental climates).
=== Subtropical zone ===
These climates are typically found in the more equatorial regions of the temperate zone, between 23.5° and 35° north or south. They are influenced more by the tropics than by other temperate climate types, usually experiencing warmer temperatures throughout the year, with longer, hotter summers and shorter, milder winters. Freezing precipitation is uncommon in this part of the temperate zone.
==== Humid subtropical (Cfa) and monsoon subtropical (Cwa) climates ====
Humid subtropical climates generally have long, hot and humid summers with frequent convective showers in summer, and a peak seasonal rainfall in the hottest months. Winters are normally mild and above freezing in the humid subtropics. Warm ocean currents are usually found in coastal areas with humid subtropical climates. This type of climate is normally located along leeward lower east coasts of continents such as in southeast and central Argentina, Uruguay and south of Brazil, Northern Vietnam, the southeast portions of East Asia, southern and portions of the northeast and midwestern United States and portions of, South Africa, Ethiopia, and eastern Australia. In some areas with a humid subtropical climate (most notably southeast China and North India), there is an even sharper wet-dry season, called a monsoon subtropical climate or subtropical monsoon (Cwa). In these regions, winters are quite chilly and dry and summers have very heavy rainfall. Some Cwa areas in southern China report more than 80% of annual precipitation in the five warmest months (southwest monsoon).
==== Mediterranean climates (Csa, Csb) ====
Mediterranean climates have the opposite rainfall pattern to dry-winter climates, with a dry summer and wet winter. This climate occurs mostly at the western edges and coasts of the continents and are bounded by arid deserts on their equatorward sides that brings dry winds causing the dry season of summer, and oceanic climates to the poleward sides that are influenced by cool ocean currents and air masses that bring the rainfall of winter. The five main Mediterranean regions of the world are the Mediterranean basin in North Africa, Southern Europe, and West Asia, coastal California in the United States, the South and West states of Australia, the Western Cape of South Africa and the south and southwestern coast of Chile.
==== Subtropical highland climates (Cwb, Cfb) ====
Subtropical highland climates are climate variants often grouped together with oceanic climates found in some mountainous areas of either the tropics or subtropics. They have characteristically mild temperatures year-round, featuring the four seasons in the subtropics and no marked seasons in the tropics, the latter usually remaining mild to cool through most of the year. Subtropical highland climates under the Cfb classification usually have rainfall spread relatively evenly in all months of the year similar to most oceanic climates while climates under the Cwb classification have significant monsoon influence, usually having dry winters and wet summers.
=== Middle latitude zone ===
These climates occur in the middle latitudes, between approximately 35° and 66.5° north and south of the equator. There is an equal climatic influence from both the polar and tropical zones in this climate region. Two types of climates are in this zone, a milder oceanic one and more severe seasonal continental one. Most prototypical temperate climates have a distinct four-season pattern, especially in the continental climate sector.
==== Oceanic climates (Cfb) ====
Oceanic climates are created by the on-shore flow from the cool high latitude oceans to their west. This causes the climate to have mild summers and cool (but not cold) winters, and relative humidity and precipitation evenly distributed throughout the year. These climates are frequently cloudy and cool, and winters are milder than those in the continental climate.
Regions with oceanic climates include northwestern Europe, northwestern North America, southeastern and southwestern South America, southeastern Australia and most of New Zealand.
==== Humid continental climates (Dfa, Dfb, Dwa, Dwb, Dsa, Dsb) ====
Humid continental climates are considered as a variety of temperate climates due to lying in the temperate zones, although they are classified separately from other temperate climates in the Köppen climate classification. In contrast to oceanic climates, they are created by large land masses and seasonal changes in wind direction. This causes humid continental climates to have severe temperatures for the season compared to other temperate climates, meaning a hot summer and cold winter. Precipitation may be evenly distributed throughout the year, while in some locations there is a summer accent on rainfall.
Regions with humid continental climates include southeastern Canada, the upper portions of the eastern United States, portions of eastern Europe, parts of China, Japan and the Korean Peninsula.
=== Subpolar zone ===
These are temperate climates that compared to the subtropics are on the poleward edge of the temperate zone. Therefore, they still have four marked seasons including a warmer one, but are far more influenced by the polar zones than any other but the very polar climates (tundra and ice cap climate).
==== Subpolar oceanic and cold subtropical highland climates (Cfc, Cwc) ====
Areas with subpolar oceanic climates feature an oceanic climate but are usually located closer to polar regions. As a result of their location, these regions tend to be on the cool end of oceanic climates. Snowfall tends to be more common here than in other oceanic climates. Subpolar oceanic climates are less prone to temperature extremes than subarctic climates or continental climates, featuring milder winters than these climates but still with similar summers. This variant of an oceanic climate is found in parts of coastal Iceland, the Faroe Islands, parts of Scotland, northwestern coastal areas of Norway such as Lofoten and reaching to 70° north on some islands, uplands near the coast of southwestern Norway, the Aleutian Islands of Alaska and northern parts of the Alaskan Panhandle, some parts of Southern Argentina and Chile (though most regions are still classified as continental subantarctic), and a few highland areas of Tasmania, the Australian Alps and Southern Alps of New Zealand. This type of climate is even found in tropical areas such as the Papuan Highlands in Indonesia. Cfc is the categorization for this regime. Even in the middle of summer, temperatures exceeding 20°C (68 °F) are exceptional weather events in the most maritime of those locations impacted by this regime. In some parts of this climate, temperatures as high as 30°C (86°F) have been recorded on rare occasions, while temperatures as low as −15 °C (5 °F) have still been recorded on rare occasions.
A cold variant of the monsoon-influenced subtropical highland climate similar to subpolar oceanic climates occurs in small areas in the Chinese provinces of Sichuan and Yunnan, and parts of the Altiplano between Bolivia, Peru and Chile, where summers are sufficiently short to be Cwc with fewer than four months over 10 °C (50 °F) due to the high altitudes at these locations. El Alto, Bolivia, is one of the few confirmed towns that features this variation of the subtropical highland climate.
==== Cold summer mediterranean climates (Csc) ====
Cold summer mediterranean climates (Csc) are present in high-elevation areas around coastal Csb climate areas, where the strong maritime influence prevents the average winter monthly temperature from dropping below 0 °C. Despite the maritime influence, they are classified alongside other mediterranean climates in the Köppen classification rather than oceanic climates like subtropical highland climates due to the opposite rainfall pattern. This climate is rare and is predominantly found in climate fringes and isolated areas of the Cascades and Andes Mountains, as the dry-summer climate extends further poleward in the Americas than elsewhere.
== Human aspects ==
=== Demography, fauna and flora ===
The vast majority of the world's human population resides in temperate zones, especially in the Northern Hemisphere, due to its greater mass of land and lack of extreme temperatures. The biggest described number of taxa in a temperate region is found in southern Africa, where some 24,000 taxa (species and infraspecific taxa) have been described.
=== Agriculture ===
Farming is a large-scale practice in the temperate regions (except for boreal/subarctic regions) due to the plentiful rainfall and warm summers, because most agricultural activity occurs in the spring and summer, cold winters have a small effect on agricultural production. Extreme winters or summers have a huge impact on the productivity of agriculture which is less common.
=== Urbanization ===
Temperate regions have the majority of the world's population, which leads to large cities. There are a couple of factors why the climate of large city landscapes differs from the climate of rural areas. One factor is the strength of the absorption rate of buildings and asphalt, which is higher than that of natural land. The other large factor is the burning of fossil fuels from buildings and vehicles. These factors have led to the average climate of cities to be warmer than surrounding areas.
== See also ==
Geographical zone
Habitat
Köppen climate classification
Middle latitudes
Polar circle
Subtropics
Tropics
Subarctic
Highland temperate climate
Humid temperate climate
Subhumid temperate climate
== References == | Wikipedia/Temperateness |
In geography, the temperate climates of Earth occur in the middle latitudes (approximately 23.5° to 66.5° N/S of the Equator), which span between the tropics and the polar regions of Earth. These zones generally have wider temperature ranges throughout the year and more distinct seasonal changes compared to tropical climates, where such variations are often small; they usually differ only in the amount of precipitation.
In temperate climates, not only do latitudinal positions influence temperature changes, but various sea currents, prevailing wind direction, continentality (how large a landmass is) and altitude also shape temperate climates.
The Köppen climate classification defines a climate as "temperate" C, when the mean temperature is above −3 °C (26.6 °F) but below 18 °C (64.4 °F) in the coldest month to account for the persistence of frost. However, some adaptations of Köppen set the minimum at 0 °C (32.0 °F). Continental climates are classified as D and considered to be varieties of temperate climates, having more extreme temperatures, with mean temperatures in the coldest month usually being below −3 °C (26.6 °F).
== Zones and climates ==
The north temperate zone extends from the Tropic of Cancer (approximately 23.5° north latitude) to the Arctic Circle (approximately 66.5° north latitude). The south temperate zone extends from the Tropic of Capricorn (approximately 23.5° south latitude) to the Antarctic Circle (at approximately 66.5° south latitude).
In some climate classifications, the temperate zone may be divided into several smaller climate zones, based on monthly temperatures, the coldest month, and rainfall. These can include the subtropical zone (humid subtropical and Mediterranean climate), and the cool temperate zone (oceanic and continental climates).
=== Subtropical zone ===
These climates are typically found in the more equatorial regions of the temperate zone, between 23.5° and 35° north or south. They are influenced more by the tropics than by other temperate climate types, usually experiencing warmer temperatures throughout the year, with longer, hotter summers and shorter, milder winters. Freezing precipitation is uncommon in this part of the temperate zone.
==== Humid subtropical (Cfa) and monsoon subtropical (Cwa) climates ====
Humid subtropical climates generally have long, hot and humid summers with frequent convective showers in summer, and a peak seasonal rainfall in the hottest months. Winters are normally mild and above freezing in the humid subtropics. Warm ocean currents are usually found in coastal areas with humid subtropical climates. This type of climate is normally located along leeward lower east coasts of continents such as in southeast and central Argentina, Uruguay and south of Brazil, Northern Vietnam, the southeast portions of East Asia, southern and portions of the northeast and midwestern United States and portions of, South Africa, Ethiopia, and eastern Australia. In some areas with a humid subtropical climate (most notably southeast China and North India), there is an even sharper wet-dry season, called a monsoon subtropical climate or subtropical monsoon (Cwa). In these regions, winters are quite chilly and dry and summers have very heavy rainfall. Some Cwa areas in southern China report more than 80% of annual precipitation in the five warmest months (southwest monsoon).
==== Mediterranean climates (Csa, Csb) ====
Mediterranean climates have the opposite rainfall pattern to dry-winter climates, with a dry summer and wet winter. This climate occurs mostly at the western edges and coasts of the continents and are bounded by arid deserts on their equatorward sides that brings dry winds causing the dry season of summer, and oceanic climates to the poleward sides that are influenced by cool ocean currents and air masses that bring the rainfall of winter. The five main Mediterranean regions of the world are the Mediterranean basin in North Africa, Southern Europe, and West Asia, coastal California in the United States, the South and West states of Australia, the Western Cape of South Africa and the south and southwestern coast of Chile.
==== Subtropical highland climates (Cwb, Cfb) ====
Subtropical highland climates are climate variants often grouped together with oceanic climates found in some mountainous areas of either the tropics or subtropics. They have characteristically mild temperatures year-round, featuring the four seasons in the subtropics and no marked seasons in the tropics, the latter usually remaining mild to cool through most of the year. Subtropical highland climates under the Cfb classification usually have rainfall spread relatively evenly in all months of the year similar to most oceanic climates while climates under the Cwb classification have significant monsoon influence, usually having dry winters and wet summers.
=== Middle latitude zone ===
These climates occur in the middle latitudes, between approximately 35° and 66.5° north and south of the equator. There is an equal climatic influence from both the polar and tropical zones in this climate region. Two types of climates are in this zone, a milder oceanic one and more severe seasonal continental one. Most prototypical temperate climates have a distinct four-season pattern, especially in the continental climate sector.
==== Oceanic climates (Cfb) ====
Oceanic climates are created by the on-shore flow from the cool high latitude oceans to their west. This causes the climate to have mild summers and cool (but not cold) winters, and relative humidity and precipitation evenly distributed throughout the year. These climates are frequently cloudy and cool, and winters are milder than those in the continental climate.
Regions with oceanic climates include northwestern Europe, northwestern North America, southeastern and southwestern South America, southeastern Australia and most of New Zealand.
==== Humid continental climates (Dfa, Dfb, Dwa, Dwb, Dsa, Dsb) ====
Humid continental climates are considered as a variety of temperate climates due to lying in the temperate zones, although they are classified separately from other temperate climates in the Köppen climate classification. In contrast to oceanic climates, they are created by large land masses and seasonal changes in wind direction. This causes humid continental climates to have severe temperatures for the season compared to other temperate climates, meaning a hot summer and cold winter. Precipitation may be evenly distributed throughout the year, while in some locations there is a summer accent on rainfall.
Regions with humid continental climates include southeastern Canada, the upper portions of the eastern United States, portions of eastern Europe, parts of China, Japan and the Korean Peninsula.
=== Subpolar zone ===
These are temperate climates that compared to the subtropics are on the poleward edge of the temperate zone. Therefore, they still have four marked seasons including a warmer one, but are far more influenced by the polar zones than any other but the very polar climates (tundra and ice cap climate).
==== Subpolar oceanic and cold subtropical highland climates (Cfc, Cwc) ====
Areas with subpolar oceanic climates feature an oceanic climate but are usually located closer to polar regions. As a result of their location, these regions tend to be on the cool end of oceanic climates. Snowfall tends to be more common here than in other oceanic climates. Subpolar oceanic climates are less prone to temperature extremes than subarctic climates or continental climates, featuring milder winters than these climates but still with similar summers. This variant of an oceanic climate is found in parts of coastal Iceland, the Faroe Islands, parts of Scotland, northwestern coastal areas of Norway such as Lofoten and reaching to 70° north on some islands, uplands near the coast of southwestern Norway, the Aleutian Islands of Alaska and northern parts of the Alaskan Panhandle, some parts of Southern Argentina and Chile (though most regions are still classified as continental subantarctic), and a few highland areas of Tasmania, the Australian Alps and Southern Alps of New Zealand. This type of climate is even found in tropical areas such as the Papuan Highlands in Indonesia. Cfc is the categorization for this regime. Even in the middle of summer, temperatures exceeding 20°C (68 °F) are exceptional weather events in the most maritime of those locations impacted by this regime. In some parts of this climate, temperatures as high as 30°C (86°F) have been recorded on rare occasions, while temperatures as low as −15 °C (5 °F) have still been recorded on rare occasions.
A cold variant of the monsoon-influenced subtropical highland climate similar to subpolar oceanic climates occurs in small areas in the Chinese provinces of Sichuan and Yunnan, and parts of the Altiplano between Bolivia, Peru and Chile, where summers are sufficiently short to be Cwc with fewer than four months over 10 °C (50 °F) due to the high altitudes at these locations. El Alto, Bolivia, is one of the few confirmed towns that features this variation of the subtropical highland climate.
==== Cold summer mediterranean climates (Csc) ====
Cold summer mediterranean climates (Csc) are present in high-elevation areas around coastal Csb climate areas, where the strong maritime influence prevents the average winter monthly temperature from dropping below 0 °C. Despite the maritime influence, they are classified alongside other mediterranean climates in the Köppen classification rather than oceanic climates like subtropical highland climates due to the opposite rainfall pattern. This climate is rare and is predominantly found in climate fringes and isolated areas of the Cascades and Andes Mountains, as the dry-summer climate extends further poleward in the Americas than elsewhere.
== Human aspects ==
=== Demography, fauna and flora ===
The vast majority of the world's human population resides in temperate zones, especially in the Northern Hemisphere, due to its greater mass of land and lack of extreme temperatures. The biggest described number of taxa in a temperate region is found in southern Africa, where some 24,000 taxa (species and infraspecific taxa) have been described.
=== Agriculture ===
Farming is a large-scale practice in the temperate regions (except for boreal/subarctic regions) due to the plentiful rainfall and warm summers, because most agricultural activity occurs in the spring and summer, cold winters have a small effect on agricultural production. Extreme winters or summers have a huge impact on the productivity of agriculture which is less common.
=== Urbanization ===
Temperate regions have the majority of the world's population, which leads to large cities. There are a couple of factors why the climate of large city landscapes differs from the climate of rural areas. One factor is the strength of the absorption rate of buildings and asphalt, which is higher than that of natural land. The other large factor is the burning of fossil fuels from buildings and vehicles. These factors have led to the average climate of cities to be warmer than surrounding areas.
== See also ==
Geographical zone
Habitat
Köppen climate classification
Middle latitudes
Polar circle
Subtropics
Tropics
Subarctic
Highland temperate climate
Humid temperate climate
Subhumid temperate climate
== References == | Wikipedia/Temperate |
The subhumid temperate climate also called monsoon temperate climate, is a temperate climate sub-type with monsoon influence, that is a climate with dry winter and wet summer. Although the terms subhumid temperate climate and monsoon temperate climate are not officially used in the Köppen climate classification, climates of this type may fall under the Cw classification for dry winters.
== Sub-types ==
=== Monsoon subtropical climate ===
A Monsoon subtropical climate, officially classified as a Subhumid subtropical climate or Monsoon-influenced humid subtropical climate under the Köppen classification (Cwa), has a hot summer. Extensively present in South and Southeast Asia, mainly India, Myanmar, and Nepal and Southern Africa, Zambia and Angola; it can also be found in South America, isolated zones of Bolivia, Brazil and Argentina. It also occurs in parts of tropical highlands of São Paulo state, Mato Grosso do Sul and near the Andean highland in northwestern Argentina. These highland areas feature summer temperatures that are warm enough to fall outside the subtropical highland climate category Cwb.
=== Highland subhumid temperate climate ===
A Highland subhumid temperate climate, officially classified as a Subtropical highland climate or Monsoon-influenced temperate oceanic climate under the Köppen classification (Cwb), exists in elevated portions of the world that are within either the tropics or subtropics, though it is typically found in mountainous locations in some tropical countries. Despite the latitude, the higher altitudes of these regions mean that the climate tends to share characteristics with oceanic climates.
=== Subpolar subhumid temperate climate ===
A Subpolar subhumid temperate climate, officially classified as a Cold subtropical highland climate or Monsoon-influenced subpolar oceanic climate under the Köppen classification (Cwc), is a sub-alpine climate. It is located only in Andean high plains in Bolivia and Perú, from 3200 m until 4000 m. It is a transition climate between Cwb and alpine climate ET.
== See also ==
Humid temperate climate
Mediterranean climate
Temperate climate
Köppen climate classification
== References == | Wikipedia/Subhumid_temperate_climate |
The humid temperate climate is a temperate climate sub-type mainly located at mid latitudes. It is characterized by humidity and rain throughout the year from oceanic influence. Although the term humid temperate climate is not used in the Köppen climate classification, this climate type may fall under the Cf classification, which indicates a temperate climate without a dry season.
== Sub-types ==
The Cf climate in Köppen classification has 3 subtypes, classified by temperature. The letter C indicates that the average monthly temperature for the coldest month is above −3 °C (27 °F) and below 18 °C (64 °F).
=== Humid subtropical climate (Cfa) ===
The humid subtropical climate, like other subtropical climates, is characterized by a hot summer, in which the average daily temperature in the warmest month is above 22 °C (72 °F).
=== Oceanic climate (Cfb) ===
The oceanic climate, also known as a marine climate, is characterized by warm summers in which the average daily temperature in the warmest month is below 22 °C (72 °F). In addition, at least 4 months have a mean monthly temperature above 10 °C (50 °F). It is found on continental western coasts.The typical vegetation in oceanic climates is humid temperate forest.
==== Subtropical highland climate (Cfb, Cwb, Cwc) ====
The subtropical highland climate is the low-latitude variation of the oceanic climate. This relatively consistent temperature and rainfall is caused by the location of this climate at up to 2500 m altitude. It is mainly found in the highlands of Andes, Central America and New Guinea.
=== Subpolar oceanic climate (Cfc) ===
The subpolar oceanic climate is located in high latitudes, at the border between the oceanic climate and polar climate. This climate has cool and short summers, with 1 to 3 months having a mean monthly temperature above 10 °C (50 °F). The vegetation of subpolar forests.
== See also ==
Temperate climate
Humid subtropical climate
Oceanic climate
Köppen climate classification
Temperate zone
== References == | Wikipedia/Humid_temperate_climate |
In virology, temperate refers to the ability of some bacteriophages (notably coliphage λ) to display a lysogenic life cycle. Many (but not all) temperate phages can integrate their genomes into their host bacterium's chromosome, together becoming a lysogen as the phage genome becomes a prophage. A temperate phage is also able to undergo a productive, typically lytic life cycle, where the prophage is expressed, replicates the phage genome, and produces phage progeny, which then leave the bacterium. With phage the term virulent is often used as an antonym to temperate, but more strictly a virulent phage is one that has lost its ability to display lysogeny through mutation rather than a phage lineage with no genetic potential to ever display lysogeny (which more properly would be described as an obligately lytic phage).
== Induction of the lytic cycle ==
At some point, temperate bacteriophages switch from the lysogenic life cycle to the lytic life cycle. This conversion may happen spontaneously, although at very low frequencies (λ displays spontaneous conversion of 10−8 to 10−5 per cell). In the majority of observed switch events, stressors - such as the cell's SOS response (due to DNA damage) or a change in nutrients - induces the switch.
== Lysogenic and lytic cycles ==
Temperate phages can switch between a lytic and lysogenic life cycle. Lytic is more drastic, killing the host whereas lysogenic impacts host cells genetically or physiologically.
Here is a chart on temperate phages that are lytic and lysogenic and how they're related. Lysogeny is characterized by the integration of the phage genome in the host genome.
== Notes == | Wikipedia/Temperateness_(virology) |
The five main latitude regions of Earth's surface comprise geographical zones, divided by the major circles of latitude. The differences between them relate to climate. They are as follows:
The North Frigid Zone, between the North Pole at 90° N and the Arctic Circle at 66°33′50.5″ N, covers 4.12% of Earth's surface.
The North Temperate Zone, between the Arctic Circle at 66°33′50.5″ N and the Tropic of Cancer at 23°26′09.5″ N, covers 25.99% of Earth's surface.
The Torrid Zone, between the Tropic of Cancer at 23°26′09.5″ N and the Tropic of Capricorn at 23°26′09.5″ S, covers 39.78% of Earth's surface.
The South Temperate Zone, between the Tropic of Capricorn at 23°26′09.5″ S and the Antarctic Circle at 66°33′50.5″ S, covers 25.99% of Earth's surface.
The South Frigid Zone, from the Antarctic Circle at 66°33′50.5″ S and the South Pole at 90° S, covers 4.12% of Earth's surface.
On the basis of latitudinal extent, the globe is divided into three broad heat zones.
== Torrid Zone ==
The Torrid Zone is also known as the tropics. This zone is bounded on the north by the Tropic of Cancer and on the south by the Tropic of Capricorn; these latitudes mark the northern and southern extremes in which the Sun passes directly overhead. This happens once annually on these cusps, but in the tropics proper, the Sun passes overhead twice a year.
Within the northern tropics, the Sun passes overhead its first time for that year before the June solstice, at which time it does so as to the Tropic of Cancer. It passes over these latitudes in turn again, on its apparent southward journey, to and before the September equinox. After then, the center of the Sun at the high point, the zenith, of the sky (which makes for the subsolar point beneath) aligns with successive latitudes in the southern tropics. The Sun passes overhead of these then does so once per year for the Tropic of Capricorn at the December solstice, then passes back again over those latitudes to return to the equator for the March equinox.
The Torrid zone includes southern Mexico, Central America, the Caribbean, northern South America (larger parts of Brazil, the Guyanas, Caribbean South America, Andean states and the northern tip of the Southern Cone), the Sudan, the southern regions of Western Sahara, Algeria, Libya and Egypt, West Africa, Central Africa, East Africa, larger parts of Southern Africa (Malawi, Zambia, Zimbabwe, northern Namibia and northern Botswana), southern Middle East (southern Saudi Arabia, southern United Arab Emirates, Oman and Yemen), southern Indian subcontinent (south-central and southern India, southern Bangladesh, Sri Lanka and Maldives), most of Southeast Asia, southern Taiwan, northern Australia (the northern regions of the Australian states of Western Australia and Queensland, the northern regions of the Northern Territory, and the entire territory of the New Guinea island), the northern tip of Zealandia (New Caledonia), and a great part of Oceania (Melanesia, Micronesia, and Polynesia, this later not including New Zealand).
== Temperate zones ==
In the two temperate zones, consisting of the tepid latitudes (including subtropical areas), the Sun is never directly overhead, and the climate is mild, generally ranging from warm to cool. The four annual seasons, spring, summer, autumn, and winter, occur in these areas.
The North Temperate Zone includes North America (including northern Mexico and the northern Bahamas), Europe, North Africa (Morocco, Tunisia and the northern regions of Western Sahara, Algeria, Libya and Egypt), Northern Asia, East Asia, Northern Vietnam, Central Asia, northern Indian subcontinent (Pakistan, northern India and northern Bangladesh) and northern Middle East (northern Saudi Arabia, Qatar, Bahrain, northern United Arab Emirates, Iraq, Iran, Afghanistan, the Levant (Syria, Lebanon, Jordan, Israel, Palestine), and Turkey).
The South Temperate Zone includes Southern Australia (the southern regions of the Australian states of Western Australia and Queensland, the southern regions of the Northern Territory, and the entire territories of the states of New South Wales, South Australia, Tasmania and Victoria), great part of Zealandia (New Zealand), southern South America (large part of the Southern Cone), and Southern Africa (southern Namibia, southern Botswana, great part of South Africa, the entire territories of Lesotho and Eswatini, and the southern tips of Mozambique and Madagascar).
== Frigid zones ==
The two frigid zones, or polar regions, experience the midnight sun and the polar night for part of the year – at the edge of the zone there remains one day, the winter solstice, when the Sun is too low to rise, and one day at the summer solstice when the Sun remains above the horizon for 24 hours. In the center of the zone (the pole), the day is one year long, with six months of daylight and six months of night. The frigid zones are the coldest regions of Earth and are generally covered in ice and snow. It receives slanting rays of the Sun, as this region lies farthest from the equator. Summer in this region lasts for about 2 to 3 months, and there is almost 24-hour sunlight during summer. The sun's rays are always slanting, so provide less heat per horizontal surface area.
The North Frigid Zone includes the United States (only the state of Alaska), the northern regions of Canada (the Northwest Territories, Nunavut, and Yukon), Greenland (Denmark), Norway, Finland, Sweden, and Russia.
The South Frigid Zone includes only Antarctica.
== History ==
The concept of a geographical zone was first hypothesized by the ancient Greek scholar Parmenides and lastingly modified by Aristotle. Both philosophers theorized the Earth divided into three types of climatic zones based on their distance from the equator.
Like Parmeneides, thinking that the area near the equator was too hot for habitation, Aristotle dubbed the region around the equator (from 23.5° N to 23.5° S) the "Torrid Zone." Both philosophers reasoned the region from the Arctic Circle to the pole to be permanently frozen. This region thought uninhabitable, was called the "Frigid Zone." The only area believed to be habitable was the northern "Temperate Zone" (the southern one not having been discovered), lying between the "Frigid Zones" and the "Torrid Zone". However, humans have inhabited almost all climates on Earth, including inside the Arctic Circle.
As knowledge of the Earth's geography improved, a second "Temperate Zone" was discovered south of the equator, and a second "Frigid Zone" was discovered around the Antarctic. Although Aristotle's map was oversimplified, the general idea was correct. Today, the most commonly used climate map is the Köppen climate classification, developed by Russian climatologist of German descent and amateur botanist Wladimir Köppen (1846–1940), which divides the world into five major climate regions, based on average annual precipitation, average monthly precipitation, and average monthly temperature.
== See also ==
Circle of latitude
Climate classification
Clime
Hardiness zone
Polar regions of Earth
Subtropics
Temperate climate
Tropics
== References and footnotes == | Wikipedia/Geographical_zone |
The highland temperate climates are a temperate climate sub-type, although located in tropical zone, isothermal and with characteristics different from others temperate climates like oceanic or mediterranean where they are often are included without proper differentiation.
The mainly difference is that it is isothermal, this mean that it has low termic range between months, whose cause is altitude and not latitude, no four seasons (spring, summer, autumn, winter) of temperate zone. However, there are rainfall variation (dry season and wet season). It is usually said that it have a Eternal Spring or a Eternal Autumn. These are sometimes called "tropical highland climates" or "highland tropical climates", though the name is a misnomer other than regional location.
A letter "i" is added to indicate its isothermal condition (Cfb, oceanic climate, Cfbi, highland humid temperate climate).
== Location ==
It is characteristic of South and central Mexico highlands, Central America mountains, North Andes in South America and East Africa mountains, among a few other areas like Baguio city which is found in the Philippines and New Guinea highlands.
== Causes and characteristics ==
Altitude generate a difference with lowlands. Temperature and atmospheric pression decrease, approximately 0,6 °C or 1 °C every 100 m. This s because to the adiabatic rate air.
In summary, this climates are generate because of temperature decrease on tropical zone, at same latitudes where appear tropical climates, located between 0 and 1500 m, while from 1500 m until 3000 m (depending on latitude) appear highland temperate climate, semihumid and isothermal. Above 3500 m is the alpine tundra climate ETH, identified with páramo and puna vegetation.
This climate often has been called oceanic Cfb or mediterranean Csb, however, it is not mediterranean since it is not found in temperate latitudes, do not limit with deserts and neither it is oceanic, because humidity here do not comes from ocean but of tropical rainforest near (Congo, Amazon, Chocó).
Temperatures are cool all year, approximately between 12 °C and 19 °C mean all months and year. Nevertheless, there are high daily range termic, between day and night, around 10 °C. There may be high nubosity and air humidity. Clear skis are rare.
Precipitations, only as rainfall, and often hail, it decrease with altitude, it is around 700–2,000 mm, that is, higher than temperate zone.
The vegetation basically is Highland Forest, beside highland wooded savanna and scrubs.
== Sub-types ==
The particular location of this highlands, many of which are just north of the Earth's equator but South of the metereological equator, what added to low termic range, makes defining between winter and summer speculative, sometimes it is confunde Cfbi, Cwbi and Csbi, just like it happens between tropical climates Aw and As.
=== Highland humid temperate climate Cfbi ===
Constant precipitation throughout the year, no dry season. Its temperature oscillates between 10 °C and 20 °C. Precipitation is higher than other highlands, about 1500 mm. It is the tropical variation of the oceanic climate Cfb. It can appear anywhere within the tropical zone with much rainfall and adequate altitude.
Cities:
Colonia Tovar, Venezuela
Mérida, Venezuela
=== Highland monsoon temperate climate Cwb ===
Rainfall come in hipotetic summer (monsoon), (usually between March and June in North Hemipshere and November and February in South Hemisphere), dry season take place in winter or cold months. Temperatures around 12 °C y 19 °C and precipitations from 800mm. Of the three subtypes, it is the one that occurs at a higher latitude, extending to subtropical areas exceeding 15° north and south latitude, which is why it usually presents a greater termic range, between 3 °C and 4°. It is located in Peru and Bolivia highlands, mountains of Brazil, center of Mexico and mountains of Central America and East Africa. Because of that, its vegetation is variable, from savanna until forests.
Most of the time it is simply called as Cwb, the Köppen classification for subtropical highland climates, because outside the intertropical zone it is existent.
Cities:
Kunming, China
Addis Ababa, Ethiopia
Nairobi, Kenya
La Paz, Bolivia
Cusco, Peru
=== Highland equatorial climate Csbi ===
Dry season math with more hot and sunny months, it has a marked wet season, with bimodal regime, where one of them is stronger than the other. Precipitation normally between 700mm y 2000mm, humidity decrease with altitude, annual rainfall decrease 100 mm every 100 m altitude. Intertropical Convergence Zone appears twice yearly, while temperature depends on altitude, generally between 12 °C and 18 °C, very stable and unchanging throughout the year.
It is located in equatorial latitudes to no more than 5°S and 5°N of equator. It is almost exclusive of Ecuadorian-Colombian Andes, located from 1500 m altitude. It consists of tropical variation of oceanic mediterranean climate Csb. Common vegetation is the highland wooded savanna. Andean forests or cloudy forests appears above 3000 m of great biodiversity.
Cities:
Bogotá, Colombia
Cuenca, Ecuador
Ibarra, Ecuador
Manizales, Colombia
Pasto, Colombia
Popayán, Colombia
Quito, Ecuador
Tunja, Colombia
== See also ==
Temperate climate
Humid temperate climate
Subhumid temperate climate
Mediterranean climate
Altitude
Köppen climate classification
== References == | Wikipedia/Highland_temperate_climate |
Ku is a dimeric protein complex that binds to DNA double-strand break ends and is required for the non-homologous end joining (NHEJ) pathway of DNA repair. Ku is evolutionarily conserved from bacteria to humans. The ancestral bacterial Ku is a homodimer (two copies of the same protein bound to each other). Eukaryotic Ku is a heterodimer of two polypeptides, Ku70 (XRCC6) and Ku80 (XRCC5), so named because the molecular weight of the human Ku proteins is around 70 kDa and 80 kDa. The two Ku subunits form a basket-shaped structure that threads onto the DNA end. Once bound, Ku can slide down the DNA strand, allowing more Ku molecules to thread onto the end. In higher eukaryotes, Ku forms a complex with the DNA-dependent protein kinase catalytic subunit (DNA-PKcs) to form the full DNA-dependent protein kinase, DNA-PK. Ku is thought to function as a molecular scaffold to which other proteins involved in NHEJ can bind, orienting the double-strand break for ligation.
The Ku70 and Ku80 proteins consist of three structural domains. The N-terminal domain is an alpha/beta domain. This domain only makes a small contribution to the dimer interface. The domain comprises a six-stranded beta sheet of the Rossmann fold. The central domain of Ku70 and Ku80 is a DNA-binding beta-barrel domain. Ku makes only a few contacts with the sugar-phosphate backbone, and none with the DNA bases, but it fits sterically to major and minor groove contours forming a ring that encircles duplex DNA, cradling two full turns of the DNA molecule. By forming a bridge between the broken DNA ends, Ku acts to structurally support and align the DNA ends, to protect them from degradation, and to prevent promiscuous binding to unbroken DNA. Ku effectively aligns the DNA, while still allowing access of polymerases, nucleases and ligases to the broken DNA ends to promote end joining. The C-terminal arm is an alpha helical region which embraces the central beta-barrel domain of the opposite subunit. In some cases a fourth domain is present at the C-terminus, which binds to DNA-dependent protein kinase catalytic subunit.
Both subunits of Ku have been experimentally knocked out in mice. These mice exhibit chromosomal instability, indicating that NHEJ is important for genome maintenance.
In many organisms, Ku has additional functions at telomeres in addition to its role in DNA repair.
Abundance of Ku80 seems to be related to species longevity.
== Aging ==
Mutant mice defective in Ku70, or Ku80, or double mutant mice deficient in both Ku70 and Ku80 exhibit early aging. The mean lifespans of the three mutant mouse strains were similar to each other, at about 37 weeks, compared to 108 weeks for the wild-type control. Six specific signs of aging were examined, and the three mutant mice were found to display the same aging signs as the control mice, but at a much earlier age. Cancer incidence was not increased in the mutant mice. These results suggest that Ku function is important for longevity assurance and that the NHEJ pathway of DNA repair (mediated by Ku) has a key role in repairing DNA double-strand breaks that would otherwise cause early aging. (Also see DNA damage theory of aging.)
== Plants ==
Ku70 and Ku80 have also been experimentally characterized in plants, where they appear to play a similar role to that in other eukaryotes. In rice, suppression of either protein has been shown to promote homologous recombination (HR) This effect was exploited to improve gene targeting (GT) efficiency in Arabidopsis thaliana. In the study, the frequency of HR-based GT using a zinc-finger nuclease (ZFN) was increased up to sixteen times in ku70 mutants This result has promising implications for genome editing across eukaryotes as DSB repair mechanisms are highly conserved. A substantial difference is that in plants, Ku is also involved in maintaining an alternate telomere morphology characterized by blunt-ends or short (≤ 3-nt) 3’ overhangs. This function is independent of the role of Ku in DSB repair, as removing the ability of the Ku complex to translocate along DNA has been shown to preserve blunt-ended telomeres while impeding DNA repair.
== Bacteria and archaea ==
Bacteria usually have only one Ku gene (if they have one at all). Unusually, Mesorhizobium loti has two, mlr9624 and mlr9623.
Archaea usually also only have one Ku gene (for the ~4% of species that have one at all). The evolutionary history is blurred by extensive horizontal gene transfer with bacteria.
Bacterial and archaeal Ku proteins are unlike their eukaryotic counterparts in that they only have the central beta-barrel domain.
== Name ==
The name 'Ku' is derived from the surname of the Japanese patient in which it was discovered.
== References ==
== External links == | Wikipedia/Ku_(protein) |
DNA photoionization is the phenomenon according to which ultraviolet radiation absorbed directly by a DNA system (mononucleotide, single or double strand, G-quadruplex…) induces the ejection of electrons, leaving electron holes on the nucleic acid.
The loss of an electron gives rise to a radical cation on the DNA. Radical cations are precursors to oxidative damage, ultimately leading to carcinogenic mutations and cell death. This aspect, detrimental to the health, is exploited in the germicidal equipments using far-UVC lamps. The electric charges photogenarated in DNA could potentially find applications in optoelectronic devices.
Two properties are crucial regarding photoionization. On the one hand, the ionization energy (also called ionization potential, IP), refers to the energy necessary to remove one electron from a molecule; the lowest IP, corresponding to the ejection of a first electron, is the most biologically relevant factor. On the other hand, the photoionization quantum yield Φ, that is the number of electrons that are ejected over the number of absorbed photons; Φ depends on the irradiation wavelength.
The mechanism underlying DNA ionization depends on the number of photons that provoke the ejection of one electron (one-photon or multiphoton, induced by intense laser pulses). And, in the case of one-photon process, it differs according to the photon energy (high-energy or low-energy). While one- and two-photon ionization in condensed phase (aqueous solutions, cells…) is mainly studied in respect with the UV-induced oxidative damage, multiphoton ionization in the gas phase, often coupled to mass spectroscopy, is used in various techniques in order to obtain broader spectroscopic,
analytical,
structural or therapeutic information.
== Ionization potentials ==
Since the end of the 20th century, numerous theoretical studies, performed using various types of quantum chemistry methods, focus on the computation of the lowest IP of nucleobases. Particular effort is being dedicated to evaluate environmental effects, such as the presence of water molecules, base-pairing, base stacking or base-sequence. All these studies agree that the IP decreases in the order: thymine, cytosine, adenine, guanine.
Experimentally, IPs are determined by photoelectron spectroscopy. A series of systematic measurements of all the elementary DNA components as well as of genomic DNA in liquid jets, associated with computations, provided important information regarding the ionization in aqueous media. The IP values measured for nucleosides/nucleotides (8.1, 8.1, 7.6 and 7.3 eV for thymidine monophosphate, cytosine, adenosine and guanosine, respectively) match those computed for vertical ionization. The latter corresponds to electron ejection without prior geometrical rearrangement of the molecular framework. Most importantly, it was evidenced that base-pairing and base-stacking do not have any significant effect.
== One photon ionization ==
=== Photoionization quantum yields ===
Photoionization quantum yields are determined for DNA in aqueous solution by means of the transient absorption spectroscopy using as excitation source nanosecond laser pulses. The ejected electrons are solvated by the water molecules (hydrated) on the sub-picosecond time scale. As the absorption spectrum of hydrated electrons, peaking 720 nm, is well known, they can be characterized in a quantitative way.
=== High-energy photoionization ===
The first experiments were reported in the 1990s using excitation at 193 nm. The quantum yields determined for the nucleobases at this wavelength amount to a few percent. Τhe Φ found for genomic DNA is the linear combination of the quantum yield values of the individual nucleobases, in agreement with the findings of the photoelectron spectroscopy.
=== Low-energy photoionization ===
The first studies on low-energy photoionization, occurring at wavelengths for which the photon energy is significantly smaller compared to the lowest ionization potential of DNA, were reported back in 2005 (G-Quadruplexes at 308 nm) and 2006 (single and double strands at 266 nm). But this unexpected phenomenon started to be studied in a systematic way only ten years later. To that effect, specific protocols regarding the purity of the nucleic acids and the ingredients of the aqueous solution as well as the intensity of the exciting laser pulses were established.
In contrast to the high-energy, low-energy photoionization strongly depends on the secondary DNA structure. It is not observed for mononucleosides, mononucleotides or purely stacked single strands (Φ<0.5x10−4). The quantum yields determined for duplexes fall in the range of (1-2)x10−3 while the highest Φ values, up to 1.4x10−2, have been detected for G-Quadruplexes. The photonization quantum yield determined for genomic DNA is similar to that reported for the formation of bipyrimidine photoproducts.
The detailed examination of the structural factors affecting the low-energy photoionization, combined to quantum chemical calculations, indicates that it occurs via a complex mechanism. The latter involves excited charge transfer states, in which an atomic charge is transferred from one nucleobase to a neighboring one; such states are known to be populated during the electronic relaxation following photon absorption. Subsequently, a small population of these states undergoes charge separation. And, eventually, the electron is ejected from the nucleobase bearing the negative charge, because its ionization potential is lower compared to those of neutral nucleobases.
== Two-photon ionization ==
Two-photon photoionization is provoked by intense laser pulses of short duration. In this case, a first photon absorbed by DNA gives rise to an electronic excited state. During its lifetime, the latter may absorb a second photon. The electron is then ejected from this excited state and not from the ground state, as happens for the one-photon ionization.
This ionization mode started to be used already from the 1980sin order to characterize chemically the final DNA lesions (single and double strand breaks, 8-oxo-7,8-dihydroguanine,..), stemming from this process. Typically, lasers emitting at 248 or 266 nm have been employed in combination to analytical or biochemical methods. Such measurements are performed both on DNA solutions and on cells.
The need to correlate the observed lesions with the ejected electrons lead to first time-resolved absorption studies on the process triggered by absorption of UV radiation directly by DNA. Thus, signatures of the nucleobase radicals were discovered either in the UV-visible spectral domain or in the infrared.
== References ==
== Further reading ==
=== Reviews and Accounts ===
Pluharova, E. (2015). "Modelling Photoionization of Aqueous DNA and Its Components". Acc. Chem. Res. 48 (5): 1209–1217. doi:10.1021/ar500366z. PMID 25738773.
Cadet, J. (2019). "Biphotonic Ionization of DNA: From Model Studies to Cell". Photochem. Photobiol. 95 (1): 59–72. doi:10.1111/php.13042. PMID 30380156.
Balanikas, E. (2021). "Guanine Radicals Induced in DNA by Low-Energy Photoionization" (PDF). Acc. Chem. Res. 53 (8): 1511–1519. doi:10.1021/acs.accounts.0c00245. PMID 32786340.
Martínez Fernández, Lara; Santoro, Fabrizio; Improta, Roberto (2022). "Nucleic Acids as a Playground for the Computational Study of the Photophysics and Photochemistry of Multichromophore Assemblies". Accounts of Chemical Research. 55 (15): 2077–2087. doi:10.1021/acs.accounts.2c00256. PMID 35833758.
Görlitz, M. (2024). "Assessing the safety of new germicidal far-UVC technologies". Photochem. Photobiol. 100 (3): 501–520. doi:10.1111/php.13866. PMID 37929787.
=== Book Chapters ===
Schwell, Martin; Hochlaf, Majdi (2014). "Photoionization Spectroscopy of Nucleobases and Analogues in the Gas Phase Using Synchrotron Radiation as Excitation Light Source". Photoinduced Phenomena in Nucleic Acids I. Topics in Current Chemistry. Vol. 355. pp. 155–208. doi:10.1007/128_2014_550. ISBN 978-3-319-13370-6. PMID 25238717.
Balanikas, E.; Markovitsi, D. (2021). "DNA photoionization: from high to low energies" (PDF). In DNA Photodamage: From Light Absorption to Cellular Responses and Skin Cancer. Comprehensive Series in Photochemical and Photobiological Science. Vol. 21. pp. 29–50. doi:10.1039/9781839165580. ISBN 978-1-83916-196-4.
Martínez Fernández, Lara; Improta, Roberto (2024). "Computational Studies on Photoinduced Charge Transfer Processes in Nucleic Acids: From Watson–Crick Dimers to Quadruple Helices". Nucleic Acid Photophysics and Photochemistry. Nucleic Acids and Molecular Biology. Vol. 36. pp. 29–50. doi:10.1007/978-3-031-68807-2_2. ISBN 978-3-031-68806-5. | Wikipedia/DNA_photoionization |
A DNA repair-deficiency disorder is a medical condition due to reduced functionality of DNA repair.
DNA repair defects can cause an accelerated aging disease or an increased risk of cancer, or sometimes both.
== DNA repair defects and accelerated aging ==
DNA repair defects are seen in nearly all of the diseases described as accelerated aging disease, in which various tissues, organs or systems of the human body age prematurely. Because the accelerated aging diseases display different aspects of aging, but never every aspect, they are often called segmental progerias by biogerontologists.
=== Human disorders with accelerated aging ===
Ataxia-telangiectasia
Bloom syndrome
Cockayne syndrome
Fanconi anemia
Progeria (Hutchinson–Gilford progeria syndrome)
Rothmund–Thomson syndrome
Trichothiodystrophy
Werner syndrome
Xeroderma pigmentosum
=== Examples ===
Some examples of DNA repair defects causing progeroid syndromes in humans or mice are shown in Table 1.
=== DNA repair defects distinguished from "accelerated aging" ===
Most of the DNA repair deficiency diseases show varying degrees of "accelerated aging" or cancer (often some of both). But elimination of any gene essential for base excision repair kills the embryo—it is too lethal to display symptoms (much less symptoms of cancer or "accelerated aging").
Rothmund-Thomson syndrome and xeroderma pigmentosum display symptoms dominated by vulnerability to cancer, whereas progeria and Werner syndrome show the most features of "accelerated aging". Hereditary nonpolyposis colorectal cancer (HNPCC) is very often caused by a defective MSH2 gene leading to defective mismatch repair, but displays no symptoms of "accelerated aging". On the other hand, Cockayne Syndrome and trichothiodystrophy show mainly features of accelerated aging, but apparently without an increased risk of cancer Some DNA repair defects manifest as neurodegeneration rather than as cancer or "accelerated aging". (Also see the "DNA damage theory of aging" for a discussion of the evidence that DNA damage is the primary underlying cause of aging.)
=== Debate concerning "accelerated aging" ===
Some biogerontologists question that such a thing as "accelerated aging" actually exists, at least partly on the grounds that all of the so-called accelerated aging diseases are segmental progerias. Many disease conditions such as diabetes, high blood pressure, etc., are associated with increased mortality. Without reliable biomarkers of aging it is hard to support the claim that a disease condition represents more than accelerated mortality.
Against this position other biogerontologists argue that premature aging phenotypes are identifiable symptoms associated with mechanisms of molecular damage. The fact that these phenotypes are widely recognized justifies classification of the relevant diseases as "accelerated aging". Such conditions, it is argued, are readily distinguishable from genetic diseases associated with increased mortality, but not associated with an aging phenotype, such as cystic fibrosis and sickle cell anemia. It is further argued that segmental aging phenotype is a natural part of aging insofar as genetic variation leads to some people being more disposed than others to aging-associated diseases such as cancer and Alzheimer's disease.
== DNA repair defects and increased cancer risk ==
Individuals with an inherited impairment in DNA repair capability are often at increased risk of cancer. When a mutation is present in a DNA repair gene, the repair gene will either not be expressed or be expressed in an altered form. Then the repair function will likely be deficient, and, as a consequence, damages will tend to accumulate. Such DNA damages can cause errors during DNA synthesis leading to mutations, some of which may give rise to cancer. Germ-line DNA repair mutations that increase the risk of cancer are listed in the Table.
== See also ==
Biogerontology
Degenerative disease
DNA damage theory of aging
Genetic disorder
Senescence
== References ==
== External links ==
BRCA - Companion Reviews and Search Terms
BRCA1 - Companion Reviews and Search Terms
BRCA2 - Companion Reviews and Search Terms
ATM - Companion Reviews and Search Terms
NBS1 - Companion Reviews and Search Terms
Bloom s syndrome - Companion Reviews and Search Terms
Fanconi s anemia - Companion Reviews and Search Terms
WRN - Companion Reviews and Search Terms
RECQ- Companion Reviews and Search Terms
RECQL4 - Companion Reviews and Search Terms
FANCJ - Companion Reviews and Search Terms
FANCM - Companion Reviews and Search Terms
FANCN - Companion Reviews and Search Terms
XPB - Companion Reviews and Search Terms
XPD - Companion Reviews and Search Terms
XPG - Companion Reviews and Search Terms
MSH6 - Companion Reviews and Search Terms
MUTYH - Companion Reviews and Search Terms
DNA repair and toxicology - Companion Reviews and Search Terms
Neoplasia inherited - Companion Reviews and Search Terms
Neoplasia carcinogenesis - Companion Reviews and Search Terms
Segmental Progeria | Wikipedia/Inherited_human_DNA_repair_gene_mutations_that_increase_cancer_risk |
In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosis, or meiosis or other types of damage to DNA (such as pyrimidine dimers caused by exposure to ultraviolet radiation), which then may undergo error-prone repair (especially microhomology-mediated end joining), cause an error during other forms of repair, or cause an error during replication (translesion synthesis). Mutations may also result from substitution, insertion or deletion of segments of DNA due to mobile genetic elements.
Mutations may or may not produce detectable changes in the observable characteristics (phenotype) of an organism. Mutations play a part in both normal and abnormal biological processes including: evolution, cancer, and the development of the immune system, including junctional diversity. Mutation is the ultimate source of all genetic variation, providing the raw material on which evolutionary forces such as natural selection can act.
Mutation can result in many different types of change in sequences. Mutations in genes can have no effect, alter the product of a gene, or prevent the gene from functioning properly or completely. Mutations can also occur in non-genic regions. A 2007 study on genetic variations between different species of Drosophila suggested that, if a mutation changes a protein produced by a gene, the result is likely to be harmful, with an estimated 70% of amino acid polymorphisms that have damaging effects, and the remainder being either neutral or marginally beneficial.
Mutation and DNA damage are the two major types of errors that occur in DNA, but they are fundamentally different. DNA damage is a physical alteration in the DNA structure, such as a single or double strand break, a modified guanosine residue in DNA such as 8-hydroxydeoxyguanosine, or a polycyclic aromatic hydrocarbon adduct. DNA damages can be recognized by enzymes, and therefore can be correctly repaired using the complementary undamaged strand in DNA as a template or an undamaged sequence in a homologous chromosome if it is available. If DNA damage remains in a cell, transcription of a gene may be prevented and thus translation into a protein may also be blocked. DNA replication may also be blocked and/or the cell may die. In contrast to a DNA damage, a mutation is an alteration of the base sequence of the DNA. Ordinarily, a mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation is not ordinarily repaired. At the cellular level, mutations can alter protein function and regulation. Unlike DNA damages, mutations are replicated when the cell replicates. At the level of cell populations, cells with mutations will increase or decrease in frequency according to the effects of the mutations on the ability of the cell to survive and reproduce. Although distinctly different from each other, DNA damages and mutations are related because DNA damages often cause errors of DNA synthesis during replication or repair and these errors are a major source of mutation.
== Overview ==
Mutations can involve the duplication of large sections of DNA, usually through genetic recombination. These duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. Most genes belong to larger gene families of shared ancestry, detectable by their sequence homology. Novel genes are produced by several methods, commonly through the duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions.
Here, protein domains act as modules, each with a particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties. For example, the human eye uses four genes to make structures that sense light: three for cone cell or colour vision and one for rod cell or night vision; all four arose from a single ancestral gene. Another advantage of duplicating a gene (or even an entire genome) is that this increases engineering redundancy; this allows one gene in the pair to acquire a new function while the other copy performs the original function. Other types of mutation occasionally create new genes from previously noncoding DNA.
Changes in chromosome number may involve even larger mutations, where segments of the DNA within chromosomes break and then rearrange. For example, in the Homininae, two chromosomes fused to produce human chromosome 2; this fusion did not occur in the lineage of the other apes, and they retain these separate chromosomes. In evolution, the most important role of such chromosomal rearrangements may be to accelerate the divergence of a population into new species by making populations less likely to interbreed, thereby preserving genetic differences between these populations.
Sequences of DNA that can move about the genome, such as transposons, make up a major fraction of the genetic material of plants and animals, and may have been important in the evolution of genomes. For example, more than a million copies of the Alu sequence are present in the human genome, and these sequences have now been recruited to perform functions such as regulating gene expression. Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity.
Nonlethal mutations accumulate within the gene pool and increase the amount of genetic variation. The abundance of some genetic changes within the gene pool can be reduced by natural selection, while other "more favorable" mutations may accumulate and result in adaptive changes.
For example, a butterfly may produce offspring with new mutations. The majority of these mutations will have no effect; but one might change the colour of one of the butterfly's offspring, making it harder (or easier) for predators to see. If this color change is advantageous, the chances of this butterfly's surviving and producing its own offspring are a little better, and over time the number of butterflies with this mutation may form a larger percentage of the population.
Neutral mutations are defined as mutations whose effects do not influence the fitness of an individual. These can increase in frequency over time due to genetic drift. It is believed that the overwhelming majority of mutations have no significant effect on an organism's fitness. Also, DNA repair mechanisms are able to mend most changes before they become permanent mutations, and many organisms have mechanisms, such as apoptotic pathways, for eliminating otherwise-permanently mutated somatic cells.
Beneficial mutations can improve reproductive success.
== Causes ==
Four classes of mutations are (1) spontaneous mutations (molecular decay), (2) mutations due to error-prone replication bypass of naturally occurring DNA damage (also called error-prone translesion synthesis), (3) errors introduced during DNA repair, and (4) induced mutations caused by mutagens. Scientists may sometimes deliberately introduce mutations into cells or research organisms for the sake of scientific experimentation.
One 2017 study claimed that 66% of cancer-causing mutations are random, 29% are due to the environment (the studied population spanned 69 countries), and 5% are inherited.
Humans on average pass 60 new mutations to their children but fathers pass more mutations depending on their age with every year adding two new mutations to a child.
=== Spontaneous mutation ===
Spontaneous mutations occur with non-zero probability even given a healthy, uncontaminated cell. Naturally occurring oxidative DNA damage is estimated to occur 10,000 times per cell per day in humans and 100,000 times per cell per day in rats. Spontaneous mutations can be characterized by the specific change:
Tautomerism – A base is changed by the repositioning of a hydrogen atom, altering the hydrogen bonding pattern of that base, resulting in incorrect base pairing during replication. Theoretical results suggest that proton tunnelling is an important factor in the spontaneous creation of GC tautomers.
Depurination – Loss of a purine base (A or G) to form an apurinic site (AP site).
Deamination – Hydrolysis changes a normal base to an atypical base containing a keto group in place of the original amine group. Examples include C → U and A → HX (hypoxanthine), which can be corrected by DNA repair mechanisms; and 5MeC (5-methylcytosine) → T, which is less likely to be detected as a mutation because thymine is a normal DNA base.
Slipped strand mispairing – Denaturation of the new strand from the template during replication, followed by renaturation in a different spot ("slipping"). This can lead to insertions or deletions.
=== Error-prone replication bypass ===
There is increasing evidence that the majority of spontaneously arising mutations are due to error-prone replication (translesion synthesis) past DNA damage in the template strand. In mice, the majority of mutations are caused by translesion synthesis. Likewise, in yeast, Kunz et al. found that more than 60% of the spontaneous single base pair substitutions and deletions were caused by translesion synthesis.
=== Errors introduced during DNA repair ===
Although naturally occurring double-strand breaks occur at a relatively low frequency in DNA, their repair often causes mutation. Non-homologous end joining (NHEJ) is a major pathway for repairing double-strand breaks. NHEJ involves removal of a few nucleotides to allow somewhat inaccurate alignment of the two ends for rejoining followed by addition of nucleotides to fill in gaps. As a consequence, NHEJ often introduces mutations.
=== Induced mutation ===
Induced mutations are alterations in the gene after it has come in contact with mutagens and environmental causes.
Induced mutations on the molecular level can be caused by:
Chemicals
Hydroxylamine
Base analogues (e.g., Bromodeoxyuridine (BrdU))
Alkylating agents (e.g., N-ethyl-N-nitrosourea (ENU). These agents can mutate both replicating and non-replicating DNA. In contrast, a base analogue can mutate the DNA only when the analogue is incorporated in replicating the DNA. Each of these classes of chemical mutagens has certain effects that then lead to transitions, transversions, or deletions.
Agents that form DNA adducts (e.g., ochratoxin A)
DNA intercalating agents (e.g., ethidium bromide)
DNA crosslinkers
Oxidative damage
Nitrous acid converts amine groups on A and C to diazo groups, altering their hydrogen bonding patterns, which leads to incorrect base pairing during replication.
Radiation
Ultraviolet light (UV) (including non-ionizing radiation). Two nucleotide bases in DNA—cytosine and thymine—are most vulnerable to radiation that can change their properties. UV light can induce adjacent pyrimidine bases in a DNA strand to become covalently joined as a pyrimidine dimer. UV radiation, in particular longer-wave UVA, can also cause oxidative damage to DNA.
Ionizing radiation. Exposure to ionizing radiation, such as gamma radiation, can result in mutation, possibly resulting in cancer or death.
Whereas in former times mutations were assumed to occur by chance, or induced by mutagens, molecular mechanisms of mutation have been discovered in bacteria and across the tree of life. As S. Rosenberg states, "These mechanisms reveal a picture of highly regulated mutagenesis, up-regulated temporally by stress responses and activated when cells/organisms are maladapted to their environments—when stressed—potentially accelerating adaptation." Since they are self-induced mutagenic mechanisms that increase the adaptation rate of organisms, they have some times been named as adaptive mutagenesis mechanisms, and include the SOS response in bacteria, ectopic intrachromosomal recombination and other chromosomal events such as duplications.
== Classification of types ==
=== By effect on structure ===
The sequence of a gene can be altered in a number of ways. Gene mutations have varying effects on health depending on where they occur and whether they alter the function of essential proteins.
Mutations in the structure of genes can be classified into several types.
==== Large-scale mutations ====
Large-scale mutations in chromosomal structure include:
Amplifications (or gene duplications) or repetition of a chromosomal segment or presence of extra piece of a chromosome broken piece of a chromosome may become attached to a homologous or non-homologous chromosome so that some of the genes are present in more than two doses leading to multiple copies of all chromosomal regions, increasing the dosage of the genes located within them.
Polyploidy, duplication of entire sets of chromosomes, potentially resulting in a separate breeding population and speciation.
Deletions of large chromosomal regions, leading to loss of the genes within those regions.
Mutations whose effect is to juxtapose previously separate pieces of DNA, potentially bringing together separate genes to form functionally distinct fusion genes (e.g., bcr-abl).
Large scale changes to the structure of chromosomes called chromosomal rearrangement that can lead to a decrease of fitness but also to speciation in isolated, inbred populations. These include:
Chromosomal translocations: interchange of genetic parts from nonhomologous chromosomes.
Chromosomal inversions: reversing the orientation of a chromosomal segment.
Non-homologous chromosomal crossover.
Interstitial deletions: an intra-chromosomal deletion that removes a segment of DNA from a single chromosome, thereby apposing previously distant genes. For example, cells isolated from a human astrocytoma, a type of brain tumour, were found to have a chromosomal deletion removing sequences between the Fused in Glioblastoma (FIG) gene and the receptor tyrosine kinase (ROS), producing a fusion protein (FIG-ROS). The abnormal FIG-ROS fusion protein has constitutively active kinase activity that causes oncogenic transformation (a transformation from normal cells to cancer cells).
Loss of heterozygosity: loss of one allele, either by a deletion or a genetic recombination event, in an organism that previously had two different alleles.
==== Small-scale mutations ====
Small-scale mutations affect a gene in one or a few nucleotides. (If only a single nucleotide is affected, they are called point mutations.) Small-scale mutations include:
Insertions add one or more extra nucleotides into the DNA. They are usually caused by transposable elements, or errors during replication of repeating elements. Insertions in the coding region of a gene may alter splicing of the mRNA (splice site mutation), or cause a shift in the reading frame (frameshift), both of which can significantly alter the gene product. Insertions can be reversed by excision of the transposable element.
Deletions remove one or more nucleotides from the DNA. Like insertions, these mutations can alter the reading frame of the gene. In general, they are irreversible: Though exactly the same sequence might, in theory, be restored by an insertion, transposable elements able to revert a very short deletion (say 1–2 bases) in any location either are highly unlikely to exist or do not exist at all.
Substitution mutations, often caused by chemicals or malfunction of DNA replication, exchange a single nucleotide for another. These changes are classified as transitions or transversions. Most common is the transition that exchanges a purine for a purine (A ↔ G) or a pyrimidine for a pyrimidine, (C ↔ T). A transition can be caused by nitrous acid, base mispairing, or mutagenic base analogues such as BrdU. Less common is a transversion, which exchanges a purine for a pyrimidine or a pyrimidine for a purine (C/T ↔ A/G). An example of a transversion is the conversion of adenine (A) into a cytosine (C). Point mutations are modifications of single base pairs of DNA or other small base pairs within a gene. A point mutation can be reversed by another point mutation, in which the nucleotide is changed back to its original state (true reversion) or by second-site reversion (a complementary mutation elsewhere that results in regained gene functionality). As discussed below, point mutations that occur within the protein coding region of a gene may be classified as synonymous or nonsynonymous substitutions, the latter of which in turn can be divided into missense or nonsense mutations.
=== By impact on protein sequence ===
The effect of a mutation on protein sequence depends in part on where in the genome it occurs, especially whether it is in a coding or non-coding region. Mutations in the non-coding regulatory sequences of a gene, such as promoters, enhancers, and silencers, can alter levels of gene expression, but are less likely to alter the protein sequence. Mutations within introns and in regions with no known biological function (e.g. pseudogenes, retrotransposons) are generally neutral, having no effect on phenotype – though intron mutations could alter the protein product if they affect mRNA splicing.
Mutations that occur in coding regions of the genome are more likely to alter the protein product, and can be categorized by their effect on amino acid sequence:
A frameshift mutation is caused by insertion or deletion of a number of nucleotides that is not evenly divisible by three from a DNA sequence. Due to the triplet nature of gene expression by codons, the insertion or deletion can disrupt the reading frame, or the grouping of the codons, resulting in a completely different translation from the original. The earlier in the sequence the deletion or insertion occurs, the more altered the protein produced is. (For example, the code CCU GAC UAC CUA codes for the amino acids proline, aspartic acid, tyrosine, and leucine. If the U in CCU was deleted, the resulting sequence would be CCG ACU ACC UAx, which would instead code for proline, threonine, threonine, and part of another amino acid or perhaps a stop codon (where the x stands for the following nucleotide).) By contrast, any insertion or deletion that is evenly divisible by three is termed an in-frame mutation.
A point substitution mutation results in a change in a single nucleotide and can be either synonymous or nonsynonymous.
A synonymous substitution replaces a codon with another codon that codes for the same amino acid, so that the produced amino acid sequence is not modified. Synonymous mutations occur due to the degenerate nature of the genetic code. If this mutation does not result in any phenotypic effects, then it is called silent, but not all synonymous substitutions are silent. (There can also be silent mutations in nucleotides outside of the coding regions, such as the introns, because the exact nucleotide sequence is not as crucial as it is in the coding regions, but these are not considered synonymous substitutions.)
A nonsynonymous substitution replaces a codon with another codon that codes for a different amino acid, so that the produced amino acid sequence is modified. Nonsynonymous substitutions can be classified as nonsense or missense mutations:
A missense mutation changes a nucleotide to cause substitution of a different amino acid. This in turn can render the resulting protein nonfunctional. Such mutations are responsible for diseases such as Epidermolysis bullosa, sickle-cell disease, and SOD1-mediated ALS. On the other hand, if a missense mutation occurs in an amino acid codon that results in the use of a different, but chemically similar, amino acid, then sometimes little or no change is rendered in the protein. For example, a change from AAA to AGA will encode arginine, a chemically similar molecule to the intended lysine. In this latter case the mutation will have little or no effect on phenotype and therefore be neutral.
A nonsense mutation is a point mutation in a sequence of DNA that results in a premature stop codon, or a nonsense codon in the transcribed mRNA, and possibly a truncated, and often nonfunctional protein product. This sort of mutation has been linked to different diseases, such as congenital adrenal hyperplasia. (See Stop codon.)
=== By effect on function ===
A mutation becomes an effect on function mutation when the exactitude of functions between a mutated protein and its direct interactor undergoes change. The interactors can be other proteins, molecules, nucleic acids, etc. There are many mutations that fall under the category of by effect on function, but depending on the specificity of the change the mutations listed below will occur.
Loss-of-function mutations, also called inactivating mutations, result in the gene product having less or no function (being partially or wholly inactivated). When the allele has a complete loss of function (null allele), it is often called an amorph or amorphic mutation in Muller's morphs schema. Phenotypes associated with such mutations are most often recessive. Exceptions are when the organism is haploid, or when the reduced dosage of a normal gene product is not enough for a normal phenotype (this is called haploinsufficiency). A disease that is caused by a loss-of-function mutation is Gitelman syndrome and cystic fibrosis.
Gain-of-function mutations also called activating mutations, change the gene product such that its effect gets stronger (enhanced activation) or even is superseded by a different and abnormal function. When the new allele is created, a heterozygote containing the newly created allele as well as the original will express the new allele; genetically this defines the mutations as dominant phenotypes. Several of Muller's morphs correspond to the gain of function, including hypermorph (increased gene expression) and neomorph (novel function).
Dominant negative mutations (also called anti-morphic mutations) have an altered gene product that acts antagonistically to the wild-type allele. These mutations usually result in an altered molecular function (often inactive) and are characterized by a dominant or semi-dominant phenotype. In humans, dominant negative mutations have been implicated in cancer (e.g., mutations in genes p53, ATM, CEBPA, and PPARgamma). Marfan syndrome is caused by mutations in the FBN1 gene, located on chromosome 15, which encodes fibrillin-1, a glycoprotein component of the extracellular matrix. Marfan syndrome is also an example of dominant negative mutation and haploinsufficiency.
Lethal mutations result in rapid organismal death when occurring during development and cause significant reductions of life expectancy for developed organisms. An example of a disease that is caused by a dominant lethal mutation is Huntington's disease.
Null mutations, also known as Amorphic mutations, are a form of loss-of-function mutations that completely prohibit the gene's function. The mutation leads to a complete loss of operation at the phenotypic level, also causing no gene product to be formed. Atopic eczema and dermatitis syndrome are common diseases caused by a null mutation of the gene that activates filaggrin.
Suppressor mutations are a type of mutation that causes the double mutation to appear normally. In suppressor mutations the phenotypic activity of a different mutation is completely suppressed, thus causing the double mutation to look normal. There are two types of suppressor mutations, there are intragenic and extragenic suppressor mutations. Intragenic mutations occur in the gene where the first mutation occurs, while extragenic mutations occur in the gene that interacts with the product of the first mutation. A common disease that results from this type of mutation is Alzheimer's disease.
Neomorphic mutations are a part of the gain-of-function mutations and are characterized by the control of new protein product synthesis. The newly synthesized gene normally contains a novel gene expression or molecular function. The result of the neomorphic mutation is the gene where the mutation occurs has a complete change in function.
A back mutation or reversion is a point mutation that restores the original sequence and hence the original phenotype.
=== By effect on fitness (harmful, beneficial, neutral mutations) ===
In genetics, it is sometimes useful to classify mutations as either harmful or beneficial (or neutral):
A harmful, or deleterious, mutation decreases the fitness of the organism. Many, but not all mutations in essential genes are harmful (if a mutation does not change the amino acid sequence in an essential protein, it is harmless in most cases).
A beneficial, or advantageous mutation increases the fitness of the organism. Examples are mutations that lead to antibiotic resistance in bacteria (which are beneficial for bacteria but usually not for humans).
A neutral mutation has no harmful or beneficial effect on the organism. Such mutations occur at a steady rate, forming the basis for the molecular clock. In the neutral theory of molecular evolution, neutral mutations provide genetic drift as the basis for most variation at the molecular level. In animals or plants, most mutations are neutral, given that the vast majority of their genomes is either non-coding or consists of repetitive sequences that have no obvious function ("junk DNA").
Large-scale quantitative mutagenesis screens, in which thousands of millions of mutations are tested, invariably find that a larger fraction of mutations has harmful effects but always returns a number of beneficial mutations as well. For instance, in a screen of all gene deletions in E. coli, 80% of mutations were negative, but 20% were positive, even though many had a very small effect on growth (depending on condition). Gene deletions involve removal of whole genes, so that point mutations almost always have a much smaller effect. In a similar screen in Streptococcus pneumoniae, but this time with transposon insertions, 76% of insertion mutants were classified as neutral, 16% had a significantly reduced fitness, but 6% were advantageous.
This classification is obviously relative and somewhat artificial: a harmful mutation can quickly turn into a beneficial mutations when conditions change. Also, there is a gradient from harmful/beneficial to neutral, as many mutations may have small and mostly neglectable effects but under certain conditions will become relevant. Also, many traits are determined by hundreds of genes (or loci), so that each locus has only a minor effect. For instance, human height is determined by hundreds of genetic variants ("mutations") but each of them has a very minor effect on height, apart from the impact of nutrition. Height (or size) itself may be more or less beneficial as the huge range of sizes in animal or plant groups shows.
==== Distribution of fitness effects (DFE) ====
Attempts have been made to infer the distribution of fitness effects (DFE) using mutagenesis experiments and theoretical models applied to molecular sequence data. DFE, as used to determine the relative abundance of different types of mutations (i.e., strongly deleterious, nearly neutral or advantageous), is relevant to many evolutionary questions, such as the maintenance of genetic variation, the rate of genomic decay, the maintenance of outcrossing sexual reproduction as opposed to inbreeding and the evolution of sex and genetic recombination. DFE can also be tracked by tracking the skewness of the distribution of mutations with putatively severe effects as compared to the distribution of mutations with putatively mild or absent effect. In summary, the DFE plays an important role in predicting evolutionary dynamics. A variety of approaches have been used to study the DFE, including theoretical, experimental and analytical methods.
Mutagenesis experiment: The direct method to investigate the DFE is to induce mutations and then measure the mutational fitness effects, which has already been done in viruses, bacteria, yeast, and Drosophila. For example, most studies of the DFE in viruses used site-directed mutagenesis to create point mutations and measure relative fitness of each mutant. In Escherichia coli, one study used transposon mutagenesis to directly measure the fitness of a random insertion of a derivative of Tn10. In yeast, a combined mutagenesis and deep sequencing approach has been developed to generate high-quality systematic mutant libraries and measure fitness in high throughput. However, given that many mutations have effects too small to be detected and that mutagenesis experiments can detect only mutations of moderately large effect; DNA sequence analysis can provide valuable information about these mutations.
Molecular sequence analysis: With rapid development of DNA sequencing technology, an enormous amount of DNA sequence data is available and even more is forthcoming in the future. Various methods have been developed to infer the DFE from DNA sequence data. By examining DNA sequence differences within and between species, we are able to infer various characteristics of the DFE for neutral, deleterious and advantageous mutations. To be specific, the DNA sequence analysis approach allows us to estimate the effects of mutations with very small effects, which are hardly detectable through mutagenesis experiments.
One of the earliest theoretical studies of the distribution of fitness effects was done by Motoo Kimura, an influential theoretical population geneticist. His neutral theory of molecular evolution proposes that most novel mutations will be highly deleterious, with a small fraction being neutral. A later proposal by Hiroshi Akashi proposed a bimodal model for the DFE, with modes centered around highly deleterious and neutral mutations. Both theories agree that the vast majority of novel mutations are neutral or deleterious and that advantageous mutations are rare, which has been supported by experimental results. One example is a study done on the DFE of random mutations in vesicular stomatitis virus. Out of all mutations, 39.6% were lethal, 31.2% were non-lethal deleterious, and 27.1% were neutral. Another example comes from a high throughput mutagenesis experiment with yeast. In this experiment it was shown that the overall DFE is bimodal, with a cluster of neutral mutations, and a broad distribution of deleterious mutations.
Though relatively few mutations are advantageous, those that are play an important role in evolutionary changes. Like neutral mutations, weakly selected advantageous mutations can be lost due to random genetic drift, but strongly selected advantageous mutations are more likely to be fixed. Knowing the DFE of advantageous mutations may lead to increased ability to predict the evolutionary dynamics. Theoretical work on the DFE for advantageous mutations has been done by John H. Gillespie and H. Allen Orr. They proposed that the distribution for advantageous mutations should be exponential under a wide range of conditions, which, in general, has been supported by experimental studies, at least for strongly selected advantageous mutations.
In general, it is accepted that the majority of mutations are neutral or deleterious, with advantageous mutations being rare; however, the proportion of types of mutations varies between species. This indicates two important points: first, the proportion of effectively neutral mutations is likely to vary between species, resulting from dependence on effective population size; second, the average effect of deleterious mutations varies dramatically between species. In addition, the DFE also differs between coding regions and noncoding regions, with the DFE of noncoding DNA containing more weakly selected mutations.
=== By inheritance ===
In multicellular organisms with dedicated reproductive cells, mutations can be subdivided into germline mutations, which can be passed on to descendants through their reproductive cells, and somatic mutations (also called acquired mutations), which involve cells outside the dedicated reproductive group and which are not usually transmitted to descendants.
Diploid organisms (e.g., humans) contain two copies of each gene—a paternal and a maternal allele. Based on the occurrence of mutation on each chromosome, we may classify mutations into three types. A wild type or homozygous non-mutated organism is one in which neither allele is mutated.
A heterozygous mutation is a mutation of only one allele.
A homozygous mutation is an identical mutation of both the paternal and maternal alleles.
Compound heterozygous mutations or a genetic compound consists of two different mutations in the paternal and maternal alleles.
==== Germline mutation ====
A germline mutation in the reproductive cells of an individual gives rise to a constitutional mutation in the offspring, that is, a mutation that is present in every cell. A constitutional mutation can also occur very soon after fertilization, or continue from a previous constitutional mutation in a parent. A germline mutation can be passed down through subsequent generations of organisms.
The distinction between germline and somatic mutations is important in animals that have a dedicated germline to produce reproductive cells. However, it is of little value in understanding the effects of mutations in plants, which lack a dedicated germline. The distinction is also blurred in those animals that reproduce asexually through mechanisms such as budding, because the cells that give rise to the daughter organisms also give rise to that organism's germline.
A new germline mutation not inherited from either parent is called a de novo mutation.
==== Somatic mutation ====
A change in the genetic structure that is not inherited from a parent, and also not passed to offspring, is called a somatic mutation. Somatic mutations are not inherited by an organism's offspring because they do not affect the germline. However, they are passed down to all the progeny of a mutated cell within the same organism during mitosis. A major section of an organism therefore might carry the same mutation. These types of mutations are usually prompted by environmental causes, such as ultraviolet radiation or any exposure to certain harmful chemicals, and can cause diseases including cancer.
With plants, some somatic mutations can be propagated without the need for seed production, for example, by grafting and stem cuttings. These type of mutation have led to new types of fruits, such as the "Delicious" apple and the "Washington" navel orange.
Human and mouse somatic cells have a mutation rate more than ten times higher than the germline mutation rate for both species; mice have a higher rate of both somatic and germline mutations per cell division than humans. The disparity in mutation rate between the germline and somatic tissues likely reflects the greater importance of genome maintenance in the germline than in the soma.
=== Special classes ===
Conditional mutation is a mutation that has wild-type (or less severe) phenotype under certain "permissive" environmental conditions and a mutant phenotype under certain "restrictive" conditions. For example, a temperature-sensitive mutation can cause cell death at high temperature (restrictive condition), but might have no deleterious consequences at a lower temperature (permissive condition). These mutations are non-autonomous, as their manifestation depends upon presence of certain conditions, as opposed to other mutations which appear autonomously. The permissive conditions may be temperature, certain chemicals, light or mutations in other parts of the genome. In vivo mechanisms like transcriptional switches can create conditional mutations. For instance, association of Steroid Binding Domain can create a transcriptional switch that can change the expression of a gene based on the presence of a steroid ligand. Conditional mutations have applications in research as they allow control over gene expression. This is especially useful studying diseases in adults by allowing expression after a certain period of growth, thus eliminating the deleterious effect of gene expression seen during stages of development in model organisms. DNA Recombinase systems like Cre-Lox recombination used in association with promoters that are activated under certain conditions can generate conditional mutations. Dual Recombinase technology can be used to induce multiple conditional mutations to study the diseases which manifest as a result of simultaneous mutations in multiple genes. Certain inteins have been identified which splice only at certain permissive temperatures, leading to improper protein synthesis and thus, loss-of-function mutations at other temperatures. Conditional mutations may also be used in genetic studies associated with ageing, as the expression can be changed after a certain time period in the organism's lifespan.
Replication timing quantitative trait loci affects DNA replication.
=== Nomenclature ===
In order to categorize a mutation as such, the "normal" sequence must be obtained from the DNA of a "normal" or "healthy" organism (as opposed to a "mutant" or "sick" one), it should be identified and reported; ideally, it should be made publicly available for a straightforward nucleotide-by-nucleotide comparison, and agreed upon by the scientific community or by a group of expert geneticists and biologists, who have the responsibility of establishing the standard or so-called "consensus" sequence. This step requires a tremendous scientific effort. Once the consensus sequence is known, the mutations in a genome can be pinpointed, described, and classified. The committee of the Human Genome Variation Society (HGVS) has developed the standard human sequence variant nomenclature, which should be used by researchers and DNA diagnostic centers to generate unambiguous mutation descriptions. In principle, this nomenclature can also be used to describe mutations in other organisms. The nomenclature specifies the type of mutation and base or amino acid changes.
Nucleotide substitution (e.g., 76A>T) – The number is the position of the nucleotide from the 5' end; the first letter represents the wild-type nucleotide, and the second letter represents the nucleotide that replaced the wild type. In the given example, the adenine at the 76th position was replaced by a thymine.
If it becomes necessary to differentiate between mutations in genomic DNA, mitochondrial DNA, and RNA, a simple convention is used. For example, if the 100th base of a nucleotide sequence mutated from G to C, then it would be written as g.100G>C if the mutation occurred in genomic DNA, m.100G>C if the mutation occurred in mitochondrial DNA, or r.100g>c if the mutation occurred in RNA. Note that, for mutations in RNA, the nucleotide code is written in lower case.
Amino acid substitution (e.g., D111E) – The first letter is the one letter code of the wild-type amino acid, the number is the position of the amino acid from the N-terminus, and the second letter is the one letter code of the amino acid present in the mutation. Nonsense mutations are represented with an X for the second amino acid (e.g. D111X).
Amino acid deletion (e.g., ΔF508) – The Greek letter Δ (delta) indicates a deletion. The letter refers to the amino acid present in the wild type and the number is the position from the N terminus of the amino acid were it to be present as in the wild type.
== Mutation rates ==
Mutation rates vary substantially across species, and the evolutionary forces that generally determine mutation are the subject of ongoing investigation.
In humans, the mutation rate is about 50–90 de novo mutations per genome per generation, that is, each human accumulates about 50–90 novel mutations that were not present in his or her parents. This number has been established by sequencing thousands of human trios, that is, two parents and at least one child.
The genomes of RNA viruses are based on RNA rather than DNA. The RNA viral genome can be double-stranded (as in DNA) or single-stranded. In some of these viruses (such as the single-stranded human immunodeficiency virus), replication occurs quickly, and there are no mechanisms to check the genome for accuracy. This error-prone process often results in mutations.
The rate of de novo mutations, whether germline or somatic, vary among organisms. Individuals within the same species can even express varying rates of mutation. Overall, rates of de novo mutations are low compared to those of inherited mutations, which categorizes them as rare forms of genetic variation. Many observations of de novo mutation rates have associated higher rates of mutation correlated to paternal age. In sexually reproducing organisms, the comparatively higher frequency of cell divisions in the parental sperm donor germline drive conclusions that rates of de novo mutation can be tracked along a common basis. The frequency of error during the DNA replication process of gametogenesis, especially amplified in the rapid production of sperm cells, can promote more opportunities for de novo mutations to replicate unregulated by DNA repair machinery. This claim combines the observed effects of increased probability for mutation in rapid spermatogenesis with short periods of time between cellular divisions that limit the efficiency of repair machinery. Rates of de novo mutations that affect an organism during its development can also increase with certain environmental factors. For example, certain intensities of exposure to radioactive elements can inflict damage to an organism's genome, heightening rates of mutation. In humans, the appearance of skin cancer during one's lifetime is induced by overexposure to UV radiation that causes mutations in the cellular and skin genome.
=== Randomness of mutations ===
There is a widespread assumption that mutations are (entirely) "random" with respect to their consequences (in terms of probability). This was shown to be wrong as mutation frequency can vary across regions of the genome, with such DNA repair- and mutation-biases being associated with various factors. For instance, Monroe and colleagues demonstrated that—in the studied plant (Arabidopsis thaliana)—more important genes mutate less frequently than less important ones. They demonstrated that mutation is "non-random in a way that benefits the plant". Additionally, previous experiments typically used to demonstrate mutations being random with respect to fitness (such as the Fluctuation Test and Replica plating) have been shown to only support the weaker claim that those mutations are random with respect to external selective constraints, not fitness as a whole.
== Disease causation ==
Changes in DNA caused by mutation in a coding region of DNA can cause errors in protein sequence that may result in partially or completely non-functional proteins. Each cell, in order to function correctly, depends on thousands of proteins to function in the right places at the right times. When a mutation alters a protein that plays a critical role in the body, a medical condition can result. One study on the comparison of genes between different species of Drosophila suggests that if a mutation does change a protein, the mutation will most likely be harmful, with an estimated 70 per cent of amino acid polymorphisms having damaging effects, and the remainder being either neutral or weakly beneficial. Some mutations alter a gene's DNA base sequence but do not change the protein made by the gene. Studies have shown that only 7% of point mutations in noncoding DNA of yeast are deleterious and 12% in coding DNA are deleterious. The rest of the mutations are either neutral or slightly beneficial.
=== Inherited disorders ===
If a mutation is present in a germ cell, it can give rise to offspring that carries the mutation in all of its cells. This is the case in hereditary diseases. In particular, if there is a mutation in a DNA repair gene within a germ cell, humans carrying such germline mutations may have an increased risk of cancer. A list of 34 such germline mutations is given in the article DNA repair-deficiency disorder. An example of one is albinism, a mutation that occurs in the OCA1 or OCA2 gene. Individuals with this disorder are more prone to many types of cancers, other disorders and have impaired vision.
DNA damage can cause an error when the DNA is replicated, and this error of replication can cause a gene mutation that, in turn, could cause a genetic disorder. DNA damages are repaired by the DNA repair system of the cell. Each cell has a number of pathways through which enzymes recognize and repair damages in DNA. Because DNA can be damaged in many ways, the process of DNA repair is an important way in which the body protects itself from disease. Once DNA damage has given rise to a mutation, the mutation cannot be repaired.
=== Role in carcinogenesis ===
On the other hand, a mutation may occur in a somatic cell of an organism. Such mutations will be present in all descendants of this cell within the same organism. The accumulation of certain mutations over generations of somatic cells is part of cause of malignant transformation, from normal cell to cancer cell.
Cells with heterozygous loss-of-function mutations (one good copy of gene and one mutated copy) may function normally with the unmutated copy until the good copy has been spontaneously somatically mutated. This kind of mutation happens often in living organisms, but it is difficult to measure the rate. Measuring this rate is important in predicting the rate at which people may develop cancer.
Point mutations may arise from spontaneous mutations that occur during DNA replication. The rate of mutation may be increased by mutagens. Mutagens can be physical, such as radiation from UV rays, X-rays or extreme heat, or chemical (molecules that misplace base pairs or disrupt the helical shape of DNA). Mutagens associated with cancers are often studied to learn about cancer and its prevention.
== Beneficial and conditional mutations ==
Although mutations that cause changes in protein sequences can be harmful to an organism, on occasions the effect may be positive in a given environment. In this case, the mutation may enable the mutant organism to withstand particular environmental stresses better than wild-type organisms, or reproduce more quickly. In these cases a mutation will tend to become more common in a population through natural selection. That said, the same mutation can be beneficial in one condition and disadvantageous in another condition. Examples include the following:
HIV resistance: a specific 32 base pair deletion in human CCR5 (CCR5-Δ32) confers HIV resistance to homozygotes and delays AIDS onset in heterozygotes. One possible explanation of the etiology of the relatively high frequency of CCR5-Δ32 in the European population is that it conferred resistance to the bubonic plague in mid-14th century Europe. People with this mutation were more likely to survive infection; thus its frequency in the population increased. This theory could explain why this mutation is not found in Southern Africa, which remained untouched by bubonic plague. A newer theory suggests that the selective pressure on the CCR5 Delta 32 mutation was caused by smallpox instead of the bubonic plague.
Malaria resistance: An example of a harmful mutation is sickle-cell disease, a blood disorder in which the body produces an abnormal type of the oxygen-carrying substance haemoglobin in the red blood cells. One-third of all indigenous inhabitants of Sub-Saharan Africa carry the allele, because, in areas where malaria is common, there is a survival value in carrying only a single sickle-cell allele (sickle cell trait). Those with only one of the two alleles of the sickle-cell disease are more resistant to malaria, since the infestation of the malaria Plasmodium is halted by the sickling of the cells that it infests.
Antibiotic resistance: Practically all bacteria develop antibiotic resistance when exposed to antibiotics. In fact, bacterial populations already have such mutations that get selected under antibiotic selection. Obviously, such mutations are only beneficial for the bacteria but not for those infected.
Lactase persistence. A mutation allowed humans to express the enzyme lactase after they are naturally weaned from breast milk, allowing adults to digest lactose, which is likely one of the most beneficial mutations in recent human evolution.
== Role in evolution ==
By introducing novel genetic qualities to a population of organisms, de novo mutations play a critical role in the combined forces of evolutionary change. However, the weight of genetic diversity generated by mutational change is often considered a generally "weak" evolutionary force. Although the random emergence of mutations alone provides the basis for genetic variation across all organic life, this force must be taken in consideration alongside all evolutionary forces at play. Spontaneous de novo mutations as cataclysmic events of speciation depend on factors introduced by natural selection, genetic flow, and genetic drift. For example, smaller populations with heavy mutational input (high rates of mutation) are prone to increases of genetic variation which lead to speciation in future generations. In contrast, larger populations tend to see lesser effects of newly introduced mutated traits. In these conditions, selective forces diminish the frequency of mutated alleles, which are most often deleterious, over time.
== Compensated pathogenic deviations ==
Compensated pathogenic deviations refer to amino acid residues in a protein sequence that are pathogenic in one species but are wild type residues in the functionally equivalent protein in another species. Although the amino acid residue is pathogenic in the first species, it is not so in the second species because its pathogenicity is compensated by one or more amino acid substitutions in the second species. The compensatory mutation can occur in the same protein or in another protein with which it interacts.
It is critical to understand the effects of compensatory mutations in the context of fixed deleterious mutations due to the population fitness decreasing because of fixation. Effective population size refers to a population that is reproducing. An increase in this population size has been correlated with a decreased rate of genetic diversity. The position of a population relative to the critical effect population size is essential to determine the effect deleterious alleles will have on fitness. If the population is below the critical effective size fitness will decrease drastically, however if the population is above the critical effect size, fitness can increase regardless of deleterious mutations due to compensatory alleles.
=== Compensatory mutations in RNA ===
As the function of a RNA molecule is dependent on its structure, the structure of RNA molecules is evolutionarily conserved. Therefore, any mutation that alters the stable structure of RNA molecules must be compensated by other compensatory mutations. In the context of RNA, the sequence of the RNA can be considered as ' genotype' and the structure of the RNA can be considered as its 'phenotype'. Since RNAs have relatively simpler composition than proteins, the structure of RNA molecules can be computationally predicted with high degree of accuracy. Because of this convenience, compensatory mutations have been studied in computational simulations using RNA folding algorithms.
=== Evolutionary mechanism of compensation ===
Compensatory mutations can be explained by the genetic phenomenon epistasis whereby the phenotypic effect of one mutation is dependent upon mutation(s) at other loci. While epistasis was originally conceived in the context of interaction between different genes, intragenic epistasis has also been studied recently. Existence of compensated pathogenic deviations can be explained by 'sign epistasis', in which the effects of a deleterious mutation can be compensated by the presence of an epistatic mutation in another loci. For a given protein, a deleterious mutation (D) and a compensatory mutation (C) can be considered, where C can be in the same protein as D or in a different interacting protein depending on the context. The fitness effect of C itself could be neutral or somewhat deleterious such that it can still exist in the population, and the effect of D is deleterious to the extent that it cannot exist in the population. However, when C and D co-occur together, the combined fitness effect becomes neutral or positive. Thus, compensatory mutations can bring novelty to proteins by forging new pathways of protein evolution : it allows individuals to travel from one fitness peak to another through the valleys of lower fitness.
DePristo et al. 2005 outlined two models to explain the dynamics of compensatory pathogenic deviations (CPD). In the first hypothesis P is a pathogenic amino acid mutation that and C is a neutral compensatory mutation. Under these conditions, if the pathogenic mutation arises after a compensatory mutation, then P can become fixed in the population. The second model of CPDs states that P and C are both deleterious mutations resulting in fitness valleys when mutations occur simultaneously. Using publicly available, Ferrer-Costa et al. 2007 obtained compensatory mutations and human pathogenic mutation datasets that were characterized to determine what causes CPDs. Results indicate that the structural constraints and the location in protein structure determine whether compensated mutations will occur.
=== Experimental evidence of compensatory mutations ===
==== Experiment in bacteria ====
Lunzer et al. tested the outcome of swapping divergent amino acids between two orthologous proteins of isopropymalate dehydrogenase (IMDH). They substituted 168 amino acids in Escherichia coli IMDH that are wild type residues in IMDH Pseudomonas aeruginosa. They found that over one third of these substitutions compromised IMDH enzymatic activity in the Escherichia coli genetic background. This demonstrated that identical amino acid states can result in different phenotypic states depending on the genetic background. Corrigan et al. 2011 demonstrated how Staphylococcus aureus was able to grow normally without the presence of lipoteichoic acid due to compensatory mutations. Whole genome sequencing results revealed that when Cyclic-di-AMP phosphodiesterase (GdpP) was disrupted in this bacterium, it compensated for the disappearance of the cell wall polymer, resulting in normal cell growth.
Research has shown that bacteria can gain drug resistance through compensatory mutations that do not impede or having little effect on fitness. Previous research from Gagneux et al. 2006 has found that laboratory grown Mycobacterium tuberculosis strains with rifampicin resistance have reduced fitness, however drug resistant clinical strains of this pathogenic bacteria do not have reduced fitness. Comas et al. 2012 used whole genome comparisons between clinical strains and lab derived mutants to determine the role and contribution of compensatory mutations in drug resistance to rifampicin. Genome analysis reveal rifampicin resistant strains have a mutation in rpoA and rpoC. A similar study investigated the bacterial fitness associated with compensatory mutations in rifampin resistant Escherichia coli. Results obtained from this study demonstrate that drug resistance is linked to bacterial fitness as higher fitness costs are linked to greater transcription errors.
==== Experiment in virus ====
Gong et al. collected obtained genotype data of influenza nucleoprotein from different timelines and temporally ordered them according to their time of origin. Then they isolated 39 amino acid substitutions that occurred in different timelines and substituted them in a genetic background that approximated the ancestral genotype. They found that 3 of the 39 substitutions significantly reduced the fitness of the ancestral background. Compensatory mutations are new mutations that arise and have a positive or neutral impact on a populations fitness. Previous research has shown that populations have can compensate detrimental mutations. Burch and Chao tested Fisher's geometric model of adaptive evolution by testing whether bacteriophage φ6 evolves by small steps. Their results showed that bacteriophage φ6 fitness declined rapidly and recovered in small steps . Viral nucleoproteins have been shown to avoid cytotoxic T lymphocytes (CTLs) through arginine-to glycine substitutions. This substitution mutations impacts the fitness of viral nucleoproteins, however compensatory co-mutations impede fitness declines and aid the virus to avoid recognition from CTLs. Mutations can have three different effects; mutations can have deleterious effects, some increase fitness through compensatory mutations, and lastly mutations can be counterbalancing resulting in compensatory neutral mutations.
== Application in human evolution and disease ==
In the human genome, the frequency and characteristics of de novo mutations have been studied as important contextual factors to our evolution. Compared to the human reference genome, a typical human genome varies at approximately 4.1 to 5.0 million loci, and the majority of this genetic diversity is shared by nearly 0.5% of the population. The typical human genome also contains 40,000 to 200,000 rare variants observed in less than 0.5% of the population that can only have occurred from at least one de novo germline mutation in the history of human evolution. De novo mutations have also been researched as playing a crucial role in the persistence of genetic disease in humans. With recents advancements in next-generation sequencing (NGS), all types of de novo mutations within the genome can be directly studied, the detection of which provides a magnitude of insight toward the causes of both rare and common genetic disorders. Currently, the best estimate of the average human germline SNV mutation rate is 1.18 x 10^-8, with an approximate ~78 novel mutations per generation. The ability to conduct whole genome sequencing of parents and offspring allows for the comparison of mutation rates between generations, narrowing down the origin possibilities of certain genetic disorders.
== See also ==
== References ==
== External links ==
Jones S, Woolfson A, Partridge L (6 December 2007). "Genetic Mutation". In Our Time. BBC Radio 4. Retrieved 18 October 2015.
Liou S (5 February 2011). "All About Mutations". HOPES. Huntington's Disease Outreach Project for Education at Stanford. Retrieved 18 October 2015.
"Locus Specific Mutation Databases". Leiden, the Netherlands: Leiden University Medical Center. Retrieved 18 October 2015.
"Welcome to the Mutalyzer website". Leiden, the Netherlands: Leiden University Medical Center. Retrieved 18 October 2015. – The Mutalyzer website. | Wikipedia/DNA_error |
FANC proteins are a network of at least 15 proteins that are associated with a cell process known as the Fanconi anemia.
== History ==
Fanconi anemia was first described in 1927 by Guido Fanconi, a Swiss pediatrician. It is a chromosome instability syndrome characterized by the progressiveness of bone marrow failure and of cancer proneness.
== Properties ==
The FA genes that code for the FANC proteins are a part of the caretaker group of cancer genes that prevent the buildup of mutations and chromosome abnormalities. The multiple FANC proteins come together to add up to the FANC/BRCA pathway.
== Components ==
There are a large number of FANC proteins that participate in the FA pathway. It has a nuclear complex also known as the ‘FA core complex’ which is formed by the interaction of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM and the accessory proteins (FAAP20, FAAP24, and FAAP100). These accessory proteins are also called Fanconi anemia associated proteins (FAAPs). There is also a group called the anchor complex which consists of FANCM, FAAP24, MHF1 (FAAP16/ CENP-S), and MHF2 (FAAP10/ CENP-X). The FANC proteins that are not a part of the core complex are FANCD1, FANCJ, and FANCN.
Components include:
core protein complex (FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM)
other: FANCD1, FANCD2, FANCI, FANCJ, FANCN, FANCP
== Function ==
They are involved in DNA replication and damage response. FANC proteins are also in charge of repairing complex DNA interstrand cross-linking lesions and maintaining the genomic stability during DNA replication. DNA cross-linking is what hinders transcription and replication from occurring in the cell so it is important that the cell has methods to repair at every stage of the cell cycle. There are multiple different repair pathways but the FA pathway is the one that involves the FANC proteins. When cross-link is detected, then the ataxia-telangiectasia and RAD3-related protein will mediate the phosphorylation (P) of the FA core complex. This phosphorylated FA core complex is what is required to have a successful monoubiquitination of the two components that form the FANCI–D2 complex. Each of the proteins of the FA core complex are needed for this phosphorylation step except for FANCM. When a typical cell senses DNA damage it targets the monoubiquitinated isoform of FANCI–D2 to the chromatid with DNA damage, which is the cross-link. Studies have also shown that there is a connection between the FA DNA repair pathway and stem cell regulation but it is still unclear. FANC proteins also play a role in redox signaling and repair of oxidative DNA damages. Recent studies have dove into the FANC protein, FANCJ, and its enzymatic function along with its roles in repair. Other studies have shown the correlation between the FANC pathway and multiple other protein post translational modifications from ubiquitin-like families.
== Pathogenesis ==
A mutation in 13 FANC genes can result in Fanconi anemia (FA), which is a cancer-prone chromosome instability disorder. Fanconi anemia occurs when there is a biallelic mutation that inactivates the genes that are in charge of the replication stress associated DNA damage response. Dysfunction of FANC proteins has been associated with a range of conditions, including the rendering of cell hypersensitivity to a type of DNA damage known as DNA interstrand cross-links (ICL) and defective DNA repair. FANC protein mutations have also lead to reduced fertility and predisposition to cancers like breast cancer and myeloid leukaemia. FANC proteins FANCD1 (BRCA2), FANCJ (BRIP), and FANCN (PALB2) have even been identified as the breast cancer susceptibility proteins. If a cell were to lack the FANC gene to code for these proteins then the cell would show a hypersensitive phenotype following H2O2 treatment.
== Similar/ Related Protein ==
FANC proteins are related to BRCA.
FANC proteins are required to promote BLM-mediated anaphase.
FANC proteins also interacts with BRCA1.
FANC proteins also interacts with LIG4.
FANC proteins also interacts with DNA-PKcs.
FANC proteins also interacts with Ku70.
FANC proteins also interacts with Ku80.
FANC proteins also interacts with FAN1.
FANC proteins also interacts with XPF.
FANCC protein interacts with cdc2.
FANCC protein interacts with PKR.
FANCC protein interactS with p53.
FANC protein FANCD1 is also known as BRCA2.
FANC protein FANCJ is also known as BRIP1.
FANC protein FANCN is also known as PALB2.
FANC protein FANCO is also known as RAD51C.
FANC protein FANCP is also known as SLX4.
== References == | Wikipedia/FANC_proteins |
Gene conversion is the process by which one DNA sequence replaces a homologous sequence such that the sequences become identical after the conversion. Gene conversion can be either allelic, meaning that one allele of the same gene replaces another allele, or ectopic, meaning that one paralogous DNA sequence converts another.
== Allelic gene conversion ==
Allelic gene conversion occurs during meiosis when homologous recombination between heterozygotic sites results in a mismatch in base pairing. This mismatch is then recognized and corrected by the cellular machinery causing one of the alleles to be converted to the other. This can cause non-Mendelian segregation of alleles in germ cells.
== Nonallelic/ectopic gene conversion ==
Recombination occurs not only during meiosis, but also as a mechanism for repair of double-strand breaks (DSBs) caused by DNA damage. These DSBs are usually repaired using the sister chromatid of the broken duplex and not the homologous chromosome, so they would not result in allelic conversion. Recombination also occurs between homologous sequences present at different genomic loci (paralogous sequences) which have resulted from previous gene duplications. Gene conversion occurring between paralogous sequences (ectopic gene conversion) is conjectured to be responsible for concerted evolution of gene families.
== Mechanism ==
Conversion of one allele to the other is often due to base mismatch repair during homologous recombination: if one of the four chromatids during meiosis pairs up with another chromatid, as can occur because of sequence homology, DNA strand transfer can occur followed by mismatch repair. This can alter the sequence of one of the chromosomes, so that it is identical to the other.
Meiotic recombination is initiated through formation of a double-strand break (DSB). The 5’ ends of the break are then degraded, leaving long 3’ overhangs of several hundred nucleotides. One of these 3’ single stranded DNA segments then invades a homologous sequence on the homologous chromosome, forming an intermediate which can be repaired through different pathways resulting either in crossovers (CO) or noncrossovers (NCO). At various steps of the recombination process, heteroduplex DNA (double-stranded DNA consisting of single strands from each of the two homologous chromosomes which may or may not be perfectly complementary) is formed. When mismatches occur in heteroduplex DNA, the sequence of one strand will be repaired to bind the other strand with perfect complementarity, leading to the conversion of one sequence to another. This repair process can follow either of two alternative pathways as illustrated in the Figure. By one pathway, a structure called a double Holliday junction (DHJ) is formed, leading to the exchange of DNA strands. By the other pathway, referred to as Synthesis Dependent Strand Annealing (SDSA), there is information exchange but not physical exchange. Gene conversion will occur during SDSA if the two DNA molecules are heterozygous at the site of the recombinational repair. Gene conversion may also occur during recombinational repair involving a DHJ, and this gene conversion may be associated with physical recombination of the DNA duplexes on the two sides of the DHJ.
== Biased vs. unbiased gene conversion ==
Biased gene conversion (BGC) occurs when one allele has a higher probability of being the donor than the other in a gene conversion event. For example, when a T:G mismatch occurs, it would be more or less likely to be corrected to a C:G pair than a T:A pair. This gives that allele a higher probability of transmission to the next generation. Unbiased gene conversion means that both possibilities occur with equal probability.
=== GC-biased gene conversion ===
GC-biased gene conversion (gBGC) is the process by which the GC content of DNA increases due to gene conversion during recombination. Evidence for gBGC exists for yeasts and humans and the theory has more recently been tested in other eukaryotic lineages. In analyzed human DNA sequences, crossover rate has been found to correlate positively with GC-content. The pseudoautosomal regions (PAR) of the X and Y chromosomes in humans, which are known to have high recombination rates also have high GC contents. Certain mammalian genes undergoing concerted evolution (for example, ribosomal operons, tRNAs, and histone genes) are very GC-rich. It has been shown that GC content is higher in paralogous human and mouse histone genes that are members of large subfamilies (presumably undergoing concerted evolution) than in paralogous histone genes with relatively unique sequences.
There is also evidence for GC bias in the mismatch repair process. It is thought that this may be an adaptation to the high rate of methyl-cytosine deamination which can lead to C→T transitions.
==== BGC of the Fxy gene in Mus musculus ====
The Fxy or Mid1 gene in some mammals closely related to house mice (humans, rats, and other Mus species) is located in the sex-linked region of the X chromosome. However, in Mus musculus, it has recently translocated such that the 3’ end of the gene overlaps with the PAR region of the X-chromosome, which is known to be a recombination hotspot. This portion of the gene has experienced a dramatic increase in GC content and substitution rate at the 3rd codon position as well as in introns but the 5’ region of the gene, which is X-linked, has not. Because this effect is present only in the region of the gene experiencing increased recombination rate, it must be due to biased gene conversion and not selective pressure.
==== Impact of GC-biased gene conversion on human genomic patterns ====
GC content varies widely in the human genome (40–80%), but there seem to be large sections of the genome where GC content is, on average, higher or lower than in other regions. These regions, although not always showing clear boundaries, are known as isochores. One possible explanation for the presence of GC-rich isochores is that they evolved due to GC-biased gene conversion in regions with high levels of recombination.
== Evolutionary importance ==
=== Adaptive function of recombination ===
Studies of gene conversion have contributed to our understanding of the adaptive function of meiotic recombination. The ordinary segregation pattern of an allele pair (Aa) among the 4 products of meiosis is 2A:2a. Detection of infrequent gene conversion events (e.g. 3:1 or 1:3 segregation patterns during individual meioses) provides insight into the alternate pathways of recombination leading either to crossover or non-crossover chromosomes. Gene conversion events are thought to arise where the "A" and "a" alleles happen to be near the exact location of a molecular recombination event. Thus, it is possible to measure the frequency with which gene conversion events are associated with crossover or non-crossover of chromosomal regions adjacent to, but outside, the immediate conversion event. Numerous studies of gene conversion in various fungi (which are especially suited for such studies) have been carried out, and the findings of these studies have been reviewed by Whitehouse. It is clear from this review that most gene conversion events are not associated with outside marker exchange. Thus, most gene conversion events in the several different fungi studied are associated with non-crossover of outside markers. Non-crossover gene conversion events are mainly produced by Synthesis Dependent Strand Annealing (SDSA). This process involves limited informational exchange, but not physical exchange of DNA, between the two participating homologous chromosomes at the site of the conversion event, and little genetic variation is produced. Thus, explanations for the adaptive function of meiotic recombination that focus exclusively on the adaptive benefit of producing new genetic variation or physical exchange seem inadequate to explain the majority of recombination events during meiosis. However, the majority of meiotic recombination events can be explained by the proposal that they are an adaptation for repair of damage in the DNA that is to be passed on to gametes.
Of particular interest, from the point of view that recombination is an adaptation for DNA repair, are the studies in yeast showing that gene conversion in mitotic cells is increased by UV and ionizing radiation
=== Evolution of humans ===
In the discussions of genetic diseases in humans, pseudogene mediated gene conversions that introduce pathogenic mutations into functional genes is a well known mechanism of mutation. In contrast, it is possible that pseudogenes could serve as templates. During the course of evolution, functional source genes which are potentially advantageous have been derived from multiple copies in their single source gene. The pseudogene-templated changes might eventually become fixed as long as they did not possess deleterious effects. So, in fact, pseudogenes can act as sources of sequence variants which can be transferred to functional genes in novel combinations and can be acted upon by selection. Lectin 11 (SIGLEC11), a human immunoglobulin that binds to sialic acid, can be considered an example of such a gene conversion event which has played a significant role in evolution. While comparing the homologous genes of human SIGLEC11 and its pseudogene in the chimpanzee, gorilla and orangutan, it appears that there was gene conversion of the sequence of 5’ upstream regions and the exons that encode the sialic acid recognition domain, approximately 2kbp from the closely flanking hSIGLECP16 pseudogene (Hayakawa et al., 2005). The three pieces of evidence concerning this event have together suggested this as an adaptive change which is very evolutionarily important in genus Homo. Those includes that only in human lineage this gene conversion happened, the brain cortex has acquired an important expression of SIGLEC11 specifically in human lineage and the exhibition of a change in substrate binding in human lineage when compared to that of its counterpart in chimpanzees. Of course the frequency of the contribution of this pseudogene-mediated gene conversion mechanism to functional and adaptive changes in evolution of human is still unknown and so far it has been scarcely explored. In spite of that, the introduction of positively selective genetic changes by such mechanism can be put forward for consideration by the example of SIGLEC11. Sometimes due to interference of transposable elements in to some members of a gene family, it causes a variation among them and finally it may also cease the rate of gene conversion due to lack of sequence similarity which leads to divergent evolution.
== Genomic analysis ==
From various genome analyses, it was concluded that the double-strand breaks (DSB) can be repaired via homologous recombination by at least two different but related pathways. In case of major pathway, homologous sequences on both sides of the DSB will be employed which seems to be analogous to the conservative DSB repair model that was originally proposed for meiotic recombination in yeast. where as the minor pathway is restricted to only one side of the DSB as postulated by nonconservative one-sided invasion model. However, in both cases the sequence of the recombination partners will be absolutely conserved. By virtue of their high degree of homology, the new gene copies that came into existence following the gene duplication naturally tend to either unequal crossover or unidirectional gene conversion events. In the latter process, there exists the acceptor and donor sequences and the acceptor sequence will be replaced by a sequence copied from the donor, while the sequence of the donor remains unchanged.
The effective homology between the interacting sequences makes the gene conversion event successful. Additionally, the frequency of gene conversion is inversely proportional to the distance between the interacting sequences in cis, and the rate of gene conversion is usually directly proportional to the length of uninterrupted sequence tract in the assumed converted region. It seems that conversion tracts accompanying crossover are longer (mean length = ~460 bp) than conversion tracts without crossover (mean length = 55–290 bp). In the studies of human globulin genes, it has long been supported that the gene conversion event or branch migration events can either be promoted or inhibited by the specific motifs that exist in the vicinity of the DNA sequence. Another basic classification of gene conversion events is the interlocus (also called nonallelic) and interallelic gene conversions. The cis or trans nonallelic or interlocus gene conversion events occur between nonallelic gene copies residing on sister chromatids or homologous chromosomes, and, in case of interallelic, the gene conversion events take place between alleles residing on homologous chromosomes. If the interlocus gene conversion events are compared, it will be frequently revealed that they exhibit biased directionality. Sometimes, such as in case of human globin genes, the gene conversion direction correlates with the relative expression levels of the genes that participate in the event, with the gene expressed at higher level, called the 'master' gene, converting that with lower expression, called the 'slave' gene. Originally formulated in an evolutionary context, the 'master/slave gene' rule should be explained with caution. In fact, the increase in gene transcription exhibits not only the increase in likelihood of it to be used as a donor but also as an acceptor.
== Effect ==
Normally, an organism that has inherited different copies of a gene from each of its parents is called heterozygous. This is generically represented as genotype: Aa (i.e. one copy of variant (allele) 'A', and one copy of allele 'a'). When a heterozygote creates gametes by meiosis, the alleles normally duplicate and end up in a 2:2 ratio in the resulting 4 cells that are the direct products of meiosis. However, in gene conversion, a ratio other than the expected 2A:2a is observed, in which A and a are the two alleles. Examples are 3A:1a and 1A:3a. In other words, there can, for example, be three times as many A alleles as a alleles expressed in the daughter cells, as is the case in 3A:1a.
== Medical relevance ==
Gene conversion resulting in mutation of the CYP21A2 gene is a common underlying genetic cause of congenital adrenal hyperplasia. Somatic gene conversion is one of the mechanisms that can result in familial retinoblastoma, a congenital cancer of the retina.
== References ==
== External links ==
Gene+conversion at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
images: http://www.web-books.com/MoBio/Free/Ch8D4.htm Archived 2022-03-20 at the Wayback Machine and http://www.web-books.com/MoBio/Free/Ch8D2.htm Archived 2022-01-27 at the Wayback Machine | Wikipedia/Gene_conversion |
Basal metabolic rate (BMR) is the rate of energy expenditure per unit time by endothermic animals at rest. It is reported in energy units per unit time ranging from watt (joule/second) to ml O2/min or joule per hour per kg body mass J/(h·kg). Proper measurement requires a strict set of criteria to be met. These criteria include being in a physically and psychologically undisturbed state and being in a thermally neutral environment while in the post-absorptive state (i.e., not actively digesting food). In bradymetabolic animals, such as fish and reptiles, the equivalent term standard metabolic rate (SMR) applies. It follows the same criteria as BMR, but requires the documentation of the temperature at which the metabolic rate was measured. This makes BMR a variant of standard metabolic rate measurement that excludes the temperature data, a practice that has led to problems in defining "standard" rates of metabolism for many mammals.
Metabolism comprises the processes that the body needs to function. Basal metabolic rate is the amount of energy per unit of time that a person needs to keep the body functioning at rest. Some of those processes are breathing, blood circulation, controlling body temperature, cell growth, brain and nerve function, and contraction of muscles. Basal metabolic rate affects the rate that a person burns calories and ultimately whether that individual maintains, gains, or loses weight. The basal metabolic rate accounts for about 70% of the daily calorie expenditure by individuals. It is influenced by several factors. In humans, BMR typically declines by 1–2% per decade after age 20, mostly due to loss of fat-free mass, although the variability between individuals is high.
== Description ==
The body's generation of heat is known as thermogenesis and it can be measured to determine the amount of energy expended. BMR generally decreases with age, and with the decrease in lean body mass (as may happen with aging). Increasing muscle mass has the effect of increasing BMR. Aerobic (resistance) fitness level, a product of cardiovascular exercise, while previously thought to have effect on BMR, has been shown in the 1990s not to correlate with BMR when adjusted for fat-free body mass. But anaerobic exercise does increase resting energy consumption (see "aerobic vs. anaerobic exercise"). Illness, previously consumed food and beverages, environmental temperature, and stress levels can affect one's overall energy expenditure as well as one's BMR.
BMR is measured under very restrictive circumstances when a person is awake. An accurate BMR measurement requires that the person's sympathetic nervous system not be stimulated, a condition which requires complete rest. A more common measurement, which uses less strict criteria, is resting metabolic rate (RMR).
BMR may be measured by gas analysis through either direct or indirect calorimetry, though a rough estimation can be acquired through an equation using age, sex, height, and weight. Studies of energy metabolism using both methods provide convincing evidence for the validity of the respiratory quotient (RQ), which measures the inherent composition and utilization of carbohydrates, fats and proteins as they are converted to energy substrate units that can be used by the body as energy.
== Phenotypic flexibility ==
BMR is a flexible trait (it can be reversibly adjusted within individuals), with, for example, lower temperatures generally resulting in higher basal metabolic rates for both birds and rodents. There are two models to explain how BMR changes in response to temperature: the variable maximum model (VMM) and variable fraction model (VFM). The VMM states that the summit metabolism (or the maximum metabolic rate in response to the cold) increases during the winter, and that the sustained metabolism (or the metabolic rate that can be indefinitely sustained) remains a constant fraction of the former. The VFM says that the summit metabolism does not change, but that the sustained metabolism is a larger fraction of it. The VMM is supported in mammals, and, when using whole-body rates, passerine birds. The VFM is supported in studies of passerine birds using mass-specific metabolic rates (or metabolic rates per unit of mass). This latter measurement has been criticized by Eric Liknes, Sarah Scott, and David Swanson, who say that mass-specific metabolic rates are inconsistent seasonally.
In addition to adjusting to temperature, BMR also may adjust before annual migration cycles. The red knot (ssp. islandica) increases its BMR by about 40% before migrating northward. This is because of the energetic demand of long-distance flights. The increase is likely primarily due to increased mass in organs related to flight. The end destination of migrants affects their BMR: yellow-rumped warblers migrating northward were found to have a 31% higher BMR than those migrating southward.
In humans, BMR is directly proportional to a person's lean body mass. In other words, the more lean body mass a person has, the higher their BMR; but BMR is also affected by acute illnesses and increases with conditions like burns, fractures, infections, fevers, etc. In menstruating females, BMR varies to some extent with the phases of their menstrual cycle. Due to the increase in progesterone, BMR rises at the start of the luteal phase and stays at its highest until this phase ends. There are different findings in research how much of an increase usually occurs. Small sample, early studies, found various figures, such as; a 6% higher postovulatory sleep metabolism, a 7% to 15% higher 24 hour expenditure following ovulation, and an increase and a luteal phase BMR increase by up to 12%. A study by the American Society of Clinical Nutrition found that an experimental group of female volunteers had an 11.5% average increase in 24 hour energy expenditure in the two weeks following ovulation, with a range of 8% to 16%. This group was measured via simultaneously direct and indirect calorimetry and had standardized daily meals and sedentary schedule in order to prevent the increase from being manipulated by change in food intake or activity level. A 2011 study conducted by the Mandya Institute of Medical Sciences found that during a woman's follicular phase and menstrual cycle is no significant difference in BMR, however the calories burned per hour is significantly higher, up to 18%, during the luteal phase. Increased state anxiety (stress level) also temporarily increased BMR.
== Physiology ==
The early work of the scientists J. Arthur Harris and Francis G. Benedict showed that approximate values for BMR could be derived using body surface area (computed from height and weight), age, and sex, along with the oxygen and carbon dioxide measures taken from calorimetry. Studies also showed that by eliminating the sex differences that occur with the accumulation of adipose tissue by expressing metabolic rate per unit of "fat-free" or lean body mass, the values between sexes for basal metabolism are essentially the same. Exercise physiology textbooks have tables to show the conversion of height and body surface area as they relate to weight and basal metabolic values.
The primary organ responsible for regulating metabolism is the hypothalamus. The hypothalamus is located on the diencephalon and forms the floor and part of the lateral walls of the third ventricle of the cerebrum. The chief functions of the hypothalamus are:
control and integration of activities of the autonomic nervous system (ANS)
The ANS regulates contraction of smooth muscle and cardiac muscle, along with secretions of many endocrine organs such as the thyroid gland (associated with many metabolic disorders).
Through the ANS, the hypothalamus is the main regulator of visceral activities, such as heart rate, movement of food through the gastrointestinal tract, and contraction of the urinary bladder.
production and regulation of feelings of rage and aggression
regulation of body temperature
regulation of food intake, through two centers:
The feeding center or hunger center is responsible for the sensations that cause us to seek food. When sufficient food or substrates have been received and leptin is high, then the satiety center is stimulated and sends impulses that inhibit the feeding center. When insufficient food is present in the stomach and ghrelin levels are high, receptors in the hypothalamus initiate the sense of hunger.
The thirst center operates similarly when certain cells in the hypothalamus are stimulated by the rising osmotic pressure of the extracellular fluid. If thirst is satisfied, osmotic pressure decreases.
All of these functions taken together form a survival mechanism that causes us to sustain the body processes that BMR measures.
=== BMR estimation formulas ===
Several equations to predict the number of calories required by humans have been published from the early 20th–21st centuries. In each of the formulas below:
P is total heat production at complete rest,
m is mass (kg),
h is height (cm),
a is age (years).
The original Harris–Benedict equation
Historically, the most notable formula was the Harris–Benedict equation, which was published in 1919:
for men,
P
=
(
13.7516
m
1
kg
+
5.0033
h
1
cm
−
6.7550
a
1
year
+
66.4730
)
kcal
day
,
{\displaystyle P=\left({\frac {13.7516m}{1~{\text{kg}}}}+{\frac {5.0033h}{1~{\text{cm}}}}-{\frac {6.7550a}{1~{\text{year}}}}+66.4730\right){\frac {\text{kcal}}{\text{day}}},}
for women,
P
=
(
9.5634
m
1
kg
+
1.8496
h
1
cm
−
4.6756
a
1
year
+
655.0955
)
kcal
day
.
{\displaystyle P=\left({\frac {9.5634m}{1~{\text{kg}}}}+{\frac {1.8496h}{1~{\text{cm}}}}-{\frac {4.6756a}{1~{\text{year}}}}+655.0955\right){\frac {\text{kcal}}{\text{day}}}.}
The difference in BMR for men and women is mainly due to differences in body mass. For example, a 55-year-old woman weighing 130 pounds (59 kg) and 66 inches (168 cm) tall would have a BMR of 1,272 kilocalories (5,320 kJ) per day.
The revised Harris–Benedict equation
In 1984, the original Harris–Benedict equations were revised using new data. In comparisons with actual expenditure, the revised equations were found to be more accurate:
for men,
P
=
(
13.397
m
1
kg
+
4.799
h
1
cm
−
5.677
a
1
year
+
88.362
)
kcal
day
,
{\displaystyle P=\left({\frac {13.397m}{1~{\text{kg}}}}+{\frac {4.799h}{1~{\text{cm}}}}-{\frac {5.677a}{1~{\text{year}}}}+88.362\right){\frac {\text{kcal}}{\text{day}}},}
for women,
P
=
(
9.247
m
1
kg
+
3.098
h
1
cm
−
4.330
a
1
year
+
447.593
)
kcal
day
.
{\displaystyle P=\left({\frac {9.247m}{1~{\text{kg}}}}+{\frac {3.098h}{1~{\text{cm}}}}-{\frac {4.330a}{1~{\text{year}}}}+447.593\right){\frac {\text{kcal}}{\text{day}}}.}
It was the best prediction equation until 1990, when Mifflin et al. introduced the equation:
The Mifflin St Jeor equation
P
=
(
10.0
m
1
kg
+
6.25
h
1
cm
−
5.0
a
1
year
+
s
)
kcal
day
,
{\displaystyle P=\left({\frac {10.0m}{1~{\text{kg}}}}+{\frac {6.25h}{1~{\text{cm}}}}-{\frac {5.0a}{1~{\text{year}}}}+s\right){\frac {\text{kcal}}{\text{day}}},}
where s is +5 for males and −161 for females.
According to this formula, the woman in the example above has a BMR of 1,204 kilocalories (5,040 kJ) per day.
During the last 100 years, lifestyles have changed, and Frankenfield et al. showed it to be about 5% more accurate.
These formulas are based on body mass, which does not take into account the difference in metabolic activity between lean body mass and body fat. Other formulas exist which take into account lean body mass, two of which are the Katch–McArdle formula and Cunningham formula.
The Katch–McArdle formula (resting daily energy expenditure)
The Katch–McArdle formula is used to predict resting daily energy expenditure (RDEE).
The Cunningham formula is commonly cited to predict RMR instead of BMR; however, the formulas provided by Katch–McArdle and Cunningham are the same.
P
=
370
+
21.6
⋅
ℓ
,
{\displaystyle P=370+21.6\cdot \ell ,}
where ℓ is the lean body mass (LBM in kg):
ℓ
=
m
(
1
−
f
100
)
,
{\displaystyle \ell =m\left(1-{\frac {f}{100}}\right),}
where f is the body fat percentage.
According to this formula, if the woman in the example has a body fat percentage of 30%, her resting daily energy expenditure (the authors use the term of basal and resting metabolism interchangeably) would be 1262 kcal per day.
=== Research on individual differences in BMR ===
The basic metabolic rate varies between individuals. One study of 150 adults representative of the population in Scotland reported basal metabolic rates from as low as 1,027 kilocalories (4,300 kJ) per day to as high as 2,499 kilocalories (10,460 kJ), with a mean BMR of 1,500 kilocalories (6,300 kJ) per day. Statistically, the researchers calculated that 62% of this variation was explained by differences in fat free mass. Other factors explaining the variation included fat mass (7%), age (2%), and experimental error including within-subject difference (2%). The rest of the variation (27%) was unexplained. This remaining difference was not explained by sex nor by differing tissue size of highly energetic organs such as the brain.
A cross-sectional study of more than 1400 subjects in Europe and the US showed that once adjusted for differences in body composition (lean and fat mass) and age, BMR has fallen over the past 35 years. The decline was also observed in a meta-analysis of more than 150 studies dating back to the early 1920s, translating into a decline in total energy expenditure of about 6%.
== Biochemistry ==
About 70% of a human's total energy expenditure is due to the basal life processes taking place in the organs of the body (see table). About 20% of one's energy expenditure comes from physical activity and another 10% from thermogenesis, or digestion of food (postprandial thermogenesis). All of these processes require an intake of oxygen along with coenzymes to provide energy for survival (usually from macronutrients like carbohydrates, fats, and proteins) and expel carbon dioxide, due to processing by the Krebs cycle.
For the BMR, most of the energy is consumed in maintaining fluid levels in tissues through osmoregulation, and only about one-tenth is consumed for mechanical work, such as digestion, heartbeat, and breathing.
What enables the Krebs cycle to perform metabolic changes to fats, carbohydrates, and proteins is energy, which can be defined as the ability or capacity to do work. The breakdown of large molecules into smaller molecules—associated with release of energy—is catabolism. The building up process is termed anabolism. The breakdown of proteins into amino acids is an example of catabolism, while the formation of proteins from amino acids is an anabolic process.
Exergonic reactions are energy-releasing reactions and are generally catabolic. Endergonic reactions require energy and include anabolic reactions and the contraction of muscle. Metabolism is the total of all catabolic, exergonic, anabolic, and endergonic reactions.
Adenosine triphosphate (ATP) is the intermediate molecule that drives the exergonic transfer of energy to switch to endergonic anabolic reactions used in muscle contraction. This is what causes muscles to work which can require a breakdown, and also to build in the rest period, which occurs during the strengthening phase associated with muscular contraction. ATP is composed of adenine, a nitrogen containing base, ribose, a five carbon sugar (collectively called adenosine), and three phosphate groups. ATP is a high energy molecule because it stores large amounts of energy in the chemical bonds of the two terminal phosphate groups. The breaking of these chemical bonds in the Krebs Cycle provides the energy needed for muscular contraction.
=== Glucose ===
Because the ratio of hydrogen to oxygen atoms in all carbohydrates is always the same as that in water—that is, 2 to 1—all of the oxygen consumed by the cells is used to oxidize the carbon in the carbohydrate molecule to form carbon dioxide. Consequently, during the complete oxidation of a glucose molecule, six molecules of carbon dioxide and six molecules of water are produced and six molecules of oxygen are consumed.
The overall equation for this reaction is
C
6
H
12
O
6
+
6
O
2
⟶
6
CO
2
+
6
H
2
O
{\displaystyle {\ce {C6H12O6 + 6 O2 -> 6 CO2 + 6 H2O}}}
(30–32 ATP molecules produced depending on type of mitochondrial shuttle, 5–5.33 ATP molecules per molecule of oxygen.)
Because the gas exchange in this reaction is equal, the respiratory quotient (R.Q.) for carbohydrate is unity or 1.0:
R.Q.
=
6
CO
2
6
O
2
=
1.0.
{\displaystyle {\text{R.Q.}}={\frac {{\ce {6 CO2}}}{{\ce {6 O2}}}}=1.0.}
=== Fats ===
The chemical composition for fats differs from that of carbohydrates in that fats contain considerably fewer oxygen atoms in proportion to atoms of carbon and hydrogen. When listed on nutritional information tables, fats are generally divided into six categories: total fats, saturated fatty acid, polyunsaturated fatty acid, monounsaturated fatty acid, dietary cholesterol, and trans fatty acid. From a basal metabolic or resting metabolic perspective, more energy is needed to burn a saturated fatty acid than an unsaturated fatty acid. The fatty acid molecule is broken down and categorized based on the number of carbon atoms in its molecular structure. The chemical equation for metabolism of the twelve to sixteen carbon atoms in a saturated fatty acid molecule shows the difference between metabolism of carbohydrates and fatty acids. Palmitic acid is a commonly studied example of the saturated fatty acid molecule.
The overall equation for the substrate utilization of palmitic acid is
C
16
H
32
O
2
+
23
O
2
⟶
16
CO
2
+
16
H
2
O
{\displaystyle {\ce {C16H32O2 + 23 O2 -> 16 CO2 + 16 H2O}}}
(106 ATP molecules produced, 4.61 ATP molecules per molecule of oxygen.)
Thus the R.Q. for palmitic acid is 0.696:
R.Q.
=
16
CO
2
23
O
2
=
0.696.
{\displaystyle {\text{R.Q.}}={\frac {{\ce {16 CO2}}}{{\ce {23 O2}}}}=0.696.}
=== Proteins ===
Proteins are composed of carbon, hydrogen, oxygen, and nitrogen arranged in a variety of ways to form a large combination of amino acids. Unlike fat the body has no storage deposits of protein. All of it is contained in the body as important parts of tissues, blood hormones, and enzymes. The structural components of the body that contain these amino acids are continually undergoing a process of breakdown and replacement. The respiratory quotient for protein metabolism can be demonstrated by the chemical equation for oxidation of albumin:
C
72
H
112
N
18
O
22
S
+
77
O
2
⟶
63
CO
2
+
38
H
2
O
+
SO
3
+
9
CO
(
NH
2
)
2
{\displaystyle {\ce {C72H112N18O22S + 77 O2 -> 63 CO2 + 38 H2O + SO3 + 9 CO(NH2)2}}}
The R.Q. for albumin is 0.818:
R.Q.
=
63
CO
2
77
O
2
=
0.818.
{\displaystyle {\text{R.Q.}}={\frac {{\ce {63 CO2}}}{{\ce {77 O2}}}}=0.818.}
The reason this is important in the process of understanding protein metabolism is that the body can blend the three macronutrients and based on the mitochondrial density, a preferred ratio can be established which determines how much fuel is utilized in which packets for work accomplished by the muscles. Protein catabolism (breakdown) has been estimated to supply 10% to 15% of the total energy requirement during a two-hour aerobic training session. This process could severely degrade the protein structures needed to maintain survival such as contractile properties of proteins in the heart, cellular mitochondria, myoglobin storage, and metabolic enzymes within muscles.
The oxidative system (aerobic) is the primary source of ATP supplied to the body at rest and during low intensity activities and uses primarily carbohydrates and fats as substrates. Protein is not normally metabolized significantly, except during long term starvation and long bouts of exercise (greater than 90 minutes.) At rest approximately 70% of the ATP produced is derived from fats and 30% from carbohydrates. Following the onset of activity, as the intensity of the exercise increases, there is a shift in substrate preference from fats to carbohydrates. During high intensity aerobic exercise, almost 100% of the energy is derived from carbohydrates, if an adequate supply is available.
=== Aerobic vs. anaerobic exercise ===
Studies published in 1992 and 1997 indicate that the level of aerobic fitness of an individual does not have any correlation with the level of resting metabolism. Both studies find that aerobic fitness levels do not improve the predictive power of fat free mass for resting metabolic rate.
However, recent research from the Journal of Applied Physiology, published in 2012, compared resistance training and aerobic training on body mass and fat mass in overweight adults (STRRIDE AT/RT). When time commitment is evaluated against health benefit, aerobic training is the optimal mode of exercise for reducing fat mass and body mass as a primary consideration, and resistance training is good as a secondary factor when aging and lean mass are a concern. Resistance training causes injuries at a much higher rate than aerobic training. Compared to resistance training, it was found that aerobic training resulted in a significantly more pronounced reduction of body weight by enhancing the cardiovascular system which is what is the principal factor in metabolic utilization of fat substrates. Resistance training if time is available is also helpful in post-exercise metabolism, but it is an adjunctive factor because the body needs to heal sufficiently between resistance training episodes, whereas the body can accept aerobic training every day. RMR and BMR are measurements of daily consumption of calories. The majority of studies that are published on this topic look at aerobic exercise because of its efficacy for health and weight management.
Anaerobic exercise, such as weight lifting, builds additional muscle mass. Muscle contributes to the fat-free mass of an individual and therefore effective results from anaerobic exercise will increase BMR. However, the actual effect on BMR is controversial and difficult to enumerate. Various studies suggest that the resting metabolic rate of trained muscle is around 55 kJ/kg per day; it then follows that even a substantial increase in muscle mass — say 5 kg — would make only a minor impact on BMR.
== Longevity ==
In 1926, Raymond Pearl proposed that longevity varies inversely with basal metabolic rate (the "rate of living hypothesis"). Support for this hypothesis comes from the fact that mammals with larger body size have longer maximum life spans (large animals do have higher total metabolic rates, but the metabolic rate at the cellular level is much lower, and the breathing rate and heartbeat are slower in larger animals) and the fact that the longevity of fruit flies varies inversely with ambient temperature. Additionally, the life span of houseflies can be extended by preventing physical activity. This theory has been bolstered by several new studies linking lower basal metabolic rate to increased life expectancy, across the animal kingdom—including humans. Calorie restriction and reduced thyroid hormone levels, both of which decrease the metabolic rate, have been associated with higher longevity in animals.
However, the ratio of total daily energy expenditure to resting metabolic rate can vary between 1.6 and 8.0 between species of mammals. Animals also vary in the degree of coupling between oxidative phosphorylation and ATP production, the amount of saturated fat in mitochondrial membranes, the amount of DNA repair, and many other factors that affect maximum life span.
One problem with understanding the associations of lifespan and metabolism is that changes in metabolism are often confounded by other factors that may affect lifespan. For example under calorie restriction whole body metabolic rate goes down with increasing levels of restriction, but body temperature also follows the same pattern. By manipulating the ambient temperature and exposure to wind it was shown in mice and hamsters that body temperature is a more important modulator of lifespan than metabolic rate.
== Medical considerations ==
A person's metabolism varies with their physical condition and activity. Weight training can have a longer impact on metabolism than aerobic training, but there are no known mathematical formulas that can exactly predict the length and duration of a raised metabolism from trophic changes with anabolic neuromuscular training.
A decrease in food intake will typically lower the metabolic rate as the body tries to conserve energy. Researcher Gary Foster estimates that a very low calorie diet of fewer than 800 calories a day would reduce the metabolic rate by more than 10 percent.
The metabolic rate can be affected by some drugs: antithyroid agents (drugs used to treat hyperthyroidism) such as propylthiouracil and methimazole bring the metabolic rate down to normal, restoring euthyroidism. Some research has focused on developing antiobesity drugs to raise the metabolic rate, such as drugs to stimulate thermogenesis in skeletal muscle.
The metabolic rate may be elevated in stress, illness, and diabetes. Menopause may also affect metabolism.
== See also ==
== References ==
== Further reading ==
Tsai AG, Wadden TA (2005). "Systematic review: An evaluation of major commercial weight loss programs in the United States". Annals of Internal Medicine. 142 (1): 56–66. doi:10.7326/0003-4819-142-1-200501040-00012. PMID 15630109. S2CID 2589699.
Gustafson D, Rothenberg E, Blennow K, Steen B, Skoog I (2003). "An 18-Year Follow-up of Overweight and Risk of Alzheimer Disease". Archives of Internal Medicine. 163 (13): 1524–8. doi:10.1001/archinte.163.13.1524. PMID 12860573.
"Clinical guidelines on the identification, evaluation, and treatment of overweight and obesity in adults: Executive summary. Expert Panel on the Identification, Evaluation, and Treatment of Overweight in Adults". The American Journal of Clinical Nutrition. 68 (4): 899–917. 1998. doi:10.1093/ajcn/68.4.899. PMID 9771869.
Segal AC (1987). "Linear Diet Model". College Mathematics Journal. 18 (1): 44–5. doi:10.2307/2686315. JSTOR 2686315.
Pike RL, Brown ML (1975). Nutrition: An Integrated Approach (2nd ed.). New York: Wiley. OCLC 474842663.
Sahlin K, Tonkonogi M, Soderlund K (1998). "Energy supply and muscle fatigue in humans". Acta Physiologica Scandinavica. 162 (3): 261–6. doi:10.1046/j.1365-201X.1998.0298f.x. PMID 9578371.
Saltin B, Gollnick PD (1983). "Skeletal muscle adaptability: Significance for metabolism and performance". In Peachey LD, Adrian RH, Geiger SR (eds.). Handbook of Physiology. Baltimore: Williams & Wilkins. pp. 540–55. OCLC 314567389. Republished as: Saltin B, Gollnick PD (2011). "Skeletal Muscle Adaptability: Significance for Metabolism and Performance". Comprehensive Physiology. doi:10.1002/cphy.cp100119. ISBN 978-0-470-65071-4.
Thorstensson (1976). "Muscle strength, fibre types and enzyme activities in man". Acta Physiologica Scandinavica. Supplementum. 443: 1–45. PMID 189574.
Thorstensson A, Sjödin B, Tesch P, Karlsson J (1977). "Actomyosin ATPase, Myokinase, CPK and LDH in Human Fast and Slow Twitch Muscle Fibres". Acta Physiologica Scandinavica. 99 (2): 225–9. doi:10.1111/j.1748-1716.1977.tb10373.x. PMID 190869.
Vanhelder WP, Radomski MW, Goode RC, Casey K (1985). "Hormonal and metabolic response to three types of exercise of equal duration and external work output". European Journal of Applied Physiology and Occupational Physiology. 54 (4): 337–42. doi:10.1007/BF02337175. PMID 3905393. S2CID 39715173.
Wells JG, Balke B, Van Fossan DD (1957). "Lactic acid accumulation during work; a suggested standardization of work classification". Journal of Applied Physiology. 10 (1): 51–5. doi:10.1152/jappl.1957.10.1.51. PMID 13405829.
McArdle WD, Katch FI, Katch VL (1986). Exercise Physiology: Energy, Nutrition, and Human Performance. Philadelphia: Lea & Febiger. ISBN 978-0-8121-0991-7. OCLC 646595478.
Harris JA, Benedict FG (1918). "A Biometric Study of Human Basal Metabolism". Proceedings of the National Academy of Sciences of the United States of America. 4 (12): 370–3. Bibcode:1918PNAS....4..370H. doi:10.1073/pnas.4.12.370. PMC 1091498. PMID 16576330. | Wikipedia/Metabolic_rate |
Signal interfering DNA (siDNA) is a class of short modified double stranded DNA molecules, 8–64 base pairs in length. siDNA molecules are capable of inhibiting DNA repair activities by interfering with multiple repair pathways. These molecules are known to act by mimicking DNA breaks and interfering with recognition and repair of DNA damage induced on chromosomes by irradiation or genotoxic products.
== Dbait ==
Dbait is a specific siDNA molecule that has been shown to mimic signalling of double-stranded DNA breaks (DSBs) in vivo. Currently, Dbait is the only type of siDNA molecule having been reviewed.
=== Mechanism of Action of Dbait ===
The siDNA family, led by Dbait, consists of 32 base pairs deoxyribonucleotide forming an intramolecular double helix, which mimicks DNA double-strand break lesions. In the event of a double-stranded break in the genome, the cell most commonly repairs the damaged segment via non-homologous end joining (NHEJ). NHEJ involves the ligation of the damaged segments without using a homologous strand as a template, and can lead to frameshift mutations and failure of the cell to properly halt the cell division cycle, which could lead to the cancerization of the cell. Dbait functions primarily by targeting the NHEJ pathway, with the cell detecting the presence of siDNA molecules as double stranded breaks (DSBs). Dbait triggers baited activation of signalling enzymes involved in NHEJ-mediated genome repair to initiate the appropriate cellular response. Dbait is first bound to by Ku protein complexes that trigger the phosphorylation of NHEJ initiation factors such as DNA-PK (DNA-dependent protein kinase) and PARP (polyadenyl-ribose polymerase). DNA-PK overactivation through Dbait in turn triggers the activity of numerous signalling proteins in the NHEJ signalling cascade. DNA-PK hyperactivation induces pan-nuclear phosphorylation of histone H2AX among all the chromatin. H2AX phosphorylation is the signal, which allows double-strand break repair proteins to form DNA repair complexes selectively on DNA double-strand breaks. Dbait-dependent unspecific phosphorylation of H2AX results in inefficient double strand break recognition and repair.
== Possible therapeutic application of Dbait ==
Most anti-cancer therapies act by induction of DNA damage (chemotherapy and radiation therapy). DNA breaks are the most lethal damage for cells, as double-stranded breaks can lead to loss of entire chromosomal fragments, and even one single double-strand break if unrepaired is sufficient to lead to cell death. Dbait enhances the efficacy of the DNA damaging agents as demonstrated with radiation therapy and/or chemotherapy in multiple in vivo experimental models such as melanoma, glioblastoma and colorectal cancer.
Preclinical proof of concept of the synergic effect of the clinical candidate, DT01, with radiation therapy lead to a first-in-human Phase I, to evaluate the tolerance and efficacy of local DT01 administration in association with RT in patients suffering from in-transit metastases of melanoma. Encouraging results were published in May 2016.
== References == | Wikipedia/SiDNA |
DNA repair is a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. A weakened capacity for DNA repair is a risk factor for the development of cancer. DNA is constantly modified in cells, by internal metabolic by-products, and by external ionizing radiation, ultraviolet light, and medicines, resulting in spontaneous DNA damage involving tens of thousands of individual molecular lesions per cell per day. DNA modifications can also be programmed.
Molecular lesions can cause structural damage to the DNA molecule, and can alter or eliminate the cell's ability for transcription and gene expression. Other lesions may induce potentially harmful mutations in the cell's genome, which affect the survival of its daughter cells following mitosis. Consequently, DNA repair as part of the DNA damage response (DDR) is constantly active. When normal repair processes fail, including apoptosis, irreparable DNA damage may occur, that may be a risk factor for cancer.
The degree of DNA repair change made within a cell depends on various factors, including the cell type, the age of the cell, and the extracellular environment. A cell that has accumulated a large amount of DNA damage or can no longer effectively repair its DNA may enter one of three possible states:
an irreversible state of dormancy, known as senescence
apoptosis a form of programmed cell death
unregulated division, which can lead to the formation of a tumor that is cancerous
The DNA repair ability of a cell is vital to the integrity of its genome and thus to the normal functionality of that organism. Many genes that were initially shown to influence life span have turned out to be involved in DNA damage repair and protection.
The 2015 Nobel Prize in Chemistry was awarded to Tomas Lindahl, Paul Modrich, and Aziz Sancar for their work on the molecular mechanisms of DNA repair processes.
== DNA damage ==
DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 10,000 to 1,000,000 molecular lesions per cell per day. While this constitutes at most only 0.03% of the human genome's approximately 3.2 billion bases, unrepaired lesions in critical genes (such as tumor suppressor genes) can impede a cell's ability to carry out its function and appreciably increase the likelihood of tumor formation and contribute to tumor heterogeneity.
The vast majority of DNA damage affects the primary structure of the double helix; that is, the bases themselves are chemically modified. These modifications can in turn disrupt the molecules' regular helical structure by introducing non-native chemical bonds or bulky adducts that do not fit in the standard double helix. Unlike proteins and RNA, DNA usually lacks tertiary structure and therefore damage or disturbance does not occur at that level. DNA is, however, supercoiled and wound around "packaging" proteins called histones (in eukaryotes), and both superstructures are vulnerable to the effects of DNA damage.
=== Sources ===
DNA damage can be subdivided into two main types:
endogenous damage such as attack by reactive oxygen species produced from normal metabolic byproducts (spontaneous mutation), especially the process of oxidative deamination
also includes replication errors
exogenous damage caused by external agents such as
ultraviolet (UV) radiation (200–400 nm) from the sun or other artificial light sources
other radiation frequencies, including x-rays and gamma rays, and particles like electrons, neutrons, or alpha particles.
hydrolysis or thermal disruption
certain plant toxins
human-made mutagenic chemicals, especially aromatic compounds that act as DNA intercalating agents
viruses
The replication of damaged DNA before cell division can lead to the incorporation of wrong bases opposite damaged ones. Daughter cells that inherit these wrong bases carry mutations from which the original DNA sequence is unrecoverable (except in the rare case of a back mutation, for example, through gene conversion).
=== Types ===
There are several types of damage to DNA due to endogenous cellular processes:
oxidation of bases [e.g. 8-oxo-7,8-dihydroguanine (8-oxoG)] and generation of DNA strand interruptions from reactive oxygen species,
alkylation of bases (usually methylation), such as formation of 7-methylguanosine, 1-methyladenine, 6-O-Methylguanine
hydrolysis of bases, such as deamination, depurination, and depyrimidination.
"bulky adduct formation" (e.g., benzo[a]pyrene diol epoxide-dG adduct, aristolactam I-dA adduct)
mismatch of bases, due to errors in DNA replication, in which the wrong DNA base is stitched into place in a newly forming DNA strand, or a DNA base is skipped over or mistakenly inserted.
Monoadduct damage cause by change in single nitrogenous base of DNA
Di adduct damage
Damage caused by exogenous agents comes in many forms. Some examples are:
Absorption of UV light directly by DNA induces photochemical reactions, leading to the formation of pyrimidine dimers, and photoionization, provoking oxidative damage.
UV-A light creates mostly free radicals. The damage caused by free radicals is called indirect DNA damage.
Ionizing radiation such as that created by radioactive decay or in cosmic rays causes breaks in DNA strands. Intermediate-level ionizing radiation may induce irreparable DNA damage (leading to replicational and transcriptional errors needed for neoplasia or may trigger viral interactions) leading to pre-mature aging and cancer.
Thermal disruption at elevated temperature increases the rate of depurination (loss of purine bases from the DNA backbone) and single-strand breaks. For example, hydrolytic depurination is seen in the thermophilic bacteria, which grow in hot springs at 40–80 °C. The rate of depurination (300 purine residues per genome per generation) is too high in these species to be repaired by normal repair machinery, hence a possibility of an adaptive response cannot be ruled out.
Industrial chemicals such as vinyl chloride and hydrogen peroxide, and environmental chemicals such as polycyclic aromatic hydrocarbons found in smoke, soot and tar create a huge diversity of DNA adducts- ethanoates, oxidized bases, alkylated phosphodiesters and crosslinking of DNA, just to name a few.
UV damage, alkylation/methylation, X-ray damage and oxidative damage are examples of induced damage. Spontaneous damage can include the loss of a base, deamination, sugar ring puckering and tautomeric shift. Constitutive (spontaneous) DNA damage caused by endogenous oxidants can be detected as a low level of histone H2AX phosphorylation in untreated cells.
=== Nuclear versus mitochondrial ===
In eukaryotic cells, DNA is found in two cellular locations – inside the nucleus and inside the mitochondria. Nuclear DNA (nDNA) exists as chromatin during non-replicative stages of the cell cycle and is condensed into aggregate structures known as chromosomes during cell division. In either state the DNA is highly compacted and wound up around bead-like proteins called histones. Whenever a cell needs to express the genetic information encoded in its nDNA the required chromosomal region is unraveled, genes located therein are expressed, and then the region is condensed back to its resting conformation. Mitochondrial DNA (mtDNA) is located inside mitochondria organelles, exists in multiple copies, and is also tightly associated with a number of proteins to form a complex known as the nucleoid. Inside mitochondria, reactive oxygen species (ROS), or free radicals, byproducts of the constant production of adenosine triphosphate (ATP) via oxidative phosphorylation, create a highly oxidative environment that is known to damage mtDNA. A critical enzyme in counteracting the toxicity of these species is superoxide dismutase, which is present in both the mitochondria and cytoplasm of eukaryotic cells.
=== Senescence and apoptosis ===
Senescence, an irreversible process in which the cell no longer divides, is a protective response to the shortening of the chromosome ends, called telomeres. The telomeres are long regions of repetitive noncoding DNA that cap chromosomes and undergo partial degradation each time a cell undergoes division (see Hayflick limit). In contrast, quiescence is a reversible state of cellular dormancy that is unrelated to genome damage (see cell cycle). Senescence in cells may serve as a functional alternative to apoptosis in cases where the physical presence of a cell for spatial reasons is required by the organism, which serves as a "last resort" mechanism to prevent a cell with damaged DNA from replicating inappropriately in the absence of pro-growth cellular signaling. Unregulated cell division can lead to the formation of a tumor (see cancer), which is potentially lethal to an organism. Therefore, the induction of senescence and apoptosis is considered to be part of a strategy of protection against cancer.
=== Mutation ===
It is important to distinguish between DNA damage and mutation, the two major types of error in DNA. DNA damage and mutation are fundamentally different. Damage results in physical abnormalities in the DNA, such as single- and double-strand breaks, 8-hydroxydeoxyguanosine residues, and polycyclic aromatic hydrocarbon adducts. DNA damage can be recognized by enzymes, and thus can be correctly repaired if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying. If a cell retains DNA damage, transcription of a gene can be prevented, and thus translation into a protein will also be blocked. Replication may also be blocked or the cell may die.
In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired. At the cellular level, mutations can cause alterations in protein function and regulation. Mutations are replicated when the cell replicates. In a population of cells, mutant cells will increase or decrease in frequency according to the effects of the mutation on the ability of the cell to survive and reproduce.
Although distinctly different from each other, DNA damage and mutation are related because DNA damage often causes errors of DNA synthesis during replication or repair; these errors are a major source of mutation.
Given these properties of DNA damage and mutation, it can be seen that DNA damage is a special problem in non-dividing or slowly-dividing cells, where unrepaired damage will tend to accumulate over time. On the other hand, in rapidly dividing cells, unrepaired DNA damage that does not kill the cell by blocking replication will tend to cause replication errors and thus mutation. The great majority of mutations that are not neutral in their effect are deleterious to a cell's survival. Thus, in a population of cells composing a tissue with replicating cells, mutant cells will tend to be lost. However, infrequent mutations that provide a survival advantage will tend to clonally expand at the expense of neighboring cells in the tissue. This advantage to the cell is disadvantageous to the whole organism because such mutant cells can give rise to cancer. Thus, DNA damage in frequently dividing cells, because it gives rise to mutations, is a prominent cause of cancer. In contrast, DNA damage in infrequently-dividing cells is likely a prominent cause of aging.
== Mechanisms ==
Cells cannot function if DNA damage corrupts the integrity and accessibility of essential information in the genome (but cells remain superficially functional when non-essential genes are missing or damaged). Depending on the type of damage inflicted on the DNA's double helical structure, a variety of repair strategies have evolved to restore lost information. If possible, cells use the unmodified complementary strand of the DNA or the sister chromatid as a template to recover the original information. Without access to a template, cells use an error-prone recovery mechanism known as translesion synthesis as a last resort.
Damage to DNA alters the spatial configuration of the helix, and such alterations can be detected by the cell. Once damage is localized, specific DNA repair molecules bind at or near the site of damage, inducing other molecules to bind and form a complex that enables the actual repair to take place.
=== Direct reversal ===
Cells are known to eliminate three types of damage to their DNA by chemically reversing it. These mechanisms do not require a template, since the types of damage they counteract can occur in only one of the four bases. Such direct reversal mechanisms are specific to the type of damage incurred and do not involve breakage of the phosphodiester backbone.
The formation of pyrimidine dimers upon irradiation with UV light results in an abnormal covalent bond between adjacent pyrimidine bases. The photoreactivation process directly reverses this damage by the action of the enzyme photolyase, whose activation is obligately dependent on energy absorbed from blue/UV light (300–500 nm wavelength) to promote catalysis. Photolyase, an old enzyme present in bacteria, fungi, and most animals no longer functions in humans, who instead use nucleotide excision repair to repair damage from UV irradiation.
Another type of damage, methylation of guanine bases, is directly reversed by the enzyme methyl guanine methyl transferase (MGMT), the bacterial equivalent of which is called ogt. This is an expensive process because each MGMT molecule can be used only once; that is, the reaction is stoichiometric rather than catalytic. A generalized response to methylating agents in bacteria is known as the adaptive response and confers a level of resistance to alkylating agents upon sustained exposure by upregulation of alkylation repair enzymes.
The third type of DNA damage reversed by cells is certain methylation of the bases cytosine and adenine.
=== Single-strand damage ===
When only one of the two strands of a double helix has a defect, the other strand can be used as a template to guide the correction of the damaged strand. In order to repair damage to one of the two paired molecules of DNA, there exist a number of excision repair mechanisms that remove the damaged nucleotide and replace it with an undamaged nucleotide complementary to that found in the undamaged DNA strand.
Base excision repair (BER): damaged single bases or nucleotides are most commonly repaired by removing the base or the nucleotide involved and then inserting the correct base or nucleotide. In base excision repair, a glycosylase enzyme removes the damaged base from the DNA by cleaving the bond between the base and the deoxyribose. These enzymes remove a single base to create an apurinic or apyrimidinic site (AP site). Enzymes called AP endonucleases nick the damaged DNA backbone at the AP site. DNA polymerase then removes the damaged region using its 5' to 3' exonuclease activity and correctly synthesizes the new strand using the complementary strand as a template. The gap is then sealed by enzyme DNA ligase.
Nucleotide excision repair (NER): bulky, helix-distorting damage, such as pyrimidine dimerization caused by UV light is usually repaired by a three-step process. First the damage is recognized, then 12-24 nucleotide-long strands of DNA are removed both upstream and downstream of the damage site by endonucleases, and the removed DNA region is then resynthesized. NER is a highly evolutionarily conserved repair mechanism and is used in nearly all eukaryotic and prokaryotic cells. In prokaryotes, NER is mediated by Uvr proteins. In eukaryotes, many more proteins are involved, although the general strategy is the same.
Mismatch repair systems are present in essentially all cells to correct errors that are not corrected by proofreading. These systems consist of at least two proteins. One detects the mismatch, and the other recruits an endonuclease that cleaves the newly synthesized DNA strand close to the region of damage. In E. coli , the proteins involved are the Mut class proteins: MutS, MutL, and MutH. In most Eukaryotes, the analog for MutS is MSH and the analog for MutL is MLH. MutH is only present in bacteria. This is followed by removal of damaged region by an exonuclease, resynthesis by DNA polymerase, and nick sealing by DNA ligase.
=== Double-strand breaks ===
Double-strand breaks, in which both strands in the double helix are severed, are particularly hazardous to the cell because they can lead to genome rearrangements. In fact, when a double-strand break is accompanied by a cross-linkage joining the two strands at the same point, neither strand can be used as a template for the repair mechanisms, so that the cell will not be able to complete mitosis when it next divides, and will either die or, in rare cases, undergo a mutation. Three mechanisms exist to repair double-strand breaks (DSBs): non-homologous end joining (NHEJ), microhomology-mediated end joining (MMEJ), and homologous recombination (HR):
In NHEJ, DNA Ligase IV, a specialized DNA ligase that forms a complex with the cofactor XRCC4, directly joins the two ends. To guide accurate repair, NHEJ relies on short homologous sequences called microhomologies present on the single-stranded tails of the DNA ends to be joined. If these overhangs are compatible, repair is usually accurate. NHEJ can also introduce mutations during repair. Loss of damaged nucleotides at the break site can lead to deletions, and joining of nonmatching termini forms insertions or translocations. NHEJ is especially important before the cell has replicated its DNA, since there is no template available for repair by homologous recombination. There are "backup" NHEJ pathways in higher eukaryotes. Besides its role as a genome caretaker, NHEJ is required for joining hairpin-capped double-strand breaks induced during V(D)J recombination, the process that generates diversity in B-cell and T-cell receptors in the vertebrate immune system.
MMEJ starts with short-range end resection by MRE11 nuclease on either side of a double-strand break to reveal microhomology regions. In further steps, Poly (ADP-ribose) polymerase 1 (PARP1) is required and may be an early step in MMEJ. There is pairing of microhomology regions followed by recruitment of flap structure-specific endonuclease 1 (FEN1) to remove overhanging flaps. This is followed by recruitment of XRCC1–LIG3 to the site for ligating the DNA ends, leading to an intact DNA. MMEJ is always accompanied by a deletion, so that MMEJ is a mutagenic pathway for DNA repair.
HR requires the presence of an identical or nearly identical sequence to be used as a template for repair of the break. The enzymatic machinery responsible for this repair process is nearly identical to the machinery responsible for chromosomal crossover during meiosis. This pathway allows a damaged chromosome to be repaired using a sister chromatid (available in G2 after DNA replication) or a homologous chromosome as a template. DSBs caused by the replication machinery attempting to synthesize across a single-strand break or unrepaired lesion cause collapse of the replication fork and are typically repaired by recombination.
In an in vitro system, MMEJ occurred in mammalian cells at the levels of 10–20% of HR when both HR and NHEJ mechanisms were also available.
The extremophile Deinococcus radiodurans has a remarkable ability to survive DNA damage from ionizing radiation and other sources. At least two copies of the genome, with random DNA breaks, can form DNA fragments through annealing. Partially overlapping fragments are then used for synthesis of homologous regions through a moving D-loop that can continue extension until complementary partner strands are found. In the final step, there is crossover by means of RecA-dependent homologous recombination.
Topoisomerases introduce both single- and double-strand breaks in the course of changing the DNA's state of supercoiling, which is especially common in regions near an open replication fork. Such breaks are not considered DNA damage because they are a natural intermediate in the topoisomerase biochemical mechanism and are immediately repaired by the enzymes that created them.
Another type of DNA double-strand breaks originates from the DNA heat-sensitive or heat-labile sites. These DNA sites are not initial DSBs. However, they convert to DSB after treating with elevated temperature. Ionizing irradiation can induces a highly complex form of DNA damage as clustered damage. It consists of different types of DNA lesions in various locations of the DNA helix. Some of these closely located lesions can probably convert to DSB by exposure to high temperatures. But the exact nature of these lesions and their interactions is not yet known
=== Translesion synthesis ===
Translesion synthesis (TLS) is a DNA damage tolerance process that allows the DNA replication machinery to replicate past DNA lesions such as thymine dimers or AP sites. It involves switching out regular DNA polymerases for specialized translesion polymerases (i.e. DNA polymerase IV or V, from the Y Polymerase family), often with larger active sites that can facilitate the insertion of bases opposite damaged nucleotides. The polymerase switching is thought to be mediated by, among other factors, the post-translational modification of the replication processivity factor PCNA. Translesion synthesis polymerases often have low fidelity (high propensity to insert wrong bases) on undamaged templates relative to regular polymerases. However, many are extremely efficient at inserting correct bases opposite specific types of damage. For example, Pol η mediates error-free bypass of lesions induced by UV irradiation, whereas Pol ι introduces mutations at these sites. Pol η is known to add the first adenine across the T^T photodimer using Watson-Crick base pairing and the second adenine will be added in its syn conformation using Hoogsteen base pairing. From a cellular perspective, risking the introduction of point mutations during translesion synthesis may be preferable to resorting to more drastic mechanisms of DNA repair, which may cause gross chromosomal aberrations or cell death. In short, the process involves specialized polymerases either bypassing or repairing lesions at locations of stalled DNA replication. For example, Human DNA polymerase eta can bypass complex DNA lesions like guanine-thymine intra-strand crosslink, G[8,5-Me]T, although it can cause targeted and semi-targeted mutations. Paromita Raychaudhury and Ashis Basu studied the toxicity and mutagenesis of the same lesion in Escherichia coli by replicating a G[8,5-Me]T-modified plasmid in E. coli with specific DNA polymerase knockouts. Viability was very low in a strain lacking pol II, pol IV, and pol V, the three SOS-inducible DNA polymerases, indicating that translesion synthesis is conducted primarily by these specialized DNA polymerases.
A bypass platform is provided to these polymerases by Proliferating cell nuclear antigen (PCNA). Under normal circumstances, PCNA bound to polymerases replicates the DNA. At a site of lesion, PCNA is ubiquitinated, or modified, by the RAD6/RAD18 proteins to provide a platform for the specialized polymerases to bypass the lesion and resume DNA replication. After translesion synthesis, extension is required. This extension can be carried out by a replicative polymerase if the TLS is error-free, as in the case of Pol η, yet if TLS results in a mismatch, a specialized polymerase is needed to extend it; Pol ζ. Pol ζ is unique in that it can extend terminal mismatches, whereas more processive polymerases cannot. So when a lesion is encountered, the replication fork will stall, PCNA will switch from a processive polymerase to a TLS polymerase such as Pol ι to fix the lesion, then PCNA may switch to Pol ζ to extend the mismatch, and last PCNA will switch to the processive polymerase to continue replication.
== Global response to DNA damage ==
Cells exposed to ionizing radiation, ultraviolet light or chemicals are prone to acquire multiple sites of bulky DNA lesions and double-strand breaks. Moreover, DNA damaging agents can damage other biomolecules such as proteins, carbohydrates, lipids, and RNA. The accumulation of damage, to be specific, double-strand breaks or adducts stalling the replication forks, are among known stimulation signals for a global response to DNA damage. The global response to damage is an act directed toward the cells' own preservation and triggers multiple pathways of macromolecular repair, lesion bypass, tolerance, or apoptosis. The common features of global response are induction of multiple genes, cell cycle arrest, and inhibition of cell division.
=== Initial steps ===
The packaging of eukaryotic DNA into chromatin presents a barrier to all DNA-based processes that require recruitment of enzymes to their sites of action. To allow DNA repair, the chromatin must be remodeled. In eukaryotes, ATP dependent chromatin remodeling complexes and histone-modifying enzymes are two predominant factors employed to accomplish this remodeling process.
Chromatin relaxation occurs rapidly at the site of a DNA damage. In one of the earliest steps, the stress-activated protein kinase, c-Jun N-terminal kinase (JNK), phosphorylates SIRT6 on serine 10 in response to double-strand breaks or other DNA damage. This post-translational modification facilitates the mobilization of SIRT6 to DNA damage sites, and is required for efficient recruitment of poly (ADP-ribose) polymerase 1 (PARP1) to DNA break sites and for efficient repair of DSBs. PARP1 protein starts to appear at DNA damage sites in less than a second, with half maximum accumulation within 1.6 seconds after the damage occurs. PARP1 synthesizes polymeric adenosine diphosphate ribose (poly (ADP-ribose) or PAR) chains on itself. Next the chromatin remodeler ALC1 quickly attaches to the product of PARP1 action, a poly-ADP ribose chain, and ALC1 completes arrival at the DNA damage within 10 seconds of the occurrence of the damage. About half of the maximum chromatin relaxation, presumably due to action of ALC1, occurs by 10 seconds. This then allows recruitment of the DNA repair enzyme MRE11, to initiate DNA repair, within 13 seconds.
γH2AX, the phosphorylated form of H2AX is also involved in the early steps leading to chromatin decondensation after DNA double-strand breaks. The histone variant H2AX constitutes about 10% of the H2A histones in human chromatin. γH2AX (H2AX phosphorylated on serine 139) can be detected as soon as 20 seconds after irradiation of cells (with DNA double-strand break formation), and half maximum accumulation of γH2AX occurs in one minute. The extent of chromatin with phosphorylated γH2AX is about two million base pairs at the site of a DNA double-strand break. γH2AX does not, itself, cause chromatin decondensation, but within 30 seconds of irradiation, RNF8 protein can be detected in association with γH2AX. RNF8 mediates extensive chromatin decondensation, through its subsequent interaction with CHD4, a component of the nucleosome remodeling and deacetylase complex NuRD.
DDB2 occurs in a heterodimeric complex with DDB1. This complex further complexes with the ubiquitin ligase protein CUL4A and with PARP1. This larger complex rapidly associates with UV-induced damage within chromatin, with half-maximum association completed in 40 seconds. The PARP1 protein, attached to both DDB1 and DDB2, then PARylates (creates a poly-ADP ribose chain) on DDB2 that attracts the DNA remodeling protein ALC1. Action of ALC1 relaxes the chromatin at the site of UV damage to DNA. This relaxation allows other proteins in the nucleotide excision repair pathway to enter the chromatin and repair UV-induced cyclobutane pyrimidine dimer damages.
After rapid chromatin remodeling, cell cycle checkpoints are activated to allow DNA repair to occur before the cell cycle progresses. First, two kinases, ATM and ATR are activated within 5 or 6 minutes after DNA is damaged. This is followed by phosphorylation of the cell cycle checkpoint protein Chk1, initiating its function, about 10 minutes after DNA is damaged.
=== DNA damage response ===
In the DNA damage response (DDR), cell cycle checkpoints are activated. Checkpoint activation pauses the cell cycle and gives the cell time to repair the damage before continuing to divide. DNA damage checkpoints occur at the G1/S and G2/M boundaries. An intra-S checkpoint also exists. Checkpoint activation is controlled by two master kinases, ATM and ATR. ATM responds to DNA double-strand breaks and disruptions in chromatin structure, whereas ATR primarily responds to stalled replication forks. These kinases phosphorylate downstream targets in a signal transduction cascade, eventually leading to cell cycle arrest. A class of checkpoint mediator proteins including BRCA1, MDC1, and 53BP1 has also been identified. These proteins seem to be required for transmitting the checkpoint activation signal to downstream proteins.
DNA damage checkpoint is a signal transduction pathway that blocks cell cycle progression in G1, G2 and metaphase and slows down the rate of S phase progression when DNA is damaged. It leads to a pause in cell cycle allowing the cell time to repair the damage before continuing to divide.
Checkpoint Proteins can be separated into four groups: phosphatidylinositol 3-kinase (PI3K)-like protein kinase, proliferating cell nuclear antigen (PCNA)-like group, two serine/threonine(S/T) kinases and their adaptors. Central to all DNA damage induced checkpoints responses is a pair of large protein kinases belonging to the first group of PI3K-like protein kinases-the ATM (Ataxia telangiectasia mutated) and ATR (Ataxia- and Rad-related) kinases, whose sequence and functions have been well conserved in evolution. All DNA damage response requires either ATM or ATR because they have the ability to bind to the chromosomes at the site of DNA damage, together with accessory proteins that are platforms on which DNA damage response components and DNA repair complexes can be assembled.
An important downstream target of ATM and ATR is p53, as it is required for inducing apoptosis following DNA damage. The cyclin-dependent kinase inhibitor p21 is induced by both p53-dependent and p53-independent mechanisms and can arrest the cell cycle at the G1/S and G2/M checkpoints by deactivating cyclin/cyclin-dependent kinase complexes.
=== The prokaryotic SOS response ===
The SOS response is the changes in gene expression in Escherichia coli and other bacteria in response to extensive DNA damage. The prokaryotic SOS system is regulated by two key proteins: LexA and RecA. The LexA homodimer is a transcriptional repressor that binds to operator sequences commonly referred to as SOS boxes. In Escherichia coli it is known that LexA regulates transcription of approximately 48 genes including the lexA and recA genes. The SOS response is known to be widespread in the Bacteria domain, but it is mostly absent in some bacterial phyla, like the Spirochetes.
The most common cellular signals activating the SOS response are regions of single-stranded DNA (ssDNA), arising from stalled replication forks or double-strand breaks, which are processed by DNA helicase to separate the two DNA strands. In the initiation step, RecA protein binds to ssDNA in an ATP hydrolysis driven reaction creating RecA–ssDNA filaments. RecA–ssDNA filaments activate LexA autoprotease activity, which ultimately leads to cleavage of LexA dimer and subsequent LexA degradation. The loss of LexA repressor induces transcription of the SOS genes and allows for further signal induction, inhibition of cell division and an increase in levels of proteins responsible for damage processing.
In Escherichia coli, SOS boxes are 20-nucleotide long sequences near promoters with palindromic structure and a high degree of sequence conservation. In other classes and phyla, the sequence of SOS boxes varies considerably, with different length and composition, but it is always highly conserved and one of the strongest short signals in the genome. The high information content of SOS boxes permits differential binding of LexA to different promoters and allows for timing of the SOS response. The lesion repair genes are induced at the beginning of SOS response. The error-prone translesion polymerases, for example, UmuCD'2 (also called DNA polymerase V), are induced later on as a last resort. Once the DNA damage is repaired or bypassed using polymerases or through recombination, the amount of single-stranded DNA in cells is decreased, lowering the amounts of RecA filaments decreases cleavage activity of LexA homodimer, which then binds to the SOS boxes near promoters and restores normal gene expression.
=== Eukaryotic transcriptional responses to DNA damage ===
Eukaryotic cells exposed to DNA damaging agents also activate important defensive pathways by inducing multiple proteins involved in DNA repair, cell cycle checkpoint control, protein trafficking and degradation. Such genome wide transcriptional response is very complex and tightly regulated, thus allowing coordinated global response to damage. Exposure of yeast Saccharomyces cerevisiae to DNA damaging agents results in overlapping but distinct transcriptional profiles. Similarities to environmental shock response indicates that a general global stress response pathway exist at the level of transcriptional activation. In contrast, different human cell types respond to damage differently indicating an absence of a common global response. The probable explanation for this difference between yeast and human cells may be in the heterogeneity of mammalian cells. In an animal different types of cells are distributed among different organs that have evolved different sensitivities to DNA damage.
In general global response to DNA damage involves expression of multiple genes responsible for postreplication repair, homologous recombination, nucleotide excision repair, DNA damage checkpoint, global transcriptional activation, genes controlling mRNA decay, and many others. A large amount of damage to a cell leaves it with an important decision: undergo apoptosis and die, or survive at the cost of living with a modified genome. An increase in tolerance to damage can lead to an increased rate of survival that will allow a greater accumulation of mutations. Yeast Rev1 and human polymerase η are members of Y family translesion DNA polymerases present during global response to DNA damage and are responsible for enhanced mutagenesis during a global response to DNA damage in eukaryotes.
== Aging ==
=== Pathological effects of poor DNA repair ===
Experimental animals with genetic deficiencies in DNA repair often show decreased life span and increased cancer incidence. For example, mice deficient in the dominant NHEJ pathway and in telomere maintenance mechanisms get lymphoma and infections more often, and, as a consequence, have shorter lifespans than wild-type mice. In similar manner, mice deficient in a key repair and transcription protein that unwinds DNA helices have premature onset of aging-related diseases and consequent shortening of lifespan. However, not every DNA repair deficiency creates exactly the predicted effects; mice deficient in the NER pathway exhibited shortened life span without correspondingly higher rates of mutation.
The maximum life spans of mice, naked mole-rats and humans are respectively ~3, ~30 and ~129 years. Of these, the shortest lived species, mouse, expresses DNA repair genes, including core genes in several DNA repair pathways, at a lower level than do humans and naked mole rats. Furthermore several DNA repair pathways in humans and naked mole-rats are up-regulated compared to mouse. These observations suggest that elevated DNA repair facilitates greater longevity.
If the rate of DNA damage exceeds the capacity of the cell to repair it, the accumulation of errors can overwhelm the cell and result in early senescence, apoptosis, or cancer. Inherited diseases associated with faulty DNA repair functioning result in premature aging, increased sensitivity to carcinogens and correspondingly increased cancer risk (see below). On the other hand, organisms with enhanced DNA repair systems, such as Deinococcus radiodurans, the most radiation-resistant known organism, exhibit remarkable resistance to the double-strand break-inducing effects of radioactivity, likely due to enhanced efficiency of DNA repair and especially NHEJ.
=== Longevity and caloric restriction ===
A number of individual genes have been identified as influencing variations in life span within a population of organisms. The effects of these genes is strongly dependent on the environment, in particular, on the organism's diet. Caloric restriction reproducibly results in extended lifespan in a variety of organisms, likely via nutrient sensing pathways and decreased metabolic rate. The molecular mechanisms by which such restriction results in lengthened lifespan are as yet unclear (see for some discussion); however, the behavior of many genes known to be involved in DNA repair is altered under conditions of caloric restriction. Several agents reported to have anti-aging properties have been shown to attenuate constitutive level of mTOR signaling, an evidence of reduction of metabolic activity, and concurrently to reduce constitutive level of DNA damage induced by endogenously generated reactive oxygen species.
For example, increasing the gene dosage of the gene SIR-2, which regulates DNA packaging in the nematode worm Caenorhabditis elegans, can significantly extend lifespan. The mammalian homolog of SIR-2 is known to induce downstream DNA repair factors involved in NHEJ, an activity that is especially promoted under conditions of caloric restriction. Caloric restriction has been closely linked to the rate of base excision repair in the nuclear DNA of rodents, although similar effects have not been observed in mitochondrial DNA.
The C. elegans gene AGE-1, an upstream effector of DNA repair pathways, confers dramatically extended life span under free-feeding conditions but leads to a decrease in reproductive fitness under conditions of caloric restriction. This observation supports the pleiotropy theory of the biological origins of aging, which suggests that genes conferring a large survival advantage early in life will be selected for even if they carry a corresponding disadvantage late in life.
== Medicine and DNA repair modulation ==
=== Hereditary DNA repair disorders ===
Defects in the NER mechanism are responsible for several genetic disorders, including:
Xeroderma pigmentosum: hypersensitivity to sunlight/UV, resulting in increased skin cancer incidence and premature aging
Cockayne syndrome: hypersensitivity to UV and chemical agents
Trichothiodystrophy: sensitive skin, brittle hair and nails
Mental retardation often accompanies the latter two disorders, suggesting increased vulnerability of developmental neurons.
Other DNA repair disorders include:
Werner's syndrome: premature aging and retarded growth
Bloom's syndrome: sunlight hypersensitivity, high incidence of malignancies (especially leukemias).
Ataxia telangiectasia: sensitivity to ionizing radiation and some chemical agents
All of the above diseases are often called "segmental progerias" ("accelerated aging diseases") because those affected appear elderly and experience aging-related diseases at an abnormally young age, while not manifesting all the symptoms of old age.
Other diseases associated with reduced DNA repair function include Fanconi anemia, hereditary breast cancer and hereditary colon cancer.
== Cancer ==
Because of inherent limitations in the DNA repair mechanisms, if humans lived long enough, they would all eventually develop cancer. There are at least 34 Inherited human DNA repair gene mutations that increase cancer risk. Many of these mutations cause DNA repair to be less effective than normal. In particular, Hereditary nonpolyposis colorectal cancer (HNPCC) is strongly associated with specific mutations in the DNA mismatch repair pathway. BRCA1 and BRCA2, two important genes whose mutations confer a hugely increased risk of breast cancer on carriers, are both associated with a large number of DNA repair pathways, especially NHEJ and homologous recombination.
Cancer therapy procedures such as chemotherapy and radiotherapy work by overwhelming the capacity of the cell to repair DNA damage, resulting in cell death. Cells that are most rapidly dividing – most typically cancer cells – are preferentially affected. The side-effect is that other non-cancerous but rapidly dividing cells such as progenitor cells in the gut, skin, and hematopoietic system are also affected. Modern cancer treatments attempt to localize the DNA damage to cells and tissues only associated with cancer, either by physical means (concentrating the therapeutic agent in the region of the tumor) or by biochemical means (exploiting a feature unique to cancer cells in the body). In the context of therapies targeting DNA damage response genes, the latter approach has been termed 'synthetic lethality'.
Perhaps the most well-known of these 'synthetic lethality' drugs is the poly(ADP-ribose) polymerase 1 (PARP1) inhibitor olaparib, which was approved by the Food and Drug Administration in 2015 for the treatment in women of BRCA-defective ovarian cancer. Tumor cells with partial loss of DNA damage response (specifically, homologous recombination repair) are dependent on another mechanism – single-strand break repair – which is a mechanism consisting, in part, of the PARP1 gene product. Olaparib is combined with chemotherapeutics to inhibit single-strand break repair induced by DNA damage caused by the co-administered chemotherapy. Tumor cells relying on this residual DNA repair mechanism are unable to repair the damage and hence are not able to survive and proliferate, whereas normal cells can repair the damage with the functioning homologous recombination mechanism.
Many other drugs for use against other residual DNA repair mechanisms commonly found in cancer are currently under investigation. However, synthetic lethality therapeutic approaches have been questioned due to emerging evidence of acquired resistance, achieved through rewiring of DNA damage response pathways and reversion of previously inhibited defects.
=== DNA repair defects in cancer ===
Studies have shown that the DNA damage response acts as a barrier to the malignant transformation of preneoplastic cells. Early studies have shown an elevated DNA damage response in cell-culture models with oncogene activation, and preneoplastic colon adenomas. DNA damage response mechanisms trigger cell-cycle arrest, and attempt to repair DNA lesions or promote cell death/senescence if repair is not possible. Replication stress is observed in preneoplastic cells due to increased proliferation signals from oncogenic mutations. Replication stress is characterized by: increased replication initiation/origin firing; increased transcription and collisions of transcription-replication complexes; nucleotide deficiency; increase in reactive oxygen species (ROS).
Replication stress, along with the selection for inactivating mutations in DNA damage response genes in the evolution of the tumor, leads to downregulation and/or loss of some DNA damage response mechanisms, and hence loss of DNA repair and/or senescence/programmed cell death. In experimental mouse models, loss of DNA damage response-mediated cell senescence was observed after using a short hairpin RNA (shRNA) to inhibit the double-strand break response kinase ataxia telangiectasia (ATM), leading to increased tumor size and invasiveness. Humans born with inherited defects in DNA repair mechanisms (for example, Li-Fraumeni syndrome) have a higher cancer risk.
The prevalence of DNA damage response mutations differs across cancer types; for example, 30% of breast invasive carcinomas have mutations in genes involved in homologous recombination. In cancer, downregulation is observed across all DNA damage response mechanisms (base excision repair (BER), nucleotide excision repair (NER), DNA mismatch repair (MMR), homologous recombination repair (HR), non-homologous end joining (NHEJ) and translesion DNA synthesis (TLS). As well as mutations to DNA damage repair genes, mutations also arise in the genes responsible for arresting the cell cycle to allow sufficient time for DNA repair to occur, and some genes are involved in both DNA damage repair and cell cycle checkpoint control, for example ATM and checkpoint kinase 2 (CHEK2) – a tumor suppressor that is often absent or downregulated in non-small cell lung cancer.
=== Epigenetic DNA repair defects in cancer ===
Classically, cancer has been viewed as a set of diseases that are driven by progressive genetic abnormalities that include mutations in tumour-suppressor genes and oncogenes, and chromosomal aberrations. However, it has become apparent that cancer is also driven by epigenetic alterations.
Epigenetic alterations refer to functionally relevant modifications to the genome that do not involve a change in the nucleotide sequence. Examples of such modifications are changes in DNA methylation (hypermethylation and hypomethylation) and histone modification, changes in chromosomal architecture (caused by inappropriate expression of proteins such as HMGA2 or HMGA1) and changes caused by microRNAs. Each of these epigenetic alterations serves to regulate gene expression without altering the underlying DNA sequence. These changes usually remain through cell divisions, last for multiple cell generations, and can be considered to be epimutations (equivalent to mutations).
While large numbers of epigenetic alterations are found in cancers, the epigenetic alterations in DNA repair genes, causing reduced expression of DNA repair proteins, appear to be particularly important. Such alterations are thought to occur early in progression to cancer and to be a likely cause of the genetic instability characteristic of cancers.
Reduced expression of DNA repair genes causes deficient DNA repair. When DNA repair is deficient DNA damages remain in cells at a higher than usual level and these excess damages cause increased frequencies of mutation or epimutation. Mutation rates increase substantially in cells defective in DNA mismatch repair or in homologous recombinational repair (HRR). Chromosomal rearrangements and aneuploidy also increase in HRR defective cells.
Higher levels of DNA damage not only cause increased mutation, but also cause increased epimutation. During repair of DNA double strand breaks, or repair of other DNA damages, incompletely cleared sites of repair can cause epigenetic gene silencing.
Deficient expression of DNA repair proteins due to an inherited mutation can cause increased risk of cancer. Individuals with an inherited impairment in any of 34 DNA repair genes (see article DNA repair-deficiency disorder) have an increased risk of cancer, with some defects causing up to a 100% lifetime chance of cancer (e.g. p53 mutations). However, such germline mutations (which cause highly penetrant cancer syndromes) are the cause of only about 1 percent of cancers.
=== Frequencies of epimutations in DNA repair genes ===
Deficiencies in DNA repair enzymes are occasionally caused by a newly arising somatic mutation in a DNA repair gene, but are much more frequently caused by epigenetic alterations that reduce or silence expression of DNA repair genes. For example, when 113 colorectal cancers were examined in sequence, only four had a missense mutation in the DNA repair gene MGMT, while the majority had reduced MGMT expression due to methylation of the MGMT promoter region (an epigenetic alteration). Five different studies found that between 40% and 90% of colorectal cancers have reduced MGMT expression due to methylation of the MGMT promoter region.
Similarly, out of 119 cases of mismatch repair-deficient colorectal cancers that lacked DNA repair gene PMS2 expression, PMS2 was deficient in 6 due to mutations in the PMS2 gene, while in 103 cases PMS2 expression was deficient because its pairing partner MLH1 was repressed due to promoter methylation (PMS2 protein is unstable in the absence of MLH1). In the other 10 cases, loss of PMS2 expression was likely due to epigenetic overexpression of the microRNA, miR-155, which down-regulates MLH1.
In a further example, epigenetic defects were found in various cancers (e.g. breast, ovarian, colorectal and head and neck). Two or three deficiencies in the expression of ERCC1, XPF or PMS2 occur simultaneously in the majority of 49 colon cancers evaluated by Facista et al.
The chart in this section shows some frequent DNA damaging agents, examples of DNA lesions they cause, and the pathways that deal with these DNA damages. At least 169 enzymes are either directly employed in DNA repair or influence DNA repair processes. Of these, 83 are directly employed in repairing the 5 types of DNA damages illustrated in the chart.
Some of the more well studied genes central to these repair processes are shown in the chart. The gene designations shown in red, gray or cyan indicate genes frequently epigenetically altered in various types of cancers. Wikipedia articles on each of the genes highlighted by red, gray or cyan describe the epigenetic alteration(s) and the cancer(s) in which these epimutations are found. Review articles, and broad experimental survey articles also document most of these epigenetic DNA repair deficiencies in cancers.
Red-highlighted genes are frequently reduced or silenced by epigenetic mechanisms in various cancers. When these genes have low or absent expression, DNA damages can accumulate. Replication errors past these damages (see translesion synthesis) can lead to increased mutations and, ultimately, cancer. Epigenetic repression of DNA repair genes in accurate DNA repair pathways appear to be central to carcinogenesis.
The two gray-highlighted genes RAD51 and BRCA2, are required for homologous recombinational repair. They are sometimes epigenetically over-expressed and sometimes under-expressed in certain cancers. As indicated in the Wikipedia articles on RAD51 and BRCA2, such cancers ordinarily have epigenetic deficiencies in other DNA repair genes. These repair deficiencies would likely cause increased unrepaired DNA damages. The over-expression of RAD51 and BRCA2 seen in these cancers may reflect selective pressures for compensatory RAD51 or BRCA2 over-expression and increased homologous recombinational repair to at least partially deal with such excess DNA damages. In those cases where RAD51 or BRCA2 are under-expressed, this would itself lead to increased unrepaired DNA damages. Replication errors past these damages (see translesion synthesis) could cause increased mutations and cancer, so that under-expression of RAD51 or BRCA2 would be carcinogenic in itself.
Cyan-highlighted genes are in the microhomology-mediated end joining (MMEJ) pathway and are up-regulated in cancer. MMEJ is an additional error-prone inaccurate repair pathway for double-strand breaks. In MMEJ repair of a double-strand break, an homology of 5–25 complementary base pairs between both paired strands is sufficient to align the strands, but mismatched ends (flaps) are usually present. MMEJ removes the extra nucleotides (flaps) where strands are joined, and then ligates the strands to create an intact DNA double helix. MMEJ almost always involves at least a small deletion, so that it is a mutagenic pathway. FEN1, the flap endonuclease in MMEJ, is epigenetically increased by promoter hypomethylation and is over-expressed in the majority of cancers of the breast, prostate, stomach, neuroblastomas, pancreas, and lung. PARP1 is also over-expressed when its promoter region ETS site is epigenetically hypomethylated, and this contributes to progression to endometrial cancer and BRCA-mutated serous ovarian cancer. Other genes in the MMEJ pathway are also over-expressed in a number of cancers (see MMEJ for summary), and are also shown in cyan.
=== Genome-wide distribution of DNA repair in human somatic cells ===
Differential activity of DNA repair pathways across various regions of the human genome causes mutations to be very unevenly distributed within tumor genomes. In particular, the gene-rich, early-replicating regions of the human genome exhibit lower mutation frequencies than the gene-poor, late-replicating heterochromatin. One mechanism underlying this involves the histone modification H3K36me3, which can recruit mismatch repair proteins, thereby lowering mutation rates in H3K36me3-marked regions. Another important mechanism concerns nucleotide excision repair, which can be recruited by the transcription machinery, lowering somatic mutation rates in active genes and other open chromatin regions.
== Epigenetic alterations due to DNA repair ==
Damage to DNA is very common and is constantly being repaired. Epigenetic alterations can accompany DNA repair of oxidative damage or double-strand breaks. In human cells, oxidative DNA damage occurs about 10,000 times a day and DNA double-strand breaks occur about 10 to 50 times a cell cycle in somatic replicating cells (see DNA damage (naturally occurring)). The selective advantage of DNA repair is to allow the cell to survive in the face of DNA damage. The selective advantage of epigenetic alterations that occur with DNA repair is not clear.
=== Repair of oxidative DNA damage can alter epigenetic markers ===
In the steady state (with endogenous damages occurring and being repaired), there are about 2,400 oxidatively damaged guanines that form 8-oxo-2'-deoxyguanosine (8-OHdG) in the average mammalian cell DNA. 8-OHdG constitutes about 5% of the oxidative damages commonly present in DNA. The oxidized guanines do not occur randomly among all guanines in DNA. There is a sequence preference for the guanine at a methylated CpG site (a cytosine followed by guanine along its 5' → 3' direction and where the cytosine is methylated (5-mCpG)). A 5-mCpG site has the lowest ionization potential for guanine oxidation.
Oxidized guanine has mispairing potential and is mutagenic. Oxoguanine glycosylase (OGG1) is the primary enzyme responsible for the excision of the oxidized guanine during DNA repair. OGG1 finds and binds to an 8-OHdG within a few seconds. However, OGG1 does not immediately excise 8-OHdG. In HeLa cells half maximum removal of 8-OHdG occurs in 30 minutes, and in irradiated mice, the 8-OHdGs induced in the mouse liver are removed with a half-life of 11 minutes.
When OGG1 is present at an oxidized guanine within a methylated CpG site it recruits TET1 to the 8-OHdG lesion (see Figure). This allows TET1 to demethylate an adjacent methylated cytosine. Demethylation of cytosine is an epigenetic alteration.
As an example, when human mammary epithelial cells were treated with H2O2 for six hours, 8-OHdG increased about 3.5-fold in DNA and this caused about 80% demethylation of the 5-methylcytosines in the genome. Demethylation of CpGs in a gene promoter by TET enzyme activity increases transcription of the gene into messenger RNA. In cells treated with H2O2, one particular gene was examined, BACE1. The methylation level of the BACE1 CpG island was reduced (an epigenetic alteration) and this allowed about 6.5 fold increase of expression of BACE1 messenger RNA.
While six-hour incubation with H2O2 causes considerable demethylation of 5-mCpG sites, shorter times of H2O2 incubation appear to promote other epigenetic alterations. Treatment of cells with H2O2 for 30 minutes causes the mismatch repair protein heterodimer MSH2-MSH6 to recruit DNA methyltransferase 1 (DNMT1) to sites of some kinds of oxidative DNA damage. This could cause increased methylation of cytosines (epigenetic alterations) at these locations.
Jiang et al. treated HEK 293 cells with agents causing oxidative DNA damage, (potassium bromate (KBrO3) or potassium chromate (K2CrO4)). Base excision repair (BER) of oxidative damage occurred with the DNA repair enzyme polymerase beta localizing to oxidized guanines. Polymerase beta is the main human polymerase in short-patch BER of oxidative DNA damage. Jiang et al. also found that polymerase beta recruited the DNA methyltransferase protein DNMT3b to BER repair sites. They then evaluated the methylation pattern at the single nucleotide level in a small region of DNA including the promoter region and the early transcription region of the BRCA1 gene. Oxidative DNA damage from bromate modulated the DNA methylation pattern (caused epigenetic alterations) at CpG sites within the region of DNA studied. In untreated cells, CpGs located at −189, −134, −29, −19, +16, and +19 of the BRCA1 gene had methylated cytosines (where numbering is from the messenger RNA transcription start site, and negative numbers indicate nucleotides in the upstream promoter region). Bromate treatment-induced oxidation resulted in the loss of cytosine methylation at −189, −134, +16 and +19 while also leading to the formation of new methylation at the CpGs located at −80, −55, −21 and +8 after DNA repair was allowed.
=== Homologous recombinational repair alters epigenetic markers ===
At least four articles report the recruitment of DNA methyltransferase 1 (DNMT1) to sites of DNA double-strand breaks. During homologous recombinational repair (HR) of the double-strand break, the involvement of DNMT1 causes the two repaired strands of DNA to have different levels of methylated cytosines. One strand becomes frequently methylated at about 21 CpG sites downstream of the repaired double-strand break. The other DNA strand loses methylation at about six CpG sites that were previously methylated downstream of the double-strand break, as well as losing methylation at about five CpG sites that were previously methylated upstream of the double-strand break. When the chromosome is replicated, this gives rise to one daughter chromosome that is heavily methylated downstream of the previous break site and one that is unmethylated in the region both upstream and downstream of the previous break site. With respect to the gene that was broken by the double-strand break, half of the progeny cells express that gene at a high level and in the other half of the progeny cells expression of that gene is repressed. When clones of these cells were maintained for three years, the new methylation patterns were maintained over that time period.
In mice with a CRISPR-mediated homology-directed recombination insertion in their genome there were a large number of increased methylations of CpG sites within the double-strand break-associated insertion.
=== Non-homologous end joining can cause some epigenetic marker alterations ===
Non-homologous end joining (NHEJ) repair of a double-strand break can cause a small number of demethylations of pre-existing cytosine DNA methylations downstream of the repaired double-strand break. Further work by Allen et al. showed that NHEJ of a DNA double-strand break in a cell could give rise to some progeny cells having repressed expression of the gene harboring the initial double-strand break and some progeny having high expression of that gene due to epigenetic alterations associated with NHEJ repair. The frequency of epigenetic alterations causing repression of a gene after an NHEJ repair of a DNA double-strand break in that gene may be about 0.9%.
== Evolution ==
The basic processes of DNA repair are highly conserved among both prokaryotes and eukaryotes and even among bacteriophages (viruses which infect bacteria); however, more complex organisms with more complex genomes have correspondingly more complex repair mechanisms. The ability of a large number of protein structural motifs to catalyze relevant chemical reactions has played a significant role in the elaboration of repair mechanisms during evolution. For an extremely detailed review of hypotheses relating to the evolution of DNA repair, see.
The fossil record indicates that single-cell life began to proliferate on the planet at some point during the Precambrian period, although exactly when recognizably modern life first emerged is unclear. Nucleic acids became the sole and universal means of encoding genetic information, requiring DNA repair mechanisms that in their basic form have been inherited by all extant life forms from their common ancestor. The emergence of Earth's oxygen-rich atmosphere (known as the "oxygen catastrophe") due to photosynthetic organisms, as well as the presence of potentially damaging free radicals in the cell due to oxidative phosphorylation, necessitated the evolution of DNA repair mechanisms that act specifically to counter the types of damage induced by oxidative stress. The mechanism by which this came about, however, is unclear.
=== Rate of evolutionary change ===
On some occasions, DNA damage is not repaired or is repaired by an error-prone mechanism that results in a change from the original sequence. When this occurs, mutations may propagate into the genomes of the cell's progeny. Should such an event occur in a germ line cell that will eventually produce a gamete, the mutation has the potential to be passed on to the organism's offspring. The rate of evolution in a particular species (or, in a particular gene) is a function of the rate of mutation. As a consequence, the rate and accuracy of DNA repair mechanisms have an influence over the process of evolutionary change. DNA damage protection and repair does not influence the rate of adaptation by gene regulation and by recombination and selection of alleles. On the other hand, DNA damage repair and protection does influence the rate of accumulation of irreparable, advantageous, code expanding, inheritable mutations, and slows down the evolutionary mechanism for expansion of the genome of organisms with new functionalities. The tension between evolvability and mutation repair and protection needs further investigation.
== Technology ==
A technology named clustered regularly interspaced short palindromic repeat (shortened to CRISPR-Cas9) was discovered in 2012. The new technology allows anyone with molecular biology training to alter the genes of any species with precision, by inducing DNA damage at a specific point and then altering DNA repair mechanisms to insert new genes. It is cheaper, more efficient, and more precise than other technologies. With the help of CRISPR–Cas9, parts of a genome can be edited by scientists by removing, adding, or altering parts in a DNA sequence.
== See also ==
== References ==
== External links ==
Media related to DNA repair at Wikimedia Commons
Roswell Park Cancer Institute DNA Repair Lectures
A comprehensive list of Human DNA Repair Genes
3D structures of some DNA repair enzymes
Machado CR, Menck CF (December 1997). "Human DNA repair diseases: From genome instability to cancer". Braz. J. Genet. 20 (4): 755–762. doi:10.1590/S0100-84551997000400032.
DNA repair special interest group
DNA Repair Archived 12 February 2018 at the Wayback Machine
DNA Damage and DNA Repair
Segmental Progeria
Hakem R (February 2008). "DNA-damage repair; the good, the bad, and the ugly". EMBO J. 27 (4): 589–605. doi:10.1038/emboj.2008.15. PMC 2262034. PMID 18285820.
Morales ME, Derbes RS, Ade CM, Ortego JC, Stark J, Deininger PL, et al. (2016). "Heavy Metal Exposure Influences Double Strand Break DNA Repair Outcomes". PLOS ONE. 11 (3): e0151367. Bibcode:2016PLoSO..1151367M. doi:10.1371/journal.pone.0151367. PMC 4788447. PMID 26966913. | Wikipedia/DNA_damage_checkpoint |
In genetics, crosslinking of DNA occurs when various exogenous or endogenous agents react with two nucleotides of DNA, forming a covalent linkage between them. This crosslink can occur within the same strand (intrastrand) or between opposite strands of double-stranded DNA (interstrand). These adducts interfere with cellular metabolism, such as DNA replication and transcription, triggering cell death. These crosslinks can, however, be repaired through excision or recombination pathways.
DNA crosslinking also has useful merit in chemotherapy and targeting cancerous cells for apoptosis, as well as in understanding how proteins interact with DNA.
== Crosslinking agents ==
Many characterized crosslinking agents have two independently reactive groups within the same molecule, each of which is able to bind with a nucleotide residue of DNA. These agents are separated based upon their source of origin and labeled either as exogenous or endogenous. Exogenous crosslinking agents are chemicals and compounds, both natural and synthetic, that stem from environmental exposures such as pharmaceuticals and cigarette smoke or automotive exhaust. Endogenous crosslinking agents are compounds and metabolites that are introduced from cellular or biochemical pathways within a cell or organism.
=== Exogenous agents ===
Nitrogen mustards are exogenous alkylating agents which react with the N7 position of guanine. These compounds have a bis-(2-ethylchloro)amine core structure, with a variable R-group, with the two reactive functional groups serving to alkylate nucleobases and form a crosslink lesion. These agents most preferentially form a 1,3 5'-d(GNC) interstrand crosslink. The introduction of this agent slightly bends the DNA duplex to accommodate for the agent's presence within the helix. These agents are often introduced as a pharmaceutical and are used in cytotoxic chemotherapy.
Cisplatin (cis-diamminedichloroplatinum(II)) and its derivatives mostly act on adjacent guanines at their N7 positions. The planar compound links to nucleobases through water displacement of one or both of its chloride groups, allowing cisplatin to form monoadducts to DNA or RNA, intrastrand DNA crosslinks, interstrand DNA crosslinks, and DNA-protein crosslinks. When cisplatin generates DNA crosslinks, it more frequently forms 1,2-intrastrand crosslinks (5'-GG), but also forms 1,3-intrastrand crosslinks (5-GNG) at lower percentages. When cisplatin forms interstrand crosslinks (5'-GC), there is a severe distortion to the DNA helix due to a shortened distance between guanines on opposite strands and a cytosine that is flipped out of the helix as a consequence of the GG interaction. Similar to nitrogen mustards, cisplatin is used frequently in chemotherapy treatment - especially for testicular and ovarian cancers.
Chloro ethyl nitroso urea (CENU), specifically carmustine (BCNU), are crosslinking agents that are widely used in chemotherapy, particularly for brain tumors. These agents differ from other crosslinkers as they alkylate O6 of guanine to form an O6-ethanoguanine. This intermediate compound then leads to an interstrand crosslink between a GC basepair. These crosslinking agents only result in small distortions to the DNA helix due to the molecules' smaller size.
Psoralens are natural compounds (furocoumarins) present in plants. These compounds intercalate into DNA at 5'-AT sequence sites and form thymidine adducts when activated in the presence of Ultra Violet-A (UV-A) rays. These covalent adducts are formed by linking the 3, 4 (pyrone) or 4', 5’ (furan) edge of psoralen to the 5, 6 double bond of thymine. Psoralens can form two types of monoadducts and one diadduct (an interstrand crosslink) with thymine. These adducts result in local distortions to DNA at the site of intercalation. Psoralens are used in the medical treatment of skin diseases, such as psoriasis and vitiligo.
Mitomycin C (MMC) is from a class of antibiotics that are used broadly in chemotherapy, often with gastrointestinal related cancers. Mitomycin C can only act as a crosslinker when a DNA nucleotide has had a reduction to its quinone ring. When two dG's have been rearranged and methylated in this manner, a 5'-GC interstrand crosslink can be formed with the exo amines of each nucleobase. Mitomycin also harbors the ability to form monoadducts and intrastrand crosslinks with DNA as well. The interstrand crosslinks of Mitomycin C are formed in the minor groove of DNA, inducing a moderate widening or stretching to the DNA helix in order to accommodate for the presence of the molecule within the two strands.
=== Endogenous agents ===
Nitrous acid is formed as a byproduct in the stomach from dietary sources of nitrites and can lead to crosslink lesions in DNA through the conversion of amino groups in DNA to carbonyls. This type of lesion occurs most frequently between two guanosines, with 1 of 4 deaminated guanosines resulting in an interstrand crosslink. It induces formation of interstrand DNA crosslinks at the amino group of exocyclic N2 of guanine at 5'-CG sequences. This lesion mildly distorts the double helix.
Bifunctional aldehydes are reactive chemicals that are formed endogenously via lipid peroxidation and prostoglandin biosynthesis. They create etheno adducts formed by aldehyde which undergo rearrangements to form crosslinks on opposite strands of DNA. Malondialdehyde is a prototypical example that can crosslink DNA via two exocyclic guanine amino groups. Other aldehydes, such as formaldehyde and acetylaldehyde, can introduce interstrand crosslinks and often act as exogenous agents as they are found in many processed foods. Often found within pesticides, tobacco smoke, and automotive exhaust, α,β unsaturated aldehydes, such as acrolein and crotonaldehyde, are further exogenous agents that may induce DNA crosslinks. Unlike other crosslinking agents, aldehyde-induced crosslinking is an intrinsically reversible process. NMR structure of these types of agents as interstrand crosslinks show that a 5'-GC adduct results in minor distortion to DNA, however a 5'-CG adduct destabilizes the helix and induces a bend and twist in the DNA.
DNA crosslinking lesions can also be formed when under conditions of oxidative stress, in which free oxygen radicals generate reactive intermediates in DNA, and these lesions have been implicated in aging and cancer. Tandem DNA lesions are formed at a substantial frequency by ionizing radiation and metal-catalyzed H2O2 reactions. Under anoxic conditions, the predominant double-base lesion is a species in which the C8 of guanine is linked to the 5-methyl group of an adjacent 3'-thymine (G[8,5- Me]T), forming intrastrand lesions.
==== Summary table of crosslinking agents ====
== Repair of DNA crosslinks ==
Crosslinked DNA is repaired in cells by a combination of enzymes and other factors from the nucleotide excision repair (NER) pathway, homologous recombination, and the base excision repair (BER) pathway. To repair interstrand crosslinks in eukaryotes, a 3’ flap endonuclease from the NER, XPF-ERCC1, is recruited to the crosslinked DNA, where it assists in ‘unhooking’ the DNA by cleaving the 3’ strand at the crosslink site. The 5’ strand is then cleaved, either by XPF-ERCC1 or another endonuclease, forming a double-strand break (DSB), which can then be repaired by the homologous recombination pathway.
The repair of interstrand crosslinks requires both nucleotide excision repair and homologous recombinational repair. The Werner syndrome (WRN) helicase and the BRCA1 protein collaborate as part of a cellular response to repair DNA interstrand crosslinks. In vitro, BRCA1 interacts directly with WRN to stimulate WRN helicase activity.
DNA crosslinks generally cause loss of overlapping sequence information from the two strands of DNA. Therefore, accurate repair of the damage depends on retrieving the lost information from an undamaged homologous chromosome in the same cell. Retrieval can occur by pairing with a sister chromatid produced during a preceding round of replication. In a diploid cell retrieval may also occur by pairing with a non-sister homologous chromosome, as occurs especially during meiosis. Once pairing has occurred, the crosslink can be removed and correct information introduced into the damaged chromosome by homologous recombination.
Cleavage of the bond between a deoxyribose sugar in DNA's sugar-phosphate backbone and its associated nucleobase leaves an abasic site in double stranded DNA. These abasic sites are often generated as an intermediate and then restored in base excision repair. However, if these sites are allowed to persist, they can inhibit DNA replication and transcription. Abasic sites can react with amine groups on proteins to form DNA-protein crosslinks or with exocyclic amines of other nucleobases to form interstrand crosslinks. To prevent interstrand or DNA-protein crosslinks, enzymes from the BER pathway tightly bind the abasic site and sequester it from nearby reactive groups, as demonstrated in human alkyladenine DNA glycosylase (AAG) and E. coli 3-methyladenine DNA glycosylase II (AlkA). in vitro evidence demonstrated that the Interstand Cross-Links induced by abasic site (DOB-ICL) is a replication-blocking and highly miscoding lesion. Compared to several other TLS pols examined, pol η is likely to contribute to the TLS-mediated repair of the DOB-ICL in vivo. By using O6-2'-deoxyguanosine-butylene-O6-2'-deoxyguanosine (O6-dG-C4-O6-dG) DNA lesions which is a chemically stable structure, the bypassing activity of several DNA polymerases had been investigated and the results demonstrated that pol η exhibited the highest bypass activity; however, 70% of the bypass products were mutagenic containing substitutions or deletions. The increase in the size of unhooked repair intermediates elevates the frequency of deletion mutation.
Treatment of E. coli with psoralen-plus-UV light (PUVA) produces interstrand crosslinks in the cells’ DNA. Cole et al. and Sinden and Cole presented evidence that a homologous recombinational repair process requiring the products of genes uvrA, uvrB, and recA can remove these crosslinks in E. coli. This process appears to be quite efficient. Even though one or two unrepaired crosslinks are sufficient to inactivate a cell, a wild-type bacterial cell can repair and therefore recover from 53 to 71 psoralen crosslinks. Eukaryotic yeast cells are also inactivated by one remaining crosslink, but wild type yeast cells can recover from 120 to 200 crosslinks.
== Applications ==
=== Crosslinking of DNA and protein ===
==== Biochemical interaction methods ====
DNA-protein crosslinking can be caused by a variety of chemical and physical agents, including transition metals, ionizing radiation, and endogenous aldehydes, in addition to chemotherapeutic agents.
Similar to DNA crosslinking, DNA-protein crosslinks are lesions in cells that are frequently damaged by UV radiation. The UV's effect can lead to reactive interactions and cause DNA and the proteins that are in contact with it to crosslink. These crosslinks are very bulky and complex lesions. They primarily occur in areas of the chromosomes that are undergoing DNA replication and interfere with cellular processes.
The advancement in structure-identification methods has progressed, and the addition in the ability to measure interactions between DNA and protein is a requirement to fully understand the biochemical processes. The structure of DNA-protein complexes can be mapped by photocrosslinking, which is the photoinduced formation of a covalent bond between two macromolecules or between two different parts of one macromolecule. The methodology involves covalently linking a DNA-binding motif of the target sequence-specific DNA-binding protein with a photoactivatable crosslinking agent capable of reacting with DNA nucleotides when exposed to UV. This method provides information on the interaction between the DNA and protein in the crosslink.
==== Clinical treatments ====
DNA repair pathways can result in the formation of tumor cells. Cancer treatments have been engineered using DNA cross-linking agents to interact with nitrogenous bases of DNA to block DNA replication. These cross-linking agents have the ability to act as single-agent therapies by targeting and destroying specific nucleotides in cancerous cells. This result is stopping the cycle and growth of cancer cells; because it inhibits specific DNA repair pathways, this approach has a potential advantage in having fewer side effects.
In humans, the leading cause of cancer deaths worldwide is lung cancer, including non small cell lung carcinoma (NSCLC) which accounts for 85% of all lung cancer cases in the United States. Individuals with NSCLC are often treated with therapeutic platinum compounds (e.g. cisplatin, carboplatin or oxaliplatin) (see Lung cancer chemotherapy) that cause interstrand DNA crosslinks. Among individuals with NSLC, low expression of the breast cancer 1 gene (BRCA1) in the primary tumor has correlated with improved survival after platinum-containing chemotherapy. This correlation implies that low BRCA1 in the cancer, and the consequent low level of DNA repair, causes vulnerability of the cancer to treatment by the DNA crosslinking agents. High BRCA1 may protect cancer cells by acting in the homologous recombinational repair pathway that removes the damages in DNA introduced by the platinum drugs. The level of BRCA1 expression is potentially an important tool for tailoring chemotherapy in lung cancer management.
Clinical chemotherapeutics can induce enzymatic and non-enzymatic DNA-protein crosslinks. An example of this induction is with platinum derivatives, such as cisplatin and oxaliplatin. They create non-enzymatic DNA-protein crosslinks through non-specific crosslinking of chromatin-interacting proteins to DNA. Crosslinking is also possible in other therapeutic agents by either stabilizing covalent DNA–protein reaction intermediates or by creating a pseudosubstrate, which traps the enzyme on DNA. Camptothecin derivatives, such as irinotecan and topotecan, target and trap specific DNA topoisomerase 1 (TOP1) by intercalating within the enzyme–DNA interface. Because the toxicity of these drugs depends on TOP1 trapping, cellular sensitivity to these compounds depends directly on TOP1 expression levels. As a result, the function of these drugs is to serve as enzyme poisons rather than inhibitors. This can be applied to treat tumor cells by utilizing TOP 2 enzyme poisons.
== References ==
== External links ==
PDB: 1AIO – Interactive structure for cisplatin and DNA adduct formation
PDB: 204D – Interactive structure for psoralen and crosslinked DNA
Psoralen Ultraviolet A Light Treatment | Wikipedia/Crosslinking_of_DNA |
Senescence () or biological aging is the gradual deterioration of functional characteristics in living organisms. Whole organism senescence involves an increase in death rates or a decrease in fecundity with increasing age, at least in the later part of an organism's life cycle. However, the resulting effects of senescence can be delayed. The 1934 discovery that calorie restriction can extend lifespans by 50% in rats, the existence of species having negligible senescence, and the existence of potentially immortal organisms such as members of the genus Hydra have motivated research into delaying senescence and thus age-related diseases. Rare human mutations can cause accelerated aging diseases.
Environmental factors may affect aging – for example, overexposure to ultraviolet radiation accelerates skin aging. Different parts of the body may age at different rates and distinctly, including the brain, the cardiovascular system, and muscle. Similarly, functions may distinctly decline with aging, including movement control and memory. Two organisms of the same species can also age at different rates, making biological aging and chronological aging distinct concepts.
== Definition and characteristics ==
Organismal senescence is the aging of whole organisms. Actuarial senescence can be defined as an increase in mortality or a decrease in fecundity with age. The Gompertz–Makeham law of mortality says that the age-dependent component of the mortality rate increases exponentially with age.
Aging is characterized by the declining ability to respond to stress, increased homeostatic imbalance, and increased risk of aging-associated diseases including cancer and heart disease. Aging has been defined as "a progressive deterioration of physiological function, an intrinsic age-related process of loss of viability and increase in vulnerability."
In 2013, a group of scientists defined nine hallmarks of aging that are common between organisms with emphasis on mammals:
genomic instability,
telomere attrition,
epigenetic alterations,
loss of proteostasis,
deregulated nutrient sensing,
mitochondrial dysfunction,
cellular senescence,
stem cell exhaustion,
altered intercellular communication
In a decadal update, three hallmarks have been added, totaling 12 proposed hallmarks:
disabled macroautophagy
chronic inflammation
dysbiosis
The environment induces damage at various levels, e.g. damage to DNA, and damage to tissues and cells by oxygen radicals (widely known as free radicals), and some of this damage is not repaired and thus accumulates with time. Cloning from somatic cells rather than germ cells may begin life with a higher initial load of damage. Dolly the sheep died young from a contagious lung disease, but data on an entire population of cloned individuals would be necessary to measure mortality rates and quantify aging.
The evolutionary theorist George Williams wrote, "It is remarkable that after a seemingly miraculous feat of morphogenesis, a complex metazoan should be unable to perform the much simpler task of merely maintaining what is already formed."
== Variation among species ==
Different speeds with which mortality increases with age correspond to different maximum life span among species. For example, a mouse is elderly at 3 years, a human is elderly at 80 years, and ginkgo trees show little effect of age even at 667 years.
Almost all organisms senesce, including bacteria which have asymmetries between "mother" and "daughter" cells upon cell division, with the mother cell experiencing aging, while the daughter is rejuvenated. There is negligible senescence in some groups, such as the genus Hydra. Planarian flatworms have "apparently limitless telomere regenerative capacity fueled by a population of highly proliferative adult stem cells." These planarians are not biologically immortal, but rather their death rate slowly increases with age. Organisms that are thought to be biologically immortal would, in one instance, be Turritopsis dohrnii, also known as the "immortal jellyfish", due to its ability to revert to its youth when it undergoes stress during adulthood. The reproductive system is observed to remain intact, and even the gonads of Turritopsis dohrnii are existing.
Some species exhibit "negative senescence", in which reproduction capability increases or is stable, and mortality falls with age, resulting from the advantages of increased body size during aging.
== Theories of aging ==
More than 300 different theories have been posited to explain the nature (mechanisms) and causes (reasons for natural emergence or factors) of aging. Good theories would both explain past observations and predict the results of future experiments. Some of the theories may complement each other, overlap, contradict, or may not preclude various other theories.
Theories of aging fall into two broad categories, evolutionary theories of aging and mechanistic theories of aging. Evolutionary theories of aging primarily explain why aging happens, but do not concern themselves with the molecular mechanism(s) that drive the process. All evolutionary theories of aging rest on the basic mechanisms that the force of natural selection declines with age. Mechanistic theories of aging can be divided into theories that propose aging is programmed, and damage accumulation theories, i.e. those that propose aging to be caused by specific molecular changes occurring over time.
=== Evolutionary aging theories ===
==== Antagonistic pleiotropy ====
One theory was proposed by George C. Williams and involves antagonistic pleiotropy. A single gene may affect multiple traits. Some traits that increase fitness early in life may also have negative effects later in life. But, because many more individuals are alive at young ages than at old ages, even small positive effects early can be strongly selected for, and large negative effects later may be very weakly selected against. Williams suggested the following example: Perhaps a gene codes for calcium deposition in bones, which promotes juvenile survival and will therefore be favored by natural selection; however, this same gene promotes calcium deposition in the arteries, causing negative atherosclerotic effects in old age. Thus, harmful biological changes in old age may result from selection for pleiotropic genes that are beneficial early in life but harmful later on. In this case, selection pressure is relatively high when Fisher's reproductive value is high and relatively low when Fisher's reproductive value is low.
==== Cancer versus cellular senescence tradeoff theory of aging ====
Senescent cells within a multicellular organism can be purged by competition between cells, but this increases the risk of cancer. This leads to an inescapable dilemma between two possibilities—the accumulation of physiologically useless senescent cells, and cancer—both of which lead to increasing rates of mortality with age.
==== Disposable soma ====
The disposable soma theory of aging was proposed by Thomas Kirkwood in 1977. The theory suggests that aging occurs due to a strategy in which an individual only invests in maintenance of the soma for as long as it has a realistic chance of survival. A species that uses resources more efficiently will live longer, and therefore be able to pass on genetic information to the next generation. The demands of reproduction are high, so less effort is invested in repair and maintenance of somatic cells, compared to germline cells, in order to focus on reproduction and species survival.
=== Programmed aging theories ===
Programmed theories of aging posit that aging is adaptive, normally invoking selection for evolvability or group selection.
The reproductive-cell cycle theory suggests that aging is regulated by changes in hormonal signaling over the lifespan.
=== Damage accumulation theories ===
==== The free radical theory of aging ====
One of the most prominent theories of aging was first proposed by Harman in 1956. It posits that free radicals produced by dissolved oxygen, radiation, cellular respiration and other sources cause damage to the molecular machines in the cell and gradually wear them down. This is also known as oxidative stress.
There is substantial evidence to back up this theory. Old animals have larger amounts of oxidized proteins, DNA and lipids than their younger counterparts.
==== Chemical damage ====
One of the earliest aging theories was the Rate of Living Hypothesis described by Raymond Pearl in 1928 (based on earlier work by Max Rubner), which states that fast basal metabolic rate corresponds to short maximum life span.
While there may be some validity to the idea that for various types of specific damage detailed below that are by-products of metabolism, all other things being equal, a fast metabolism may reduce lifespan, in general this theory does not adequately explain the differences in lifespan either within, or between, species. Calorically restricted animals process as much, or more, calories per gram of body mass, as their ad libitum fed counterparts, yet exhibit substantially longer lifespans. Similarly, metabolic rate is a poor predictor of lifespan for birds, bats and other species that, it is presumed, have reduced mortality from predation, and therefore have evolved long lifespans even in the presence of very high metabolic rates. In a 2007 analysis it was shown that, when modern statistical methods for correcting for the effects of body size and phylogeny are employed, metabolic rate does not correlate with longevity in mammals or birds.
With respect to specific types of chemical damage caused by metabolism, it is suggested that damage to long-lived biopolymers, such as structural proteins or DNA, caused by ubiquitous chemical agents in the body such as oxygen and sugars, are in part responsible for aging. The damage can include breakage of biopolymer chains, cross-linking of biopolymers, or chemical attachment of unnatural substituents (haptens) to biopolymers.
Under normal aerobic conditions, approximately 4% of the oxygen metabolized by mitochondria is converted to superoxide ion, which can subsequently be converted to hydrogen peroxide, hydroxyl radical and eventually other reactive species including other peroxides and singlet oxygen, which can, in turn, generate free radicals capable of damaging structural proteins and DNA. Certain metal ions found in the body, such as copper and iron, may participate in the process. (In Wilson's disease, a hereditary defect that causes the body to retain copper, some of the symptoms resemble accelerated senescence.) These processes termed oxidative stress are linked to the potential benefits of dietary polyphenol antioxidants, for example in coffee, and tea. However their typically positive effects on lifespans when consumption is moderate have also been explained by effects on autophagy, glucose metabolism and AMPK.
Sugars such as glucose and fructose can react with certain amino acids such as lysine and arginine and certain DNA bases such as guanine to produce sugar adducts, in a process called glycation. These adducts can further rearrange to form reactive species, which can then cross-link the structural proteins or DNA to similar biopolymers or other biomolecules such as non-structural proteins. People with diabetes, who have elevated blood sugar, develop senescence-associated disorders much earlier than the general population, but can delay such disorders by rigorous control of their blood sugar levels. There is evidence that sugar damage is linked to oxidant damage in a process termed glycoxidation.
Free radicals can damage proteins, lipids or DNA. Glycation mainly damages proteins. Damaged proteins and lipids accumulate in lysosomes as lipofuscin. Chemical damage to structural proteins can lead to loss of function; for example, damage to collagen of blood vessel walls can lead to vessel-wall stiffness and, thus, hypertension, and vessel wall thickening and reactive tissue formation (atherosclerosis); similar processes in the kidney can lead to kidney failure. Damage to enzymes reduces cellular functionality. Lipid peroxidation of the inner mitochondrial membrane reduces the electric potential and the ability to generate energy. It is probably no accident that nearly all of the so-called "accelerated aging diseases" are due to defective DNA repair enzymes.
It is believed that the impact of alcohol on aging can be partly explained by alcohol's activation of the HPA axis, which stimulates glucocorticoid secretion, long-term exposure to which produces symptoms of aging.
==== DNA damage ====
DNA damage was proposed in a 2021 review to be the underlying cause of aging because of the mechanistic link of DNA damage to nearly every aspect of the aging phenotype. Slower rate of accumulation of DNA damage as measured by the DNA damage marker gamma H2AX in leukocytes was found to correlate with longer lifespans in comparisons of dolphins, goats, reindeer, American flamingos and griffon vultures. DNA damage-induced epigenetic alterations, such as DNA methylation and many histone modifications, appear to be of particular importance to the aging process. Evidence for the theory that DNA damage is the fundamental cause of aging was first reviewed in 1981.
==== Mutation accumulation ====
Natural selection can support lethal and harmful alleles, if their effects are felt after reproduction. The geneticist J. B. S. Haldane wondered why the dominant mutation that causes Huntington's disease remained in the population, and why natural selection had not eliminated it. The onset of this neurological disease is (on average) at age 45 and is invariably fatal within 10–20 years. Haldane assumed that, in human prehistory, few survived until age 45. Since few were alive at older ages and their contribution to the next generation was therefore small relative to the large cohorts of younger age groups, the force of selection against such late-acting deleterious mutations was correspondingly small. Therefore, a genetic load of late-acting deleterious mutations could be substantial at mutation–selection balance. This concept came to be known as the selection shadow.
Peter Medawar formalised this observation in his mutation accumulation theory of aging. "The force of natural selection weakens with increasing age—even in a theoretically immortal population, provided only that it is exposed to real hazards of mortality. If a genetic disaster... happens late enough in individual life, its consequences may be completely unimportant". Age-independent hazards such as predation, disease, and accidents, called 'extrinsic mortality', mean that even a population with negligible senescence will have fewer individuals alive in older age groups.
==== Other damage ====
A study concluded that retroviruses in the human genomes can become awakened from dormant states and contribute to aging which can be blocked by neutralizing antibodies, alleviating "cellular senescence and tissue degeneration and, to some extent, organismal aging".
=== Stem cell theories of aging ===
Hematopoietic stem cell aging
Hematopoietic stem cell diversity aging
Hematopoietic mosaic loss of chromosome Y
== Biomarkers of aging ==
If different individuals age at different rates, then fecundity, mortality, and functional capacity might be better predicted by biomarkers than by chronological age. However, graying of hair, face aging, skin wrinkles and other common changes seen with aging are not better indicators of future functionality than chronological age. Biogerontologists have continued efforts to find and validate biomarkers of aging, but success thus far has been limited.
Levels of CD4 and CD8 memory T cells and naive T cells have been used to give good predictions of the expected lifespan of middle-aged mice.
=== Aging clocks ===
There is interest in an epigenetic clock as a biomarker of aging, based on its ability to predict human chronological age. Basic blood biochemistry and cell counts can also be used to accurately predict the chronological age. It is also possible to predict the human chronological age using transcriptomic aging clocks.
There is research and development of further biomarkers, detection systems and software systems to measure biological age of different tissues or systems or overall. For example, a deep learning (DL) software using anatomic magnetic resonance images estimated brain age with relatively high accuracy, including detecting early signs of Alzheimer's disease and varying neuroanatomical patterns of neurological aging, and a DL tool was reported as to calculate a person's inflammatory age based on patterns of systemic age-related inflammation.
Aging clocks have been used to evaluate impacts of interventions on humans, including combination therapies. Employing aging clocks to identify and evaluate longevity interventions represents a fundamental goal in aging biology research. However, achieving this goal requires overcoming numerous challenges and implementing additional validation steps.
== Genetic determinants of aging ==
A number of genetic components of aging have been identified using model organisms, ranging from the simple budding yeast Saccharomyces cerevisiae to worms such as Caenorhabditis elegans and fruit flies (Drosophila melanogaster). Study of these organisms has revealed the presence of at least two conserved aging pathways.
Gene expression is imperfectly controlled, and it is possible that random fluctuations in the expression levels of many genes contribute to the aging process as suggested by a study of such genes in yeast. Individual cells, which are genetically identical, nonetheless can have substantially different responses to outside stimuli, and markedly different lifespans, indicating the epigenetic factors play an important role in gene expression and aging as well as genetic factors. There is research into epigenetics of aging.
The ability to repair DNA double-strand breaks declines with aging in mice and humans.
A set of rare hereditary (genetics) disorders, each called progeria, has been known for some time. Sufferers exhibit symptoms resembling accelerated aging, including wrinkled skin. The cause of Hutchinson–Gilford progeria syndrome was reported in the journal Nature in May 2003.
This report suggests that DNA damage, not oxidative stress, is the cause of this form of accelerated aging.
A study indicates that aging may shift activity toward short genes or shorter transcript length and that this can be countered by interventions.
== Healthspans and aging in society ==
Healthspan can broadly be defined as the period of one's life that one is healthy, such as free of significant diseases or declines of capacities (e.g. of senses, muscle, endurance and cognition).
Biological aging or the LHG comes with a great cost burden to society, including potentially rising health care costs (also depending on types and costs of treatments). This, along with global quality of life or wellbeing, highlight the importance of extending healthspans.
Many measures that may extend lifespans may simultaneously also extend healthspans, albeit that is not necessarily the case, indicating that "lifespan can no longer be the sole parameter of interest" in related research. While recent life expectancy increases were not followed by "parallel" healthspan expansion, awareness of the concept and issues of healthspan lags as of 2017. Scientists have noted that "[c]hronic diseases of aging are increasing and are inflicting untold costs on human quality of life".
== Interventions ==
== See also ==
== References ==
== External links == | Wikipedia/Aging_DNA |
A nick is a discontinuity in a double stranded DNA molecule where there is no phosphodiester bond between adjacent nucleotides of one strand. They typically occur through damage or enzyme action. Nicks allow DNA strands to untwist during replication, and are also thought to play a role in the DNA mismatch repair mechanisms that fix errors on both the leading and lagging daughter strands.
== Formation of nicks ==
The diagram shows the effects of nicks on intersecting DNA in a twisted plasmid. Nicking can be used to dissipate the energy held up by intersecting states. The nicks allow the DNA to take on a circular shape.
Nicked DNA can be the result of DNA damage or purposeful, regulated biomolecular reactions carried out in the cell. During processing, DNA can be nicked by physical shearing, over-drying, or enzymes. Excessive rough handling in pipetting or vortexing creates physical stress that can lead to breaks and nicks in DNA. Overdrying of DNA can also break the phosphodiester bond in DNA and result in nicks. Nicking enzymes can assist with this process. A nick in DNA can be formed by the hydrolysis and subsequent removal of a phosphate group within the helical backbone. This leads to a different DNA conformation, where a hydrogen bond forms in place of the missing piece of the DNA backbone in order to preserve the structure.
== Repair of nicks ==
Ligases are versatile and ubiquitous enzymes that join the 3’ hydroxyl and 5’ phosphate ends to form a phosphodiester bond, making them essential in nicked DNA repair, and ultimately genome fidelity. This biological role has also been extremely valuable in sealing the sticky ends of plasmids in molecular cloning. Their importance is attested by the fact most organisms have multiple ligases dedicated to specific pathways of repairing DNA. In eubacteria, these ligases are powered by NAD+ rather than ATP. Each nick site requires 1 ATP or 1 NAD+ to power the ligase repair.
In order to join these fragments, the ligase progresses through three steps:
Addition of an adenosine monophosphate (AMP) group to the enzyme, referred to as adenylylation
Adenosine monophosphate transfer to the DNA
Nick sealing, or phosphodiester bond formation.
One particular example of a ligase catalyzing nick closure is the E. coli NAD+ dependent DNA ligase, LigA. LigA is a relevant example as it is structurally similar to a clade of enzymes found across all types of bacteria.
Ligases have a metal binding site which is capable of recognizing nicks in DNA. The ligase forms a DNA-adenylate complex, assisting recognition. With human DNA ligase, this forms a crystallized complex. The complex, which has a DNA–adenylate intermediate, allows DNA ligase I to institute a conformational change in the DNA for the isolation and subsequent repair of the DNA nick.
== Biological implications ==
=== Role in mismatch repair ===
Single-stranded nicks act as recognizable markers to help the repair machinery distinguish the newly synthesized strand (daughter strand) from the template strand (parental strand). DNA mismatch repair (MMR) is an important DNA repair system that helps maintain genome plasticity by correcting mismatches, or non Watson-Crick base pairs in a DNA duplex. Some sources of mismatched base pairs include replication errors and deamination of 5-methylcytosine DNA to form thymine.
MMR in most bacteria and eukaryotes is directed to the erroneous strand of the mismatched duplex through recognition of strand discontinuities, while MMR in E. coli and closely related bacteria is directed to the strand on the basis of the absence of methylation. Nicking endonucleases introduce strand discontinuities, or DNA nicks, for both respective systems. Mut L homologues from eukaryotes and most bacteria incise the discontinuous strand to introduce the entry or termination point for the excision reaction. Similarly, in E. coli, Mut H nicks the unmethylated strand of the duplex to introduce the entry point of excision.
For eukaryotes specifically, the mechanism of DNA replication elongation between the leading and lagging strand differs. On the lagging strand, nicks exist between Okazaki fragments and are easily recognizable by the DNA mismatch repair machinery prior to ligation. Due to the continuous replication that occurs on the leading strand, the mechanism there is slightly more complex. During replication, ribonucleotides are added by replication enzymes and these ribonucleotides are nicked by an enzyme called RNase H2. Together, the presence of a nick and a ribonucleotide make the leading strand easily recognizable to the DNA mismatch repair machinery.
Nick translation is a biological process in which a single-stranded DNA nick serves as the marker for DNA polymerase to excise and replace possibly damaged nucleotides. At the end of the segment that DNA polymerase acts on, DNA ligase must repair the final segment of the DNA backbone in order to complete the repair process. In a lab setting, this can be used to introduce fluorescent or other tagged nucleotides by purposefully inducing site-specific, single-stranded nicks in DNA in vitro and then adding the nicked DNA to an environment rich in DNA polymerase and tagged nucleotide. The DNA polymerase then replaces the DNA nucleotides with the tagged ones, starting at the site of the single-stranded nick.
=== Role in replication and transcription ===
Nicked DNA plays an important role in many biological functions. For instance, single-stranded nicks in DNA may serve as purposeful biological markers for the enzyme topoisomerase that unwinds packed DNA and is critical to DNA replication and transcription. In these instances, nicked DNA is not the result of unwanted cell damage.
Topoisomerase-1 preferentially acts at nicks in DNA to cleave adjacent to the nick and then winds or unwinds the complex topologies associated with packed DNA. Here, the nick in the DNA serves as a marker for single strand breakage and subsequent unwinding. It is possible that this is not a highly conserved process. Topoisomerase may cause short deletions when it cleaves bonds, because both full-length DNA products and short deletion strands are seen as products of topoisomerase cleavage while inactive mutants only produced full-length DNA strands.
Nicks in DNA also give rise to different structural properties, can be involved in repairing damages caused by ultraviolet radiation, and are used in the primary steps that allow for genetic recombination.
Nick idling is a biological process in which DNA polymerase may slow or stop its activity of adding bases to a new daughter strand during DNA replication at a nick site. This is particularly relevant to Okazaki fragments in lagging strand in double stranded DNA replication because the direction of replication is opposite to the direction of DNA polymerase, therefore nick idling plays a role in stalling the complex as it replicates in the reverse direction in small fragments (Okazaki fragments) and has to stop and reposition itself in between each and every fragment length of DNA.
DNA structure changes when a single-stranded nick is introduced. Stability is decreased as a break in the phosphodiester backbone allows DNA to unwind, as the built up stress from twisting and packing is not being resisted as strongly anymore. Nicked DNA is more susceptible to degradation due to this reduced stability.
==== In bacteria ====
The nic site or nick region is found within the origin of transfer (oriT) site and is a key in starting bacterial conjugation. A single strand of DNA, called the T-strand, is cut at nic by an enzyme called relaxase. This single strand is eventually transferred to the recipient cell during the process of bacterial conjugation. Before this cleavage can occur, however, it is necessary for a group of proteins to attach to the oriT site. This group of proteins is called the relaxosome. It is thought that portions of the oriT site are bent in a way that creates interaction between the relaxosome proteins and the nic site.
Cleaving the T-strand involves relaxase cutting a phosphodiester bond at the nic site. The cleaved strand is left with a hydroxyl group at the 3' end, which may allow for the strand to form a circular plasmid after moving into the recipient cell.
=== Role in meiosis ===
DNA nicks promote crossover formation during meiosis, and such nicks are protected from ligation by Exonuclease 1 (Exo1).
== References == | Wikipedia/Nick_(DNA) |
DNA end resection, also called 5′–3′ degradation, is a biochemical process where the blunt end of a section of double-stranded DNA (dsDNA) is modified by cutting away some nucleotides from the 5' end to produce a 3' single-stranded sequence. The presence of a section of single-stranded DNA (ssDNA) allows the broken end of the DNA to line up accurately with a matching sequence, so that it can be accurately repaired.Double-strand breaks (DSBs) can occur at any phase of the cell cycle causing DNA end resection and repair activities to take place, but they are also normal intermediates in mitosis recombination. Furthermore, the natural ends of the linear chromosomes resemble DSBs, and although DNA breaks can cause damage to the integrity of genomic DNA, the natural ends are packed into complex specialized DNA protective packages called telomeres that prevent DNA repair activities. Telomeres and mitotic DSBs have different functionality, but both experience the same 5′–3′ degradation process.
== Background ==
A double-strand break is a kind of DNA damage in which both strands in the double helix are severed. DSBs only occur during DNA replication of the cell cycle. Furthermore, DSBs can lead to genome rearrangements and instability. Cases where two complementary strands are linked at the point of the DSB have potential to be catastrophic, such that the cell will not be able to complete mitosis when it next divides, and will either die or, in rare cases, undergo chromosomal loss, duplications, and even mutations. Three mechanisms exist to repair DSBs: non-homologous end joining (NHEJ), microhomology-mediated end joining (MMEJ), and homologous recombination HR. Of these, only NHEJ does not rely on DNA end resection.
== Mechanism ==
Accurate repair of DSBs are essential in the upkeep of genome integrity. From the three mechanisms that exists to repair DSBs, NHEJ and HR repair mechanisms are the dominant pathways. Several highly conservative proteins trigger the DNA Damage Checkpoint for detection of DSBs ensuing repair by either NHEJ or HR repair pathways. NHEJ mechanism functions in ligating two different DSBs with high fidelity, while HR relies on a homologous template to repair DSB ends.
DNA end resection in the HR pathway only occurs at two specific phases: S and G2 phases. Since HR pathway requires sister chromatids for activation, this event only happens in the G2 and S phases of the cell cycle during replication. DSBs that have not begun DNA end resection can be ligated by NHEJ pathway, but resection of a few nucleotides inhibits the NHEJ pathway and commits' DNA repair by the HR pathway. The NHEJ pathway is involved throughout the cell cycle, but it is critical to DNA repair during the G1 phase. In G1 phase there is no sister chromatids to repair DSBs via the HR pathway making the NHEJ pathway a critical repair mechanism.
Before resection can take place, the break needs to be detected. In animals, this detection is done by PARP1; similar systems exist in other eukaryotes: in plants, PARP2 seems to play this role. PARP binding then recruits the MRN complex to the breakage site. This is a highly conserved complex consisting of Mre11, Rad50 and NBS1 (known as Nibrin in mammals, or Xrs2 in yeast, where this complex is called the MRX complex).
Before resection can start, CtBP1-interacting protein (CtIP) needs to bind to the MRN complex so that the first phase of resection can begin, namely short-range end resection. After phosphorylated CtIP binds, the Mre11 subunit is able to cut the 5'-terminated strand endonucleolytically, probably about 300 base pairs from the end, and then acts as a 3'→5' exonuclease to strip away the end of the 5' strand.
== Resection of telomere DSBs ==
Linear chromosomes are packed into complex specialized DNA protective packages called telomeres. The structure of telomeres is highly conserve and is organized in multiple short tandem DNA repeats. Telomeres and DSBs have different functionality, such that telomeres prevent DNA repair activities. During telomeric DNA replication in the S/G2 and G1 phases of the cell cycle, the 3' lagging strand leaves a short overhang called a G-tail. Telomeric DNA ends at the 3' G tail end because the 3' lagging strand extends without its complementary 5' C leading strand. The G tail provide a major function to telomeric DNA such that the G tails control telomere homeostasis.
=== Telomeres in G1 phase ===
In the G1 phase of the cell cycle, the telomere-associated proteins RIF1, RIF2, and RAP2 bind to telomeric DNA and prevent access to the MRX complex. Such process in S. Cerevisiae for example is negatively regulated by this activity. The MRX complex and the Ku complex bind simultaneously and independently to DSBs ends. In the presence of the telomere-associated proteins, MRX fails to bind to the DSB ends while the Ku complex binds to DSB ends. The bound Ku complex to the DSB ends protect the telomeres from nucleolytic degradation by exo1. This results in an inhibition of telomerase elongation at the DSB ends and prevents further telomere action at the G1 phase of the cell cycle.
=== Telomeres in the late S/G2 phase ===
In the late S/G2 phase of the cell cycle, the telomere-associated proteins RIF1, RIF2, and RAP2 exhibit their inhibitory effect by binding to telomeric DNA. In the Late S/G2 phase, the protein kinase CDK1 (cyclin-dependent) promotes telomeric resection. This control is exerted by cyclin-dependent kinases, which phosphorylate parts of the resection machinery. This process alleviates the inhibitory effect of the telomere-associated proteins, and allows Cdc13 (a binding protein on both the lagging strand, and leading strand) to cover telomeric DNA. The binding of cdc13 to DNA suppresses DNA damage checkpoint and allows resection to occur while allowing for telomerase elongation at the DSB ends.
== Resection of mitotic DSBs ==
One of the important regulatory controls in mitotic cells is deciding which specific DSB repair pathway to take. Once a DSB is detected, the highly conserved complexes are recruited by the DNA ends. If the cell is in the G1 phase of the cell cycle, the complex Ku prevents resection to occur and triggers the NHEJ pathway factors. DSBs in the NHEJ pathway are ligated, a step in the NHEJ pathway that requires DNA ligase activity of Dnl4-Lif1/XRCC4 heterodimer and the Nej1/XLF protein. This process results in error-prone religation of DSB ends at the G1 phase of the cell cycle.
If the cells are in S/G2 phase, mitotic DSBs are controlled through Cdk1 activity and involves phosphorylation of Sae2 Ser267. After phosphorylation occurs by Cdk1, MRX complex binds to dsDNA ends and generates short ssDNA that stretches in the 5' direction. The 5' ssDNA continues resection by the activity of the helicase enzyme, Sgs1 enzyme, and the nucleases Exo1 and Dna2. Involvement of Sae2 Sar267 in DSB processing is highly conserved throughout eukaryotes, such that the Sae2 along with the MRX complex are involved in two major functions: single-strand annealing, and processing of hairpin DNA structures. Like all ssDNA in the nucleus, the resected region is first coated by Replication protein A (RPA) complex, but RPA is then replaced with RAD51 to form a nucleoprotein filament which can take part in the search for a matching region, allowing HR to take place. The 3' ssDNA coated by a RPA promotes the recruitment of Mec1. Mec1 further phosphorylates Sae2 along with cdk1. The resulting phosphorylation by Sae2 by Mec1 helps increase the effect of resection and this in turn leads to the DNA damage checkpoint activation.
== Regulators ==
The pathway of choice in DNA repair is highly regulated to guarantee that cells in the S/G2 and G1 phase use the appropriate mechanism. Regulators in both the NHEJ and HR pathway mediate the appropriate DNA repair response pathway. Furthermore, recent studies into DNA repair show that regulation of DNA end resection is governed by the activity of cdk1 in the cell replication cycle.
=== NHEJ pathway ===
DNA end resection is key in determining the correct pathway in NHEJ. For NHEJ pathway to occur, positive regulators such as the Ku and MRX complex mediate recruitment of other NHEJ-associated proteins such as Tel1, Lif1, Dnl4, and Nej1. Since NHEJ does not rely on end resection, NHEJ could only happen in the G1 phase of the cell cycle. Both Ku and NHEJ-associated proteins prevent initiation of resection.
Resection ensures that DSBs are not repaired by NHEJ (which joins broken DNA ends together without ensuring that they match), but rather by methods based on homology (matching DNA sequences). Cyclin-dependent protein kinase such as cdk1 in yeast serves as a negative regulator of the NHEJ pathway. Any activity associated with the presence of cyclin dependent protein kinases inhibit the NHEJ pathway
=== Positive regulators ===
The presence of a ssDNA allows the broken end of the DNA to line up accurately with a matching sequence, so that it can be accurately repaired. For HR pathway to occur in the S and G2 phases of the cell cycle, availability of a sister chromatid is required. 5′–3′ resection automatically links a DSB to the HR pathway. Cyclin-dependent protein kinase such as cdk1 serve as a positive regulator of the HR pathway. This positive regulator promotes 5′–3′ nucleolytic degradation of DNA ends. Along with cdk1, the MRX complex, B1 cyclin, and Spo11-induced DSBs serve as a positive regulators to the HR pathway.
== See also ==
Exonuclease
Double-strand breaks
Blunt ends
Non-homologous end joining
Nucleotide
Cell cycle
Telomere
NHEJ
Homologous Recombination
Microhomology-mediated end joining
== References == | Wikipedia/DNA_end_resection |
Protein O-GlcNAc transferase also known as OGT or O-linked N-acetylglucosaminyltransferase is an enzyme (EC 2.4.1.255) that in humans is encoded by the OGT gene. OGT catalyzes the addition of the O-GlcNAc post-translational modification to proteins.
== Nomenclature ==
Other names include:
O-GlcNAc transferase
OGTase
O-linked N-acetylglucosaminyltransferase
Uridine diphospho-N-acetylglucosamine:polypeptide β-N-acetylglucosaminyltransferase
Systematic name: UDP-N-α-acetyl-d-glucosamine:[protein]-3-O-N-acetyl-β-d-glucosaminyl transferase
== Function ==
=== Glycosyltransferase ===
OGT catalyzes the addition of a single N-acetylglucosamine through an O-glycosidic linkage to serine or threonine and an S-glycosidic linkage to cysteine residues of nucleocytoplasmic proteins. Since both phosphorylation and O-GlcNAcylation compete for similar serine or threonine residues, the two processes may compete for sites, or they may alter the substrate specificity of nearby sites by steric or electrostatic effects. Two transcript variants encoding cytoplasmic and mitochondrial isoforms have been found for this gene. OGT glycosylates many proteins including: Histone H2B, AKT1, PFKL, KMT2E/MLL5, MAPT/TAU, Host cell factor C1, and SIN3A.
O-GlcNAc transferase is a part of a host of biological functions within the human body. OGT is involved in the resistance of insulin in muscle cells and adipocytes by inhibiting the Threonine 308 phosphorylation of AKT1, increasing the rate of IRS1 phosphorylation (at serine 307 and serine 632/635), reducing insulin signaling, and glycosylating components of insulin signals. Additionally, O-GlcNAc transferase catalyzes intracellular glycosylation of serine and threonine residues with the addition of N-acetylglucosamine. Studies show that OGT alleles are vital for embryogenesis, and that OGT is necessary for intracellular glycosylation and embryonic stem cell vitality. O-GlcNAc transferase also catalyzes the posttranslational modification that modifies transcription factors and RNA polymerase II, however the specific function of this modification is mostly unknown.
=== Protease ===
OGT cleaves Host Cell Factor C1, at one or more of 6 repeating 26 amino acid sequences. The TPR domain of OGT binds to the carboxyl terminal portion of an HCF1 proteolytic repeat so that the cleavage region is in the glycosyltransferase active site above uridine-diphosphate-GlcNAc The large proportion of OGT complexed with HCF1 is necessary for HCF1 cleavage, and HCFC1 is required for OGT stabilization in the nucleus. HCF1 regulates OGT stability using a post-transcriptional mechanism, however the mechanism of the interaction with HCFC1 is still unknown.
== Structure ==
The human OGT gene has 1046 amino acid residues, and is a heterotrimer consisting of two 110 kDa subunits and one 78 kDa subunit. The 110 kDa subunit contains 13 tetratricopeptide repeats (TPRs); the 13th repeat is truncated. These subunits are dimerized by TPR repeats 6 and 7. OGT is highly expressed in the pancreas and also expressed in the heart, brain, skeletal muscle, and the placenta. There have been trace amounts found in the lung and the liver. The binding sites have been determined for the 110 kDa subunit. It has 3 binding sites at amino acid residues 849, 852, and 935. The probable active site is at residue 508.
The crystal structure of O-GlcNAc transferase has not been well studied, but the structure of a binary complex with UDP and a ternary complex with UDP and a peptide substrate has been researched. The OGT-UDP complex contains three domains in its catalytic region: the amino (N)-terminal domain, the carboxy (C)-terminal domain, and the intervening domain (Int-D). The catalytic region is linked to TPR repeats by a translational helix (H3), which loops from the C-cat domain to the N-cat domain along the upper surface of the catalytic region. The OGT-UDP-peptide complex has a larger space between the TPR domain and the catalytic region than the OGT-UDP complex. The CKII peptide, which contains three serine residues and a threonine residue, binds in this space. In 2021 a 5Å CryoEM analysis revealed the relationship between the catalytic domains and the intact TPR regions confirming the dimer arrangement first seen in the TPR alone X ray structure. This structure supports an ordered sequential bi-bi mechanism that matches the fact that “at saturating peptide concentrations, a competitive inhibition pattern was obtained for UDP with respect to UDP-GlcNAc.”
== Mechanism of catalysis ==
The molecular mechanism of O-linked N-acetylglucosamine transferase has not been extensively studied either, since there is not a confirmed crystal structure of the enzyme. A proposed mechanism by Lazarus et al. is supported by product inhibition patterns of UDP at saturating peptide conditions. This mechanism proceeds with starting materials Uridine diphosphate N-acetylglucosamine, and a peptide chain with a reactive serine or threonine hydroxyl group. The proposed reaction is an ordered sequential bi-bi mechanism.
The chemical reaction can be written as:
UDP-N-acetyl-D-glucosamine + [protein]-L-serine → UDP + [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-serine
UDP-N-acetyl-D-glucosamine + [protein]-L-threonine → UDP + [protein]-3-O-(N-acetyl-D-glucosaminyl)-L-threonine
First, the hydroxyl group of serine is deprotonated by histidine 498, a catalytic base in this proposed reaction. Lysine 842 is also present to stabilize the UDP moiety. The oxygen ion then attacks the sugar-phosphate bond between the glucosamine and UDP. This results in the splitting of UDP-N-acetylglucosamine into N-acetylglucosamine – peptide and UDP. Proton transfers take place at the phosphate and histidine 498. This mechanism is spurred by OGT gene containing O-linked N-acetylglucosamine transferase. Aside from proton transfers the reaction proceeds in one step, as shown in Figure 2. Figure 2 uses a lone serine residue as a representative of the peptide with a reactive hydroxyl group. Threonine could have also been used in the mechanism.
== Inhibitors ==
Many inhibitors of OGT enzymatic activity have been reported. OGT inhibition results in global downregulation of O-GlcNAc. Cells appear to upregulate OGT and downregulate OGA in response to OGT inhibition.
=== 5S-GlcNAc ===
Ac45S-GlcNAc is converted intracellularly into UDP-5S-GlcNAc, a substrate analogue inhibitor of OGT. UDP-5S-GlcNAc is not efficiently utilized as a donor sugar by OGT, possibly due to distortion of the pyranose ring by replacement of oxygen with sulfur. As other glycosyltransferases utilize UDP-GlcNAc as a donor sugar, UDP-5S-GlcNAc has some non-specific effects on cell-surface glycosylation.
=== OSMI ===
OSMI-1 was first identified from high-throughput screening using fluorescence polarization. Further optimization led to the development of OSMI-2, OSMI-3, and OSMI-4, which bind OGT with low-nanomolar affinity. X-ray crystallography showed that the quinolinone-6-sulfonamide scaffold of OSMI compounds act as a uridine mimetic. OSMI-2, OSMI-3, and OSMI-4 have negatively charged carboxylate groups; esterification renders these inhibitors cell-permeable.
== Regulation ==
O-GlcNAc transferase is part of a dynamic competition for a serine or threonine hydroxyl functional group in a peptide unit. Figure 3 shows an example of both reciprocal same-site occupancy and adjacent-site occupancy. For the same-site occupancy, OGT competes with kinase to catalyze the glycosylation of the protein instead of phosphorylation. The adjacent-site occupancy example shows the naked protein catalyzed by OGT converted to a glycoprotein, which can increase the turnover of proteins such as the tumor repressor p53.
The post-translational modification of proteins by O-GlcNAc is spurred by glucose flux through the hexosamine biosynthetic pathway. OGT catalyzes attachment of the O-GlcNAc group to serine and threonine, while O-GlcNAcase spurs sugar removal.
This regulation is important for multiple cellular processes including transcription, signal transduction, and proteasomal degradation. Also, there is competitive regulation between OGT and kinase for the protein to attach to a phosphate group or O-GlcNAc, which can alter the function of proteins in the body through downstream effects.
OGT inhibits the activity of 6-phosophofructosekinase PFKL by mediating the glycosylation process. This then acts as a part of glycolysis regulation. O-GlcNAc has been defined as a negative transcription regulator in response to steroid hormone signaling.
Studies show that O-GlcNAc transferase interacts directly with the Ten eleven translocation 2 (TET2) enzyme, which converts 5-methylcytosine to 5-hydroxymethylcytosine and regulates gene transcription. Additionally, increasing levels of OGT for O-GlcNAcylation may have therapeutic effects for Alzheimer's disease patients. Brain glucose metabolism is impaired in Alzheimer's disease, and a study suggests that this leads to hyperphosphorylation of tau and degerenation of tau O-GlcNCAcylation. Replenishing tau O-GlcNacylation in the brain along with protein phosphatase could deter this process and improve brain glucose metabolism.
== See also ==
O-GlcNAc
O-GlcNAcase (OGA)
O-linked glycosylation
== References ==
== External links ==
The O-GlcNAc Database - A curated database for protein O-GlcNAcylation and referencing more than 14 000 protein entries and 10 000 O-GlcNAc sites.
Protein+O-GlcNAc+transferase at the U.S. National Library of Medicine Medical Subject Headings (MeSH) | Wikipedia/Protein_O-GlcNAc_transferase |
Indirect DNA damage occurs when a UV-photon is absorbed in the human skin by a chromophore that does not have the ability to convert the energy into harmless heat very quickly. Molecules that do not have this ability have a long-lived excited state. This long lifetime leads to a high probability for reactions with other molecules—so-called bimolecular reactions. Melanin and DNA have extremely short excited state lifetimes in the range of a few femtoseconds (10−15s). The excited state lifetime of compounds used in sunscreens such as menthyl anthranilate, avobenzone or padimate O is 1,000 to 1,000,000 times longer than that of melanin, and therefore they may cause damage to living cells that come in contact with them.
The molecule that originally absorbs the UV-photon is called a "chromophore". Bimolecular reactions can occur either between the excited chromophore and DNA or between the excited chromophore and another species, to produce free radicals and reactive oxygen species. These reactive chemical species can reach DNA by diffusion and the bimolecular reaction damages the DNA (oxidative stress). Unlike direct DNA damage which causes sunburn, indirect DNA damage does not result in any warning signal or pain in the human body.
The bimolecular reactions that cause the indirect DNA damage are illustrated in the figure:
(
C
h
r
o
m
o
p
h
o
r
e
)
∗
+
3
O
2
→
C
h
r
o
m
o
p
h
o
r
e
+
1
O
2
{\displaystyle \mathrm {(Chromophore)^{*}+{}^{3}O_{2}\ {\xrightarrow {}}\ Chromophore+{}^{1}O_{2}} }
1O2 is reactive harmful singlet oxygen:
1
O
2
+
i
n
t
a
c
t
D
N
A
→
3
O
2
+
d
a
m
a
g
e
d
D
N
A
{\displaystyle \mathrm {{}^{1}O_{2}+intact\ DNA\ {\xrightarrow {}}\ {}^{3}O_{2}+damaged\ DNA} }
== Location of the damage ==
Unlike direct DNA damage, which occurs in areas directly exposed to UV-B light, reactive chemical species can travel through the body and affect other areas—possibly even inner organs. The traveling nature of the indirect DNA damage can be seen in the fact that the malignant melanoma can occur in places that are not directly illuminated by the sun—in contrast to basal-cell carcinoma and squamous cell carcinoma, which appear only on directly illuminated locations on the body.
== See also ==
Free radical damage to DNA
Photoprotection
Sunscreen
== References == | Wikipedia/Indirect_DNA_damage |
DNA glycosylases are a family of enzymes involved in base excision repair, classified under EC number EC 3.2.2. Base excision repair is the mechanism by which damaged bases in DNA are removed and replaced. DNA glycosylases catalyze the first step of this process. They remove the damaged nitrogenous base while leaving the sugar-phosphate backbone intact, creating an apurinic/apyrimidinic site, commonly referred to as an AP site. This is accomplished by flipping the damaged base out of the double helix followed by cleavage of the N-glycosidic bond.
Glycosylases were first discovered in bacteria, and have since been found in all kingdoms of life. In addition to their role in base excision repair, DNA glycosylase enzymes have been implicated in the repression of gene silencing in A. thaliana, N. tabacum and other plants by active demethylation. 5-methylcytosine residues are excised and replaced with unmethylated cytosines allowing access to the chromatin structure of the enzymes and proteins necessary for transcription and subsequent translation.
== Monofunctional vs. bifunctional glycosylases ==
There are two main classes of glycosylases: monofunctional and bifunctional. Monofunctional glycosylases have only glycosylase activity, whereas bifunctional glycosylases also possess AP lyase activity that permits them to cut the phosphodiester bond of DNA, creating a single-strand break without the need for an AP endonuclease. β-Elimination of an AP site by a glycosylase-lyase yields a 3' α,β-unsaturated aldehyde adjacent to a 5' phosphate, which differs from the AP endonuclease cleavage product. Some glycosylase-lyases can further perform δ-elimination, which converts the 3' aldehyde to a 3' phosphate.
== Biochemical mechanism ==
The first crystal structure of a DNA glycosylase was obtained for E. coli Nth. This structure revealed that the enzyme flips the damaged base out of the double helix into an active site pocket in order to excise it. Other glycosylases have since been found to follow the same general paradigm, including human UNG pictured below. To cleave the N-glycosidic bond, monofunctional glycosylases use an activated water molecule to attack carbon 1 of the substrate. Bifunctional glycosylases, instead, use an amine residue as a nucleophile to attack the same carbon, going through a Schiff base intermediate.
== Types of glycosylases ==
Crystal structures of many glycosylases have been solved. Based on structural similarity, glycosylases are grouped into four superfamilies. The UDG and AAG families contain small, compact glycosylases, whereas the MutM/Fpg and HhH-GPD families comprise larger enzymes with multiple domains.
A wide variety of glycosylases have evolved to recognize different damaged bases. The table below summarizes the properties of known glycosylases in commonly studied model organisms.
DNA glycosylases can be grouped into the following categories based on their substrate(s):
=== Uracil DNA glycosylases ===
In molecular biology, the protein family, Uracil-DNA glycosylase (UDG) is an enzyme that reverts mutations in DNA. The most common mutation is the deamination of cytosine to uracil. UDG repairs these mutations. UDG is crucial in DNA repair, without it these mutations may lead to cancer.
This entry represents various uracil-DNA glycosylases and related DNA glycosylases (EC), such as uracil-DNA glycosylase, thermophilic uracil-DNA glycosylase, G:T/U mismatch-specific DNA glycosylase (Mug), and single-strand selective monofunctional uracil-DNA glycosylase (SMUG1).
Uracil DNA glycosylases remove uracil from DNA, which can arise either by spontaneous deamination of cytosine or by the misincorporation of dU opposite dA during DNA replication. The prototypical member of this family is E. coli UDG, which was among the first glycosylases discovered. Four different uracil-DNA glycosylase activities have been identified in mammalian cells, including UNG, SMUG1, TDG, and MBD4. They vary in substrate specificity and subcellular localization. SMUG1 prefers single-stranded DNA as substrate, but also removes U from double-stranded DNA. In addition to unmodified uracil, SMUG1 can excise 5-hydroxyuracil, 5-hydroxymethyluracil and 5-formyluracil bearing an oxidized group at ring C5. TDG and MBD4 are strictly specific for double-stranded DNA. TDG can remove thymine glycol when present opposite guanine, as well as derivatives of U with modifications at carbon 5. Current evidence suggests that, in human cells, TDG and SMUG1 are the major enzymes responsible for the repair of the U:G mispairs caused by spontaneous cytosine deamination, whereas uracil arising in DNA through dU misincorporation is mainly dealt with by UNG. MBD4 is thought to correct T:G mismatches that arise from deamination of 5-methylcytosine to thymine in CpG sites. MBD4 mutant mice develop normally and do not show increased cancer susceptibility or reduced survival. But they acquire more C T mutations at CpG sequences in epithelial cells of the small intestine.
The structure of human UNG in complex with DNA revealed that, like other glycosylases, it flips the target nucleotide out of the double helix and into the active site pocket. UDG undergoes a conformational change from an ‘‘open’’ unbound state to a ‘‘closed’’ DNA-bound state.
== History ==
Lindahl was the first to observe repair of uracil in DNA. UDG was purified from Escherichia coli, and this hydrolysed the N-glycosidic bond connecting the base to the deoxyribose sugar of the DNA backbone.
== Function ==
The function of UDG is to remove mutations in DNA, more specifically removing uracil.
== Structure ==
These proteins have a 3-layer alpha/beta/alpha structure.
The polypeptide topology of UDG is that of a classic alpha/beta protein. The structure consists primarily of a central, four-stranded, all parallel beta sheet surrounded on either side by a total of eight alpha helices and is termed a parallel doubly wound beta sheet.
== Mechanism ==
Uracil-DNA glycosylases are DNA repair enzymes that excise uracil residues from DNA by cleaving the N-glycosydic bond, initiating the base excision repair pathway. Uracil in DNA can arise either through the deamination of cytosine to form mutagenic U:G mispairs, or through the incorporation of dUMP by DNA polymerase to form U:A pairs. These aberrant uracil residues are genotoxic.
== Localisation ==
In eukaryotic cells, UNG activity is found in both the nucleus and the mitochondria. Human UNG1 protein is transported to both the mitochondria and the nucleus.
== Conservation ==
The sequence of uracil-DNA glycosylase is extremely well conserved in bacteria and eukaryotes as well as in herpes viruses. More distantly related uracil-DNA glycosylases are also found in poxviruses.
The N-terminal 77 amino acids of UNG1 seem to be required for mitochondrial localization, but the presence of a mitochondrial transit peptide has not been directly demonstrated. The most N-terminal conserved region contains an aspartic acid residue which has been proposed, based on X-ray structures to act as a general base in the catalytic mechanism.
== Family ==
There are two UDG families, named Family 1 and Family 2. Family 1 is active
against uracil in ssDNA and dsDNA. Family 2 excise uracil from mismatches with guanine.
=== Glycosylases of oxidized bases ===
A variety of glycosylases have evolved to recognize oxidized bases, which are commonly formed by reactive oxygen species generated during cellular metabolism. The most abundant lesions formed at guanine residues are 2,6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG) and 8-oxoguanine. Due to mispairing with adenine during replication, 8-oxoG is highly mutagenic, resulting in G to T transversions. Repair of this lesion is initiated by the bifunctional DNA glycosylase OGG1, which recognizes 8-oxoG paired with C.
hOGG1 is a bifunctional glycosylase that belongs to the helix-hairpin-helix (HhH) family. MYH recognizes adenine mispaired with 8-oxoG but excises the A, leaving the 8-oxoG intact. OGG1 knockout mice do not show an increased tumor incidence, but accumulate 8-oxoG in the liver as they age. A similar phenotype is observed with the inactivation of MYH, but simultaneous inactivation of both MYH and OGG1 causes 8-oxoG accumulation in multiple tissues including lung and small intestine. In humans, mutations in MYH are associated with increased risk of developing colon polyps and colon cancer. In addition to OGG1 and MYH, human cells contain three additional DNA glycosylases, NEIL1, NEIL2, and NEIL3. These are homologous to bacterial Nei, and their presence likely explains the mild phenotypes of the OGG1 and MYH knockout mice.
=== Glycosylases of alkylated bases ===
This group includes E. coli AlkA and related proteins in higher eukaryotes. These glycosylases are monofunctional and recognize methylated bases, such as 3-methyladenine.
==== AlkA ====
AlkA refers to 3-methyladenine DNA glycosylase II.
== Pathology ==
DNA glycosylases involved in base excision repair (BER) may be associated with cancer risk in BRCA1 and BRCA2 mutation carriers.
== Epigenetic deficiencies in cancers ==
Epigenetic alterations (epimutations) in DNA glycosylase genes have only recently begun to be evaluated in a few cancers, compared to the numerous previous studies of epimutations in genes acting in other DNA repair pathways (such as MLH1 in mismatch repair and MGMT in direct reversal). Two examples of epimutations in DNA glycosylase genes that occur in cancers are summarized below.
=== MBD4 ===
MBD4 (methyl-CpG-binding domain protein 4) is a glycosylase employed in an initial step of base excision repair. MBD4 protein binds preferentially to fully methylated CpG sites. These altered bases arise from the frequent hydrolysis of cytosine to uracil (see image) and hydrolysis of 5-methylcytosine to thymine, producing G:U and G:T base pairs. If the improper uracils or thymines in these base pairs are not removed before DNA replication, they will cause transition mutations. MBD4 specifically catalyzes the removal of T and U paired with guanine (G) within CpG sites. This is an important repair function since about 1/3 of all intragenic single base pair mutations in human cancers occur in CpG dinucleotides and are the result of G:C to A:T transitions. These transitions comprise the most frequent mutations in human cancer. For example, nearly 50% of somatic mutations of the tumor suppressor gene p53 in colorectal cancer are G:C to A:T transitions within CpG sites. Thus, a decrease in expression of MBD4 could cause an increase in carcinogenic mutations.
MBD4 expression is reduced in almost all colorectal neoplasms due to methylation of the promoter region of MBD4. Also MBD4 is deficient due to mutation in about 4% of colorectal cancers,
A majority of histologically normal fields surrounding neoplastic growths (adenomas and colon cancers) in the colon also show reduced MBD4 mRNA expression (a field defect) compared to histologically normal tissue from individuals who never had a colonic neoplasm. This finding suggests that epigenetic silencing of MBD4 is an early step in colorectal carcinogenesis.
In a Chinese population that was evaluated, the MBD4 Glu346Lys polymorphism was associated with about a 50% reduced risk of cervical cancer, suggesting that alterations in MBD4 is important in this cancer.
=== NEIL1 ===
Nei-like (NEIL) 1 is a DNA glycosylase of the Nei family (which also contains NEIL2 and NEIL3). NEIL1 is a component of the DNA replication complex needed for surveillance of oxidized bases before replication, and appears to act as a “cowcatcher” to slow replication until NEIL1 can act as a glycosylase and remove the oxidatively damaged base.
NEIL1 protein recognizes (targets) and removes certain oxidatively-damaged bases and then incises the abasic site via β,δ elimination, leaving 3′ and 5′ phosphate ends. NEIL1 recognizes oxidized pyrimidines, formamidopyrimidines, thymine residues oxidized at the methyl group, and both stereoisomers of thymine glycol. The best substrates for human NEIL1 appear to be the hydantoin lesions, guanidinohydantoin, and spiroiminodihydantoin that are further oxidation products of 8-oxoG. NEIL1 is also capable of removing lesions from single-stranded DNA as well as from bubble and forked DNA structures. A deficiency in NEIL1 causes increased mutagenesis at the site of an 8-oxo-Gua:C pair, with most mutations being G:C to T:A transversions.
A study in 2004 found that 46% of primary gastric cancers had reduced expression of NEIL1 mRNA, though the mechanism of reduction was not known. This study also found that 4% of gastric cancers had mutations in the NEIL1 gene. The authors suggested that low NEIL1 activity arising from reduced expression and/or mutation of the NEIL1 gene was often involved in gastric carcinogenesis.
A screen of 145 DNA repair genes for aberrant promoter methylation was performed on head and neck squamous cell carcinoma (HNSCC) tissues from 20 patients and from head and neck mucosa samples from 5 non-cancer patients. This screen showed that the NEIL1 gene had substantially increased hypermethylation, and of the 145 DNA repair genes evaluated, NEIL1 had the most significantly different frequency of methylation. Furthermore, the hypermethylation corresponded to a decrease in NEIL1 mRNA expression. Further work with 135 tumor and 38 normal tissues also showed that 71% of HNSCC tissue samples had elevated NEIL1 promoter methylation.
When 8 DNA repair genes were evaluated in non-small cell lung cancer (NSCLC) tumors, 42% were hypermethylated in the NEIL1 promoter region. This was the most frequent DNA repair abnormality found among the 8 DNA repair genes tested. NEIL1 was also one of six DNA repair genes found to be hypermethylated in their promoter regions in colorectal cancer.
== References ==
== External links ==
Media related to DNA-glycosylase at Wikimedia Commons
DNA+Glycosylases at the U.S. National Library of Medicine Medical Subject Headings (MeSH) | Wikipedia/DNA_glycosylase |
Bloom syndrome protein is a protein that in humans is encoded by the BLM gene and is not expressed in Bloom syndrome.
The Bloom syndrome gene product is related to the RecQ subset of DExH box-containing DNA helicases and has both DNA-stimulated ATPase and ATP-dependent DNA helicase activities. Mutations causing Bloom syndrome delete or alter helicase motifs and may disable the 3' → 5' helicase activity. The normal protein may act to suppress inappropriate homologous recombination.
== Meiosis ==
Recombination during meiosis is often initiated by a DNA double-strand break (DSB). During recombination, sections of DNA at the 5' ends of the break are cut away in a process called resection. In the strand invasion step that follows, an overhanging 3' end of the broken DNA molecule then "invades" the DNA of an homologous chromosome that is not broken. After strand invasion, the further sequence of events may follow either of two main pathways leading to a crossover (CO) or a non-crossover (NCO) recombinant (see Genetic recombination and bottom of Figure in this section).
The budding yeast Saccharomyces cerevisiae encodes an ortholog of the Bloom syndrome (BLM) protein that is designated Sgs1 (Small growth suppressor 1). Sgs1(BLM) is a helicase that functions in homologous recombinational repair of DSBs. The Sgs1(BLM) helicase appears to be a central regulator of most of the recombination events that occur during S. cerevisiae meiosis. During normal meiosis Sgs1(BLM) is responsible for directing recombination towards the alternate formation of either early NCOs or Holliday junction joint molecules, the latter being subsequently resolved as COs.
In the plant Arabidopsis thaliana, homologs of the Sgs1(BLM) helicase act as major barriers to meiotic CO formation. These helicases are thought to displace the invading strand allowing its annealing with the other 3’overhang end of the DSB, leading to NCO recombinant formation by a process called synthesis dependent strand annealing (SDSA) (see Genetic recombination and Figure in this section). It is estimated that only about 4% of DSBs are repaired by CO recombination. Sequela-Arnaud et al. suggested that CO numbers are restricted because of the long-term costs of CO recombination, that is, the breaking up of favorable genetic combinations of alleles built up by past natural selection.
== DNA repair and apoptosis ==
Bloom syndrome protein facilitates DNA repair when cells are stressed by agents that cause DNA damage, specifically when DNA replication forks are stalled. Damage present during S phase of the cell cycle causes Bloom syndrome protein to rapidly form foci with gamma H2AFX protein at replication forks that develop DNA breaks. These BLM foci then recruit repair complexes composed of BRCA1 and NBS1 proteins to the stalled replication forks. In addition to its role in repairing DNA damages, Bloom syndrome protein facilitates apoptosis (programmed cell death), a process dependent on p53 protein when cells are stressed by agents that cause unrepairable DNA damage, particularly damage that causes stalled DNA replication forks.
Both DNA repair and apoptosis are enzymatic processes necessary for maintaining genome integrity in humans. Cells that are deficient in DNA repair tend to accumulate DNA damages, and when such cells are also defective in apoptosis they tend to survive even though excessive DNA damage is present. Replication of DNA in such cells tends to lead to mutations and such mutations may cause cancer. Thus Bloom syndrome protein appears to have two roles related to the prevention of cancer, where the first role is to promote repair of a specific class of damages and the second role is to induce apoptosis if the level of such DNA damage is beyond the cell's repair capability
== Interactions ==
Bloom syndrome protein has been shown to interact with:
== References ==
== Further reading ==
== External links ==
Human BLM genome location and BLM gene details page in the UCSC Genome Browser.
Overview of all the structural information available in the PDB for UniProt: P54132 (Bloom syndrome protein) at the PDBe-KB. | Wikipedia/Bloom_syndrome_protein |
Uracil-DNA glycosylase (also known as UNG or UDG) is an enzyme. Its most important function is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosidic bond and initiating the base-excision repair (BER) pathway.
== Function ==
The human gene encodes one of several uracil-DNA glycosylases. Alternative promoter usage and splicing of this gene leads to two different isoforms: the mitochondrial UNG1 and the nuclear UNG2. One important function of uracil-DNA glycosylases is to prevent mutagenesis by eliminating uracil from DNA molecules by cleaving the N-glycosidic bond and initiating the base-excision repair (BER) pathway. Uracil bases occur from cytosine deamination or misincorporation of dUMP residues. After a mutation occurs, the mutagenic threat of uracil propagates through any subsequent DNA replication steps. Once unzipped, mismatched guanine and uracil pairs are separated, and DNA polymerase inserts complementary bases to form a guanine-cytosine (GC) pair in one daughter strand and an adenine-uracil (AU) pair in the other. Half of all progeny DNA derived from the mutated template inherit a shift from GC to AU at the mutation site. UDG excises uracil in both AU and GU pairs to prevent propagation of the base mismatch to downstream transcription and translation processes. With high efficiency and specificity, this glycosylase repairs 100–500 bases damaged daily in the human cell. Human cells express five to six types of DNA glycosylases, all of which share a common mechanism of base eversion and excision as a means of DNA repair.
== Structure ==
UDG is made of a four-stranded parallel β-sheet surrounded by eight α-helices. The active site comprises five highly conserved motifs that collectively catalyze glycosidic bond cleavage:
Water-activating loop: 63-QDPYH-67
Pro-rich loop: 165-PPPPS-169
Uracil-binding motif: 199-GVLLLN-204
Gly-Ser loop: 246-GS-247
Minor groove intercalation loop: 268-HPSPLS-273
== Mechanism ==
Glycosidic bond cleavage follows a “pinch-push-pull” mechanism using the five
conserved motifs.
Pinch:
UDG scans DNA for uracil by nonspecifically binding to the strand and creating a
kink in the backbone, thereby positioning the selected base for detection. The Pro-rich and Gly-Ser loops form polar contacts with the 3’ and 5’ phosphates flanking the examined base. This compression of the DNA backbone, or “pinch,” allows for close contact between UDG and base of interest.
Push:
To fully assess the nucleotide identity, the intercalation loop penetrates, or pushes into, the DNA minor groove and induces a conformational change to flip the nucleotide out of the helix. Backbone compression favors eversion of the now extrahelical nucleotide, which is positioned for recognition by the uracil-binding motif. The coupling of intercalation and eversion helps compensate for the disruption of favorable base stacking interactions within the DNA helix. Leu272 fills the void left by the flipped nucleotide to create dispersion interactions with neighboring bases and restore stacking stability.
Pull:
Now accessible to the active site, the nucleotide interacts with the uracil binding motif. The active site shape complements the everted uracil structure, allowing for high substrate specificity. Purines are too large to fit in the active site, while unfavorable interactions with other pyrimidines discourage binding alternative substrates. The side chain of Tyr147 interferes sterically with the thymine C5 methyl group, while a specific hydrogen bond between the uracil O2 carbonyl and Gln144 discriminates against a cytosine substrate, which lacks the necessary carbonyl. Once uracil is recognized, cleavage of the glycosidic bond proceeds according to the mechanism below.
The position of the residues that activate the water nucleophile and protonate the uracil leaving group are widely debated, though the most commonly followed mechanism employs the water activating loop detailed in the enzyme structure. Regardless of position, the identities of the aspartic acid and histidine residues are consistent across catalytic studies.
== Laboratory use ==
Uracil N-glycosylase (UNG) is utilized to eliminate carryover polymerase chain reaction (PCR) products in PCR. This method modifies PCR products such that in a new reaction, any residual products from previous PCR amplifications will be digested and prevented from amplifying, but the true DNA templates will be unaffected. PCR synthesizes abundant amplification products each round, but contamination of further rounds of PCR with trace amounts of these products, called carry-over contamination, yields false positive results. Carry-over contamination from some previous PCR can be a significant problem, due both to the abundance of PCR products, and to the ideal structure of the contaminant material for re-amplification. However carry-over contamination can be controlled by the following two steps: (i) incorporating dUTP in all PCR products (by substituting dUTP for dTTP, or by incorporating uracil during synthesis of primers; and (ii) treating all subsequent fully preassembled starting reactions with uracil DNA glycosylase (UDG), followed by thermal inactivation of UDG. UDG cleaves the uracil base from the phosphodiester backbone of uracil-containing DNA, but has no effect on natural (i.e., thymine-containing) DNA. The resulting apyrimidinic sites block replication by DNA polymerases, and are very labile to acid/base hydrolysis. Because UDG does not react with dTTP, and is also inactivated by heat denaturation prior to the actual PCR, carry-over contamination of PCRs can be controlled effectively if the contaminants contain uracils in place of thymines.
Uracil N-glycosylase was also used in a study to detect evidence of ongoing low-level metabolic activity and DNA repair in ancient bacteria. Long-term survival of bacteria can occur either through endospore formation (in which the bacterium enters total dormancy, with no metabolic activity at all taking place, and, thus, no DNA repair), or else through reduction of metabolic activity to a very low rate, just sufficient to carry out ongoing DNA repair and prevent the depletion of other unstable molecules (such as ATP), in which the microbe is able to repair damage to its DNA but also continues to slowly consume nutrients. DNA sequences from bacteria in permafrost were amplified using PCR. One series of runs amplified the DNA sequences as-is (to detect all live bacterial DNA in the samples), while the other series looked specifically for DNA that had been undergoing ongoing repair; to do this, the DNA was treated with UNG to remove uracils. This prevented amplification of unrepaired DNA in two ways: firstly, the abasic sites generated by the removal of uracils prevented the DNA polymerase used in PCR from proceeding past the site of damage, while these abasic sites also directly weakened the DNA and made it more likely to fragment upon heating. In this way, the researchers were able to show evidence of ongoing DNA repair in high-GC Gram-positive bacteria up to 600,000 years old.
Uracil N glycosylase has also been used in a method for cloning of PCR amplified DNA fragments. In this method the primers used in PCR are synthesized with uracil residues instead of thymine. When these primers are incorporated into PCR amplified fragments the primer sequence becomes susceptible to digestion with Uracil N Glycosylase and produce 3' protruding ends that can be annealed to an appropriately prepared vector DNA. The resulting chimeric molecules can be transformed into competent cells with high efficiency, without the need for in vitro ligation.
== Interactions ==
Uracil-DNA glycosylase has been shown to interact with RPA2.
== See also ==
Double-stranded uracil-DNA glycosylase
DNA-deoxyinosine glycosylase
SMUG1
Thymine-DNA glycosylase
== References == | Wikipedia/Uracil-DNA_glycosylase |
Progeroid syndromes (PS) are a group of rare genetic disorders that mimic physiological aging, making affected individuals appear to be older than they are. The term progeroid syndrome does not necessarily imply progeria (Hutchinson–Gilford progeria syndrome), which is a specific type of progeroid syndrome.
Progeroid means "resembling premature aging", a definition that can apply to a broad range of diseases. Familial Alzheimer's disease and familial Parkinson's disease are two well-known accelerated-aging diseases that are more frequent in older individuals. They affect only one tissue and can be classified as unimodal progeroid syndromes. Segmental progeria, which is more frequently associated with the term progeroid syndrome, tends to affect multiple or all tissues while causing affected individuals to exhibit only some of the features associated with aging.
All disorders within this group are thought to be monogenic, meaning they arise from mutations of a single gene. Most known PS are due to genetic mutations that lead to either defects in the DNA repair mechanism or defects in lamin A/C.
Examples of PS include Werner syndrome (WS), Bloom syndrome (BS), Rothmund–Thomson syndrome (RTS), Cockayne syndrome (CS), xeroderma pigmentosum (XP), trichothiodystrophy (TTD), combined xeroderma pigmentosum-Cockayne syndrome (XP-CS), restrictive dermopathy (RD), and Hutchinson–Gilford progeria syndrome (HGPS). Individuals with these disorders tend to have a reduced lifespan. Progeroid syndromes have been widely studied in the fields of aging, regeneration, stem cells, and cancer. The most widely studied of the progeroid syndromes are Werner syndrome and Hutchinson–Gilford progeria, as they are seen to most resemble natural aging.
== Defects in DNA repair ==
One of the main causes of progeroid syndromes are genetic mutations, which lead to defects in the cellular processes which repair DNA. The DNA damage theory of aging proposes that aging is a consequence of the accumulation of naturally occurring DNA damages. The accumulated damage may arise from reactive oxygen species (ROS), chemical reactions (e.g. with intercalating agents), radiation, depurination, and deamination.
Mutations in three classes of DNA repair proteins, RecQ protein-like helicases (RECQLs), nucleotide excision repair (NER) proteins, and nuclear envelope proteins LMNA (lamins) have been associated with the following progeroid syndromes:
Werner syndrome (WS)
Bloom syndrome (BS)
Rothmund–Thomson syndrome (RTS)
Cockayne syndrome (CS)
Xeroderma pigmentosum (XP)
Trichothiodystrophy (TTD)
=== RecQ-associated PS ===
RecQ is a family of conserved ATP-dependent helicases required for repairing DNA and preventing deleterious recombination and genomic instability. DNA helicases are enzymes that bind to double-stranded DNA and temporarily separate them. This unwinding is required during replication of the genome under mitosis, but in the context of PS, it is a required step in repairing damaged DNA. Thus, DNA helicases, maintain the integrity of a cell, and defects in these helicases are linked to an increased predisposition to cancer and aging phenotypes. Thus, individuals with RecQ-associated PS show an increased risk of developing cancer, which is caused by genomic instability and increased rates of mutation.
There are five genes encoding RecQ in humans (RECQ1-5), and defects in RECQL2/WRN, RECQL3/BLM and RECQL4 lead to Werner syndrome (WS), Bloom syndrome (BS), and Rothmund–Thomson syndrome (RTS), respectively. On the cellular level, cells of affected individuals exhibit chromosomal abnormalities, genomic instability, and sensitivity to mutagens.
==== Werner syndrome ====
Werner syndrome (WS) is a rare autosomal recessive disorder. It has a global incidence rate of less than 1 in 100,000 live births, although incidences in Japan and Sardinia are higher, where it affects 1 in 20,000-40,000 and 1 in 50,000, respectively. As of 2006, there were approximately 1,300 reported cases of WS worldwide. Affected individuals typically grow and develop normally until puberty, when they do not experience the typical adolescent growth spurt. The mean age of diagnosis is twenty-four. The median and mean age of death are 47-48 and 54 years, respectively; the main cause of death is cardiovascular disease or cancer.
Affected individuals can exhibit growth retardation, short stature, premature graying of hair, hair loss, wrinkling, prematurely aged faces, beaked noses, skin atrophy (wasting away) with scleroderma-like lesions, loss of fat tissues, abnormal fat deposition leading to thin legs and arms, and severe ulcerations around the Achilles tendon and malleoli. Other signs include change in voice, making it weak, hoarse, or high-pitched; atrophy of gonads, leading to reduced fertility; bilateral cataracts (clouding of lens); premature arteriosclerosis (thickening and loss of elasticity of arteries); calcinosis (calcium deposits in blood vessels); atherosclerosis (blockage of blood vessels); type 2 diabetes; loss of bone mass; telangiectasia; and malignancies. In fact, the prevalence of rare cancers, such as meningiomas, are increased in individuals with Werner syndrome.
Approximately 90% of individuals with Werner Syndrome have any of a range of mutations in the eponymous gene, WRN, the only gene currently connected to Werner syndrome. WRN encodes the WRNp protein, a 1432 amino acid protein with a central domain resembling members of the RecQ helicases. WRNp is active in unwinding DNA, a step necessary in DNA repair and DNA replication. Since WRNp's function depends on DNA, it is only functional when localized to the nucleus.
Mutations that cause Werner syndrome only occur at the regions of the gene that encode for protein and not at non-coding regions. These mutations can have a range of effects. They may decrease the stability of the transcribed messenger RNA (mRNA), which increases the rate at which they are degraded. With fewer mRNA, fewer are available to be translated into the WRNp protein. Mutations may also lead to the truncation (shortening) of the WRNp protein, leading to the loss of its nuclear localization signal sequence, which would normally transport it to the nucleus where it can interact with the DNA. This leads to a reduction in DNA repair. Furthermore, mutated proteins are more likely to be degraded than normal WRNp. Apart from causing defects in DNA repair, its aberrant association with p53 down-regulates the function of p53, leading to a reduction in p53-dependent apoptosis and increase the survival of these dysfunctional cells.
Cells of affected individuals have reduced lifespan in culture, more chromosome breaks and translocations and extensive deletions. These DNA damages, chromosome aberrations and mutations may in turn cause more RecQ-independent aging phenotypes.
==== Bloom syndrome ====
Bloom syndrome (BS) is a very rare autosomal recessive disorder. Incidence rates are unknown, although it is known to be higher in people of Ashkenazi Jewish background, presenting in around 1 in 50,000. Approximately one-third of individuals who have BS are of Ashkenazi Jewish descent.
There is no evidence from the Bloom's Syndrome Registry or from the peer-reviewed medical literature that BS is a progeroid condition associated with advanced aging. It is, however, associated with early-onset cancer and adult-type diabetes and also with Werner syndrome, which is a progeroid syndrome, through mutation in the RecQ helicases. These associations have led to the speculation that BS could be associated with aging. Unfortunately, the average lifespan of persons with Bloom syndrome is 27 years; consequently, there is insufficient information to completely rule out the possibility that BS is associated with some features of aging.
People with BS start their life with a low weight and length when they are born. Even as adults, they typically remain under 5 feet tall. Individuals with BS are characterized by low weight and height and abnormal facial features, particularly a long, narrow face with a small lower jaw, a large nose and prominent ears. Most also develop photosensitivity, which causes the blood vessels to be dilated and leads to reddening of the skin, usually presented as a "butterfly-shaped patch of reddened skin across the nose and cheeks".
Other characteristics of BS include learning disabilities, an increased risk of diabetes, gastroesophageal reflux (GER), and chronic obstructive pulmonary disease (COPD). GER may also lead to recurrent infections of the upper respiratory tract, ears, and lungs during infancy. BS causes infertility in males and reduced fertility and early-onset menopause in females. In line with any RecQ-associated PS, people with BS have an increased risk of developing cancer, often more than one type.
BS is caused by mutations in the BLM gene, which encodes for the Bloom syndrome protein, a RecQ helicase. These mutations may be frameshift, missense, non-sense, or mutations of other kinds and are likely to cause deletions in the gene product. Apart from helicase activity that is common to all RecQ helices, it also acts to prevent inappropriate homologous recombination. During replication of the genome, the two copies of DNA, called sister chromatids, are held together through a structure called the centromere. During this time, the homologous (corresponding) copies are in close physical proximity to each other, allowing them to 'cross' and exchange genetic information, a process called homologous recombination. Defective homologous recombination can cause mutation and genetic instability. Such defective recombination can introduce gaps and breaks within the genome and disrupt the function of genes, possibly causing growth retardation, aging and elevated risk of cancer. It introduces gaps and breaks within the genome and disrupts the function of genes, often causing retardation of growth, aging and elevated risks of cancers. The Bloom syndrome protein interacts with other proteins, such as topoisomerase IIIα and RMI2, and suppresses illegitimate recombination events between sequences that are divergent from strict homology, thus maintaining genome stability. Individuals with BS have a loss-of-function mutation, which means that the illegitimate recombination is no longer suppressed, leading to higher rates of mutation (~10-100 times above normal, depending on cell type).
=== NER protein-associated PS ===
Nucleotide excision repair is a DNA repair mechanism. There are three excision repair pathways: nucleotide excision repair (NER), base excision repair (BER), and DNA mismatch repair (MMR). In NER, the damaged DNA strand is removed and the undamaged strand is kept as a template for the formation of a complementary sequence with DNA polymerase. DNA ligase joins the strands together to form dsDNA. There are two subpathways for NER, which differ only in their mechanism for recognition: global genomic NER (GG-NER) and transcription coupled NER (TC-NER).
Defects in the NER pathway have been linked to progeroid syndromes. There are 28 genes in this pathway. Individuals with defects in these genes often have developmental defects and exhibit neurodegeneration. They can also develop CS, XP, and TTD, often in combination with each other, as with combined xeroderma pigmentosa-Cockayne syndrome (XP-CS). Variants of these diseases, such as DeSanctis–Cacchione syndrome and Cerebro-oculo-facio-skeletal (COFS) syndrome, can also be caused by defects in the NER pathway. However, unlike RecQ-associated PS, not all individuals affected by these diseases have increased risk of cancer. All these disorders can be caused by mutations in a single gene, XPD, or in other genes.
==== Cockayne syndrome ====
Cockayne syndrome (CS) is a rare autosomal recessive PS. There are three types of CS, distinguished by severity and age of onset. It occurs at a rate of about 1 in 300,000-500,000 in the United States and Europe.
The mean age of death is ~12 years, although the different forms differ significantly. Individuals with the type I (or classical) form of the disorder usually first show symptoms between one and three years and have lifespans of between 20 and 40 years. Type II Cockayne syndrome (CSB) is more severe: symptoms present at birth and individuals live to approximately 6–7 years of age. Type III has the mildest symptoms, first presents later in childhood, and the cause of death is often severe nervous system deterioration and respiratory tract infections.
Individuals with CS appear prematurely aged and exhibit severe growth retardation leading to short stature. They have a small head (less than the -3 standard deviation), fail to gain weight and failure to thrive. They also have extreme cutaneous photosensitivity (sensitivity to sunlight), neurodevelopmental abnormalities, and deafness, and often exhibit lipoatrophy, atrophic skin, severe tooth decay, sparse hair, calcium deposits in neurons, cataracts, sensorineural hearing loss, pigmentary retinopathy, and bone abnormalities. However, they do not have a higher risk of cancer.
Type I and II are known to be caused by mutation of a specific gene. CSA is caused by mutations in the cross-complementing gene 8 (ERCC8), which encodes for the CSA protein. These mutations are thought to cause alternate splicing of the pre-mRNA which leads to an abnormal protein. CSB is caused by mutations in the ERCC6 gene, which encodes the CSB protein. CSA and CSB are involved in transcription-coupled NER (TC-NER), which is involved in repairing DNA; they ubiquitinate RNA polymerase II, halting its progress thus allowing the TC-NER mechanism to be carried out. The ubiquitinated RNAP II then dissociates and is degraded via the proteasome. Mutations in ERCC8, ERCC6, or both mean DNA is no longer repaired through TC-NER, and the accumulation of mutations leads to cell death, which may contribute to the symptoms of Cockayne syndrome.
==== Xeroderma pigmentosum ====
Xeroderma pigmentosum (XP) is a rare autosomal recessive disorder, affecting about one per million in the United States and autochthonic Europe populations but with a higher incidence rate in Japan, North Africa, and the Middle East. There have been 830 published cases from 1874 to 1982. The disorder presents at infancy or early childhood.
Xeroderma pigmentosum mostly affects the eye and skin. Individuals with XP have extreme sensitivity to light in the ultraviolet range starting from one to two years of age, and causes sunburn, freckling of skin, dry skin and pigmentation after exposure. When the eye is exposed to sunlight, it becomes irritated and bloodshot, and the cornea becomes cloudy. Around 30% of affected individuals also develop neurological abnormalities, including deafness, poor coordination, decreased intellectual abilities, difficulty swallowing and talking, and seizures; these effects tend to become progressively worse over time. All affected individuals have a 1000-fold higher risk of developing skin cancer: half of the affected population develop skin cancer by age 10, usually at areas most exposed to sunlight (e.g. face, head, or neck). The risk for other cancers such as brain tumors, lung cancer and eye cancers also increase.
There are eight types of XP (XP-A through XP-G), plus a variant type (XP-V), all categorized based on the genetic cause. XP can be caused by mutations in any of these genes: DDB2, ERCC2, ERCC3, ERCC4, ERCC5, XPA, XPC. These genes are all involved in the NER repair pathway that repairs damaged DNA. The variant form, XP-V, is caused by mutations in the POLH gene, which unlike the rest does not code for components of the NER pathway but produces a DNA polymerase that allows accurate translesion synthesis of DNA damage resulting from UV radiation; its mutation leads to an overall increase in UV-dependent mutation, which ultimately causes the symptoms of XP.
==== Trichothiodystrophy ====
Trichothiodystrophy (TTD) is a rare autosomal recessive disease whose symptoms span across multiple systems and can vary greatly in severity. The incidence rate of TTD is estimated to be 1.2 per million in Western Europe. Milder cases cause sparse and brittle hair, which is due to the lack of sulfur, an element that is part of the matrix proteins that give hair its strength. More severe cases cause delayed development, significant intellectual disability, and recurrent infection; the most severe cases see death at infancy or early childhood.
TTD also affects the mother of the affected child during pregnancy, when she may experience pregnancy-induced high blood pressure and develop HELLP syndrome. The baby has a high risk of being born prematurely and will have a low birth weight. After birth, the child's normal growth is retarded, resulting in a short stature.
Other symptoms include scaly skin, abnormalities of the fingernails and toenails, clouding of the lens of the eye from birth (congenital cataracts), poor co-ordination, and ocular and skeletal abnormalities. Half of affected individuals also experience photosensitivity to UV light.
TTD is caused by mutations in one of three genes, ERCC2, ERCC3, or GTF2H5, the first two of which are also linked to xeroderma pigmentosum. However, patients with TTD do not show a higher risk of developing skin cancer, in contrast to patients with XP. The three genes associated with TTD encode for XPB, XPD and p8/TTDA of the general transcription factor IIH (TFIIH) complex, which is involved in transcription and DNA damage repair. Mutations in one of these genes cause reduction of gene transcription, which may be involved in development (including placental development), and thus may explain retardation in intellectual abilities, in some cases; these mutations also lead to reduction in DNA repair, causing photosensitivity.
A form of TTD without photosensitivity also exists, although its mechanism is unclear. The MPLKIP gene has been associated with this form of TTD, although it accounts for only 20% of all known cases of the non-photosensitive form of TTD, and the function of its gene product is also unclear. Mutations in the TTDN1 gene explain another 10% of non-photosensitive TTD. The function of the gene product of TTDN1 is unknown, but the sex organs of individuals with this form of TTD often produce no hormones, a condition known as hypogonadism.
== Defects in Lamin A/C ==
Hutchinson–Gilford progeria syndrome (HGPS) and restrictive dermopathy (RD) are two PS caused by a defect in lamin A/C, which is encoded by the LMNA gene. Lamin A is a major nuclear component that determines the shape and integrity of the nucleus, by acting as a scaffold protein that forms a filamentous meshwork underlying the inner nuclear envelope, the membrane that surrounds the nucleus.
=== Hutchinson–Gilford progeria syndrome ===
Hutchinson–Gilford progeria syndrome is an extremely rare developmental autosomal dominant condition, characterized by premature and accelerated aging (~7 times the normal rate) beginning at childhood. It affects 1 in ~4 million newborns; over 130 cases have been reported in the literature since the first described case in 1886. The mean age of diagnosis is ~3 years and the mean age of death is ~13 years. The cause of death is usually myocardial infarction, caused by the severe hardening of the arteries (arteriosclerosis). There is currently no treatment available.
Individuals with HGPS typically appear normal at birth, but their growth is severely retarded, resulting in short stature, a very low body weight and delayed tooth eruption. Their facial/cranial proportions and facial features are abnormal, characterized by larger-than-normal eyes, a thin, beaked nose, thin lips, small chin and jaw (micrognathia), protruding ears, scalp hair, eyebrows, and lashes, hair loss, large head, large fontanelle and generally appearing aged. Other features include skeletal alterations (osteolysis, osteoporosis), amyotrophy (wasting of muscle), lipodystrophy and skin atrophy (loss of subcutaneous tissue and fat) with sclerodermatous focal lesions, severe atherosclerosis and prominent scalp veins. However, the level of cognitive function, motor skills, and risk of developing cancer is not affected significantly.
HGPS is caused by sporadic mutations (not inherited from parent) in the LMNA gene, which encodes for lamin A. Specifically, most HGPS are caused by a dominant, de novo, point mutation p.G608G (GGC > GGT). This mutation causes a splice site within exon 11 of the pre-mRNA to come into action, leading to the last 150 base pairs of that exon, and consequently, the 50 amino acids near the C-terminus, being deleted. This results in a truncated lamin A precursor (a.k.a. progerin or LaminAΔ50).
After being translated, a farnesol is added to prelamin A using protein farnesyltransferase; this farnesylation is important in targeting lamin to the nuclear envelope, where it maintains its integrity. Normally, lamin A is recognized by ZMPSTE24 (FACE1, a metalloprotease) and cleaved, removing the farnesol and a few other amino acids.
In the truncated lamin A precursor, this cleavage is not possible and the prelamin A cannot mature. When the truncated prelamin A is localized to the nuclear envelope, it will not be processed and accumulates, leading to "lobulation of the nuclear envelope, thickening of the nuclear lamina, loss of peripheral heterochromatin, and clustering of nuclear pores", causing the nucleus to lose its shape and integrity. The prelamin A also maintains the farnesyl and a methyl moiety on its C-terminal cysteine residue, ensuring their continued localization at the membrane. When this farnesylation is prevented using farnesyltransferase inhibitor (FTI), the abnormalities in nuclear shape are significantly reduced.
HGPS is considered autosomal dominant, which means that only one of the two copies of the LMNA gene needs to be mutated to produce this phenotype. As the phenotype is caused by an accumulation of the truncated prelamin A, only mutation in one of the two genes is sufficient. At least 16 Other mutations in lamin A/C, or defects in the ZMPSTE24 gene, have been shown to cause HGPS and other progeria-like symptoms, although these are less studied.
Repair of DNA double-strand breaks can occur by one of two processes, non-homologous end joining (NHEJ) or homologous recombination (HR). A-type lamins promote genetic stability by maintaining levels of proteins which have key roles in NHEJ and HR. Mouse cells deficient for maturation of prelamin A show increased DNA damage and chromosome aberrations and have increased sensitivity to DNA damaging agents. In HGPS, the inability to adequately repair DNA damages due to defective A-type lamin may cause aspects of premature aging (see DNA damage theory of aging).
=== Restrictive dermopathy ===
Restrictive dermopathy (RD), also called tight skin contracture syndrome, is a rare, lethal autosomal recessive perinatal genodermatosis. Two known causes of RD are mutations in the LMNA gene, which lead to the production of truncated prelamin A precursor, and insertions in the ZMPSTE24, which lead to a premature stop codon.
Individuals with RD exhibit growth retardation starting in the uterus, tight and rigid skin with erosions, prominent superficial vasculature and epidermal hyperkeratosis, abnormal facial features (small mouth, small pinched nose and micrognathia), sparse or absent eyelashes and eyebrows, mineralization defects of the skull, thin dysplastic clavicles, pulmonary hypoplasia and multiple joint contractures. Most affected individuals die in the uterus or are stillbirths, and liveborns usually die within a week.
== Defects in FBN1 ==
Patients with Marfan-progeroid-lipodystrophy syndrome typically exhibit congenital lipodystrophy and a neonatal progeroid appearance. Sometimes identified as having neonatal progeroid syndrome, the term is a misnomer since they do not exhibit accelerated aging. The condition is caused by mutations near the 3'-terminus of the FBN1 gene.
== A common cause for premature aging ==
Hutchinson–Gilford progeria syndrome, Werner syndrome, and Cockayne syndrome are the three genetic disorders in which patients have premature aging features. Premature aging also develops on some animal models which have genetic alterations. Although the patients with these syndromes and the animal models with premature aging symptoms have different genetic backgrounds, they all have abnormal structures of tissues/organs as a result of defective development. Misrepair-accumulation aging theory suggests that the abnormality of tissue structure is the common point between premature aging and normal aging.
Premature aging is a result of Mis-construction during development as a consequence of gene mutations, whereas normal aging is a result of accumulation of Misrepairs for the survival of an organism. Thus the process of development and that of aging are coupled by Mis-construction and Mis-re-construction (Misrepair) of the structure of an organism.
== Unknown causes ==
=== Wiedemann–Rautenstrauch syndrome ===
Wiedemann–Rautenstrauch (WR) syndrome, also known as neonatal progeroid syndrome, is an autosomal recessive progeroid syndrome. More than 30 cases have been reported. Most affected individuals die by seven months of age, but some do survive into their teens.
WR is associated with abnormalities in bone maturation, and lipids and hormone metabolism. Affected individuals exhibit intrauterine and postnatal growth retardation, leading to short stature and an aged appearance from birth. They have physical abnormalities including a large head (macrocephaly), sparse hair, prominent scalp veins, inward-folded eyelids, widened anterior fontanelles, hollow cheeks (malar hypoplasia), general loss of fat tissues under the skin, delayed tooth eruption, abnormal hair pattern, beaked noses, mild to severe intellectual disability and dysmorphism.
The cause of WR is unknown, although defects in DNA repair have been implicated.
==== Rothmund–Thomson syndrome ====
Classified as an autosomal recessive defect, but the pathology has still yet to be well researched.
== Cancer ==
Some segmental progeroid syndromes, such as Werner syndrome (WS), Bloom syndrome (BS), Rothmund-Thomson syndromes (RTS) and combined xeroderma pigmentosa-Cockayne syndrome (XP-CS), are associated with an increased risk of developing cancer in the affected individual; two exceptions are Hutchinson–Gilford progeria (HGPS) and Cockayne syndrome.
== Animal models ==
Within animal models for progeroid syndromes, early observations have detected abnormalities within overall mitochondrial function, signal transduction between membrane receptors, and nuclear regulatory proteins.
== Other ==
Alterations in lipid and carbohydrate metabolism, a triplet-repeat disorder (myotonic dystrophy) and an idiopathic disorder
== Society and popular culture ==
=== People ===
Hayley Okines was an English girl with classic progeria famed for her efforts in spreading awareness of the condition. She was featured in the media.
Lizzie Velásquez is an American motivational speaker who has a syndrome that resembles progeria, although the exact nature is unclear; it is now thought to be a form of neonatal progeroid syndrome. Velásquez is an advocate of anti-bullying.
Jesper Sørensen is widely recognized in Denmark as the only child in Denmark and Scandinavia with progeria (as of 2008). His fame came about after a documentary in 2008 on TV 2 about Sørensen.
=== Literature and Theatre ===
F. Scott Fitzgerald's 1922 short story The Curious Case of Benjamin Button is about a boy who was born with the appearance of a 70-year-old and who ages backwards. This short story is thought to be inspired by progeria. The description of the fictitious Smallweed family in the Charles Dickens' Bleak House suggests the characters had progeria. Christopher Snow, the main character in Dean Koontz's Moonlight Bay Trilogy, has xeroderma pigmentosum, as does Luke from the 2002 novel Going Out by Scarlett Thomas. In the visual novel Chaos;Head, the character Shogun eventually dies of a progeroid syndrome, and in its sequel Chaos;Child, more characters get this same fictional progeroid syndrome, which by then is called Chaos Child Syndrome. In Kimberly Akimbo, a 2000 play by David Lindsay-Abaire, and its Tony Award for Best Musical-winning adaptation of the same name, the main character, Kimberly Levaco, has an unnamed progeria-like condition.
=== Film ===
Paa, a 2009 Indian comedy-drama film, features a protagonist, Auro (Amitabh Bachchan), who has progeria. Jack is a 1996 American comedy-drama film, in which the titular character (portrayed by Robin Williams) has Werner syndrome. Taiyou no Uta, a 2006 Japanese film, features Kaoru Amane (portrayed by Yui), a 16-year-old girl has xeroderma pigmentosum.
== See also ==
DeSanctis–Cacchione syndrome, an extremely rare variant of xeroderma pigmentosum (XP)
Dyskeratosis congenita, a rare progressive congenital disorder of the skin and bone marrow in some ways resembling progeria
Fanconi anemia, a rare genetic defect in a cluster of proteins responsible for DNA repair
Li–Fraumeni syndrome, a rare autosomal genetic disorder caused by defects in DNA repair
Nijmegen breakage syndrome, a rare autosomal recessive genetic disorder caused by defect(s) in the Double Holliday junction DNA repair mechanism
Nestor-Guillermo progeria syndrome, an extremely rare genetic disorder which is unique from other PS because of the absence of any cardiovascular abnormalities (which lead to premature death in cases where they are present)
== References ==
== Further reading ==
Riedl, T.; Hanaoka, F; Egly, JM (2003). "The comings and goings of nucleotide excision repair factors on damaged DNA". The EMBO Journal. 22 (19): 5293–303. doi:10.1093/emboj/cdg489. PMC 204472. PMID 14517266.
Park, CJ; Choi, BS (2006). "The protein shuffle. Sequential interactions among components of the human nucleotide excision repair pathway". The FEBS Journal. 273 (8): 1600–8. doi:10.1111/j.1742-4658.2006.05189.x. PMID 16623697. S2CID 19820776.
Singh, DK; Ahn, B; Bohr, VA (2009). "Roles of RECQ helicases in recombination based DNA repair, genomic stability and aging". Biogerontology. 10 (3): 235–52. doi:10.1007/s10522-008-9205-z. PMC 2713741. PMID 19083132.
Mallory, Susan B.; Krafchik, Bernice R.; Bender, Matthew M.; Potocki, Lorraine; Metry, Denise W. (2003). "Cockayne Syndrome". Pediatric Dermatology. 20 (6): 538–40. doi:10.1111/j.1525-1470.2003.20619.x. PMID 14651579. S2CID 39698691.
== External links ==
Hutchinson–Gilford Progeria Syndrome described in GeneReviews™
NIH Office of Rare Diseases Research (ORDR) - a National Institutes of Health branch which coordinates and supports rare diseases research
Orphanet, a reference portal for information on rare diseases and orphan drugs | Wikipedia/Accelerated_aging_disease |
A double-strand break repair model refers to the various models of pathways that cells undertake to repair double-strand breaks (DSB). DSB repair is an important cellular process, as the accumulation of unrepaired DSB could lead to chromosomal rearrangements, tumorigenesis or even cell death. In human cells, there are two main DSB repair mechanisms: Homologous recombination (HR) and non-homologous end joining (NHEJ). HR can be seen as a more accurate site specific form of repair. It requires much more larger and intricate protein complexes. These complexes that involve proteins such as RAD51 (searches for homology and mediates strand invasion) and BRCA2 (the well studied RAD51 localizer) are critical in support of DNA replication and the recovery of stalled or broken replication forks. NHEJ modifies and ligates the damaged ends regardless of homology. In terms of DSB repair pathway choice, most mammalian cells appear to favor NHEJ rather than HR. This is because the employment of HR may lead to gene deletion or amplification in cells which contains repetitive sequences. In terms of repair models in the cell cycle, HR is only possible during the S and G2 phases, while NHEJ can occur throughout whole process. These repair pathways are all regulated by the overarching DNA damage response mechanism. Besides HR and NHEJ, there are also other repair models which exists in cells. Some are categorized under HR, such as synthesis-dependent strand annealing, break-induced replication, and single-strand annealing; while others are an entirely alternate repair model, namely, the pathway microhomology-mediated end joining (MMEJ).
== Causes ==
DSB can occur naturally by exogenous sources or endogenous sources. Exoogenously due to the presence of reactive species generated by metabolism, as well as replication stress and various external factors such as ionizing radiation or chemotherapeutic drugs. Endogenous breaks are due to DNA replication, transcription, as well as normal cellular processes.
The exogenous source of ionization causing DSB's can be a result of radiation directly hitting a sequence of DNA or localized radiation by neighboring molecules, resulting in a chain reaction of molecular breaks. Each lesion or break is completely dependent on the type of radiation it is exposed to. Examples such as proton particles and X rays effect strands differently, while the former directly disrupts the bonds created by the negatively charged backbone of DNA, the ladder is effected by indirect exposure.
Not all DSB damage results in catastrophic cell cycling (i.e. endogenous reactions). Regularly DNA goes through oxidative damage which quickly arise and are then quickly resolved and repaired. These are referred to as programmed DSB's. This controlled damage and repair promotes diversity during the cell cycle and subsequent division. Programmed DSB's have been proven to be imperative for mammalian cell development. The breaks caused be a RAG protein complex are integral for sexual reproduction. The breaks induce a crossover formation for faithful segregation of homologous chromosomes.
In mammalian cells, there are numerous cellular processes that induce DSB. Firstly, DNA topological strain from topoisomerase during normal cell growth can cause the majority a cell’s DSB. Secondly, cellular processes such as meiosis and the maturation of antibodies can cause nuclease-induced DSB. Thirdly, the cleavage of different DNA structures such as reversed or blocked DNA replication forks, R-loops and DNA interstrand crosslinks can also cause DSB.
== Different models ==
=== Homologous recombination ===
Homologous recombination involves the exchange of DNA materials between homologous chromosomes. There are multiple pathways of HR to repair DSBs, which includes double-strand break repair (DSBR), synthesis-dependent strand annealing (SDSA), break-induced replication (BIR), and single-strand annealing (SSA).
The basis of homologous recombination stems from the central reaction of homology search and DNA strand invasion by specific protein and single strand DNA presynaptic filaments. Which is then followed by synapsis; that is the action of strand invasion and the formation of a displacement loop (D-loop) which is formed during strand invasion between the invading 3' overhang strand and the homologous chromosome. After DNA is newly synthesized the invading strand is disengaged and annealed during post-synapse leading to genetic crossover.
The regulation of HR in mammalian cells involves key HR proteins (or mediator proteins) such as BRCA1 and BRCA2. It has well been supported that BRCA1 plays a role in end resection. Its role has been proven to be associated with different mechanisms such as antagonizing, promoting, and inhibiting certain protein/ssDNA complexes. BRCA2, a tumor suppressor gene that is the center of a wide variety of research; has experimentally been seen to act in concert with BRCA1-PALB2 to form a complex and load RAD51 onto ssDNA that is coated with RPA. In vivo, BRCA2 mutations lead to predisposed ovarian or breast cancer so it is apparent that is function is integral for dsDNA break repair.
==== Double-strand break repair ====
HR repairs DSB by copying intact and homologous DNA molecules. The blunt ends of the DSB are processed into ssDNA with 3’ extensions, which allows RAD51 recombinase (eukaryotic homologue of prokaryotic RecA) to bind to it to form a nucleoprotein filament. The function of the filament is to locate the template DNA and form a joint heteroduplex molecule. Other proteins such as RP-A protein and RAD52 also coordinate in the heteroduplex formation, the RP-A protein has to be removed for the RAD51 to form the filament, whereas the RAD52 is a key HR mediator. Afterwards, the 3’ ssDNA invades the template DNA, and displaces a DNA strand to form a D-loop. DNA polymerase and other accessory factors follows by replacing the missing DNA via DNA synthesis. Ligase then attaches the DNA strand break, resulting in the formation of 2 Holliday junctions. The recombined DNA strands then undergoes resolution by cleavage. The orientation of the cleavage determines whether the resolution results in either cross-over or noncross-over products. Lastly, the strands finally separate and revert to its original form.
, the main pathway for resolution relies on the BTR (BLM helicase-TopoisomeraseIIIα-RMI1-RM2) complex, where it induces the resolution of the 2 Holliday junctions, but this pathway favors the noncross-over cleavage.
==== Synthesis-dependent strand annealing ====
Source:
Synthesis-dependent strain annealing is the most preferred repair mechanism in somatic cells. The pathway of SDSA is similar to DSBR until just after the D-loop formation. Instead of forming Holliday junctions after DNA synthesis, the nascent strand dissociates via RETL1 helicase and anneals back to the other end of the resected strand. This explains why SDSA results in a non-crossover pathway. The remaining gap is filled in and the nick is attached by the ligase.
==== Break-induced replication ====
Although there is little research in regards of break-induced replication, it is known through multiple experiments utilizing yeast as a model that it is a one-ended recombination mechanism, where only of the one ends of a DSB will be involved in strand invasion. BIR however, has been proven to work during replication restart and repair of eroded telomeres as well as unexpectedly RAD51's independence from the BIR process. This means that unlike DSBR, BIR does not link back to the second DSB end after the strand invasion and replication. Seeing as HR is a strictly regulated process and BIR is another possible stage of regulation, it will drive further interest into the mechanism in the near future.
==== Single-strand annealing ====
Single-strand annealing involves homologous/repeated sequences flanking a DSB. The process starts with the key end resection factor CtlP, which mediates the end resection of DSBs, resulting in the formation of a 3' ssDNA extension. Meditated by RAD52, the flanking homologous sequences are annealed, and forms a synapse intermediate. Then, the nonhomologous 3’ extension is removed by the ERCC1-XPF complex through endonucleolytic cleavage, with RAD52 increasing the efficiency of the ERCC1-XPF complex activity. It is only after the removal of 3’ ssDNA, where the polymerase will fill the missing gaps and the ligase to ligate the strands. Since SSA results in the deletion of repetitive sequences, this could potentially lead to error-prone repair.
Single-strand annealing differs from SDSA and DSBR in numerous ways. For instance, the 3’ extension after the end resection in SSA anneals to the repeated/homologous sequences of the other end, whereas in other pathways the strand invasion to another homologous DNA template. Moreover, SSA does not require RAD51, because it does not involve strand invasion, but rather the annealing of homologous sequences.
=== Non-homologous end joining ===
Non-homologous end joining (NHEJ) is one of the major pathways in DSB repair besides HR. The basic concept of NHEJ involves three steps. First, the ends of a DSB is captured by a group of enzymes. The enzymes then form a bridge which connects the DSB ends together, and is lastly followed by religation of the DNA strands. To initiate whole process, the Ku70/80 protein complex binds to the damaged ends of the DSB strands. This forms a preliminary scaffold which allows the recruitment of various NHEJ factors, such as the DNA-dependent protein kinase catalytic subunit (DNA-PKcs), DNA Ligase IV and X-ray cross complementing protein 4 (XRCC4) to form a bridge and bring both ends of the damaged DNA strands together. This is then followed by the processing of any non-ligatable DNA termini by a group of proteins including Artemis, PNKP, APLF and Ku, before the XRCC4 and DNA Ligase IV ligate the bridged DNA.
=== Microhomology-mediated end joining ===
Microhomology-mediated end joining (MMEJ), also known as alt-non-homologous end joining, is another pathway to repair DSBs. The process of MMEJ can be summarized in five steps: the 5' to 3' cutting of DNA ends, annealing of microhomology, removing heterologous flaps, and ligation and synthesis of gap filling DNA. It was found that the selection between MMEJ and NHEJ is mainly dependent on Ku levels and the concurrent cell cycle.
== The regulation of double-strand break repair pathways ==
=== DNA damage response ===
DNA damage response (DDR) is the overarching mechanism which mediates the cell's detection and response to DNA damage. This includes the process of detecting DSB within the cell, and the subsequent triggering and regulation of DSB repair pathways. Upstream detections of DNA damage via DDR will lead to the activation of downstream responses such as senescence, cell apoptosis, halting transcription and activating DNA repair mechanisms. Proteins such as the proteins ATM, ATR and DNA-dependent protein kinase (DNA-PK) are vital for the process of detection of DSB in DDR, and these proteins are recruited to the DSB site in the DNA. In particular, ATM has been identified as the protein kinase in charge of the global meditation of cellular responses to DSB, which includes various DSB repair pathways. Following the recruitment of the aforementioned proteins to DNA damage sites, they will in turn trigger cellular responses and repair pathways to mitigate and repair the damage caused. In short, these vital upstream proteins and downstream repair pathways altogether forms the DDR, which plays a vital role in DSB repair pathways regulation.
=== Fanconi anemia complex in one DNA damage response pathway ===
The image in this section illustrates molecular steps in a DNA damage response pathway in which a Fanconi anemia complex is activated during repair of a double-strand break. ATM (ATM) is also a protein kinase that is recruited and activated by DNA double-strand breaks. DNA double-strand damages
activate the Fanconi anemia core complex (FANCA/B/C/E/F/G/L/M). The FA core complex monoubiquitinates the downstream targets FANCD2 and FANCI. ATM activates (phosphorylates) CHEK2 and FANCD2 CHEK2 phosphorylates BRCA1. Ubiquinated FANCD2 complexes with BRCA1 and RAD51. The PALB2 protein acts as a hub, bringing together BRCA1, BRCA2 and RAD51 at the site of a DNA double-strand break, and also binds to RAD51C, a member of the RAD51 paralog complex RAD51B-RAD51C-RAD51D-XRCC2 (BCDX2). The BCDX2 complex is responsible for RAD51 recruitment or stabilization at damage sites. RAD51 plays a major role in homologous recombinational repair of DNA during double strand break repair. In this process, an ATP dependent DNA strand exchange takes place in which a template strand invades base-paired strands of homologous DNA molecules. RAD51 is involved in the search for homology and strand pairing stages of the process.
=== Double-strand break repair pathway choice ===
As cells have developed various DSB repair models, it is said that specific pathways are favoured for their ability to repair DSB depending on the cellular context. These conditions include the type of DSB involved, the species of cells involved, and the stage of the cell cycle.
==== In various types of DSB ====
Cells have evolved a multitude of DSB repair pathways in response to the various types of DSB. Hence, various pathways are favoured in different situations. For instance, frank DSB, which are DSB induced by substances like as ionizing radiation, and nucleases, can be repaired by both HR and NHEJ. On the other hand, DSB due to replication fork collapse mainly favours HR.
==== In higher eukaryotes and yeast cells ====
It is said that the favoured pathway in a particular situations is also largely dependent on the species of the cell, the cell type, and cell cycle phases; and are all modulated and triggered by different upstream regulatory proteins. As compared to higher eukaryotes, yeast cells have adopted HR as the main repair pathway for DSB. Imprecise NHEJ, the primary pathway for NHEJ to repair "dirty" ends due to IR, was found to be inefficient at repairing DSB in yeast cells. It was hypothesized that this inefficiency as compared to mammalian cells is due to the lack of three vital NHEJ proteins, including DNA-PKcs, BRCA1, and Artemis. Contrary to yests, higher eukaryotes has a much higher frequency and efficiency at adopting NHEJ pathways. Research hypothesize that this is due to the higher eukaryote's larger genome size, as it means that more NHEJ related proteins are encoded for NHEJ repair pathways; and a larger genome implies a challenging obstacle to find a homologous template for HR.
==== In cell cycle ====
HR and NHEJ pathways are favoured in various phases of cell cycles for a multitude of factors. As S and G2 phases of the cell cycle generate more chromatids, the increased availability of template access for HR results in the up-regulation of the pathway. This rise is further increased due to the activation of CDK1 and the increase of RAD51 and RAD52 levels during G1 phase. Despite this, NHEJ not is inactive during the HR up-regulation. In fact, NHEJ was shown to be active throughout all stages of the cell cycle, and is favoured in G1 phase during low resection action intervals. This suggests the competition between HR and NHEJ for DSB repair in cells. It should be noted, however, that there is a shift of favour from NHEJ to HR when the cell cycle is progressing from G1 to S/G2 phases in eukaryotic cells.
==== During meiosis ====
In diploid eukaryotic organisms, the events of meiosis can be viewed as occurring in three steps. (1) Haploid gametes undergo syngamy/fertilisation with the result that chromosome sets of different parental origin come together to share the same nucleus. (2) Homologous chromosomes originating from different cells (i.e. non-sister chromosomes) align in pairs and undergo recombination involving double-strand break repair. (3) Two successive cell divisions (without duplication of chromosomes) result in haploid gametes that can then repeat the meiotic cycle. During step (2), damages in DNA of the germline can be removed by double-strand break repair. In particular, double-strand breaks in one duplex DNA molecule can be accurately repaired using information from a homologous intact DNA molecule by the process of homologous recombination.
== Defective DSB repair ==
Although there is no universal model to explain disease etiology caused by DNA repair deficiency, it is said that the accumulation of unrepaired DNA damage may lead to various diseases, including various metabolic syndromes and types of cancers. Some examples of diseases caused by defects of DSB repair mechanisms are listed below:
Fanconi Anemia (FA) and Hereditary breast and ovarian cancer (HBOC) syndrome are caused by defects in homologous recombination. Biallelic mutation of either BRCA1/2 gene results in the loss of homologous recombination activity.
Chordomas, a rare bone tumour, might suggest defects in homologous recombination and mutations affecting HR-related genes. Other syndromes and defects that have been proven to be associated with HR defects in mouse models are developmental defects, early onset breast cancer, and genetic instability.
Defects in the NHEJ mechanism are related to the mutations in hRAD50 and/or hMRE11 genes in mismatch repair deficient tumors. Other complications associated with in vivo deficient NHEJ include; genomic instability, immunodeficiency, growth retardation, embryonic development, and cancer predisposition.
=== Aging ===
Women tend to live longer than men and the gender gap in life expectancy suggests differences in the ageing process between the sexes. Sex specific differences in DNA double-strand break repair of cycling human lymphocytes during aging were studied. It was found that the repair of DNA double-strand breaks changes upon aging and the changes are distinct in men and women.
=== Cancer ===
Activation of gene transcription during oncogenesis is often associated with the introduction of DNA double-strand breaks and their repair by a process employing RAD51. This transcription-coupled DNA repair tends to occur in specific regions of the DNA termed super-enhancers.
== See also ==
DNA damage & repair
Homologous Recombination
Synthesis-dependent strain annealing
Non-homologous end joining
Microhomology-mediated end joining
Cell cycle
DNA synthesis
== References == | Wikipedia/Double-strand_break_repair_model |
A blood-borne disease is a disease that can be spread through contamination by blood and other body fluids. Blood can contain pathogens of various types, chief among which are microorganisms, like bacteria and parasites, and non-living infectious agents such as viruses. Three blood-borne pathogens in particular, all viruses, are cited as of primary concern to health workers by the CDC-NIOSH: human immunodeficiency virus, hepatitis B, and hepatitis C.
Diseases that are not usually transmitted directly by blood contact, but rather by insect or other vector, are more usefully classified as vector-borne disease, even though the causative agent can be found in blood. Vector-borne diseases include West Nile virus, zika fever and malaria.
Many blood-borne diseases can also be contracted by other means, including high-risk sexual behavior or intravenous drug use. These diseases have also been identified in sports medicine.
Since it is difficult to determine what pathogens any given sample of blood contains, and some blood-borne diseases are lethal, standard medical practice regards all blood (and any body fluid) as potentially infectious. "Blood and body fluid precautions" are a type of infection control practice that seeks to minimize this sort of disease transmission.
== Global epidemiology and statistics ==
Blood-borne diseases pose significant global health challenges, especially in regions with limited healthcare access. Recent Statistics include:
HIV/AIDS: as of 2023, approximately 39.9 million people globally were living with HIV infection in 2023.
Hepatitis B: 2.4 million people are chronically infected in United States.
Hepatitis C: approximately 50 million people are infected with hepatitis C worldwide, with about 1 million new infections annually.
== Emerging blood-borne pathogens ==
While well-known blood-borne diseases such as human immunodeficiency virus, hepatitis B, and hepatitis C continue to be of major concern, new and emerging pathogens are also being identified. These include:
Zika Virus – although primarily transmitted by mosquitoes, Zika virus has been detected in blood transfusions, raising concerns about its potential as a blood-borne pathogen.
Ebola Virus – the Ebola virus can be transmitted through blood and bodily fluids, particularly in healthcare settings. Studies suggest that survivors may carry the virus for months.
Babesia microti – a parasite causing babesiosis, which is transmitted via tick bites but has also been found in blood transfusions, leading to increased screening measures.
HTLV-1 (Human T-lymphotropic virus type 1) – a retrovirus that affects white blood cells and is linked to adult T-cell leukemia, myelopathy, and other neurological disorders.
== Transmission routes ==
Percutaneous exposure: Injuries from needlesticks or cuts with contaminated sharp instruments.
Mucous membrane exposure: Contact of mucous membranes with infected blood or body fluids.
Non-intact skin exposure: Blood contact with broken skin.
== Occupational exposure ==
Blood poses the greatest threat to health in a laboratory or clinical setting due to needlestick injuries (e.g., lack of proper needle disposal techniques and/or safety syringes). Needles are not the only issue, as direct splashes of blood also cause transmission. These risks are greatest among healthcare workers, including: nurses, surgeons, laboratory assistants, doctors, phlebotomists, and laboratory technicians. These roles often require the use of syringes for blood draws or to administer medications.
The Occupational Safety and Health Administration (OSHA) prescribes 5 rules that are required for a healthcare facility to follow in order to reduce the risk of employee exposure to blood-borne pathogens. They are:
Written exposure control plan
Engineering controls (Sharps containers, detachable and retractable needles, syringe caps, etc.)
Safe work practices and safety devices
Vaccines available to employees
Education and post-exposure follow up
These controls, while general, serve to greatly reduce the incidence of blood-borne disease transmission in occupational settings of healthcare workers.
There are 26 different viruses that have been shown to present in healthcare workers as a result of occupational exposure. The most common blood-borne diseases are hepatitis B, hepatitis C, and human immunodeficiency virus. Exposure is possible through blood of an infected patient splashing onto mucous membranes; however, the greatest exposure risk was shown to occur during percutaneous injections performed for vascular access. These include blood draws, as well as catheter placement, as both typically use hollow bore needles. Preventive measures for occupational exposure include standard precautions (hand washing, sharp disposal containers), as well as additional education. Advancements in the design of safety engineered devices have played a significant role in decreasing rates of occupational exposure to blood-borne disease. According to the Massachusetts Sharps Injury Surveillance System, needle devices without safety features accounted for 53% of the 2010 reported sharps injuries. Safer sharps devices now have engineering controls, such as a protective shield over the needle, and sharps containers that have helped to decrease this statistic. These safer alternatives are highly effective in substantially reducing injuries. For instance, almost 83% of injuries from hollow bore needles can be prevented with the use of safer sharps devices. There have been reports of HCW transferring disease to patients. This happens usually when surgeons perform using these sharps as well.
== Advances in detection and prevention ==
Recent innovations in biomedical technology have significantly improved the early detection and prevention of blood-borne pathogens. One such advancement is Next-Generation Sequencing (NGS), a high-throughput genomic sequencing technique that allows for the precise identification of pathogens at the molecular level, even in asymptomatic individuals. In addition, Point-of-Care Testing (POCT) has revolutionized screening accessibility by enabling rapid diagnostic tests for infections such as HIV and hepatitis C, delivering accurate results within minutes, particularly beneficial in remote or resource-limited settings. Emerging CRISPR based diagnostics are also showing promise. These utilize gene-editing technology to detect viral RNA in blood samples with high sensitivity and specificity, offering potential for rapid and cost effective pathogen identification. Furthermore, Universal Pathogen Inactivation methods are being developed to neutralize a broad range of viruses and bacteria in donated blood, significantly lowering the risk of transfusion transmitted infections.
== Blood transfusions ==
Blood for blood transfusion is screened for many blood-borne diseases. Additionally, a technique that uses a combination of riboflavin and UV light to inhibit the replication of these pathogens by altering their nucleic acids can be used to treat blood components prior to their transfusion, and can reduce the risk of disease transmission.
A technology using the synthetic psoralen (amotosalen HCl) and UVA light (320–400 nm) has been implemented in European blood centers for the treatment of platelet and plasma components to prevent transmission of blood-borne diseases caused by bacteria, viruses and protozoa.
== Needle exchange programs ==
Needle exchange programs (NEPs) are an attempt to reduce the spread of blood-borne diseases between intravenous drug users. They often also provide addiction counseling services, infectious disease testing, and in some cases mental health care and other case management. NEPs acquired their name as they were initially places where intravenous (IV) illicit substance users were provided with clean, unused needles in exchange for their used needles. This allows for proper disposal of the needles. Empirical studies confirm the benefits of NEPs. NEPs can affect behaviors that result in the transmission of human immunodeficiency virus. These behaviors include decreased sharing of used syringes, which reduces contaminated syringes from circulation and replaces them with sterile ones, among other risk reductions.
== Prevention ==
Follow standard precautions to help prevent the spread of blood-borne pathogens and other diseases whenever there is a risk of exposure to blood or other bodily fluids. Standard precautions include maintaining personal hygiene and using personal protective equipment (PPE), engineering controls, and work practice controls among others. Always avoid contact with blood and other bodily fluids. Wear disposable gloves when providing care, particularly if you may come into contact with blood or bodily fluids. Dispose of gloves properly and change gloves when providing care to a new patient. Use needles with safety devices to help prevent needlestick injury and exposure to blood-borne pathogens. It is also recommended healthcare workers who come often in contact with contaminated material should get vaccinated against hepatitis B. A hierarchy of controls can help to prevent environmental and occupational exposures and subsequent diseases. These include:
Elimination: Physically remove hazards, including needles that lack a safety device. Additionally, eliminate the use of needle devices whenever safe and effective alternatives are available.
Substitution: Replace needles without safety devices with ones that have a safety feature built in. This has been shown to reduce blood-borne diseases transmitted via needlestick injuries.
Engineering controls: Isolate people from the hazard by providing sharps containers for workers to immediately place needles in after use, which means putting them within arm's reach of wherever patient treatment occurs, such as in every physician's exam room, every draw station in a medical lab, and every bedside in a hospital ward or wing.
Administrative controls: Change the way people work by creating a culture of safety such as avoiding recapping or bending needles that may be contaminated and promptly disposing of used needle devices and other sharps.
Personal protective equipment: Protect workers with PPE such as gloves and masks to avoid transmission of blood and other bodily fluids.
There have been reports of HCW transferring disease to patients. This happens usually when surgeons perform EPPs, which are procedures requiring sharp tools.
== Post-exposure protocol ==
Immediate actions: Wash needlesticks and cuts with soap and water; flush splashes to nose, mouth, or skin with water; irrigate eyes with clean water, saline, or sterile wash.
Reporting: Promptly report exposures to receive appropriate follow-up care.
== See also ==
BTSB anti-D scandal
Contaminated haemophilia blood products
Contaminated blood scandal in the United Kingdom
Hematology
HIV-tainted blood scandal (Japan)
Infected blood scandal (France)
Plasma Economy
Royal Commission of Inquiry on the Blood System in Canada
== References == | Wikipedia/Blood-borne_disease |
Protein production is the biotechnological process of generating a specific protein. It is typically achieved by the manipulation of gene expression in an organism such that it expresses large amounts of a recombinant gene. This includes the transcription of the recombinant DNA to messenger RNA (mRNA), the translation of mRNA into polypeptide chains, which are ultimately folded into functional proteins and may be targeted to specific subcellular or extracellular locations.
Protein production systems (also known as expression systems) are used in the life sciences, biotechnology, and medicine. Molecular biology research uses numerous proteins and enzymes, many of which are from expression systems; particularly DNA polymerase for PCR, reverse transcriptase for RNA analysis, restriction endonucleases for cloning, and to make proteins that are screened in drug discovery as biological targets or as potential drugs themselves. There are also significant applications for expression systems in industrial fermentation, notably the production of biopharmaceuticals such as human insulin to treat diabetes, and to manufacture enzymes.
== Protein production systems ==
Commonly used protein production systems include those derived from bacteria, yeast, baculovirus/insect, mammalian cells, and more recently filamentous fungi such as Myceliophthora thermophila. When biopharmaceuticals are produced with one of these systems, process-related impurities termed host cell proteins also arrive in the final product in trace amounts.
=== Cell-based systems ===
The oldest and most widely used expression systems are cell-based and may be defined as the "combination of an expression vector, its cloned DNA, and the host for the vector that provide a context to allow foreign gene function in a host cell, that is, produce proteins at a high level". Overexpression is an abnormally and excessively high level of gene expression which produces a pronounced gene-related phenotype.
There are many ways to introduce foreign DNA to a cell for expression, and many different host cells may be used for expression — each expression system has distinct advantages and liabilities. Expression systems are normally referred to by the host and the DNA source or the delivery mechanism for the genetic material. For example, common hosts are bacteria (such as E. coli, B. subtilis), yeast (such as S. cerevisiae) or eukaryotic cell lines. Common DNA sources and delivery mechanisms are viruses (such as baculovirus, retrovirus, adenovirus), plasmids, artificial chromosomes and bacteriophage (such as lambda). The best expression system depends on the gene involved, for example the Saccharomyces cerevisiae is often preferred for proteins that require significant posttranslational modification. Insect or mammal cell lines are used when human-like splicing of mRNA is required. Nonetheless, bacterial expression has the advantage of easily producing large amounts of protein, which is required for X-ray crystallography or nuclear magnetic resonance experiments for structure determination.
Because bacteria are prokaryotes, they are not equipped with the full enzymatic machinery to accomplish the required post-translational modifications or molecular folding. Hence, multi-domain eukaryotic proteins expressed in bacteria often are non-functional. Also, many proteins become insoluble as inclusion bodies that are difficult to recover without harsh denaturants and subsequent cumbersome protein-refolding.
To address these concerns, expressions systems using multiple eukaryotic cells were developed for applications requiring the proteins be conformed as in, or closer to eukaryotic organisms: cells of plants (i.e. tobacco), of insects or mammalians (i.e. bovines) are transfected with genes and cultured in suspension and even as tissues or whole organisms, to produce fully folded proteins. Mammalian in vivo expression systems have however low yield and other limitations (time-consuming, toxicity to host cells,..). To combine the high yield/productivity and scalable protein features of bacteria and yeast, and advanced epigenetic features of plants, insects and mammalians systems, other protein production systems are developed using unicellular eukaryotes (i.e. non-pathogenic 'Leishmania' cells).
==== Bacterial systems ====
===== Escherichia coli =====
E. coli is one of the most widely used expression hosts, and DNA is normally introduced in a plasmid expression vector. The techniques for overexpression in E. coli are well developed and work by increasing the number of copies of the gene or increasing the binding strength of the promoter region so assisting transcription.
For example, a DNA sequence for a protein of interest could be cloned or subcloned into a high copy-number plasmid containing the lac (often LacUV5) promoter, which is then transformed into the bacterium E. coli. Addition of IPTG (a lactose analog) activates the lac promoter and causes the bacteria to express the protein of interest.
E. coli strain BL21 and BL21(DE3) are two strains commonly used for protein production. As members of the B lineage, they lack lon and OmpT proteases, protecting the produced proteins from degradation. The DE3 prophage found in BL21(DE3) provides T7 RNA polymerase (driven by the LacUV5 promoter), allowing for vectors with the T7 promoter to be used instead.
===== Corynebacterium =====
Non-pathogenic species of the gram-positive Corynebacterium are used for the commercial production of various amino acids. The C. glutamicum species is widely used for producing glutamate and lysine, components of human food, animal feed and pharmaceutical products.
Expression of functionally active human epidermal growth factor has been done in C. glutamicum, thus demonstrating a potential for industrial-scale production of human proteins. Expressed proteins can be targeted for secretion through either the general, secretory pathway (Sec) or the twin-arginine translocation pathway (Tat).
Unlike gram-negative bacteria, the gram-positive Corynebacterium lack lipopolysaccharides that function as antigenic endotoxins in humans.
===== Pseudomonas fluorescens =====
The non-pathogenic and gram-negative bacteria, Pseudomonas fluorescens, is used for high level production of recombinant proteins; commonly for the development bio-therapeutics and vaccines. P. fluorescens is a metabolically versatile organism, allowing for high throughput screening and rapid development of complex proteins. P. fluorescens is most well known for its ability to rapid and successfully produce high titers of active, soluble protein.
==== Eukaryotic systems ====
===== Yeasts =====
Expression systems using either S. cerevisiae or Pichia pastoris allow stable and lasting production of proteins that are processed similarly to mammalian cells, at high yield, in chemically defined media of proteins.
===== Filamentous fungi =====
Filamentous fungi, especially Aspergillus and Trichoderma, have long been used to produce diverse industrial enzymes from their own genomes ("native", "homologous") and from recombinant DNA ("heterologous").
More recently, Myceliophthora thermophila C1 has been developed into an expression platform for screening and production of native and heterologous proteins.The expression system C1 shows a low viscosity morphology in submerged culture, enabling the use of complex growth and production media. C1 also does not "hyperglycosylate" heterologous proteins, as Aspergillus and Trichoderma tend to do.
===== Baculovirus-infected cells =====
Baculovirus-infected insect cells (Sf9, Sf21, High Five strains) or mammalian cells (HeLa, HEK 293) allow production of glycosylated or membrane proteins that cannot be produced using fungal or bacterial systems. It is useful for production of proteins in high quantity. Genes are not expressed continuously because infected host cells eventually lyse and die during each infection cycle.
===== Non-lytic insect cell expression =====
Non-lytic insect cell expression is an alternative to the lytic baculovirus expression system. In non-lytic expression, vectors are transiently or stably transfected into the chromosomal DNA of insect cells for subsequent gene expression. This is followed by selection and screening of recombinant clones. The non-lytic system has been used to give higher protein yield and quicker expression of recombinant genes compared to baculovirus-infected cell expression. Cell lines used for this system include: Sf9, Sf21 from Spodoptera frugiperda cells, Hi-5 from Trichoplusia ni cells, and Schneider 2 cells and Schneider 3 cells from Drosophila melanogaster cells. With this system, cells do not lyse and several cultivation modes can be used. Additionally, protein production runs are reproducible. This system gives a homogeneous product. A drawback of this system is the requirement of an additional screening step for selecting viable clones.
===== Excavata =====
Leishmania tarentolae (cannot infect mammals) expression systems allow stable and lasting production of proteins at high yield, in chemically defined media. Produced proteins exhibit fully eukaryotic post-translational modifications, including glycosylation and disulfide bond formation.
===== Mammalian systems =====
The most common mammalian expression systems are Chinese Hamster ovary (CHO) and Human embryonic kidney (HEK) cells.
Chinese hamster ovary cell
Mouse myeloma lymphoblstoid (e.g. NS0 cell)
Fully Human
Human embryonic kidney cells (HEK-293)
Human embryonic retinal cells (Crucell's Per.C6)
Human amniocyte cells (Glycotope and CEVEC)
=== Cell-free systems ===
Cell-free production of proteins is performed in vitro using purified RNA polymerase, ribosomes, tRNA and ribonucleotides. These reagents may be produced by extraction from cells or from a cell-based expression system. Due to the low expression levels and high cost of cell-free systems, cell-based systems are more widely used.
== See also ==
Cellosaurus, a database of cell lines
Gene expression
Single-cell protein
Protein purification
Precision fermentation
Host cell protein
List of recombinant proteins
== References ==
== Further reading ==
Higgins SJ, Hames BD (1999). Protein Expression: A Practical Approach. Oxford University Press. ISBN 978-0-19-963623-5.
Baneyx, François (2004). Protein Expression Technologies: Current Status and Future Trends. Garland Science. ISBN 978-0-9545232-5-1.
== External links == | Wikipedia/Protein_expression_(biotechnology) |
RDNA (Radeon DNA) is a graphics processing unit (GPU) microarchitecture and accompanying instruction set architecture developed by AMD. It is the successor to their Graphics Core Next (GCN) microarchitecture/instruction set. The first product lineup featuring RDNA was the Radeon RX 5000 series of video cards, launched on July 7, 2019. The architecture is also used in mobile products. It is manufactured and fabricated with TSMC's N7 FinFET graphics chips used in the Navi series of AMD Radeon graphics cards.
The second iteration of RDNA was first featured in the PlayStation 5 and Xbox Series X/S consoles. Both consoles utilize a custom RDNA 2-based graphics solution as the basis for their GPU microarchitecture. On PC, RDNA 2 is featured in the Radeon RX 6000 series of video cards, which first launched in November 2020. RDNA 2 is also featured in Samsung's Exynos 2200 as the graphics architecture.
The third iteration of RDNA was announced on November 3, 2022, and is featured in the Radeon RX 7000 series of consumer desktop and mobile graphics cards.
The fourth iteration of RDNA was unveiled on January 6, 2025 at CES and is used in the Radeon RX 9070 series of desktop graphics cards.
== RDNA 1 ==
RDNA 1 (also RDNA1) is the first implementation of the RDNA microarchitecture and is the successor to the Radeon RX Vega series. The launch occurred on July 7, 2019.
=== Architecture ===
The architecture features a new processor design, although the first details released at AMD's Computex keynote hints at aspects from the previous Graphics Core Next (GCN) architecture being present for backwards compatibility purposes, which is especially important for its use (in the form of RDNA 2) in the major ninth generation game consoles (the Xbox Series X/S and PlayStation 5) to preserve native compatibility with their pre-existing eighth generation game libraries designed for GCN. It features multi-level cache hierarchy and an improved rendering pipeline, with support for GDDR6 memory.
Starting with the architecture itself, one of the biggest changes for RDNA is the width of a wavefront, the fundamental group of work. GCN in all of its iterations was 64 threads wide, meaning 64 threads were bundled together into a single wavefront for execution. RDNA drops this to a native 32 threads wide. At the same time, AMD has expanded the width of their SIMDs from 16 slots to 32 (aka SIMD32), meaning the size of a wavefront now matches the SIMD size.: 2
RDNA also introduces working primitive shaders. While the feature was present in the hardware of the Vega architecture, it was difficult to get a real-world performance boost from and thus AMD never enabled it. Primitive shaders in RDNA are compiler-controlled.: 2
The display controller in RDNA has been updated to support Display Stream Compression 1.2a, allowing output in 4K@240 Hz, HDR 4K@120 Hz, and HDR 8K@60 Hz.: 2
=== Instruction set ===
AMD's GPUOpen website hosts a PDF document aiming to describe the environment, the organization and the program state of RDNA devices. It details the instruction set and the microcode formats native to this family of processors that are accessible to programmers and compilers.
Documentation is available for:
the Radeon DNA 1 instruction set,
the Radeon DNA 2 instruction set,
the Radeon DNA 3 instruction set,
the Radeon DNA 3.5 instruction set,
the Radeon DNA 4 instruction set,
=== Differences between GCN and RDNA ===
There are architectural changes which affect how code is scheduled:
Single cycle instruction issue:
GCN issued one instruction per wave once every 4 cycles.
RDNA issues instructions every cycle.
Wave32:
GCN used a wavefront size of 64 threads (work items).
RDNA supports both wavefront sizes of 32 and 64 threads.
Workgroup Processors:
GCN grouped the shader hardware into "compute units" (CUs) which contained scalar ALUs and vector ALUs, LDS and memory access. One CU contains 4 SIMD16s which share one path to memory.
RDNA introduced the "workgroup processor" ("WGP"). The WGP replaces the compute unit as the basic unit of shader computation hardware/computing. One WGP encompasses 2 CUs. This allows significantly more compute power and memory bandwidth to be directed at a single workgroup.
=== Chips ===
Discrete GPUs:
Navi 10 found on Radeon RX 5600, Radeon RX 5600 XT, Radeon RX 5600M, Radeon RX 5700, Radeon RX 5700M, Radeon RX 5700 XT, Radeon Pro 5700, Radeon Pro 5700 XT, Radeon Pro W5700X, and Radeon Pro W5700 graphics cards
Navi 12 found on Radeon Pro V520 branded graphics card, Radeon Pro 5600M branded mobile graphics card and BC-160 mining card for cryptocurrency
Navi 14 found on Radeon RX 5300, Radeon RX 5300 XT, Radeon Pro 5300, Radeon Pro W5300, Radeon RX 5500, Radeon RX 5500 XT, Radeon Pro 5500, Radeon Pro 5500 XT, and Radeon Pro W5500, branded graphics cards; Radeon RX 5300M, Radeon Pro 5300M, Radeon Pro W5300M, Radeon RX 5500M, Radeon Pro 5500M, and Radeon Pro W5500M branded mobile graphics cards
== RDNA 2 ==
RDNA 2 (also RDNA2) is the successor to the RDNA microarchitecture. It was first publicly announced in early 2020 with a projected release in Q4 2020. According to statements from AMD, RDNA 2 would be a "refresh" of the RDNA architecture.
More information about RDNA 2 was made public on AMD's Financial Analyst Day on March 5, 2020. AMD claimed that it would provide a 50% performance-per-watt improvement over RDNA, with increases in clock speed and instructions-per-clock. Additional features confirmed by AMD include real-time, hardware accelerated ray tracing, "Infinity Cache", mesh shaders, sampler feedback and variable rate shading. The company announced that RDNA 2 would be used in next-generation gaming consoles and PC graphics cards code-named "Navi 2X" and also nicknamed as "Big Navi".
AMD unveiled the Radeon RX 6000 series, its next-gen RDNA 2 graphics cards at an online event on October 28, 2020. The lineup initially consisted of the RX 6800, RX 6800 XT and RX 6900 XT. The RX 6800 and 6800 XT launched on November 18, 2020, with the RX 6900 XT being released on December 8, 2020. Further variants including a Radeon RX 6700 (XT) series based on Navi 22, later launched on March 18, 2021.
On May 31, 2021, AMD launched the RX 6000M series of GPUs designed for laptops. These include the RX 6600M, RX 6700M, and RX 6800M. These were made available beginning on June 1, 2021.
On June 1, 2021, AMD's CEO Dr. Lisa Su and Tesla, Inc.'s CEO Elon Musk confirmed that the entertainment systems of Tesla's new Model S and Model X are powered by RDNA 2. The same microarchitecture was also announced to be used for an upcoming flagship Samsung Exynos SoC, later introduced in January 2022 as Exynos 2200, utilizing a custom Xclipse 920 GPU with 3 workgroup processors.
An RDNA 2 integrated GPU with 2 compute units is included in the I/O die on AMD's Zen 4-based Ryzen 7000 Series CPUs. According to AMD, the integrated RDNA 2 graphics in Ryzen 7000 are not intended for gaming and is instead intended for diagnostic purposes and offering video encode and decode capabilities.
=== Chips ===
Discrete GPUs:
Navi 21
Navi 22
Navi 23
Navi 24
Integrated into APUs/CPUs:
Rembrandt (as "Radeon 660M" and "Radeon 680M" models found on Ryzen 6000 series mobile APUs)
Raphael (as "Radeon Graphics" branded iGPU found on Ryzen 7000 series desktop CPUs)
Mendocino (as "Radeon 610M" model found on Ryzen 7020 series mobile APUs)
Rembrandt-R (as "Radeon 660M" and "Radeon 680M" models found on Ryzen 7035 series mobile APUs)
Dragon Range (as "Radeon 610M" model found on Ryzen 7045 series mobile APUs)
=== Usage in video game consoles ===
Custom configurations of the RDNA 2 graphics microarchitecture are used in the PlayStation 5 from Sony, Xbox Series X and Series S consoles from Microsoft, with proprietary tweaks and different GPU modifications in each system's implementation.
Valve announced on July 15, 2021, that their Steam Deck would feature the RDNA 2 architecture. The Steam Deck was released in February 2022.
== RDNA 3 ==
RDNA 3 (also RDNA3) is the successor to the RDNA 2 microarchitecture and was projected for a launch in Q4 2022 per AMD's gaming GPU roadmap. At an August 29 reveal event for Ryzen 7000 series CPUs, AMD CEO Lisa Su teased RDNA 3 and revealed that it would utilize chiplets built on TSMC's N5 node. On September 19, 2022, Sam Naffziger, the current senior vice president at AMD, stated in a blogpost that improvements made to the RDNA 3 microarchitecture allow for considerable performance gains and efficiency, with an estimated 50% increase in performance-per-watt compared to the RDNA 2 microarchitecture. Additionally, the RDNA 3 architecture features the next generation of Infinity Cache, a modified graphics pipeline, adaptive power management and rearchitected compute units, leading to an overall robust uplift in rasterization and ray-tracing performance over the previous consumer architecture.
On November 3, 2022, AMD unveiled the RX 7900 XTX and RX 7900 XT graphics cards, based on the RDNA 3 microarchitecture. These are the first commercial GPUs to be based on multi-chip module (MCM) design.
On October 5, 2023 and October 24, 2024 respectively, Samsung announced Exynos 2400 and Exynos 1580, which utilized RDNA 3 microarchitecture-based custom-design GPU, Xclipse 940 and 540.
=== Chips ===
Discrete GPUs:
Navi 31 found on Radeon RX 7900 GRE, Radeon RX 7900 XT, Radeon RX 7900 XTX, Radeon Pro W7800 and Radeon Pro W7900 branded graphics cards; Radeon RX 7900M branded mobile graphics cards
Navi 32 found on Radeon RX 7700 XT and Radeon RX 7800 XT branded graphics cards
Navi 33 found on Radeon RX 7600, Radeon RX 7600 XT, Radeon Pro W7500 and Radeon Pro W7600 branded graphics cards; Radeon RX 7600S, Radeon RX 7600M, Radeon RX 7600M XT and Radeon RX 7700S branded mobile graphics cards
Integrated into APUs/CPUs:
Phoenix (as "Radeon 740M", "Radeon 760M" and "Radeon 780M" models found on Ryzen 7040 series and Ryzen Z1 series mobile APUs)
Hawk Point (as "Radeon 740M", "Radeon 760M" and "Radeon 780M" models found on Ryzen 8040 series mobile APUs)
== Comparison of RDNA chips ==
== See also ==
List of AMD graphics processing units
AMD Radeon Software
GPUOpen
ROCm
== References ==
== External links ==
RDNA's official page on AMD.com
AMD RDNA 1.0 Instruction Set Architecture – Reference Guide - developer.amd.com
AMD RDNA 2 Instruction Set Architecture – Reference Guide - developer.amd.com
AMD RDNA3 Instruction Set Architecture – Reference Guide - developer.amd.com | Wikipedia/RDNA_(microarchitecture) |
The Infinite sites model (ISM) is a mathematical model of molecular evolution first proposed by Motoo Kimura in 1969. Like other mutation models, the ISM provides a basis for understanding how mutation develops new alleles in DNA sequences. Using allele frequencies, it allows for the calculation of heterozygosity, or genetic diversity, in a finite population and for the estimation of genetic distances between populations of interest.
The assumptions of the ISM are that (1) there are an infinite number of sites where mutations can occur, (2) every new mutation occurs at a novel site, and (3) there is no recombination. The term ‘site’ refers to a single nucleotide base pair. Because every new mutation has to occur at a novel site, there can be no homoplasy, or back-mutation to an allele that previously existed. All identical alleles are identical by descent. The four gamete rule can be applied to the data to ensure that they do not violate the model assumption of no recombination.
The mutation rate (
θ
{\displaystyle \theta }
) can be estimated as follows, where
μ
∗
{\displaystyle \mu ^{*}}
is the number of mutations found within a randomly selected DNA sequence (per generation),
N
e
{\displaystyle N_{e}}
is the effective population size. The coefficient is the product of twice the gene copies in individuals of the population; in the case of diploid, biparentally-inherited genes the appropriate coefficient is 4 whereas for uniparental, haploid genes, such as mitochondrial genes, the coefficient would be 2 but applied to the female effective population size which is, for most species, roughly half of
N
e
{\displaystyle N_{e}}
.
θ
=
4
N
e
μ
∗
{\displaystyle \theta =4N_{e}\mu ^{*}}
When considering the length of a DNA sequence, the expected number of mutations is calculated as follows
μ
∗
=
k
μ
{\displaystyle \mu ^{*}=k\mu }
Where k is the length of a DNA sequence and
μ
{\displaystyle \mu }
is the probability a mutation will occur at a site.
Watterson developed an estimator for mutation rate that incorporates the number of segregating sites (Watterson's estimator).
One way to think of the ISM is in how it applies to genome evolution. To understand the ISM as it applies to genome evolution, we must think of this model as it applies to chromosomes. Chromosomes are made up of sites, which are nucleotides represented by either A, C, G, or T. While individual chromosomes are not infinite, we must think of chromosomes as continuous intervals or continuous circles.
Multiple assumptions are applied to understanding the ISM in terms of genome evolution:
k breaks are made in these chromosomes, which leaves 2k free ends available. The 2k free ends will rejoin in a new manner rearranging the set of chromosomes (i.e. reciprocal translocation, fusion, fission, inversion, circularized incision, circularized excision).
No break point is ever used twice.
A set of chromosomes can be duplicated or lost.
DNA that never existed before can be observed in the chromosomes, such as horizontal gene transfer of DNA or viral integration.
If the chromosomes become different enough, evolution can form a new species.
Substitutions that alter a single base pair are individually invisible and substitutions occur at a finite rate per site.
The substitution rate is the same for all sites in a species, but is allowed to vary between species (i.e. no molecular clock is assumed).
Instead of thinking about substitutions themselves, think about the effect of the substitution at each point along the chromosome as a continuous increase in evolutionary distance between the previous version of the genome at that site and the next version of the genome at the corresponding site in the descendant.
== References ==
== Further reading ==
Degnan, James H.; Salter, Laura A. (2005). "Gene tree distributions under the coalescent process". Evolution. 59 (1): 24–37. doi:10.1111/j.0014-3820.2005.tb00891.x. PMID 15792224. S2CID 592613.
Hobolth, Asger; Uyenoyama, Marcy K.; Wiuf, Carsten (2008). "Importance sampling for the infinite sites model". Statistical Applications in Genetics and Molecular Biology. 7 (1): Article32. doi:10.2202/1544-6115.1400. PMC 2832804. PMID 18976228.
Ma, Jian; et al. (2008). "The infinite sites model of genome evolution". Proceedings of the National Academy of Sciences. 105 (38): 14254–14261. doi:10.1073/pnas.0805217105. PMC 2533685. PMID 18787111.
Tsitrone, Anne; Rousset, François; David, Patrice (2001). "Heterosis, marker mutational processes and population inbreeding history". Genetics. 159 (4): 1845–1859. doi:10.1093/genetics/159.4.1845. PMC 1461896. PMID 11779819. | Wikipedia/Infinite_sites_model |
Haldane's dilemma, also known as the waiting time problem, is a limit on the speed of beneficial evolution, calculated by J. B. S. Haldane in 1957. Before the invention of DNA sequencing technologies, it was not known how much polymorphism DNA harbored, although alloenzymes (variant forms of an enzyme which differ structurally but not functionally from other alloenzymes coded for by different alleles at the same locus) were beginning to make it clear that substantial polymorphism existed. This was puzzling because the amount of polymorphism known to exist seemed to exceed the theoretical limits that Haldane calculated, that is, the limits imposed if polymorphisms present in the population generally influence an organism's fitness. Motoo Kimura's landmark paper on neutral theory in 1968 built on Haldane's work to suggest that most molecular evolution is neutral, resolving the dilemma. Although neutral evolution remains the consensus theory among modern biologists, and thus Kimura's resolution of Haldane's dilemma is widely regarded as correct, some biologists argue that adaptive evolution explains a large fraction of substitutions in protein coding sequence, and they propose alternative solutions to Haldane's dilemma.
== Substitution cost ==
In the introduction to The Cost of Natural Selection Haldane writes that it is difficult for breeders to simultaneously select all the desired qualities, partly because the required genes may not be found together in the stock; but, he writes,
especially in slowly breeding animals such as cattle, one cannot cull even half the females, even though only one in a hundred of them combines the various qualities desired.
That is, the problem for the cattle breeder is that keeping only the specimens with the desired qualities will lower the reproductive capability too much to keep a useful breeding stock.
Haldane states that this same problem arises with respect to natural selection. Characters that are positively correlated at one time may be negatively correlated at a later time, so simultaneous optimization of more than one character is a problem also in nature. And, as Haldane writes
[i]n this paper I shall try to make quantitative the fairly obvious statement that natural selection cannot occur with great intensity for a number of characters at once unless they happen to be controlled by the same genes.
In faster breeding species there is less of a problem. Haldane mentions the peppered moth, Biston betularia, whose variation in pigmentation is determined by several alleles at a single gene. One of these alleles, "C", is dominant to all the others, and any CC or Cx moths are dark (where "x" is any other allele). Another allele, "c", is recessive to all the others, and cc moths are light. Against the originally pale lichens the darker moths were easier for birds to pick out, but in areas, where pollution has darkened the lichens, the cc moths had become rare. Haldane mentions that in a single day the frequency of cc moths might be halved.
Another potential problem is that if "ten other independently inherited characters had been subject to selection of the same intensity as that for colour, only
(
1
/
2
)
10
{\displaystyle (1/2)^{10}}
, or one in 1024, of the original genotype would have survived." The species would most likely have become extinct; but it might well survive ten other selective periods of comparable selectivity, if they happened in different centuries.
== Selection intensity ==
Haldane proceeds to define the intensity of selection regarding "juvenile survival" (that is, survival to reproductive age) as
I
=
ln
(
s
0
/
S
)
{\displaystyle I=\ln(s_{0}/S)}
, where
s
0
{\displaystyle s_{0}}
is the proportion of those with the optimal genotype (or genotypes) that survive to reproduce, and
S
{\displaystyle S}
is the proportion of the entire population that similarly so survive. The proportion for the entire population that die without reproducing is thus
1
−
S
{\displaystyle 1-S}
, and this would have been
1
−
s
0
{\displaystyle 1-s_{0}}
if all genotypes had survived as well as the optimal. Hence
s
0
−
S
{\displaystyle s_{0}-S}
is the proportion of "genetic" deaths due to selection. As Haldane mentions, if
s
0
≈
S
{\displaystyle s_{0}\approx S}
, then
I
≈
s
0
−
S
{\displaystyle I\approx s_{0}-S}
.
== The cost ==
Haldane writes
I shall investigate the following case mathematically. A population is in equilibrium under selection and mutation. One or more genes are rare because their appearance by mutation is balanced by natural selection. A sudden change occurs in the environment, for example, pollution by smoke, a change of climate, the introduction of a new food source, predator, or pathogen, and above all migration to a new habitat. It will be shown later that the general conclusions are not affected if the change is slow. The species is less adapted to the new environment, and its reproductive capacity is lowered. It is gradually improved as a result of natural selection. But meanwhile, a number of deaths, or their equivalents in lowered fertility, have occurred. If selection at the
i
t
h
{\displaystyle i^{th}}
selected locus is responsible for
d
i
{\displaystyle d_{i}}
of these deaths in any generation the reproductive capacity of the species will be
∏
(
1
−
d
i
)
{\displaystyle \prod \left(1-d_{i}\right)}
of that of the optimal genotype, or
exp
(
−
∑
d
i
)
{\displaystyle \exp \left(-\sum d_{i}\right)}
nearly, if every
d
i
{\displaystyle d_{i}}
is small. Thus the intensity of selection approximates to
∑
d
i
{\displaystyle \sum d_{i}}
.
Comparing to the above, we have that
d
i
=
s
0
i
−
S
{\displaystyle d_{i}=s_{0i}-S}
, if we say that
s
0
i
{\displaystyle s_{0i}}
is the quotient of deaths for the
i
t
h
{\displaystyle i^{th}}
selected locus and
S
{\displaystyle S}
is again the quotient of deaths for the entire population.
The problem statement is therefore that the alleles in question are not particularly beneficial under the previous circumstances; but a change in environment favors these genes by natural selection. The individuals without the genes are therefore disfavored, and the favorable genes spread in the population by the death (or lowered fertility) of the individuals without the genes. Note that Haldane's model as stated here allows for more than one gene to move towards fixation at a time; but each such will add to the cost of substitution.
The total cost of substitution of the
i
t
h
{\displaystyle i^{th}}
gene is the sum
D
i
{\displaystyle D_{i}}
of all values of
d
i
{\displaystyle d_{i}}
over all generations of selection; that is, until fixation of the gene. Haldane states that he will show that
D
i
{\displaystyle D_{i}}
depends mainly on
p
0
{\displaystyle p_{0}}
, the small frequency of the gene in question, as selection begins – that is, at the time that the environmental change occurs (or begins to occur).
== A mathematical model of the cost of diploids ==
Let A and a be two alleles with frequencies
p
n
{\displaystyle p_{n}}
and
q
n
{\displaystyle q_{n}}
in the
n
th
{\displaystyle n^{\mbox{th}}}
generation. Their relative fitness is given by
where 0 ≤
K
{\displaystyle K}
≤ 1, and 0 ≤ λ ≤ 1.
If λ = 0, then Aa has the same fitness as AA, e.g. if Aa is phenotypically equivalent with AA (A dominant), and if λ = 1, then Aa has the same fitness as aa, e.g. if Aa is phenotypically equivalent with aa (A recessive). In general λ indicates how close in fitness Aa is to aa.
The fraction of selective deaths in the
n
th
{\displaystyle n^{\mbox{th}}}
generation then is
d
n
=
2
λ
K
p
n
q
n
+
K
q
n
2
=
K
q
n
[
2
λ
+
(
1
−
2
λ
)
q
n
]
{\displaystyle d_{n}=2\lambda Kp_{n}q_{n}+Kq_{n}^{2}=Kq_{n}[2\lambda +(1-2\lambda )q_{n}]}
and the total number of deaths is the population size multiplied by
D
=
K
∑
0
∞
q
n
[
2
λ
+
(
1
−
2
λ
)
q
n
]
.
{\displaystyle D=K\sum _{0}^{\infty }q_{n}\;[2\lambda +(1-2\lambda )q_{n}].}
== Important number 300 ==
Haldane approximates the above equation by taking the continuum limit of the above equation. This is done by multiplying and dividing it by dq so that it is in integral form
d
q
n
=
−
K
p
n
q
n
[
λ
+
(
1
−
2
λ
)
q
n
]
{\displaystyle dq_{n}=-Kp_{n}q_{n}[\lambda +(1-2\lambda )q_{n}]}
substituting q=1-p, the cost (given by the total number of deaths, 'D', required to make a substitution) is given by
D
=
∫
0
q
0
[
2
λ
+
(
1
−
2
λ
)
q
]
(
1
−
q
)
[
λ
+
(
1
−
2
λ
)
q
]
d
q
=
1
1
−
λ
∫
0
q
0
[
1
1
−
q
+
λ
(
1
−
2
λ
)
λ
+
(
1
−
2
λ
)
q
]
d
q
.
{\displaystyle D=\int _{0}^{q_{_{0}}}{\frac {[2\lambda +(1-2\lambda )q]}{(1-q)[\lambda +(1-2\lambda )q]}}dq={\frac {1}{1-\lambda }}\int _{0}^{q_{_{0}}}\left[{\frac {1}{1-q}}+{\frac {\lambda (1-2\lambda )}{\lambda +(1-2\lambda )q}}\right]dq.}
Assuming λ < 1, this gives
D
=
1
1
−
λ
[
−
ln
p
0
+
λ
ln
(
1
−
λ
−
(
1
−
2
λ
)
p
0
λ
)
]
≈
1
1
−
λ
[
−
ln
p
0
+
λ
ln
(
1
−
λ
λ
)
]
{\displaystyle D={\frac {1}{1-\lambda }}\left[-{\mbox{ln }}p_{0}+\lambda {\mbox{ ln }}\left({\frac {1-\lambda -(1-2\lambda )p_{0}}{\lambda }}\right)\right]\approx {\frac {1}{1-\lambda }}\left[-{\mbox{ln }}p_{0}+\lambda {\mbox{ ln }}\left({\frac {1-\lambda }{\lambda }}\right)\right]}
where the last approximation assumes
p
0
{\displaystyle p_{0}}
to be small.
If λ = 1, then we have
D
=
∫
0
q
0
2
−
q
(
1
−
q
)
2
d
q
=
∫
0
q
0
[
1
1
−
q
+
1
(
1
−
q
)
2
]
d
q
=
p
0
−
1
−
ln
p
0
+
O
(
λ
K
)
.
{\displaystyle D=\int _{0}^{q_{_{0}}}{\frac {2-q}{(1-q)^{2}}}dq=\int _{0}^{q_{_{0}}}\left[{\frac {1}{1-q}}+{\frac {1}{(1-q)^{2}}}\right]dq=p_{0}^{-1}-{\mbox{ ln }}p_{0}+O(\lambda K).}
In his discussion Haldane writes that the substitution cost, if it is paid by juvenile deaths, "usually involves a number of deaths equal to about 10 or 20 times the number in a generation" – the minimum being the population size (= "the number in a generation") and rarely being 100 times that number. Haldane assumes 30 to be the mean value.
Assuming substitution of genes to take place slowly, one gene at a time over n generations, the fitness of the species will fall below the optimum (achieved when the substitution is complete) by a factor of about 30/n, so long as this is small – small enough to prevent extinction. Haldane doubts that high intensities – such as in the case of the peppered moth – have occurred frequently and estimates that a value of n = 300 is a probable number of generations. This gives a selection intensity of
I
=
30
/
300
=
0.1
{\displaystyle I=30/300=0.1}
.
Haldane then continues:
The number of loci in a vertebrate species has been estimated at about 40,000. 'Good' species, even when closely related, may differ at several thousand loci, even if the differences at most of them are very slight. But it takes as many deaths, or their equivalents, to replace a gene by one producing a barely distinguishable phenotype as by one producing a very different one. If two species differ at 1000 loci, and the mean rate of gene substitution, as has been suggested, is one per 300 generations, it will take 300,000 generations to generate an interspecific difference. It may take a good deal more, for if an allele a1 is replaced by a10, the population may pass through stages where the commonest genotype is a1a1, a2a2, a3a3, and so on, successively, the various alleles in turn giving maximal fitness in the existing environment and the residual environment.
The number 300 of generations is a conservative estimate for a slowly evolving species not at the brink of extinction by Haldane's calculation. For a difference of at least 1,000 genes, 300,000 generations might be needed – maybe more, if some gene runs through more than one optimisation.
== Origin of the term "Haldane's dilemma" ==
Apparently the first use of the term "Haldane's dilemma" was by paleontologist Leigh Van Valen in his 1963 paper "Haldane's Dilemma, Evolutionary Rates, and Heterosis".
Van Valen writes:
Haldane (1957 [= The Cost of Natural Selection]) drew attention to the fact that in the process of the evolutionary substitution of one allele for another, at any intensity of selection and no matter how slight the importance of the locus, a substantial number of individuals would usually be lost because they did not already possess the new allele. Kimura (1960, 1961) has referred to this loss as the substitutional (or evolutional) load, but because it necessarily involves either a completely new mutation or (more usually) previous change in the environment or the genome, I like to think of it as a dilemma for the population: for most organisms, rapid turnover in a few genes precludes rapid turnover in the others. A corollary of this is that, if an environmental change occurs that necessitates the rather rapid replacement of several genes if a population is to survive, the population becomes extinct.
That is, since a high number of deaths are required to fix one gene rapidly, and dead organisms do not reproduce, fixation of more than one gene simultaneously would conflict. Note that Haldane's model assumes independence of genes at different loci; if the selection intensity is 0.1 for each gene moving towards fixation, and there are N such genes, then the reproductive capacity of the species will be lowered to 0.9N times the original capacity. Therefore, if it is necessary for the population to fix more than one gene, it may not have reproductive capacity to counter the deaths.
== Evolution above Haldane's limit ==
Various models evolve at rates above Haldane's limit.
J. A. Sved showed that a threshold model of selection, where individuals with a phenotype less than the threshold die and individuals with a phenotype above the threshold are all equally fit, allows for a greater substitution rate than Haldane's model (though no obvious upper limit was found, though tentative paths to calculate one were examined e.g. the death rate). John Maynard Smith and Peter O'Donald followed on the same track.
Additionally, the effects of density-dependent processes, epistasis, and soft selective sweeps on the maximum rate of substitution have been examined.
By looking at the polymorphisms within species and divergence between species an estimate can be obtained for the fraction of substitutions that occur due to selection. This parameter is generally called alpha (hence DFE-alpha), and appears to be large in some species, although almost all approaches suggest that the human-chimp divergence was primarily neutral. However, if divergence between Drosophila species was as adaptive as the alpha parameter suggests, then it would exceed Haldane's limit.
== See also ==
Error catastrophe
Genetic drift
Genetic load
Muller's ratchet
== References ==
== Further reading == | Wikipedia/Haldane's_dilemma |
Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. Under this model, the expected time between successive coalescence events increases almost exponentially back in time (with wide variance). Variance in the model comes from both the random passing of alleles from one generation to the next, and the random occurrence of mutations in these alleles.
The mathematical theory of the coalescent was developed independently by several groups in the early 1980s as a natural extension of classical population genetics theory and models,[1][2][3][4] but can be primarily attributed to John Kingman.[5] Advances in coalescent theory include recombination, selection, overlapping generations and virtually any arbitrarily complex evolutionary or demographic model in population genetic analysis.
The model can be used to produce many theoretical genealogies, and then compare observed data to these simulations to test assumptions about the demographic history of a population. Coalescent theory can be used to make inferences about population genetic parameters, such as migration, population size and recombination.
== Theory ==
=== Time to coalescence ===
Consider a single gene locus sampled from two haploid individuals in a population. The ancestry of this sample is traced backwards in time to the point where these two lineages coalesce in their most recent common ancestor (MRCA). Coalescent theory seeks to estimate the expectation of this time period and its variance.
The probability that two lineages coalesce in the immediately preceding generation is the probability that they share a parental DNA sequence. In a population with a constant effective population size with 2Ne copies of each locus, there are 2Ne "potential parents" in the previous generation. Under a random mating model, the probability that two alleles originate from the same parental copy is thus 1/(2Ne) and, correspondingly, the probability that they do not coalesce is 1 − 1/(2Ne).
At each successive preceding generation, the probability of coalescence is geometrically distributed—that is, it is the probability of noncoalescence at the t − 1 preceding generations multiplied by the probability of coalescence at the generation of interest:
P
c
(
t
)
=
(
1
−
1
2
N
e
)
t
−
1
(
1
2
N
e
)
.
{\displaystyle P_{c}(t)=\left(1-{\frac {1}{2N_{e}}}\right)^{t-1}\left({\frac {1}{2N_{e}}}\right).}
For sufficiently large values of Ne, this distribution is well approximated by the continuously defined exponential distribution
P
c
(
t
)
=
1
2
N
e
e
−
t
−
1
2
N
e
.
{\displaystyle P_{c}(t)={\frac {1}{2N_{e}}}e^{-{\frac {t-1}{2N_{e}}}}.}
This is mathematically convenient, as the standard exponential distribution has both the expected value and the standard deviation equal to 2Ne. Therefore, although the expected time to coalescence is 2Ne, actual coalescence times have a wide range of variation. Note that coalescent time is the number of preceding generations where the coalescence took place and not calendar time, though an estimation of the latter can be made multiplying 2Ne with the average time between generations. The above calculations apply equally to a diploid population of effective size Ne (in other words, for a non-recombining segment of DNA, each chromosome can be treated as equivalent to an independent haploid individual; in the absence of inbreeding, sister chromosomes in a single individual are no more closely related than two chromosomes randomly sampled from the population). Some effectively haploid DNA elements, such as mitochondrial DNA, however, are only passed on by one sex, and therefore have one quarter the effective size of the equivalent diploid population (Ne/2)
The mathematical object one formally obtains by letting Ne go to infinity is known as the Kingman coalescent.
=== Neutral variation ===
Coalescent theory can also be used to model the amount of variation in DNA sequences expected from genetic drift and mutation. This value is termed the mean heterozygosity, represented as
H
¯
{\displaystyle {\bar {H}}}
. Mean heterozygosity is calculated as the probability of a mutation occurring at a given generation divided by the probability of any "event" at that generation (either a mutation or a coalescence). The probability that the event is a mutation is the probability of a mutation in either of the two lineages:
2
μ
{\displaystyle 2\mu }
. Thus the mean heterozygosity is equal to
H
¯
=
2
μ
2
μ
+
1
2
N
e
=
4
N
e
μ
1
+
4
N
e
μ
=
θ
1
+
θ
{\displaystyle {\begin{aligned}{\bar {H}}&={\frac {2\mu }{2\mu +{\frac {1}{2N_{e}}}}}\\[6pt]&={\frac {4N_{e}\mu }{1+4N_{e}\mu }}\\[6pt]&={\frac {\theta }{1+\theta }}\end{aligned}}}
For
4
N
e
μ
≫
1
{\displaystyle 4N_{e}\mu \gg 1}
, the vast majority of allele pairs have at least one difference in nucleotide sequence.
=== Extensions ===
There are numerous extensions to the coalescent model, such as the Λ-coalescent which allows for the possibility of multifurcations.[6]
== Graphical representation ==
Coalescents can be visualised using dendrograms which show the relationship of branches of the population to each other. The point where two branches meet indicates a coalescent event.
== Applications ==
=== Disease gene mapping ===
The utility of coalescent theory in the mapping of disease is slowly gaining more appreciation; although the application of the theory is still in its infancy, there are a number of researchers who are actively developing algorithms for the analysis of human genetic data that utilise coalescent theory.[7][8][9]
A considerable number of human diseases can be attributed to genetics, from simple Mendelian diseases like sickle-cell anemia and cystic fibrosis, to more complicated maladies like cancers and mental illnesses. The latter are polygenic diseases, controlled by multiple genes that may occur on different chromosomes, but diseases that are precipitated by a single abnormality are relatively simple to pinpoint and trace – although not so simple that this has been achieved for all diseases. It is immensely useful in understanding these diseases and their processes to know where they are located on chromosomes, and how they have been inherited through generations of a family, as can be accomplished through coalescent analysis.
Genetic diseases are passed from one generation to another just like other genes. While any gene may be shuffled from one chromosome to another during homologous recombination, it is unlikely that one gene alone will be shifted. Thus, other genes that are close enough to the disease gene to be linked to it can be used to trace it.
Polygenic diseases have a genetic basis even though they don't follow Mendelian inheritance models, and these may have relatively high occurrence in populations, and have severe health effects. Such diseases may have incomplete penetrance, and tend to be polygenic, complicating their study. These traits may arise due to many small mutations, which together have a severe and deleterious effect on the health of the individual.
Linkage mapping methods, including Coalescent theory can be put to work on these diseases, since they use family pedigrees to figure out which markers accompany a disease, and how it is inherited. At the very least, this method helps narrow down the portion, or portions, of the genome on which the deleterious mutations may occur. Complications in these approaches include epistatic effects, the polygenic nature of the mutations, and environmental factors. That said, genes whose effects are additive carry a fixed risk of developing the disease, and when they exist in a disease genotype, they can be used to predict risk and map the gene. Both the regular coalescent and the shattered coalescent (which allows that multiple mutations may have occurred in the founding event, and that the disease may occasionally be triggered by environmental factors) have been put to work in understanding disease genes.
Studies have been carried out correlating disease occurrence in fraternal and identical twins, and the results of these studies can be used to inform coalescent modeling. Since identical twins share all of their genome, but fraternal twins only share half their genome, the difference in correlation between the identical and fraternal twins can be used to work out if a disease is heritable, and if so how strongly.
=== The genomic distribution of heterozygosity ===
The human single-nucleotide polymorphism (SNP) map has revealed large regional variations in heterozygosity, more so than can be explained on the basis of (Poisson-distributed) random chance.[10] In part, these variations could be explained on the basis of assessment methods, the availability of genomic sequences, and possibly the standard coalescent population genetic model. Population genetic influences could have a major influence on this variation: some loci presumably would have comparatively recent common ancestors, others might have much older genealogies, and so the regional accumulation of SNPs over time could be quite different. The local density of SNPs along chromosomes appears to cluster in accordance with a variance to mean power law and to obey the Tweedie compound Poisson distribution.[11] In this model the regional variations in the SNP map would be explained by the accumulation of multiple small genomic segments through recombination, where the mean number of SNPs per segment would be gamma distributed in proportion to a gamma distributed time to the most recent common ancestor for each segment.[12]
== History ==
Coalescent theory is a natural extension of the more classical population genetics concept of neutral evolution and is an approximation to the Fisher–Wright (or Wright–Fisher) model for large populations. It was discovered independently by several researchers in the 1980s.[13][14][15][16]
== Software ==
A large body of software exists for both simulating data sets under the coalescent process as well as inferring parameters such as population size and migration rates from genetic data.
BEAST and BEAST 2 – Bayesian inference package via MCMC with a wide range of coalescent models including the use of temporally sampled sequences.[17]
BPP – software package for inferring phylogeny and divergence times among populations under a multispecies coalescent process.
CoaSim – software for simulating genetic data under the coalescent model.
DIYABC – a user-friendly approach to ABC for inference on population history using molecular markers.[18]
DendroPy – a Python library for phylogenetic computing, with classes and methods for simulating pure (unconstrained) coalescent trees as well as constrained coalescent trees under the multispecies coalescent model (i.e., "gene trees in species trees").
GeneRecon – software for the fine-scale mapping of linkage disequilibrium mapping of disease genes using coalescent theory based on a Bayesian MCMC framework.
genetree Archived 2012-02-05 at the Wayback Machine software for estimation of population genetics parameters using coalescent theory and simulation (the R package "popgen"). See also Oxford Mathematical Genetics and Bioinformatics Group
GENOME – rapid coalescent-based whole-genome simulation[19]
IBDSim – a computer package for the simulation of genotypic data under general isolation by distance models.[20]
IMa – IMa implements the same Isolation with Migration model, but does so using a new method that provides estimates of the joint posterior probability density of the model parameters. IMa also allows log likelihood ratio tests of nested demographic models. IMa is based on a method described in Hey and Nielsen (2007 PNAS 104:2785–2790). IMa is faster and better than IM (i.e. by virtue of providing access to the joint posterior density function), and it can be used for most (but not all) of the situations and options that IM can be used for.
Lamarc – software for estimation of rates of population growth, migration, and recombination.
Migraine – a program which implements coalescent algorithms for a maximum likelihood analysis (using Importance Sampling algorithms) of genetic data with a focus on spatially structured populations.[21]
Migrate – maximum likelihood and Bayesian inference of migration rates under the n-coalescent. The inference is implemented using MCMC
MaCS – Markovian Coalescent Simulator – simulates genealogies spatially across chromosomes as a Markovian process. Similar to the SMC algorithm of McVean and Cardin, and supports all demographic scenarios found in Hudson's ms.
ms & msHOT – Richard Hudson's original program for generating samples under neutral models[22] and an extension which allows recombination hotspots.[23]
msms – an extended version of ms that includes selective sweeps.[24]
msprime – a fast and scalable ms-compatible simulator, allowing demographic simulations, producing compact output files for thousands or millions of genomes.
PhyloCoalSimulations - a Julia package to simulate gene trees under the coalescent along a phylogenetic network / admixture graph. The model allows for possible correlated inheritance at reticulations, which represent introgression, gene flow or hybridization events.
Recodon and NetRecodon – software to simulate coding sequences with inter/intracodon recombination, migration, growth rate and longitudinal sampling.[25][26]
CoalEvol and SGWE – software to simulate nucleotide, coding and amino acid sequences under the coalescent with demographics, recombination, population structure with migration and longitudinal sampling.[27]
SARG – structure Ancestral Recombination Graph by Magnus Nordborg
simcoal2 – software to simulate genetic data under the coalescent model with complex demography and recombination
TreesimJ – forward simulation software allowing sampling of genealogies and data sets under diverse selective and demographic models.
== References ==
== Sources ==
=== Articles ===
=== Books ===
== External links ==
EvoMath 3: Genetic Drift and Coalescence, Briefly — overview, with probability equations for genetic drift, and simulation graphs | Wikipedia/Coalescent_theory |
The Neutral Theory of Molecular Evolution is an influential monograph written in 1983 by Japanese evolutionary biologist Motoo Kimura. While the neutral theory of molecular evolution existed since his article in 1968, Kimura felt the need to write a monograph with up-to-date information and evidences showing the importance of his theory in evolution.
Evolution is a change in the frequency of alleles in a population over time. Mutations occur at random and in the Darwinian evolution model natural selection acts on the genetic variation in a population that has arisen through this mutation. These mutations can be beneficial or deleterious and are selected for or against based on that factor. In this theory, every evolutionary event, mutation, and gene polymorphism (neutral differences in phenotype or genotype) would have to be positively or negatively selected for and show some kind of change over many generations. If these genetic differences grow between different populations speciation events can occur. When this theory was first introduced to the scientific community, there was no understanding of genetic principles such as drift or synonymous mutation.
When molecular biologists, like Motoo Kimura (1979), began to examine the DNA evidence, they found that far more mutations occur in non-protein coding regions or are synonymous mutations in coding regions (which do not change the protein structure or function) and are, therefore, not involved in selection as they do not impact an organism’s fitness. These findings began to show that the positive or negative selection in Darwinian evolution was too simplistic to describe every evolutionary process. Through various experiments Kimura was able to determine that proteins in mammalian lineages were polymorphisms of each other, having only one or two point mutations that did not affect the actions of the protein in any way, whereas in Darwinian evolution a slow pattern of selection in genetic lineages with increasing fitness through generations is expected. The molecular evidence showed that DNA changes more often than what was originally expected and no real pattern was found. Polymorphisms in proteins that have no effect to the function are neutral or nearly neutral and do not get selected for or against at all. This theory would mean that each change in DNA that is passed on to the next generation does not result in a morphological change that can be acted upon by natural selection.
Genetic drift, or the result of a limited population size, can also cause a change in allele frequencies over time that can look like Darwinian evolution while actually being an entirely random or as Kimura puts it "neutral" process. In this scenario a relatively small population can lose neutral alleles through the random deaths or migrations of individuals that have them. It may appear to an onlooker that one trait is being selected for over another but in actuality it is a neutral process that is not necessarily undergoing selection as it would in Darwinian evolution.
== Neutral theory in research ==
=== Selective constraint in mammalian genes ===
Within the neutral theory, selective constraint is a type of negative selection that can occur in populations. When selective constraint is reached at a locus negative selection becomes so small that it is effectively neutral. This concept (also brought to prominence by Motoo Kimura (1979) in his expansion of the Neutral Theory of Molecular Evolution (1979) has been put to use in work concerning mammalian genes. In a study done by Price and Graur in 2015, the pair tried to find evidence on whether genes in primates and rodents were either undergoing Darwinian selection or were neutrally evolving under Kimura's model. The number of guanine/cytosine base pairs were utilized in pseudogenes that mimicked nonsynonymous and synonymous mutations that began at what would be expected in a truly neutrally evolving genome for both rodents and primates. Their findings showed that in rodents, the pseudogenes were evolving as one would expect under neutral conditions whereas in primates purifying selection was having an effect on as many as 20% of the pseudogenes tested. By these estimates in primates, 20-40% of their genes could be under selective constraint in the neutral model.
== Content ==
From Lamarck to population genetics
Overdevelopment of the synthetic theory and the proposal of the neutral theory
The neutral mutation-random drift hypothesis as an evolutionary paradigm
Molecular evolutionary rates contrasted with phenotypic evolutionary rates
Some features of molecular evolution
Definition, types and action of natural selection
Molecular structure, selective constraint and the rate of evolution
Population genetics at the molecular level
Summary and conclusion
== See also ==
Molecular evolution
Molecular clock
Population genetics
== References ==
== Further reading ==
Kimura, M. (1983). The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge. ISBN 978-0-521-23109-1.
== External links ==
Review of the book by Gert Korthof | Wikipedia/The_Neutral_Theory_of_Molecular_Evolution |
In population genetics, the Balding–Nichols model is a statistical description of the allele frequencies in the components of a sub-divided population. With background allele frequency p the allele frequencies, in sub-populations separated by Wright's FST F, are distributed according to independent draws from
B
(
1
−
F
F
p
,
1
−
F
F
(
1
−
p
)
)
{\displaystyle B\left({\frac {1-F}{F}}p,{\frac {1-F}{F}}(1-p)\right)}
where B is the Beta distribution. This distribution has mean p and variance Fp(1 – p).
The model is due to David Balding and Richard Nichols and is widely used in the forensic analysis of DNA profiles and in population models for genetic epidemiology.
== References == | Wikipedia/Balding–Nichols_model |
The shifting balance theory is a theory of evolution proposed in 1932 by Sewall Wright, suggesting that adaptive evolution may proceed most quickly when a population divides into subpopulations with restricted gene flow. The name of the theory is borrowed from Wright's metaphor of fitness landscapes (evolutionary landscapes), attempting to explain how a population may move across an adaptive valley to a higher adaptive peak. According to the theory, this movement occurs in three steps:
Genetic drift allows a locally adapted subpopulation to move across an adaptive valley to the base of a higher adaptive peak.
Natural selection will move the subpopulation up the higher peak.
This new superiorly adapted subpopulation may then expand its range and outcompete or interbreed with other subpopulations, causing the spread of new adaptations and movement of the global population toward the new fitness peak.
Although shifting balance theory has been influential in evolutionary biology, inspiring the theories of quantum evolution and punctuated equilibrium, little empirical evidence exists to support the shifting balance process as an important factor in evolution.
== References ==
== Further reading ==
Wade, M.J.; Goodnight, C.J. (1998). "Perspective: the theories of Fisher and Wright in the context of metapopulations: when nature does many small experiments". Evolution. 52 (6): 1537–1553. doi:10.1111/j.1558-5646.1998.tb02235.x. PMID 28565332. S2CID 20901475.
Wright, S (1931). "Evolution in Mendelian populations". Genetics. 16 (2): 97–159. doi:10.1093/genetics/16.2.97. PMC 1201098. PMID 17246615.
Wright, S. 1932. The roles of mutation, inbreeding, crossbreeding and selection in evolution. Proceedings of the 6th International Congress of Genetics: 356–366.
Wright, S.W. (1948). "On the roles of directed and random changes in gene frequency in the genetics of populations". Evolution. 2 (4): 279–294. doi:10.1111/j.1558-5646.1948.tb02746.x. PMID 18104586. S2CID 30360594.
Wright, S.W. (1982). "The shifting balance theory and macroevolution". Annual Review of Genetics. 16: 1–19. doi:10.1146/annurev.ge.16.120182.000245. PMID 6760797. | Wikipedia/Shifting_balance_theory |
The unified neutral theory of biodiversity and biogeography (here "Unified Theory" or "UNTB") is a theory and the title of a monograph by ecologist Stephen P. Hubbell. It aims to explain the diversity and relative abundance of species in ecological communities. Like other neutral theories of ecology, Hubbell assumes that the differences between members of an ecological community of trophically similar species are "neutral", or irrelevant to their success. This implies that niche differences do not influence abundance and the abundance of each species follows a random walk. The theory has sparked controversy, and some authors consider it a more complex version of other null models that fit the data better.
"Neutrality" means that at a given trophic level in a food web, species are equivalent in birth rates, death rates, dispersal rates and speciation rates, when measured on a per-capita basis. This can be considered a null hypothesis to niche theory. Hubbell built on earlier neutral models, including Robert MacArthur and E.O. Wilson's theory of island biogeography and Stephen Jay Gould's concepts of symmetry and null models.
An "ecological community" is a group of trophically similar, sympatric species that actually or potentially compete in a local area for the same or similar resources. Under the Unified Theory, complex ecological interactions are permitted among individuals of an ecological community (such as competition and cooperation), provided that all individuals obey the same rules. Asymmetric phenomena such as parasitism and predation are ruled out by the terms of reference; but cooperative strategies such as swarming, and negative interaction such as competing for limited food or light are allowed (so long as all individuals behave alike).
The theory predicts the existence of a fundamental biodiversity constant, conventionally written θ, that appears to govern species richness on a wide variety of spatial and temporal scales.
== Saturation ==
Although not strictly necessary for a neutral theory, many stochastic models of biodiversity assume a fixed, finite community size (total number of individual organisms). There are unavoidable physical constraints on the total number of individuals that can be packed into a given space (although space per se isn't necessarily a resource, it is often a useful surrogate variable for a limiting resource that is distributed over the landscape; examples would include sunlight or hosts, in the case of parasites).
If a wide range of species are considered (say, giant sequoia trees and duckweed, two species that have very different saturation densities), then the assumption of constant community size might not be very good, because density would be higher if the smaller species were monodominant. Because the Unified Theory refers only to communities of trophically similar, competing species, it is unlikely that population density will vary too widely from one place to another.
Hubbell considers the fact that community sizes are constant and interprets it as a general principle: large landscapes are always biotically saturated with individuals. Hubbell thus treats communities as being of a fixed number of individuals, usually denoted by J.
Exceptions to the saturation principle include disturbed ecosystems such as the Serengeti, where saplings are trampled by elephants and Blue wildebeests; or gardens, where certain species are systematically removed.
=== Species abundances ===
When abundance data on natural populations are collected, two observations are almost universal:
The most common species accounts for a substantial fraction of the individuals sampled;
A substantial fraction of the species sampled are very rare. Indeed, a substantial fraction of the species sampled are singletons, that is, species which are sufficiently rare for only a single individual to have been sampled.
Such observations typically generate a large number of questions. Why are the rare species rare? Why is the most abundant species so much more abundant than the median species abundance?
A non neutral explanation for the rarity of rare species might suggest that rarity is a result of poor adaptation to local conditions. The UNTB suggests that it is not necessary to invoke adaptation or niche differences because neutral dynamics alone can generate such patterns.
Species composition in any community will change randomly with time. Any particular abundance structure will have an associated probability. The UNTB predicts that the probability of a community of J individuals composed of S distinct species with abundances
n
1
{\displaystyle n_{1}}
for species 1,
n
2
{\displaystyle n_{2}}
for species 2, and so on up to
n
S
{\displaystyle n_{S}}
for species S is given by
Pr
(
n
1
,
n
2
,
…
,
n
S
|
θ
,
J
)
=
J
!
θ
S
1
ϕ
1
2
ϕ
2
⋯
J
ϕ
J
ϕ
1
!
ϕ
2
!
⋯
ϕ
J
!
Π
k
=
1
J
(
θ
+
k
−
1
)
{\displaystyle \Pr(n_{1},n_{2},\ldots ,n_{S}|\theta ,J)={\frac {J!\theta ^{S}}{1^{\phi _{1}}2^{\phi _{2}}\cdots J^{\phi _{J}}\phi _{1}!\phi _{2}!\cdots \phi _{J}!\Pi _{k=1}^{J}(\theta +k-1)}}}
where
θ
=
2
J
ν
{\displaystyle \theta =2J\nu }
is the fundamental biodiversity number (
ν
{\displaystyle \nu }
is the speciation rate), and
ϕ
i
{\displaystyle \phi _{i}}
is the number of species that have i individuals in the sample.
This equation shows that the UNTB implies a nontrivial dominance-diversity equilibrium between speciation and extinction.
As an example, consider a community with 10 individuals and three species "a", "b", and "c" with abundances 3, 6 and 1 respectively. Then the formula above would allow us to assess the likelihood of different values of θ. There are thus S = 3 species and
ϕ
1
=
ϕ
3
=
ϕ
6
=
1
{\displaystyle \phi _{1}=\phi _{3}=\phi _{6}=1}
, all other
ϕ
{\displaystyle \phi }
's being zero. The formula would give
Pr
(
3
,
6
,
1
|
θ
,
10
)
=
10
!
θ
3
1
1
⋅
3
1
⋅
6
1
⋅
1
!
1
!
1
!
⋅
θ
(
θ
+
1
)
(
θ
+
2
)
⋯
(
θ
+
9
)
{\displaystyle \Pr(3,6,1|\theta ,10)={\frac {10!\theta ^{3}}{1^{1}\cdot 3^{1}\cdot 6^{1}\cdot 1!1!1!\cdot \theta (\theta +1)(\theta +2)\cdots (\theta +9)}}}
which could be maximized to yield an estimate for θ (in practice, numerical methods are used). The maximum likelihood estimate for θ is about 1.1478.
We could have labelled the species another way and counted the abundances being 1,3,6 instead (or 3,1,6, etc. etc.). Logic tells us that the probability of observing a pattern of abundances will be the same observing any permutation of those abundances. Here we would have
Pr
(
3
;
3
,
6
,
1
)
=
Pr
(
3
;
1
,
3
,
6
)
=
Pr
(
3
;
3
,
1
,
6
)
{\displaystyle \Pr(3;3,6,1)=\Pr(3;1,3,6)=\Pr(3;3,1,6)}
and so on.
To account for this, it is helpful to consider only ranked abundances (that is, to sort the abundances before inserting into the formula). A ranked dominance-diversity configuration is usually written as
Pr
(
S
;
r
1
,
r
2
,
…
,
r
s
,
0
,
…
,
0
)
{\displaystyle \Pr(S;r_{1},r_{2},\ldots ,r_{s},0,\ldots ,0)}
where
r
i
{\displaystyle r_{i}}
is the abundance of the ith most abundant species:
r
1
{\displaystyle r_{1}}
is the abundance of the most abundant,
r
2
{\displaystyle r_{2}}
the abundance of the second most abundant species, and so on. For convenience, the expression is usually "padded" with enough zeros to ensure that there are J species (the zeros indicating that the extra species have zero abundance).
It is now possible to determine the expected abundance of the ith most abundant species:
E
(
r
i
)
=
∑
k
=
1
C
r
i
(
k
)
⋅
Pr
(
S
;
r
1
,
r
2
,
…
,
r
s
,
0
,
…
,
0
)
{\displaystyle E(r_{i})=\sum _{k=1}^{C}r_{i}(k)\cdot \Pr(S;r_{1},r_{2},\ldots ,r_{s},0,\ldots ,0)}
where C is the total number of configurations,
r
i
(
k
)
{\displaystyle r_{i}(k)}
is the abundance of the ith ranked species in the kth configuration, and
P
r
(
…
)
{\displaystyle Pr(\ldots )}
is the dominance-diversity probability. This formula is difficult to manipulate mathematically, but relatively simple to simulate computationally.
The model discussed so far is a model of a regional community, which Hubbell calls the metacommunity. Hubbell also acknowledged that on a local scale, dispersal plays an important role. For example, seeds are more likely to come from nearby parents than from distant parents. Hubbell introduced the parameter m, which denotes the probability of immigration in the local community from the metacommunity. If m = 1, dispersal is unlimited; the local community is just a random sample from the metacommunity and the formulas above apply. If m < 1, dispersal is limited and the local community is a dispersal-limited sample from the metacommunity for which different formulas apply.
It has been shown that
⟨
ϕ
n
⟩
{\displaystyle \langle \phi _{n}\rangle }
, the expected number of species with abundance n, may be calculated by
θ
J
!
n
!
(
J
−
n
)
!
Γ
(
γ
)
Γ
(
J
+
γ
)
∫
y
=
0
γ
Γ
(
n
+
y
)
Γ
(
1
+
y
)
Γ
(
J
−
n
+
γ
−
y
)
Γ
(
γ
−
y
)
exp
(
−
y
θ
/
γ
)
d
y
{\displaystyle \theta {\frac {J!}{n!(J-n)!}}{\frac {\Gamma (\gamma )}{\Gamma (J+\gamma )}}\int _{y=0}^{\gamma }{\frac {\Gamma (n+y)}{\Gamma (1+y)}}{\frac {\Gamma (J-n+\gamma -y)}{\Gamma (\gamma -y)}}\exp(-y\theta /\gamma )\,dy}
where θ is the fundamental biodiversity number, J the community size,
Γ
{\displaystyle \Gamma }
is the gamma function, and
γ
=
(
J
−
1
)
m
/
(
1
−
m
)
{\displaystyle \gamma =(J-1)m/(1-m)}
. This formula is an approximation. The correct formula is derived in a series of papers, reviewed and synthesized by Etienne and Alonso in 2005:
θ
(
I
)
J
(
J
n
)
∫
0
1
(
I
x
)
n
(
I
(
1
−
x
)
)
J
−
n
(
1
−
x
)
θ
−
1
x
d
x
{\displaystyle {\frac {\theta }{(I)_{J}}}{J \choose n}\int _{0}^{1}(Ix)_{n}(I(1-x))_{J-n}{\frac {(1-x)^{\theta -1}}{x}}\,dx}
where
I
=
(
J
−
1
)
∗
m
/
(
1
−
m
)
{\displaystyle I=(J-1)*m/(1-m)}
is a parameter that measures dispersal limitation.
⟨
ϕ
n
⟩
{\displaystyle \langle \phi _{n}\rangle }
is zero for n > J, as there cannot be more species than individuals.
This formula is important because it allows a quick evaluation of the Unified Theory. It is not suitable for testing the theory. For this purpose, the appropriate likelihood function should be used. For the metacommunity this was given above. For the local community with dispersal limitation it is given by:
Pr
(
n
1
,
n
2
,
…
,
n
S
|
θ
,
m
,
J
)
=
J
!
∏
i
=
1
S
n
i
∏
j
=
1
J
Φ
j
!
θ
S
(
I
)
J
∑
A
=
S
J
K
(
D
→
,
A
)
I
A
(
θ
)
A
{\displaystyle \Pr(n_{1},n_{2},\ldots ,n_{S}|\theta ,m,J)={\frac {J!}{\prod _{i=1}^{S}n_{i}\prod _{j=1}^{J}\Phi _{j}!}}{\frac {\theta ^{S}}{(I)_{J}}}\sum _{A=S}^{J}K({\overrightarrow {D}},A){\frac {I^{A}}{(\theta )_{A}}}}
Here, the
K
(
D
→
,
A
)
{\displaystyle K({\overrightarrow {D}},A)}
for
A
=
S
,
.
.
.
,
J
{\displaystyle A=S,...,J}
are coefficients fully determined by the data, being defined as
K
(
D
→
,
A
)
:=
∑
{
a
1
,
.
.
.
,
a
S
|
∑
i
=
1
S
a
i
=
A
}
∏
i
=
1
S
s
¯
(
n
i
,
a
i
)
s
¯
(
a
i
,
1
)
s
¯
(
n
i
,
1
)
{\displaystyle K({\overrightarrow {D}},A):=\sum _{\{a_{1},...,a_{S}|\sum _{i=1}^{S}a_{i}=A\}}\prod _{i=1}^{S}{\frac {{\overline {s}}\left(n_{i},a_{i}\right){\overline {s}}\left(a_{i},1\right)}{{\overline {s}}\left(n_{i},1\right)}}}
This seemingly complicated formula involves Stirling numbers and Pochhammer symbols, but can be very easily calculated.
An example of a species abundance curve can be found in Scientific American.
== Stochastic modelling of species abundances ==
UNTB distinguishes between a dispersal-limited local community of size
J
{\displaystyle J}
and a so-called metacommunity from which species can (re)immigrate and which acts as a heat bath to the local community. The distribution of species in the metacommunity is given by a dynamic equilibrium of speciation and extinction. Both community dynamics are modelled by appropriate urn processes, where each individual is represented by a ball with a color corresponding to its species. With a certain rate
r
{\displaystyle r}
randomly chosen individuals reproduce, i.e. add another ball of their own color to the urn. Since one basic assumption is saturation, this reproduction has to happen at the cost of another random individual from the urn which is removed. At a different rate
μ
{\displaystyle \mu }
single individuals in the metacommunity are replaced by mutants of an entirely new species. Hubbell calls this simplified model for speciation a point mutation, using the terminology of the Neutral theory of molecular evolution. The urn scheme for the metacommunity of
J
M
{\displaystyle J_{M}}
individuals is the following.
At each time step take one of the two possible actions :
With probability
(
1
−
ν
)
{\displaystyle (1-\nu )}
draw an individual at random and replace another random individual from the urn with a copy of the first one.
With probability
ν
{\displaystyle \nu }
draw an individual and replace it with an individual of a new species.
The size
J
M
{\displaystyle J_{M}}
of the metacommunity does not change. This is a point process in time. The length of the time steps is distributed exponentially. For simplicity one can assume that each time step is as long as the mean time between two changes which can be derived from the reproduction and mutation rates
r
{\displaystyle r}
and
μ
{\displaystyle \mu }
. The probability
ν
{\displaystyle \nu }
is given as
ν
=
μ
/
(
r
+
μ
)
{\displaystyle \nu =\mu /(r+\mu )}
.
The species abundance distribution for this urn process is given by Ewens's sampling formula which was originally derived in 1972 for the distribution of alleles under neutral mutations. The expected number
S
M
(
n
)
{\displaystyle S_{M}(n)}
of species in the metacommunity having exactly
n
{\displaystyle n}
individuals is:
S
M
(
n
)
=
θ
n
Γ
(
J
M
+
1
)
Γ
(
J
M
+
θ
−
n
)
Γ
(
J
M
+
1
−
n
)
Γ
(
J
M
+
θ
)
{\displaystyle S_{M}(n)={\frac {\theta }{n}}{\frac {\Gamma (J_{M}+1)\Gamma (J_{M}+\theta -n)}{\Gamma (J_{M}+1-n)\Gamma (J_{M}+\theta )}}}
where
θ
=
(
J
M
−
1
)
ν
/
(
1
−
ν
)
≈
J
M
ν
{\displaystyle \theta =(J_{M}-1)\nu /(1-\nu )\approx J_{M}\nu }
is called the fundamental biodiversity number. For large
metacommunities and
n
≪
J
M
{\displaystyle n\ll J_{M}}
one recovers the Fisher Log-Series as species distribution.
S
M
(
n
)
≈
θ
n
(
J
M
J
M
+
θ
)
n
{\displaystyle S_{M}(n)\approx {\frac {\theta }{n}}\left({\frac {J_{M}}{J_{M}+\theta }}\right)^{n}}
The urn scheme for the local community of fixed size
J
{\displaystyle J}
is very similar to the one for the metacommunity.
At each time step take one of the two actions :
With probability
(
1
−
m
)
{\displaystyle (1-m)}
draw an individual at random and replace another random individual from the urn with a copy of the first one.
With probability
m
{\displaystyle m}
replace a random individual with an immigrant drawn from the metacommunity.
The metacommunity is changing on a much larger timescale and is assumed to be fixed during the evolution of the local community. The resulting distribution of species in the local community and expected values depend on four parameters,
J
{\displaystyle J}
,
J
M
{\displaystyle J_{M}}
,
θ
{\displaystyle \theta }
and
m
{\displaystyle m}
(or
I
{\displaystyle I}
) and are derived by Etienne and Alonso (2005), including several simplifying limit cases like the one presented in the previous section (there called
⟨
ϕ
n
⟩
{\displaystyle \langle \phi _{n}\rangle }
). The parameter
m
{\displaystyle m}
is a dispersal parameter. If
m
=
1
{\displaystyle m=1}
then the local community is just a sample from the metacommunity. For
m
=
0
{\displaystyle m=0}
the local community is completely isolated from the metacommunity and all species will go extinct except one. This case has been analyzed by Hubbell himself. The case
0
<
m
<
1
{\displaystyle 0<m<1}
is characterized by a unimodal species distribution in a Preston Diagram and often fitted by a log-normal distribution. This is understood as an intermediate state between domination of the most common species and a sampling from the metacommunity, where singleton species are most abundant. UNTB thus predicts that in dispersal limited communities rare species become even rarer. The log-normal distribution describes the maximum and the abundance of common species very well but underestimates the number of very rare species considerably which becomes only apparent for very large sample sizes.
== Species-area relationships ==
The Unified Theory unifies biodiversity, as measured by species-abundance curves, with biogeography, as measured by species-area curves. Species-area relationships show the rate at which species diversity increases with area. The topic is of great interest to conservation biologists in the design of reserves, as it is often desired to harbour as many species as possible.
The most commonly encountered relationship is the power law given by
S
=
c
A
z
{\displaystyle S=cA^{z}}
where S is the number of species found, A is the area sampled, and c and z are constants. This relationship, with different constants, has been found to fit a wide range of empirical data.
From the perspective of Unified Theory, it is convenient to consider S as a function of total community size J. Then
S
=
k
J
z
{\displaystyle S=kJ^{z}}
for some constant k, and if this relationship were exactly true, the species area line would be straight on log scales. It is typically found that the curve is not straight, but the slope changes from being steep at small areas, shallower at intermediate areas, and steep at the largest areas.
The formula for species composition may be used to calculate the expected number of species present in a community under the assumptions of the Unified Theory. In symbols
E
{
S
|
θ
,
J
}
=
θ
θ
+
θ
θ
+
1
+
θ
θ
+
2
+
⋯
+
θ
θ
+
J
−
1
{\displaystyle E\left\{S|\theta ,J\right\}={\frac {\theta }{\theta }}+{\frac {\theta }{\theta +1}}+{\frac {\theta }{\theta +2}}+\cdots +{\frac {\theta }{\theta +J-1}}}
where θ is the fundamental biodiversity number. This formula specifies the expected number of species sampled in a community of size J. The last term,
θ
/
(
θ
+
J
−
1
)
{\displaystyle \theta /(\theta +J-1)}
, is the expected number of new species encountered when adding one new individual to the community. This is an increasing function of θ and a decreasing function of J, as expected.
By making the substitution
J
=
ρ
A
{\displaystyle J=\rho A}
(see section on saturation above), then the expected number of species becomes
Σ
θ
/
(
θ
+
ρ
A
−
1
)
{\displaystyle \Sigma \theta /(\theta +\rho A-1)}
.
The formula above may be approximated to an integral giving
S
(
θ
)
=
1
+
θ
ln
(
1
+
J
−
1
θ
)
.
{\displaystyle S(\theta )=1+\theta \ln \left(1+{\frac {J-1}{\theta }}\right).}
This formulation is predicated on a random placement of individuals.
=== Example ===
Consider the following (synthetic) dataset of 27 individuals:
a,a,a,a,a,a,a,a,a,a,b,b,b,b,c,c,c,c,d,d,d,d,e,f,g,h,i
There are thus 27 individuals of 9 species ("a" to "i") in the sample. Tabulating this would give:
a b c d e f g h i
10 4 4 4 1 1 1 1 1
indicating that species "a" is the most abundant with 10 individuals and species "e" to "i" are singletons. Tabulating the table gives:
species abundance 1 2 3 4 5 6 7 8 9 10
number of species 5 0 0 3 0 0 0 0 0 1
On the second row, the 5 in the first column means that five species, species "e" through "i", have abundance one. The following two zeros in columns 2 and 3 mean that zero species have abundance 2 or 3. The 3 in column 4 means that three species, species "b", "c", and "d", have abundance four. The final 1 in column 10 means that one species, species "a", has abundance 10.
This type of dataset is typical in biodiversity studies. Observe how more than half the biodiversity (as measured by species count) is due to singletons.
For real datasets, the species abundances are binned into logarithmic categories, usually using base 2, which gives bins of abundance 0–1, abundance 1–2, abundance 2–4, abundance 4–8, etc. Such abundance classes are called octaves; early developers of this concept included F. W. Preston and histograms showing number of species as a function of abundance octave are known as Preston diagrams.
These bins are not mutually exclusive: a species with abundance 4, for example, could be considered as lying in the 2-4 abundance class or the 4-8 abundance class. Species with an abundance of an exact power of 2 (i.e. 2,4,8,16, etc.) are conventionally considered as having 50% membership in the lower abundance class 50% membership in the upper class. Such species are thus considered to be evenly split between the two adjacent classes (apart from singletons which are classified into the rarest category). Thus in the example above, the Preston abundances would be
abundance class 1 1-2 2-4 4-8 8-16
species 5 0 1.5 1.5 1
The three species of abundance four thus appear, 1.5 in abundance class 2–4, and 1.5 in 4–8.
The above method of analysis cannot account for species that are unsampled: that is, species sufficiently rare to have been recorded zero times. Preston diagrams are thus truncated at zero abundance. Preston called this the veil line and noted that the cutoff point would move as more individuals are sampled.
== Dynamics ==
All biodiversity patterns previously described are related to time-independent quantities. For biodiversity evolution and species preservation, it is crucial to compare the dynamics of ecosystems with models (Leigh, 2007). An easily accessible index of the underlying evolution is the so-called species turnover distribution (STD), defined as the probability P(r,t) that the population of any species has varied by a fraction r after a given time t.
A neutral model that can analytically predict both the relative species abundance (RSA) at steady-state and the STD at time t has been presented in Azaele et al. (2006). Within this framework the population of any species is represented by a continuous (random) variable x, whose evolution is governed by the following Langevin equation:
x
˙
=
b
−
x
/
τ
+
D
x
ξ
(
t
)
{\displaystyle {\dot {x}}=b-x/\tau +{\sqrt {Dx}}\xi (t)}
where b is the immigration rate from a large regional community,
−
x
/
τ
{\displaystyle -x/\tau }
represents competition for finite resources and D is related to demographic stochasticity;
ξ
(
t
)
{\displaystyle \xi (t)}
is a Gaussian white noise. The model can also be derived as a continuous approximation of a master equation, where birth and death rates are independent of species, and predicts that at steady-state the RSA is simply a gamma distribution.
From the exact time-dependent solution of the previous equation, one can exactly calculate the STD at time t under stationary conditions:
P
(
r
,
t
)
=
A
λ
+
1
λ
(
e
t
/
τ
)
b
/
2
D
1
−
e
−
t
/
τ
(
sinh
(
t
2
τ
)
λ
)
b
D
+
1
(
4
λ
2
(
λ
+
1
)
2
e
t
/
τ
−
4
λ
)
b
D
+
1
2
.
{\displaystyle P(r,t)=A{\frac {\lambda +1}{\lambda }}{\frac {(e^{t/\tau })^{b/2D}}{1-e^{-t/\tau }}}\left({\frac {\sinh({\frac {t}{2\tau }})}{\lambda }}\right)^{{\frac {b}{D}}+1}\left({\frac {4\lambda ^{2}}{(\lambda +1)^{2}e^{t/\tau }-4\lambda }}\right)^{{\frac {b}{D}}+{\frac {1}{2}}}.}
This formula provides good fits of data collected in the Barro Colorado tropical forest from 1990 to 2000. From the best fit one can estimate
τ
{\displaystyle \tau }
~ 3500 years with a broad uncertainty due to the relative short time interval of the sample. This parameter can be interpreted as the relaxation time of the system, i.e. the time the system needs to recover from a perturbation of species distribution. In the same framework, the estimated mean species lifetime is very close to the fitted temporal scale
τ
{\displaystyle \tau }
. This suggests that the neutral assumption could correspond to a scenario in which species originate and become extinct on the same timescales of fluctuations of the whole ecosystem.
== Testing ==
The theory has provoked much controversy as it "abandons" the role of ecology when modelling ecosystems. The theory has been criticized as it requires an equilibrium, yet climatic and geographical conditions are thought to change too frequently for this to be attained.
Tests on bird and tree abundance data demonstrate that the theory is usually a poorer match to the data than alternative null hypotheses that use fewer parameters (a log-normal model with two tunable parameters, compared to the neutral theory's three), and are thus more parsimonious. The theory also fails to describe coral reef communities, studied by Dornelas et al., and is a poor fit to data in intertidal communities. It also fails to explain why families of tropical trees have statistically highly correlated numbers of species in phylogenetically unrelated and geographically distant forest plots in Central and South America, Africa, and South East Asia.
While the theory has been heralded as a valuable tool for palaeontologists, little work has so far been done to test the theory against the fossil record.
== See also ==
Biodiversity Action Plan
Functional equivalence (ecology)
Ewens's sampling formula
Metabolic Scaling Theory (Metabolic theory of ecology)
Neutral theory of molecular evolution
Warren Ewens
== References ==
== Further reading ==
Gilbert, B; Lechowicz MJ (2004). "Neutrality, niches, and dispersal in a temperate forest understory". PNAS. 101 (20): 7651–7656. Bibcode:2004PNAS..101.7651G. doi:10.1073/pnas.0400814101. PMC 419661. PMID 15128948.
Leigh E.G. (Jr) (2007). "Neutral theory: a historical perspective". Journal of Evolutionary Biology. 20 (6): 2075–2091. doi:10.1111/j.1420-9101.2007.01410.x. PMID 17956380.
Preston, F. W. (1962). "The Canonical Distribution of Commonness and Rarity: Part I". Ecology. 43 (2). Ecology, Vol. 43, No. 2: 185–215. Bibcode:1962Ecol...43..185P. doi:10.2307/1931976. JSTOR 1931976.
Pueyo, S.; He, F.; Zillio, T. (2007). "The maximum entropy formalism and the idiosyncratic theory of biodiversity". Ecology Letters. 10 (11): 1017–1028. Bibcode:2007EcolL..10.1017P. doi:10.1111/j.1461-0248.2007.01096.x. PMC 2121135. PMID 17692099.
== External links ==
Scientific American Interview with Steve Hubbell
R package for implementing UNTB Archived September 18, 2019, at the Wayback Machine
"Ecological neutral theory: useful model or statement of ignorance?" in Cell Press Discussions | Wikipedia/Unified_neutral_theory_of_biodiversity |
In the theory of evolution and natural selection, the Price equation (also known as Price's equation or Price's theorem) describes how a trait or allele changes in frequency over time. The equation uses a covariance between a trait and fitness, to give a mathematical description of evolution and natural selection. It provides a way to understand the effects that gene transmission and natural selection have on the frequency of alleles within each new generation of a population. The Price equation was derived by George R. Price, working in London to re-derive W.D. Hamilton's work on kin selection. Examples of the Price equation have been constructed for various evolutionary cases. The Price equation also has applications in economics.
The Price equation is a mathematical relationship between various statistical descriptors of population dynamics, rather than a physical or biological law, and as such is not subject to experimental verification. In simple terms, it is a mathematical statement of the expression "survival of the fittest".
== Statement ==
The Price equation shows that a change in the average amount
z
{\displaystyle z}
of a trait in a population from one generation to the next (
Δ
z
{\displaystyle \Delta z}
) is determined by the covariance between the amounts
z
i
{\displaystyle z_{i}}
of the trait for subpopulation
i
{\displaystyle i}
and the fitnesses
w
i
{\displaystyle w_{i}}
of the subpopulations, together with the expected change in the amount of the trait value due to fitness, namely
E
(
w
i
Δ
z
i
)
{\displaystyle \mathrm {E} (w_{i}\Delta z_{i})}
:
Δ
z
=
1
w
cov
(
w
i
,
z
i
)
+
1
w
E
(
w
i
Δ
z
i
)
.
{\displaystyle \Delta {z}={\frac {1}{w}}\operatorname {cov} (w_{i},z_{i})+{\frac {1}{w}}\operatorname {E} (w_{i}\,\Delta z_{i}).}
Here
w
{\displaystyle w}
is the average fitness over the population, and
E
{\displaystyle \operatorname {E} }
and
cov
{\displaystyle \operatorname {cov} }
represent the population mean and covariance respectively. 'Fitness'
w
{\displaystyle w}
is the ratio of the average number of offspring for the whole population per the number of adult individuals in the population, and
w
i
{\displaystyle w_{i}}
is that same ratio only for subpopulation
i
{\displaystyle i}
.
If the covariance between fitness (
w
i
{\displaystyle w_{i}}
) and trait value (
z
i
{\displaystyle z_{i}}
) is positive, the trait value is expected to rise on average across population
i
{\displaystyle i}
. If the covariance is negative, the characteristic is harmful, and its frequency is expected to drop.
The second term,
E
(
w
i
Δ
z
i
)
{\displaystyle \mathrm {E} (w_{i}\Delta z_{i})}
, represents the portion of
Δ
z
{\displaystyle \Delta z}
due to all factors other than direct selection which can affect trait evolution. This term can encompass genetic drift, mutation bias, or meiotic drive. Additionally, this term can encompass the effects of multi-level selection or group selection. Price (1972) referred to this as the "environment change" term, and denoted both terms using partial derivative notation (∂NS and ∂EC). This concept of environment includes interspecies and ecological effects. Price describes this as follows:
Fisher adopted the somewhat unusual point of view of regarding dominance and epistasis as being environment effects. For example, he writes (1941): ‘A change in the proportion of any pair of genes itself constitutes a change in the environment in which individuals of the species find themselves.’ Hence he regarded the natural selection effect on M as being limited to the additive or linear effects of changes in gene frequencies, while everything else – dominance, epistasis, population pressure, climate, and interactions with other species – he regarded as a matter of the environment.
== Proof ==
Suppose we are given four equal-length lists of real numbers
n
i
{\displaystyle n_{i}}
,
z
i
{\displaystyle z_{i}}
,
n
i
′
{\displaystyle n_{i}'}
,
z
i
′
{\displaystyle z_{i}'}
from which we may define
w
i
=
n
i
′
/
n
i
{\displaystyle w_{i}=n_{i}'/n_{i}}
.
n
i
{\displaystyle n_{i}}
and
z
i
{\displaystyle z_{i}}
will be called the parent population numbers and characteristics associated with each index i. Likewise
n
i
′
{\displaystyle n_{i}'}
and
z
i
′
{\displaystyle z_{i}'}
will be called the child population numbers and characteristics, and
w
i
′
{\displaystyle w_{i}'}
will be called the fitness associated with index i. (Equivalently, we could have been given
n
i
{\displaystyle n_{i}}
,
z
i
{\displaystyle z_{i}}
,
w
i
{\displaystyle w_{i}}
,
z
i
′
{\displaystyle z_{i}'}
with
n
i
′
=
w
i
n
i
{\displaystyle n_{i}'=w_{i}n_{i}}
.) Define the parent and child population totals:
and the probabilities (or frequencies):
Note that these are of the form of probability mass functions in that
∑
i
q
i
=
∑
i
q
i
′
=
1
{\displaystyle \sum _{i}q_{i}=\sum _{i}q_{i}'=1}
and are in fact the probabilities that a random individual drawn from the parent or child population has a characteristic
z
i
{\displaystyle z_{i}}
. Define the fitnesses:
w
i
=
d
e
f
n
i
′
/
n
i
{\displaystyle w_{i}\;{\stackrel {\mathrm {def} }{=}}\;n_{i}'/n_{i}}
The average of any list
x
i
{\displaystyle x_{i}}
is given by:
E
(
x
i
)
=
∑
i
q
i
x
i
{\displaystyle E(x_{i})=\sum _{i}q_{i}x_{i}}
so the average characteristics are defined as:
and the average fitness is:
w
=
d
e
f
∑
i
q
i
w
i
{\displaystyle w\;{\stackrel {\mathrm {def} }{=}}\;\sum _{i}q_{i}w_{i}}
A simple theorem can be proved:
q
i
w
i
=
(
n
i
n
)
(
n
i
′
n
i
)
=
(
n
i
′
n
′
)
(
n
′
n
)
=
q
i
′
(
n
′
n
)
{\displaystyle q_{i}w_{i}=\left({\frac {n_{i}}{n}}\right)\left({\frac {n_{i}'}{n_{i}}}\right)=\left({\frac {n_{i}'}{n'}}\right)\left({\frac {n'}{n}}\right)=q_{i}'\left({\frac {n'}{n}}\right)}
so that:
w
=
n
′
n
∑
i
q
i
′
=
n
′
n
{\displaystyle w={\frac {n'}{n}}\sum _{i}q_{i}'={\frac {n'}{n}}}
and
q
i
w
i
=
w
q
i
′
{\displaystyle q_{i}w_{i}=w\,q_{i}'}
The covariance of
w
i
{\displaystyle w_{i}}
and
z
i
{\displaystyle z_{i}}
is defined by:
cov
(
w
i
,
z
i
)
=
d
e
f
E
(
w
i
z
i
)
−
E
(
w
i
)
E
(
z
i
)
=
∑
i
q
i
w
i
z
i
−
w
z
{\displaystyle \operatorname {cov} (w_{i},z_{i})\;{\stackrel {\mathrm {def} }{=}}\;E(w_{i}z_{i})-E(w_{i})E(z_{i})=\sum _{i}q_{i}w_{i}z_{i}-wz}
Defining
Δ
z
i
=
d
e
f
z
i
′
−
z
i
{\displaystyle \Delta z_{i}\;{\stackrel {\mathrm {def} }{=}}\;z_{i}'-z_{i}}
, the expectation value of
w
i
Δ
z
i
{\displaystyle w_{i}\Delta z_{i}}
is
E
(
w
i
Δ
z
i
)
=
∑
q
i
w
i
(
z
i
′
−
z
i
)
=
∑
i
q
i
w
i
z
i
′
−
∑
i
q
i
w
i
z
i
{\displaystyle E(w_{i}\Delta z_{i})=\sum q_{i}w_{i}(z_{i}'-z_{i})=\sum _{i}q_{i}w_{i}z_{i}'-\sum _{i}q_{i}w_{i}z_{i}}
The sum of the two terms is:
cov
(
w
i
,
z
i
)
+
E
(
w
i
Δ
z
i
)
=
∑
i
q
i
w
i
z
i
−
w
z
+
∑
i
q
i
w
i
z
i
′
−
∑
i
q
i
w
i
z
i
=
∑
i
q
i
w
i
z
i
′
−
w
z
{\displaystyle \operatorname {cov} (w_{i},z_{i})+E(w_{i}\Delta z_{i})=\sum _{i}q_{i}w_{i}z_{i}-wz+\sum _{i}q_{i}w_{i}z_{i}'-\sum _{i}q_{i}w_{i}z_{i}=\sum _{i}q_{i}w_{i}z_{i}'-wz}
Using the above mentioned simple theorem, the sum becomes
cov
(
w
i
,
z
i
)
+
E
(
w
i
Δ
z
i
)
=
w
∑
i
q
i
′
z
i
′
−
w
z
=
w
z
′
−
w
z
=
w
Δ
z
{\displaystyle \operatorname {cov} (w_{i},z_{i})+E(w_{i}\Delta z_{i})=w\sum _{i}q_{i}'z_{i}'-wz=wz'-wz=w\Delta z}
where
Δ
z
=
d
e
f
z
′
−
z
{\displaystyle \Delta z\;{\stackrel {\mathrm {def} }{=}}\;z'-z}
.
=== Derivation of the continuous-time Price equation ===
Consider a set of groups with
i
=
1
,
.
.
.
,
n
{\displaystyle i=1,...,n}
that are characterized by a particular trait, denoted by
x
i
{\displaystyle x_{i}}
. The number
n
i
{\displaystyle n_{i}}
of individuals belonging to group
i
{\displaystyle i}
experiences exponential growth:
d
n
i
d
t
=
f
i
n
i
{\displaystyle {dn_{i} \over {dt}}=f_{i}n_{i}}
where
f
i
{\displaystyle f_{i}}
corresponds to the fitness of the group. We want to derive an equation describing the time-evolution of the expected value of the trait:
E
(
x
)
=
∑
i
p
i
x
i
≡
μ
,
p
i
=
n
i
∑
i
n
i
{\displaystyle \mathbb {E} (x)=\sum _{i}p_{i}x_{i}\equiv \mu ,\quad p_{i}={n_{i} \over {\sum _{i}n_{i}}}}
Based on the chain rule, we may derive an ordinary differential equation:
d
μ
d
t
=
∑
i
∂
μ
∂
p
i
d
p
i
d
t
+
∑
i
∂
μ
∂
x
i
d
x
i
d
t
=
∑
i
x
i
d
p
i
d
t
+
∑
i
p
i
d
x
i
d
t
=
∑
i
x
i
d
p
i
d
t
+
E
(
d
x
d
t
)
{\displaystyle {\begin{aligned}{d\mu \over {dt}}&=\sum _{i}{\partial \mu \over {\partial p_{i}}}{dp_{i} \over {dt}}+\sum _{i}{\partial \mu \over {\partial x_{i}}}{dx_{i} \over {dt}}\\&=\sum _{i}x_{i}{dp_{i} \over {dt}}+\sum _{i}p_{i}{dx_{i} \over {dt}}\\&=\sum _{i}x_{i}{dp_{i} \over {dt}}+\mathbb {E} \left({dx \over {dt}}\right)\end{aligned}}}
A further application of the chain rule for
d
p
i
/
d
t
{\displaystyle dp_{i}/dt}
gives us:
d
p
i
d
t
=
∑
j
∂
p
i
∂
n
j
d
n
j
d
t
,
∂
p
i
∂
n
j
=
{
−
p
i
/
N
,
i
≠
j
(
1
−
p
i
)
/
N
,
i
=
j
{\displaystyle {dp_{i} \over {dt}}=\sum _{j}{\partial p_{i} \over {\partial n_{j}}}{dn_{j} \over {dt}},\quad {\partial p_{i} \over {\partial n_{j}}}={\begin{cases}-p_{i}/N,\quad &i\neq j\\(1-p_{i})/N,\quad &i=j\end{cases}}}
Summing up the components gives us that:
d
p
i
d
t
=
p
i
(
f
i
−
∑
j
p
j
f
j
)
=
p
i
[
f
i
−
E
(
f
)
]
{\displaystyle {\begin{aligned}{dp_{i} \over {dt}}&=p_{i}\left(f_{i}-\sum _{j}p_{j}f_{j}\right)\\&=p_{i}\left[f_{i}-\mathbb {E} (f)\right]\end{aligned}}}
which is also known as the replicator equation. Now, note that:
∑
i
x
i
d
p
i
d
t
=
∑
i
p
i
x
i
[
f
i
−
E
(
f
)
]
=
E
{
x
i
[
f
i
−
E
(
f
)
]
}
=
Cov
(
x
,
f
)
{\displaystyle {\begin{aligned}\sum _{i}x_{i}{dp_{i} \over {dt}}&=\sum _{i}p_{i}x_{i}\left[f_{i}-\mathbb {E} (f)\right]\\&=\mathbb {E} \left\{x_{i}\left[f_{i}-\mathbb {E} (f)\right]\right\}\\&={\text{Cov}}(x,f)\end{aligned}}}
Therefore, putting all of these components together, we arrive at the continuous-time Price equation:
d
d
t
E
(
x
)
=
Cov
(
x
,
f
)
⏟
Selection effect
+
E
(
x
˙
)
⏟
Dynamic effect
{\displaystyle {d \over {dt}}\mathbb {E} (x)=\underbrace {{\text{Cov}}(x,f)} _{\text{Selection effect}}+\underbrace {\mathbb {E} ({\dot {x}})} _{\text{Dynamic effect}}}
== Simple Price equation ==
When the characteristic values
z
i
{\displaystyle z_{i}}
do not change from the parent to the child generation, the second term in the Price equation becomes zero resulting in a simplified version of the Price equation:
w
Δ
z
=
cov
(
w
i
,
z
i
)
{\displaystyle w\,\Delta z=\operatorname {cov} \left(w_{i},z_{i}\right)}
which can be restated as:
Δ
z
=
cov
(
v
i
,
z
i
)
{\displaystyle \Delta z=\operatorname {cov} \left(v_{i},z_{i}\right)}
where
v
i
{\displaystyle v_{i}}
is the fractional fitness:
v
i
=
w
i
/
w
{\displaystyle v_{i}=w_{i}/w}
.
This simple Price equation can be proven using the definition in Equation (2) above. It makes this fundamental statement about evolution: "If a certain inheritable characteristic is correlated with an increase in fractional fitness, the average value of that characteristic in the child population will be increased over that in the parent population."
=== Applications ===
The Price equation can describe any system that changes over time, but is most often applied in evolutionary biology. The evolution of sight provides an example of simple directional selection. The evolution of sickle cell anemia shows how a heterozygote advantage can affect trait evolution. The Price equation can also be applied to population context dependent traits such as the evolution of sex ratios. Additionally, the Price equation is flexible enough to model second order traits such as the evolution of mutability. The Price equation also provides an extension to Founder effect which shows change in population traits in different settlements
=== Dynamical sufficiency and the simple Price equation ===
Sometimes the genetic model being used encodes enough information into the parameters used by the Price equation to allow the calculation of the parameters for all subsequent generations. This property is referred to as dynamical sufficiency. For simplicity, the following looks at dynamical sufficiency for the simple Price equation, but is also valid for the full Price equation.
Referring to the definition in Equation (2), the simple Price equation for the character
z
{\displaystyle z}
can be written:
w
(
z
′
−
z
)
=
⟨
w
i
z
i
⟩
−
w
z
{\displaystyle w(z'-z)=\langle w_{i}z_{i}\rangle -wz}
For the second generation:
w
′
(
z
″
−
z
′
)
=
⟨
w
i
′
z
i
′
⟩
−
w
′
z
′
{\displaystyle w'(z''-z')=\langle w'_{i}z'_{i}\rangle -w'z'}
The simple Price equation for
z
{\displaystyle z}
only gives us the value of
z
′
{\displaystyle z'}
for the first generation, but does not give us the value of
w
′
{\displaystyle w'}
and
⟨
w
i
z
i
⟩
{\displaystyle \langle w_{i}z_{i}\rangle }
, which are needed to calculate
z
″
{\displaystyle z''}
for the second generation. The variables
w
i
{\displaystyle w_{i}}
and
⟨
w
i
z
i
⟩
{\displaystyle \langle w_{i}z_{i}\rangle }
can both be thought of as characteristics of the first generation, so the Price equation can be used to calculate them as well:
w
(
w
′
−
w
)
=
⟨
w
i
2
⟩
−
w
2
w
(
⟨
w
i
′
z
i
′
⟩
−
⟨
w
i
z
i
⟩
)
=
⟨
w
i
2
z
i
⟩
−
w
⟨
w
i
z
i
⟩
{\displaystyle {\begin{aligned}w(w'-w)&=\langle w_{i}^{2}\rangle -w^{2}\\w\left(\langle w'_{i}z'_{i}\rangle -\langle w_{i}z_{i}\rangle \right)&=\langle w_{i}^{2}z_{i}\rangle -w\langle w_{i}z_{i}\rangle \end{aligned}}}
The five 0-generation variables
w
{\displaystyle w}
,
z
{\displaystyle z}
,
⟨
w
i
z
i
⟩
{\displaystyle \langle w_{i}z_{i}\rangle }
,
⟨
w
i
2
⟩
{\displaystyle \langle w_{i}^{2}\rangle }
, and
⟨
w
i
2
z
i
{\displaystyle \langle w_{i}^{2}z_{i}}
must be known before proceeding to calculate the three first generation variables
w
′
{\displaystyle w'}
,
z
′
{\displaystyle z'}
, and
⟨
w
i
′
z
i
′
⟩
{\displaystyle \langle w'_{i}z'_{i}\rangle }
, which are needed to calculate
z
″
{\displaystyle z''}
for the second generation. It can be seen that in general the Price equation cannot be used to propagate forward in time unless there is a way of calculating the higher moments
⟨
w
i
n
⟩
{\displaystyle \langle w_{i}^{n}\rangle }
and
⟨
w
i
n
z
i
⟩
{\displaystyle \langle w_{i}^{n}z_{i}\rangle }
from the lower moments in a way that is independent of the generation. Dynamical sufficiency means that such equations can be found in the genetic model, allowing the Price equation to be used alone as a propagator of the dynamics of the model forward in time.
== Full Price equation ==
The simple Price equation was based on the assumption that the characters
z
i
{\displaystyle z_{i}}
do not change over one generation. If it is assumed that they do change, with
z
i
{\displaystyle z_{i}}
being the value of the character in the child population, then the full Price equation must be used. A change in character can come about in a number of ways. The following two examples illustrate two such possibilities, each of which introduces new insight into the Price equation.
=== Genotype fitness ===
We focus on the idea of the fitness of the genotype. The index
i
{\displaystyle i}
indicates the genotype and the number of type
i
{\displaystyle i}
genotypes in the child population is:
n
i
′
=
∑
j
w
j
i
n
j
{\displaystyle n'_{i}=\sum _{j}w_{ji}n_{j}\,}
which gives fitness:
w
i
=
n
i
′
n
i
{\displaystyle w_{i}={\frac {n'_{i}}{n_{i}}}}
Since the individual mutability
z
i
{\displaystyle z_{i}}
does not change, the average mutabilities will be:
z
=
1
n
∑
i
z
i
n
i
z
′
=
1
n
′
∑
i
z
i
n
i
′
{\displaystyle {\begin{aligned}z&={\frac {1}{n}}\sum _{i}z_{i}n_{i}\\z'&={\frac {1}{n'}}\sum _{i}z_{i}n'_{i}\end{aligned}}}
with these definitions, the simple Price equation now applies.
=== Lineage fitness ===
In this case we want to look at the idea that fitness is measured by the number of children an organism has, regardless of their genotype. Note that we now have two methods of grouping, by lineage, and by genotype. It is this complication that will introduce the need for the full Price equation. The number of children an
i
{\displaystyle i}
-type organism has is:
n
i
′
=
n
i
∑
j
w
i
j
{\displaystyle n'_{i}=n_{i}\sum _{j}w_{ij}\,}
which gives fitness:
w
i
=
n
i
′
n
i
=
∑
j
w
i
j
{\displaystyle w_{i}={\frac {n'_{i}}{n_{i}}}=\sum _{j}w_{ij}}
We now have characters in the child population which are the average character of the
i
{\displaystyle i}
-th parent.
z
j
′
=
∑
i
n
i
z
i
w
i
j
∑
i
n
i
w
i
j
{\displaystyle z'_{j}={\frac {\sum _{i}n_{i}z_{i}w_{ij}}{\sum _{i}n_{i}w_{ij}}}}
with global characters:
z
=
1
n
∑
i
z
i
n
i
z
′
=
1
n
′
∑
i
z
i
n
i
′
{\displaystyle {\begin{aligned}z&={\frac {1}{n}}\sum _{i}z_{i}n_{i}\\z'&={\frac {1}{n'}}\sum _{i}z_{i}n'_{i}\end{aligned}}}
with these definitions, the full Price equation now applies.
== Criticism ==
The use of the change in average characteristic (
z
′
−
z
{\displaystyle z'-z}
) per generation as a measure of evolutionary progress is not always appropriate. There may be cases where the average remains unchanged (and the covariance between fitness and characteristic is zero) while evolution is nevertheless in progress. For example, if we have
z
i
=
(
1
,
2
,
3
)
{\displaystyle z_{i}=(1,2,3)}
,
n
i
=
(
1
,
1
,
1
)
{\displaystyle n_{i}=(1,1,1)}
, and
w
i
=
(
1
,
4
,
1
)
{\displaystyle w_{i}=(1,4,1)}
, then for the child population,
n
i
′
=
(
1
,
4
,
1
)
{\displaystyle n_{i}'=(1,4,1)}
showing that the peak fitness at
w
2
=
4
{\displaystyle w_{2}=4}
is in fact fractionally increasing the population of individuals with
z
i
=
2
{\displaystyle z_{i}=2}
. However, the average characteristics are z=2 and z'=2 so that
Δ
z
=
0
{\displaystyle \Delta z=0}
. The covariance
c
o
v
(
z
i
,
w
i
)
{\displaystyle \mathrm {cov} (z_{i},w_{i})}
is also zero. The simple Price equation is required here, and it yields 0=0. In other words, it yields no information regarding the progress of evolution in this system.
A critical discussion of the use of the Price equation can be found in van Veelen (2005), van Veelen et al. (2012), and van Veelen (2020). Frank (2012) discusses the criticism in van Veelen et al. (2012).
== Cultural references ==
Price's equation features in the plot and title of the 2008 thriller film WΔZ.
The Price equation also features in posters in the computer game BioShock 2, in which a consumer of a "Brain Boost" tonic is seen deriving the Price equation while simultaneously reading a book. The game is set in the 1950s, substantially before Price's work.
== See also ==
The breeder's equation, which is a special case of the Price equation.
== References ==
== Further reading == | Wikipedia/Price_equation |
Microbiology (from Ancient Greek μῑκρος (mīkros) 'small' βίος (bíos) 'life' and -λογία (-logía) 'study of') is the scientific study of microorganisms, those being of unicellular (single-celled), multicellular (consisting of complex cells), or acellular (lacking cells). Microbiology encompasses numerous sub-disciplines including virology, bacteriology, protistology, mycology, immunology, and parasitology.
The organisms that constitute the microbial world are characterized as either prokaryotes or eukaryotes; Eukaryotic microorganisms possess membrane-bound organelles and include fungi and protists, whereas prokaryotic organisms are conventionally classified as lacking membrane-bound organelles and include Bacteria and Archaea. Microbiologists traditionally relied on culture, staining, and microscopy for the isolation and identification of microorganisms. However, less than 1% of the microorganisms present in common environments can be cultured in isolation using current means. With the emergence of biotechnology, Microbiologists currently rely on molecular biology tools such as DNA sequence-based identification, for example, the 16S rRNA gene sequence used for bacterial identification.
Viruses have been variably classified as organisms because they have been considered either very simple microorganisms or very complex molecules. Prions, never considered microorganisms, have been investigated by virologists; however, as the clinical effects traced to them were originally presumed due to chronic viral infections, virologists took a search—discovering "infectious proteins".
The existence of microorganisms was predicted many centuries before they were first observed, for example by the Jains in India and by Marcus Terentius Varro in ancient Rome. The first recorded microscope observation was of the fruiting bodies of moulds, by Robert Hooke in 1666, but the Jesuit priest Athanasius Kircher was likely the first to see microbes, which he mentioned observing in milk and putrid material in 1658. Antonie van Leeuwenhoek is considered a father of microbiology as he observed and experimented with microscopic organisms in the 1670s, using simple microscopes of his design. Scientific microbiology developed in the 19th century through the work of Louis Pasteur and in medical microbiology Robert Koch.
== History ==
The existence of microorganisms was hypothesized for many centuries before their actual discovery. The existence of unseen microbiological life was postulated by Jainism which is based on Mahavira's teachings as early as 6th century BCE (599 BC - 527 BC).: 24 Paul Dundas notes that Mahavira asserted the existence of unseen microbiological creatures living in earth, water, air and fire.: 88 Jain scriptures describe nigodas which are sub-microscopic creatures living in large clusters and having a very short life, said to pervade every part of the universe, even in tissues of plants and flesh of animals. The Roman Marcus Terentius Varro made references to microbes when he warned against locating a homestead in the vicinity of swamps "because there are bred certain minute creatures which cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and thereby cause serious diseases."
Persian scientists hypothesized the existence of microorganisms, such as Avicenna in his book The Canon of Medicine, Ibn Zuhr (also known as Avenzoar) who discovered scabies mites, and Al-Razi who gave the earliest known description of smallpox in his book The Virtuous Life (al-Hawi). The tenth-century Taoist Baoshengjing describes "countless micro organic worms" which resemble vegetable seeds, which prompted Dutch sinologist Kristofer Schipper to claim that "the existence of harmful bacteria was known to the Chinese of the time."
In 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or vehicle transmission.
In 1676, Antonie van Leeuwenhoek, who lived most of his life in Delft, Netherlands, observed bacteria and other microorganisms using a single-lens microscope of his own design. He is considered a father of microbiology as he used simple single-lensed microscopes of his own design. While Van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke made his first recorded microscopic observation, of the fruiting bodies of moulds, in 1665. It has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe microorganisms.
Kircher was among the first to design magic lanterns for projection purposes, and so he was well acquainted with the properties of lenses. He wrote "Concerning the wonderful structure of things in nature, investigated by Microscope" in 1646, stating "who would believe that vinegar and milk abound with an innumerable multitude of worms." He also noted that putrid material is full of innumerable creeping animalcules. He published his Scrutinium Pestis (Examination of the Plague) in 1658, stating correctly that the disease was caused by microbes, though what he saw was most likely red or white blood cells rather than the plague agent itself.
== The birth of bacteriology ==
The field of bacteriology (later a subdiscipline of microbiology) was founded in the 19th century by Ferdinand Cohn, a botanist whose studies on algae and photosynthetic bacteria led him to describe several bacteria including Bacillus and Beggiatoa. Cohn was also the first to formulate a scheme for the taxonomic classification of bacteria, and to discover endospores. Louis Pasteur and Robert Koch were contemporaries of Cohn, and are often considered to be the fathers of modern microbiology and medical microbiology, respectively. Pasteur is most famous for his series of experiments designed to disprove the then widely held theory of spontaneous generation, thereby solidifying microbiology's identity as a biological science. One of his students, Adrien Certes, is considered the founder of marine microbiology. Pasteur also designed methods for food preservation (pasteurization) and vaccines against several diseases such as anthrax, fowl cholera and rabies. Koch is best known for his contributions to the germ theory of disease, proving that specific diseases were caused by specific pathogenic microorganisms. He developed a series of criteria that have become known as the Koch's postulates. Koch was one of the first scientists to focus on the isolation of bacteria in pure culture resulting in his description of several novel bacteria including Mycobacterium tuberculosis, the causative agent of tuberculosis.
While Pasteur and Koch are often considered the founders of microbiology, their work did not accurately reflect the true diversity of the microbial world because of their exclusive focus on microorganisms having direct medical relevance. It was not until the late 19th century and the work of Martinus Beijerinck and Sergei Winogradsky that the true breadth of microbiology was revealed. Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques. While his work on the tobacco mosaic virus established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemolithotrophy and to thereby reveal the essential role played by microorganisms in geochemical processes. He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria. French-Canadian microbiologist Felix d'Herelle co-discovered bacteriophages in 1917 and was one of the earliest applied microbiologists.
Joseph Lister was the first to use phenol disinfectant on the open wounds of patients.
== Branches ==
The branches of microbiology can be classified into applied sciences, or divided according to taxonomy, as is the case with bacteriology, mycology, protozoology, virology, phycology, and microbial ecology. There is considerable overlap between the specific branches of microbiology with each other and with other disciplines, and certain aspects of these branches can extend beyond the traditional scope of microbiology. A pure research branch of microbiology is termed cellular microbiology.
== Applications ==
While some people have fear of microbes due to the association of some microbes with various human diseases, many microbes are also responsible for numerous beneficial processes such as industrial fermentation (e.g. the production of alcohol, vinegar and dairy products), antibiotic production can act as molecular vehicles to transfer DNA to complex organisms such as plants and animals. Scientists have also exploited their knowledge of microbes to produce biotechnologically important enzymes such as Taq polymerase, reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system.
Bacteria can be used for the industrial production of amino acids. organic acids, vitamin, proteins, antibiotics and other commercially used metabolites which are produced by microorganisms. Corynebacterium glutamicum is one of the most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine. Since some bacteria have the ability to synthesize antibiotics, they are used for medicinal purposes, such as Streptomyces to make aminoglycoside antibiotics.
A variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are produced by microorganisms. Microorganisms are used for the biotechnological production of biopolymers with tailored properties suitable for high-value medical application such as tissue engineering and drug delivery. Microorganisms are for example used for the biosynthesis of xanthan, alginate, cellulose, cyanophycin, poly(gamma-glutamic acid), levan, hyaluronic acid, organic acids, oligosaccharides polysaccharide and polyhydroxyalkanoates.
Microorganisms are beneficial for microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since sites typically have multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial and fungal species and strains, each specific to the biodegradation of one or more types of contaminants.
Symbiotic microbial communities confer benefits to their human and animal hosts health including aiding digestion, producing beneficial vitamins and amino acids, and suppressing pathogenic microbes. Some benefit may be conferred by eating fermented foods, probiotics (bacteria potentially beneficial to the digestive system) or prebiotics (substances consumed to promote the growth of probiotic microorganisms). The ways the microbiome influences human and animal health, as well as methods to influence the microbiome are active areas of research.
Research has suggested that microorganisms could be useful in the treatment of cancer. Various strains of non-pathogenic clostridia can infiltrate and replicate within solid tumors. Clostridial vectors can be safely administered and their potential to deliver therapeutic proteins has been demonstrated in a variety of preclinical models.
Some bacteria are used to study fundamental mechanisms. An example of model bacteria used to study motility or the production of polysaccharides and development is Myxococcus xanthus.
== See also ==
== References ==
== Further reading ==
== External links ==
Media related to Microbiology at Wikimedia Commons
Quotations related to Microbiology at Wikiquote
nature.com Latest Research, reviews and news on microbiology
Microbes.info is a microbiology information portal containing a vast collection of resources including articles, news, frequently asked questions, and links pertaining to the field of microbiology.
Microbiology on In Our Time at the BBC
Immunology, Bacteriology, Virology, Parasitology, Mycology and Infectious Disease
Annual Review of Microbiology Archived 2009-01-20 at the Wayback Machine | Wikipedia/microbiology |
A viral disease (or viral infection) occurs when an organism's body is invaded by pathogenic viruses, and infectious virus particles (virions) attach to and enter susceptible cells.
Examples include the common cold, gastroenteritis, COVID-19, the flu, and rabies.
== Structural characteristics ==
Basic structural characteristics, such as genome type, virion shape and replication site, generally share the same features among virus species within the same family.
Double-stranded DNA families: three are non-enveloped (Adenoviridae, Papillomaviridae and Polyomaviridae) and two are enveloped (Herpesviridae and Poxviridae). All of the non-enveloped families have icosahedral capsids.
Partly double-stranded DNA viruses: Hepadnaviridae. These viruses are enveloped.
One family of single-stranded DNA viruses infects humans: Parvoviridae. These viruses are non-enveloped.
Positive single-stranded RNA families: three non-enveloped (Astroviridae, Caliciviridae and Picornaviridae) and four enveloped (Coronaviridae, Flaviviridae, Retroviridae and Togaviridae). All the non-enveloped families have icosahedral nucleocapsids.
Negative single-stranded RNA families: Arenaviridae, Bunyaviridae, Filoviridae, Orthomyxoviridae, Paramyxoviridae and Rhabdoviridae. All are enveloped with helical nucleocapsids.
Double-stranded RNA genome: Reoviridae.
The Hepatitis D virus has not yet been assigned to a family, but is clearly distinct from the other families infecting humans.
Viruses known to infect humans that have not been associated with disease: the family Anelloviridae and the genus Dependovirus. Both of these taxa are non-enveloped single-stranded DNA viruses.
=== Pragmatic rules ===
Human-infecting virus families offer rules that may assist physicians and medical microbiologists/virologists.
As a general rule, DNA viruses replicate within the cell nucleus while RNA viruses replicate within the cytoplasm. Exceptions are known to this rule: poxviruses replicate within the cytoplasm and orthomyxoviruses and hepatitis D virus (RNA viruses) replicate within the nucleus.
Segmented genomes: Bunyaviridae, Orthomyxoviridae, Arenaviridae, and Reoviridae (acronym BOAR). All are RNA viruses.
Viruses transmitted almost exclusively by arthropods: Bunyavirus, Flavivirus, and Togavirus. Some Reoviruses are transmitted from arthropod vectors. All are RNA viruses.
One family of enveloped viruses causes gastroenteritis (Coronaviridae). All other viruses associated with gastroenteritis are non-enveloped.
=== Baltimore group ===
This group of analysts defined multiple categories of virus. Groups:
I - dsDNA
II - ssDNA
III - dsRNA
IV - positive-sense ssRNA
V - negative-sense ssRNA
VI - ssRNA-RT
VII - dsDNA-RT
=== Clinical characteristics ===
The clinical characteristics of viruses may differ substantially among species within the same family:
== See also ==
List of latent human viral infections
Pathogenic bacteria
== References ==
== External links == | Wikipedia/Viral_disease |
The term viral protein refers to both the products of the genome of a virus and any host proteins incorporated into the viral particle. Viral proteins are grouped according to their functions, and groups of viral proteins include structural proteins, nonstructural proteins, regulatory proteins, and accessory proteins. Viruses are non-living and do not have the means to reproduce on their own, instead depending on their host cell's machinery to do this. Thus, viruses do not code for most of the proteins required for their replication and the translation of their mRNA into viral proteins, but use proteins encoded by the host cell for this purpose.
== Viral structural proteins ==
Most viral structural proteins are components for the capsid and the envelope of the virus.
=== Capsid ===
The genetic material of a virus is stored within a viral protein structure called the capsid. The capsid is a "shield" that protects the viral nucleic acids from getting degraded by host enzymes or other types of pesticides or pestilences. It also functions to attach the virion to its host, and enable the virion to penetrate the host cell membrane. Many copies of a single viral protein or a number of different viral proteins make up the capsid, and each of these viral proteins are coded for by one gene from the viral genome. The structure of the capsid allows the virus to use a small number of viral genes to make a large capsid.
Several protomers, oligomeric (viral) protein subunits, combine to form capsomeres, and capsomeres come together to form the capsid. Capsomeres can arrange into an icosahedral, helical, or complex capsid, but in many viruses, such as the herpes simplex virus, an icosahedral capsid is assembled. Three asymmetric and nonidentical viral protein units make up each of the twenty identical triangular faces in the icosahedral capsid.
=== Viral envelope ===
The capsid of some viruses are enclosed in a membrane called the viral envelope. In most cases, the viral envelope is obtained by the capsid from the host cell's plasma membrane when a virus leaves its host cell through a process called budding. The viral envelope is made up of a lipid bilayer embedded with viral proteins, including viral glycoproteins. These viral glycoproteins bind to specific receptors and coreceptors on the membrane of host cells, and they allow viruses to attach onto their target host cells. Some of these glycoproteins include:
Hemagglutinin, neuraminidase, and M2 protein in the influenza virus
gp160, composed of subunits gp120 and gp41, in the human immunodeficiency virus (HIV).
Viral glycoproteins play a critical role in virus-to-cell fusion. Virus-to-cell fusion is initiated when viral glycoproteins bind to cellular receptors.
==== Viral membrane fusion proteins ====
The fusion of the viral envelope with the cellular membrane requires high energy to occur. Viral membrane fusion proteins act as catalysts to overcome this high energy barrier. Following viral glycoprotein binding to cellular receptors, viral membrane fusion proteins undergo a change in structure conformation. This change in conformation then facilitates the destabilization and fusion of the viral envelope with the cellular membrane by allowing fusion loops (FLs) or hydrophobic fusion peptides (FPs) on the viral envelope to interact with the cell membrane. Most viral membrane fusion proteins would end up in a hairpin-like conformation after fusion, in which FLs/FPs and the transmembrane domain are all on the same side of the protein.
Viral glycoproteins and their three-dimensional structures, before and after fusion, have allowed a wide range of structural conformations to be discovered. Viral membrane fusion proteins have been grouped into four different classes, and each class is identified by characteristic structural conformations:
Class I: Post-fusion conformation has a distinct central coiled-coil structure composed of signature trimer of α-helical hairpins. An example of a Class I viral fusion protein is the HIV glycoprotein, gp41.
Class II: Protein lacks the central coiled-coil structure. Contains a characteristic elongated β- sheet ectodomain structure that refolds to give a trimer of hairpins. Examples of class II viral fusion proteins include the dengue virus E protein, and the west nile virus E protein.
Class III: Structural conformation is a combination of features from Class I and Class II viral membrane fusion proteins. An example of a Class III viral fusion protein is the rabies virus glycoprotein, G.
Class IV: Class IV viral fusion proteins are fusion-associated small transmembrane (FAST) proteins. They do not form trimers of hairpins or hairpin structures themselves, and they are the smallest known viral fusion proteins. FAST proteins are coded for by members of the nonenveloped reoviridae family of viruses.
== Viral nonstructural proteins ==
Viral nonstructural proteins are proteins coded for by the genome of the virus and are expressed in infected cells. However, these proteins are not assembled in the virion. During the replication of viruses, some viral nonstructural proteins carry out important functions that affect the replication process itself. Similarly, during the assembly of viruses, some of these proteins also carry out important functions that affect the assembly process. Some of these viral nonstructural protein functions are replicon formation, immunomodulation, and transactivation of viral structural protein encoding genes.
=== Replicon formation ===
Viral nonstructural proteins interact with host cell proteins to form the replicon, otherwise known as the replication complex. In the hepatitis C virus, viral nonstructural proteins interact with cellular vesicle membrane transport protein, hVAP-33, to assemble the replicon. Viral nonstructural 4b (NS4B) protein alters the host cell's membrane and starts the formation process of the replication complex. Other viral nonstructural proteins such as NS5A, NS5B, and NS3, are also recruited to the complex, and NS4B interacts with them and binds to viral RNA.
=== Immunomodulation ===
The immune response of a host to an infected cell can be adjusted through the immunomodulatory properties of viral nonstructural proteins. Many species of large DNA viruses encode proteins which subvert host immune response, allowing proliferation of the virus. Such proteins hold potential in developing new bio-pharmaceutical treatments for inflammatory disease in humans, as the proteins have been proven to subvert inflammatory immune mediators. Viral nonstructural protein NS1 in the West Nile virus prevents complement activation through its binding to a complement control protein, factor H. As a result, complement recognition of infected cells is reduced, and infected cells remain unharmed by the host's immune system.
== Viral regulatory and accessory proteins ==
Viral regulatory and accessory proteins have many functions. These viral proteins control and influence viral gene expressions in the viral genome, including viral structural gene transcription rates. Viral regulatory and accessory proteins also influence and adjust cellular functions of the host cell, such as the regulation of genes, and apoptosis.
In DNA viruses and retroviruses, viral regulatory proteins can enhance viral gene transcription, likewise, these proteins can also enhance host cellular gene transcription too.
Viral accessory proteins, also known as auxiliary proteins, are coded for by the genome of retroviruses. Most viral accessory proteins only carry out their functions in specific types of cells. Also, they do not have much influence on the replication of the virus. However, in some instances, maintaining the replication of viruses would require the help (and function) of viral accessory proteins.
== Endogenous retroviral proteins ==
Syncytin is an endogenous retrovirus protein that has been captured in the mammalian genome to allow membrane fusion in placental morphogenesis.
== References ==
== External links ==
List of all known Viral Proteins in UniProtKB
VirusMint | Wikipedia/Viral_protein |
Spontaneous generation is a superseded scientific theory that held that living creatures could arise from non-living matter and that such processes were commonplace and regular. It was hypothesized that certain forms, such as fleas, could arise from inanimate matter such as dust, or that maggots could arise from dead flesh. The doctrine of spontaneous generation was coherently synthesized by the Greek philosopher and naturalist Aristotle, who compiled and expanded the work of earlier natural philosophers and the various ancient explanations for the appearance of organisms. Spontaneous generation was taken as scientific fact for two millennia. Though challenged in the 17th and 18th centuries by the experiments of the Italian biologists Francesco Redi and Lazzaro Spallanzani, it was not discredited until the work of the French chemist Louis Pasteur and the Irish physicist John Tyndall in the mid-19th century.
Among biologists, rejecting spontaneous genesis is no longer controversial. Experiments conducted by Pasteur and others were thought to have refuted the conventional notion of spontaneous generation by the mid-1800s. Since all life appears to have evolved from a single form approximately four billion years ago, attention has instead turned to the origin of life.
== Description ==
"Spontaneous generation" means both the supposed processes by which different types of life might repeatedly emerge from specific sources other than seeds, eggs, or parents, and the theoretical principles presented in support of any such phenomena. Crucial to this doctrine are the ideas that life comes from non-life and that no causal agent, such as a parent, is needed. Supposed examples included the seasonal generation of mice and other animals from the mud of the Nile, the emergence of fleas from inanimate matter such as dust, or the appearance of maggots in dead flesh. Such ideas have something in common with the modern hypothesis of the origin of life, which asserts that life emerged some four billion years ago from non-living materials, over a time span of millions of years, and subsequently diversified into all the forms that now exist.
The term equivocal generation, sometimes known as heterogenesis or xenogenesis, describes the supposed process by which one form of life arises from a different, unrelated form, such as tapeworms from the bodies of their hosts.
== Antiquity ==
=== Pre-Socratic philosophers ===
Active in the 6th and 5th centuries BCE, early Greek philosophers, called physiologoi in antiquity (Greek: φυσιολόγοι; in English, physical or natural philosophers), attempted to give natural explanations of phenomena that had previously been ascribed to the agency of the gods. The physiologoi sought the material principle or arche (Greek: ἀρχή) of things, emphasizing the rational unity of the external world and rejecting theological or mythological explanations.
Anaximander, who believed that all things arose from the elemental nature of the universe, the apeiron (ἄπειρον) or the "unbounded" or "infinite", was likely the first western thinker to propose that life developed spontaneously from nonliving matter. The primal chaos of the apeiron, eternally in motion, served as a platform on which elemental opposites (e.g., wet and dry, hot and cold) generated and shaped the many and varied things in the world. According to Hippolytus of Rome in the third century CE, Anaximander claimed that fish or fish-like creatures were first formed in the "wet" when acted on by the heat of the sun and that these aquatic creatures gave rise to human beings. The Roman author Censorinus, writing in the 3rd century, reported:
Anaximander of Miletus considered that from warmed up water and earth emerged either fish or entirely fishlike animals. Inside these animals, men took form and embryos were held prisoners until puberty; only then, after these animals burst open, could men and women come out, now able to feed themselves.
The Greek philosopher Anaximenes, a pupil of Anaximander, thought that air was the element that imparted life and endowed creatures with motion and thought. He proposed that plants and animals, including human beings, arose from a primordial terrestrial slime, a mixture of earth and water, combined with the sun's heat. The philosopher Anaxagoras, too, believed that life emerged from a terrestrial slime. However, Anaximenes held that the seeds of plants existed in the air from the beginning, and those of animals in the aether. Another philosopher, Xenophanes, traced the origin of man back to the transitional period between the fluid stage of the Earth and the formation of land, under the influence of the Sun.
In what has occasionally been seen as a prefiguration of a concept of natural selection, Empedocles accepted the spontaneous generation of life, but held that different forms, made up of differing combinations of parts, spontaneously arose as though by trial and error: successful combinations formed the individuals present in the observer's lifetime, whereas unsuccessful forms failed to reproduce.
=== Aristotle ===
In his biological works, the natural philosopher Aristotle theorized extensively the reproduction of various animals, whether by sexual, parthenogenetic, or spontaneous generation. In accordance with his fundamental theory of hylomorphism, which held that every physical entity was a compound of matter and form, Aristotle's basic theory of sexual reproduction contended that the male's seed imposed form, the set of characteristics passed down to offspring on the "matter" (menstrual blood) supplied by the female. Thus female matter is the material cause of generation—it supplies the matter that will constitute the offspring—while the male semen is the efficient cause, the factor that instigates and delineates the thing's existence. Yet, Aristotle proposed in the History of Animals, many creatures form not through sexual processes but by spontaneous generation:
Now there is one property that animals are found to have in common with plants. For some plants are generated from the seed of plants, whilst other plants are self-generated through the formation of some elemental principle similar to a seed; and of these latter plants some derive their nutriment from the ground, whilst others grow inside other plants ... So with animals, some spring from parent animals according to their kind, whilst others grow spontaneously and not from kindred stock; and of these instances of spontaneous generation some come from putrefying earth or vegetable matter, as is the case with a number of insects, while others are spontaneously generated in the inside of animals out of the secretions of their several organs.
According to this theory, living things may come forth from nonliving things in a manner roughly analogous to the "enformation of the female matter by the agency of the male seed" seen in sexual reproduction. Nonliving materials, like the seminal fluid present in sexual generation, contain pneuma (πνεῦμα, "breath"), or "vital heat". According to Aristotle, pneuma had more "heat" than regular air did, and this heat endowed the substance with certain vital properties:
The power of every soul seems to have shared in a different and more divine body than the so called [four] elements ... For every [animal], what makes the seed generative inheres in the seed and is called its "heat". But this is not fire or some such power, but instead the pneuma that is enclosed in the seed and in foamy matter, this being analogous to the element of the stars. This is why fire does not generate any animal ... but the heat of the sun and the heat of animals does, not only the heat that fills the seed, but also any other residue of [the animal's] nature that may exist similarly possesses this vital principle.
Aristotle drew an analogy between the "foamy matter" (τὸ ἀφρῶδες, to aphrodes) found in nature and the "seed" of an animal, which he viewed as being a kind of foam itself (composed, as it was, from a mixture of water and pneuma). For Aristotle, the generative materials of male and female animals (semen and menstrual fluid) were essentially refinements, made by male and female bodies according to their respective proportions of heat, of ingested food, which was, in turn, a byproduct of the elements earth and water. Thus any creature, whether generated sexually from parents or spontaneously through the interaction of vital heat and elemental matter, was dependent on the proportions of pneuma and the various elements which Aristotle believed comprised all things. While Aristotle recognized that many living things emerged from putrefying matter, he pointed out that the putrefaction was not the source of life, but the byproduct of the action of the "sweet" element of water.
Animals and plants come into being in earth and in liquid because there is water in earth, and air in water, and in all air is vital heat so that in a sense all things are full of soul. Therefore living things form quickly whenever this air and vital heat are enclosed in anything. When they are so enclosed, the corporeal liquids being heated, there arises as it were a frothy bubble.
With varying degrees of observational confidence, Aristotle theorized the spontaneous generation of a range of creatures from different sorts of inanimate matter. The testaceans (a genus which for Aristotle included bivalves and snails), for instance, were characterized by spontaneous generation from mud, but differed based upon the precise material they grew in—for example, clams and scallops in sand, oysters in slime, and the barnacle and the limpet in the hollows of rocks.
=== Latin and early Christian sources ===
Athenaeus dissented towards spontaneous generation, claiming that a variety of anchovy did not generate from roe, as Aristotle stated, but rather, from sea foam.
As the dominant view of philosophers and thinkers continued to be in favour of spontaneous generation, some Christian theologians accepted the view. The Berber theologian and philosopher Augustine of Hippo discussed spontaneous generation in The City of God and The Literal Meaning of Genesis, citing Biblical passages such as "Let the waters bring forth abundantly the moving creature that hath life" (Genesis 1:20) as decrees that would enable ongoing creation.
== Middle Ages ==
From the fall of the Roman Empire in 5th century to the East–West Schism in 1054, the influence of Greek science declined, although spontaneous generation generally went unchallenged. New descriptions were made. Of the beliefs, some had doctrinal implications. In 1188, Gerald of Wales, after having traveled in Ireland, argued that the barnacle goose myth was evidence for the virgin birth of Jesus. Where the practice of fasting during Lent allowed fish, but prohibited fowl, the idea that the goose was in fact a fish suggested that its consumption be permitted during Lent. The practice was eventually prohibited by decree of Pope Innocent III in 1215.
After Aristotle’s works were reintroduced to Western Europe, they were translated into Latin from the original Greek or Arabic. They reached their greatest level of acceptance during the 13th century. With the availability of Latin translations, the German philosopher Albertus Magnus and his student Thomas Aquinas raised Aristotelianism to its greatest prominence. Albert wrote a paraphrase of Aristotle, De causis et processu universitatis, in which he removed some commentaries by Arabic scholars and incorporated others. The influential writings of Aquinas, on both the physical and metaphysical, are predominantly Aristotelian, but show numerous other influences.
Spontaneous generation is described in literature as if it were a fact well into the Renaissance. Shakespeare wrote of snakes and crocodiles forming from the mud of the Nile:
Shakespeare: Antony and Cleopatra: Act 2, scene 7
The author of The Compleat Angler, Izaak Walton repeats the question of the origin of eels "as rats and mice, and many other living creatures, are bred in Egypt, by the sun's heat when it shines upon the overflowing of the river...". While the ancient question of the origin of eels remained unanswered and the additional idea that eels reproduced from corruption of age was mentioned, the spontaneous generation of rats and mice stirred up no debate.
The Dutch biologist and microscopist Jan Swammerdam rejected the concept that one animal could arise from another or from putrification by chance because it was impious; he found the concept of spontaneous generation irreligious, and he associated it with atheism.
== Previous beliefs ==
Frogs were believed to have spontaneously generated from mud.
Mice were believed to become pregnant though the act of licking salt, or grew from the moisture of the earth.
Barnacle geese were thought to have emerged from a crustacean, the goose barnacle (see the barnacle goose myth).
Snakes could generate from the marrow of the human spine, and had previously generated from the blood of Medusa.
Eels had multiple stories. Aristotle claimed that eels emerged from earthworms, and were lacking in sex and milt, spawn and passages for these. Later authors dissented. The Roman author and natural historian Pliny the Elder did not argue against the anatomic limits of eels, but stated that eels reproduce by budding, scraping themselves against rocks, liberating particles that become eels. The Greek author Athenaeus described eels as entwining and discharging a fluid which would settle on mud and generate life.
Bookworms could generate from excessive wind. Vitruvius, a Roman architect and writer of the 1st century BCE, advised that to stop their generation, libraries be placed facing eastwards to benefit from morning light, but not towards the south or the west as those winds were particularly offensive.
Bees were generated in decomposing cows, through a process known as bugonia. Samson's riddle led some to believe they could also generate through the body of a lion.
Wasps could be generated from decomposing horses.
Cicada were generated from the spittle of the cuckoo.
== Experimental approach ==
=== Early tests ===
The Brussels physician Jan Baptist van Helmont described a recipe for mice (a piece of dirty cloth plus wheat for 21 days) and scorpions (basil, placed between two bricks and left in sunlight). His notes suggest he may have attempted to do these things.
Where Aristotle held that the embryo was formed by a coagulation in the uterus, the English physician William Harvey showed by way of dissection of deer that there was no visible embryo during the first month. Although his work predated the microscope, this led him to suggest that life came from invisible eggs. In the frontispiece of his 1651 book Exercitationes de Generatione Animalium (Essays on the Generation of Animals), he denied spontaneous generation with the motto omnia ex ovo ("everything from eggs").
The ancient beliefs were subjected to testing. In 1668, the Italian physician and parasitologist Francesco Redi challenged the idea that maggots arose spontaneously from rotting meat. In the first major experiment to challenge spontaneous generation, he placed meat in a variety of sealed, open, and partially covered containers. Realizing that the sealed containers were deprived of air, he used "fine Naples veil", and observed no worms on the meat, but they appeared on the cloth. Redi used his experiments to support the preexistence theory put forth by the Catholic Church at that time, which maintained that living things originated from parents. In scientific circles Redi's work very soon had great influence, as evidenced in a letter from the English natural theologian John Ray in 1671 to members of the Royal Society of London, in which he calls the spontaneous generation of insects "unlikely".
Pier Antonio Micheli, c. 1729, observed that when fungal spores were placed on slices of melon, the same type of fungi were produced that the spores came from, and from this observation he noted that fungi did not arise from spontaneous generation.
In 1745, John Needham performed a series of experiments on boiled broths. Believing that boiling would kill all living things, he showed that when sealed right after boiling, the broths would cloud, allowing the belief in spontaneous generation to persist. His studies were rigorously scrutinized by his peers, and many of them agreed.
Lazzaro Spallanzani did an extensive variety of observations and experiments that modified the experiments of Needham in 1768, where he attempted to exclude the possibility of introducing a contaminating factor between boiling and sealing. His technique involved boiling the broth in a sealed container with the air partially evacuated to prevent explosions. Although he did not see growth, the exclusion of air left the question of whether air was an essential factor in spontaneous generation. But attitudes were changing; by the start of the 19th century, a scientist such as Joseph Priestley could write that "There is nothing in modern philosophy that appears to me so extraordinary, as the revival of what has long been considered as the exploded doctrine of equivocal, or, as Dr. [Erasmus] Darwin calls it, spontaneous generation."
In 1837, Charles Cagniard de la Tour, a physicist, and Theodor Schwann, one of the founders of cell theory, published their independent discovery of yeast in alcoholic fermentation. They used the microscope to examine foam left over from the process of brewing beer. Where the Dutch microscopist Antonie van Leeuwenhoek described "small spheroid globules", they observed yeast cells undergo cell division. Fermentation would not occur when sterile air or pure oxygen was introduced if yeast were not present. This suggested that airborne microorganisms, not spontaneous generation, was responsible.
However, although the idea of spontaneous generation had been in decline for nearly a century, its supporters did not abandon it all at once. As James Rennie wrote in 1838, despite Redi's experiments, "distinguished naturalists, such as Blumenbach, Cuvier, Bory de St. Vincent, R. Brown, &c." continued to support the theory.
=== Pasteur and Tyndall ===
Louis Pasteur's experiment's in the late 1850's are widely seen as having settled the question of spontaneous generation. He boiled a meat broth in a swan neck flask; the bend in the neck of the flask prevented falling particles from reaching the broth, while still allowing the free flow of air. The flask remained free of growth for an extended period. When the flask was turned so that particles could fall down the bends, the broth quickly became clouded. However, minority objections were persistent and not always unreasonable, given that the experimental difficulties were far more challenging than the popular accounts suggest. The investigations of the Irish physician John Tyndall, a correspondent of Pasteur and an admirer of his work, were decisive in disproving spontaneous generation. All the same, Tyndall encountered difficulties in dealing with microbial spores, which were not well understood in his day. Like Pasteur, he boiled his cultures to sterilize them, and some types of bacterial spores can survive boiling. The autoclave, which eventually came into universal application in medical practice and microbiology to sterilise equipment, was introduced after these experiments.
In 1862, the French Academy of Sciences paid special attention to the issue, establishing a prize "to him who by well-conducted experiments throws new light on the question of the so-called spontaneous generation" and appointed a commission to judge the winner. Pasteur and others used the term biogenesis as the opposite of spontaneous generation, to mean that life was generated only from other life. Pasteur's claim followed the German physician Rudolf Virchow's doctrine Omnis cellula e cellula ("all cells from cells"), itself derived from the work of Robert Remak. After Pasteur's 1859 experiment, the term "spontaneous generation" fell out of favor. Experimentalists used a variety of terms for the study of the origin of life from nonliving materials. Heterogenesis was applied to the generation of living things from once-living organic matter (such as boiled broths), and the English physiologist Henry Charlton Bastian proposed the term archebiosis for life originating from non-living materials. Disliking the randomness and unpredictability implied by the term spontaneous generation, in 1870 Bastian coined the term biogenesis for the formation of life from nonliving matter. Soon thereafter, however, the English biologist Thomas Henry Huxley proposed the term abiogenesis for this same process, and adopted biogenesis for the process by which life arises from existing life.
== See also ==
Bugonia
Barnacle goose myth
Origin of life
== References == | Wikipedia/Theory_of_spontaneous_generation |
In the diagnostic laboratory, virus infections can be confirmed by a myriad of methods. Diagnostic virology has changed rapidly due to the advent of molecular techniques and increased clinical sensitivity of serological assays.
== Sampling ==
A wide variety of samples can be used for virological testing. The type of sample sent to the laboratory often depends on the type of viral infection being diagnosed and the test required. Proper sampling technique is essential to avoid potential pre-analytical errors. For example, different types of samples must be collected in appropriate tubes to maintain the integrity of the sample and stored at appropriate temperatures (usually 4 °C) to preserve the virus and prevent bacterial or fungal growth. Sometimes multiple sites may also be sampled.
Types of samples include the following:
Nasopharyngeal swab
Blood
Skin
Sputum, gargles and bronchial washings
Urine
Semen
Faeces
Cerebrospinal fluid
Tissues (biopsies or post-mortem)
Dried blood spots
For example, a nasal mucus test may be done to diagnose rhinovirus.
== Virus isolation ==
Viruses are often isolated from the initial patient sample. This allows the virus sample to be grown into larger quantities and allows a larger number of tests to be run on them. This is particularly important for samples that contain new or rare viruses for which diagnostic tests are not yet developed.
Many viruses can be grown in cell culture in the lab. To do this, the virus sample is mixed with cells, a process called adsorption, after which the cells become infected and produce more copies of the virus. Although different viruses often only grow in certain types of cells, there are cells that support the growth of a large variety of viruses and are a good starting point, for example, the African monkey kidney cell line (Vero cells), human lung fibroblasts (MRC-5), and human epidermoid carcinoma cells (HEp-2). One means of determining whether the cells are successfully replicating the virus is to check for a change in cell morphology or for the presence of cell death using a microscope.
Other viruses may require alternative methods for growth such as the inoculation of embryonated chicken eggs (e.g. avian influenza viruses) or the intracranial inoculation of virus using newborn mice (e.g. lyssaviruses).
== Nucleic acid based methods ==
Molecular techniques are the most specific and sensitive diagnostic tests. They are capable of detecting either the whole viral genome or parts of the viral genome. In the past nucleic acid tests have mainly been used as a secondary test to confirm positive serological results. However, as they become cheaper and more automated, they are increasingly becoming the primary tool for diagnostics and can also be use for monitoring of treatment of viral infected individuals t.
=== Polymerase chain reaction ===
Detection of viral RNA and DNA genomes can be performed using polymerase chain reaction. This technique makes many copies of the virus genome using virus-specific probes. Variations of PCR such as nested reverse transcriptase PCR and real time PCR can also be used to determine viral loads in patient serum. This is often used to monitor treatment success in HIV cases.
=== Sequencing ===
Sequencing is the only diagnostic method that will provide the full sequence of a virus genome. Hence, it provides the most information about very small differences between two viruses that would look the same using other diagnostic tests. Currently it is only used when this depth of information is required. For example, sequencing is useful when specific mutations in the patient are tested for in order to determine antiviral therapy and susceptibility to infection. However, as the tests are getting cheaper, faster and more automated, sequencing will likely become the primary diagnostic tool in the future.
== Microscopy based methods ==
=== Immunofluorescence or immunoperoxidase ===
Immunofluorescence or immunoperoxidase assays are commonly used to detect whether a virus is present in a tissue sample. These tests are based on the principle that if the tissue is infected with a virus, an antibody specific to that virus will be able to bind to it. To do this, antibodies that are specific to different types of viruses are mixed with the tissue sample. After the tissue is exposed to a specific wavelength of light or a chemical that allows the antibody to be visualized.
These tests require specialized antibodies that are produced and purchased from commercial companies. These commercial antibodies are usually well characterized and are known to bind to only one specific type of virus. They are also conjugated to a special kind of tag that allows the antibody to be visualized in the lab, i.e.so that it will emit fluorescence or a color. Hence, immunofluorescence refers
to the detection of a fluorescent antibody (immuno) and immunoperoxidase refers to the detection of a colored antibody (peroxidase produces a dark brown color).
=== Electron microscopy ===
Electron microscopy is a method that can take a picture of a whole virus and can reveal its shape and structure. It is not typically used as a routine diagnostic test as it requires a highly specialized type of sample preparation, microscope and technical expertise. However, electron microscopy is highly versatile due to its ability to analyze any type of sample and identify any type of virus. Therefore, it remains the gold standard for identifying viruses that do not show up on routine diagnostic tests or for which routine tests present conflicting results.
== Host antibody detection ==
A person who has recently been infected by a virus will produce antibodies in their bloodstream that specifically recognize that virus. This is called humoral immunity. Two types of antibodies are important. The first called IgM is highly effective at neutralizing viruses but is only produced by the cells of the immune system for a few weeks. The second, called, IgG is produced indefinitely. Therefore, the presence of IgM in the blood of the host is used to test for acute infection, whereas IgG indicates an infection sometime in the past. Both types of antibodies are measured when tests for immunity are carried out.
Antibody testing has become widely available. It can be done for individual viruses (e.g. using an ELISA assay) but automated panels that can screen for many viruses at once are becoming increasingly common.
== Hemagglutination assay ==
Some viruses attach to molecules present on the surface of red blood cells, for example, influenza virus. A consequence of this is that – at certain concentrations – a viral suspension may bind together (agglutinate) the red blood cells thus preventing them from settling out of suspension.
== See also ==
Serology
Molecular diagnostics
== References == | Wikipedia/Laboratory_diagnosis_of_viral_infections |
Microbial DNA barcoding is the use of DNA metabarcoding to characterize a mixture of microorganisms. DNA metabarcoding is a method of DNA barcoding that uses universal genetic markers to identify DNA of a mixture of organisms.
== History ==
Using metabarcoding to assess microbial communities has a long history. Back in 1972, Carl Woese, Mitchell Sogin and Stephen Sogin first tried to detect several families within bacteria using the 5S rRNA gene. Only a few years later, a new tree of life with three domains was proposed by again Woese and colleagues, who were the first to use the small subunit of the ribosomal RNA (SSU rRNA) gene to distinguish between bacteria, archaea and eukaryotes. Out of this approach, the SSU rRNA gene made its way to be the most frequently used genetic marker for both prokaryotes (16S rRNA) and eukaryotes (18S rRNA). The tedious process of cloning those DNA fragments for sequencing got fastened up by the steady improvement of sequencing technologies. With the development of HTS (High-Throughput-Sequencing) in the early 2000s and the ability to deal with this massive data using modern bioinformatics and cluster algorithms, investigating microbial life got much easier.
== Genetic markers ==
Genetic diversity is varying from species to species. Therefore, it is possible to identify distinct species by the recovery of a short DNA sequence from a standard part of the genome. This short sequence is defined as barcode sequence. Requirements for a specific part of the genome to serve as barcode should be a high variation between two different species, but not much differences in the gene between two individuals of the same species to make differentiating individual species easier. For both bacteria and archaea the 16S rRNA/rDNA gene is used. It is a common housekeeping gene in all prokaryotic organisms and therefore is used as a standard barcode to assess prokaryotic diversity. For protists, the corresponding 18S rRNA/rDNA gene is used. To distinguish different species of fungi, the ITS (Internal Transcribed Spacer) region of the ribosomal cistron is used.
== Advantages ==
The existing diversity of the microbial world is not unraveled completely yet, although we know that it is mainly composed by bacteria, fungi and unicellular eukaryotes. Taxonomic identification of microbial eukaryotes requires exceedingly skillful expertise and is often difficult due to small sizes of the organisms, fragmented individuals, hidden diversity and cryptic species. Further, prokaryotes can simply not be taxonomically assigned using traditional methods like microscopy, because they are too small and morphologically indistinguishable. Therefore, via the use of DNA metabarcoding, it is possible to identify organisms without taxonomic expertise by matching short High Throughput Sequences (HTS)-derived gene fragments to a reference sequence database, e.g. NCBI. These mentioned qualities make DNA barcoding a cost-effective, reliable and less time-consuming method, compared to the traditional ones, to meet the increasing need for large-scale environmental assessments.
== Applications ==
A lot of studies followed the first usage of Woese et al., and are now covering a variety of applications. Not only in biological or ecological research metabarcoding is used. Also in medicine and human biology bacterial barcodes are used, e.g. to investigate the microbiome and bacterial colonization of the human gut in normal and obese twins or comparison studies of newborn, child and adult gut bacteria composition. Additionally, barcoding plays a major role in biomonitoring of e.g. rivers and streams and grassland restoration. Conservation parasitology, environmental parasitology and paleoparasitology rely on barcoding as a useful tool in disease investigating and management, too.
=== Cyanobacteria ===
Cyanobacteria are a group of photosynthetic prokaryotes. Similar as in other prokaryotes, taxonomy of cyanobacteria using DNA sequences is mostly based on similarity within the 16S ribosomal gene. Thus, the most common barcode used for identification of cyanobacteria is 16S rDNA marker. While it is difficult to define species within prokaryotic organisms, 16S marker can be used for determining individual operational taxonomic units (OTUs). In some cases, these OTUs can also be linked to traditionally defined species and can therefore be considered a reliable representation of the evolutionary relationships.
However, when analyzing a taxonomic structure or biodiversity of a whole cyanobacterial community (see DNA metabarcoding), it is more informative to use markers specific for cyanobacteria. Universal 16S bacterial primers have been used successfully to isolate cyanobacterial rDNA from environmental samples, but they also recover many bacterial sequences. The use of cyanobacteria-specific or phyto-specific 16S markers is commonly used for focusing on cyanobacteria only. A few sets of such primers have been tested for barcoding or metabarcoding of environmental samples and gave good results, screening out majority of non-photosynthetic or non-cyanobacterial organisms.
Number of sequenced cyanobacterial genomes available in databases is increasing. Besides 16S marker, phylogenetic studies could therefore include also more variable sequences, such as sequences of protein-coding genes (gyrB, rpoC, rpoD, rbcL, hetR, psbA, rnpB, nifH, nifD), internal transcribed spacer of ribosomal RNA genes (16S-23S rRNA-ITS) or phycocyanin intergenic spacer (PC-IGS). However, nifD and nifH can only be used for identification of nitrogen-fixing cyanobacterial strains.
DNA barcoding of cyanobacteria can be applied in various ecological, evolutionary and taxonomical studies. Some examples include assessment of cyanobacterial diversity and community structure, identification of harmful cyanobacteria in ecologically and economically important waterbodies and assessment of cyanobacterial symbionts in marine invertebrates. It has a potential to serve as a part of routine monitoring programs for occurrence of cyanobacteria, as well as early detection of potentially toxic species in waterbodies. This might help us detect harmful species before they start to form blooms and thus improve our water management strategies. Species identification based on environmental DNA could be particularly useful for cyanobacteria, as traditional identification using microscopy is challenging. Their morphological characteristics which are the basis for species delimitation vary in different growth conditions. Identification under microscope is also time-consuming and therefore relatively costly. Molecular methods can detect much lower concentration of cyanobacterial cells in the sample than traditional identification methods.
== Reference databases ==
The reference database is a collection of DNA sequences, which are assigned to either a species or a function. It can be used to link molecular obtained sequences of an organism to pre-existing taxonomy. General databases like the NCBI platform include all kind of sequences, either whole genomes or specific marker genes of all organisms. There are also different platforms where only sequences from a distinct group of organisms are stored, e.g. UNITE database exclusively for fungi sequences or the PR2 database solely for protist ribosomal sequences. Some databases are curated, which allows a taxonomic assignment with higher accuracy than using uncurated databases as a reference.
== See also ==
Consortium for the Barcode of Life
Algae DNA barcoding
DNA Barcoding
DNA barcoding in diet assessment
Fish DNA barcoding
== References == | Wikipedia/Microbial_DNA_barcoding |
A disease is a particular abnormal condition that adversely affects the structure or function of all or part of an organism and is not immediately due to any external injury. Diseases are often known to be medical conditions that are associated with specific signs and symptoms. A disease may be caused by external factors such as pathogens or by internal dysfunctions. For example, internal dysfunctions of the immune system can produce a variety of different diseases, including various forms of immunodeficiency, hypersensitivity, allergies, and autoimmune disorders.
In humans, disease is often used more broadly to refer to any condition that causes pain, dysfunction, distress, social problems, or death to the person affected, or similar problems for those in contact with the person. In this broader sense, it sometimes includes injuries, disabilities, disorders, syndromes, infections, isolated symptoms, deviant behaviors, and atypical variations of structure and function, while in other contexts and for other purposes these may be considered distinguishable categories. Diseases can affect people not only physically but also mentally, as contracting and living with a disease can alter the affected person's perspective on life.
Death due to disease is called death by natural causes. There are four main types of disease: infectious diseases, deficiency diseases, hereditary diseases (including both genetic and non-genetic hereditary diseases), and physiological diseases. Diseases can also be classified in other ways, such as communicable versus non-communicable diseases. The deadliest diseases in humans are coronary artery disease (blood flow obstruction), followed by cerebrovascular disease and lower respiratory infections. In developed countries, the diseases that cause the most sickness overall are neuropsychiatric conditions, such as depression and anxiety.
Pathology, the study of disease, includes etiology, or the study of cause.
== Terminology ==
=== Concepts ===
In many cases, terms such as disease, disorder, morbidity, sickness and illness are used interchangeably; however, there are situations when specific terms are considered preferable.
Disease
The term disease broadly refers to any condition that impairs the normal functioning of the body. For this reason, diseases are associated with the dysfunction of the body's normal homeostatic processes. Commonly, the term is used to refer specifically to infectious diseases, which are clinically evident diseases that result from the presence of pathogenic microbial agents, including viruses, bacteria, fungi, protozoa, multicellular organisms, and aberrant proteins known as prions. An infection or colonization that does not and will not produce clinically evident impairment of normal functioning, such as the presence of the normal bacteria and yeasts in the gut, or of a passenger virus, is not considered a disease. By contrast, an infection that is asymptomatic during its incubation period, but expected to produce symptoms later, is usually considered a disease. Non-infectious diseases are all other diseases, including most forms of cancer, heart disease, and genetic disease.
Acquired disease
An acquired disease is one that began at some point during one's lifetime, as opposed to disease that was already present at birth, which is congenital disease. Acquired sounds like it could mean "caught via contagion", but it simply means acquired sometime after birth. It also sounds like it could imply secondary disease, but acquired disease can be primary disease.
Acute disease
An acute disease is one of a short-term nature (acute); the term sometimes also connotes a fulminant nature
Chronic condition or chronic disease
A chronic disease is one that persists over time, often for at least six months, but may also include illnesses that are expected to last for the entirety of one's natural life.
Congenital disorder or congenital disease
A congenital disorder is one that is present at birth. It is often a genetic disease or disorder and can be inherited. It can also be the result of a vertically transmitted infection from the mother, such as HIV/AIDS.
Genetic disease
A genetic disorder or disease is caused by one or more genetic mutations. It is often inherited, but some mutations are random and de novo.
Hereditary or inherited disease
A hereditary disease is a type of genetic disease caused by genetic mutations that are hereditary (and can run in families)
Iatrogenic disease
An iatrogenic disease or condition is one that is caused by medical intervention, whether as a side effect of a treatment or as an inadvertent outcome.
Idiopathic disease
An idiopathic disease has an unknown cause or source. As medical science has advanced, many diseases with entirely unknown causes have had some aspects of their sources explained and therefore shed their idiopathic status. For example, when germs were discovered, it became known that they were a cause of infection, but particular germs and diseases had not been linked. In another example, it is known that autoimmunity is the cause of some forms of diabetes mellitus type 1, even though the particular molecular pathways by which it works are not yet understood. It is also common to know certain factors are associated with certain diseases; however, association does not necessarily imply causality. For example, a third factor might be causing both the disease, and the associated phenomenon.
Incurable disease
A disease that cannot be cured. Incurable diseases are not necessarily terminal diseases, and sometimes a disease's symptoms can be treated sufficiently for the disease to have little or no impact on quality of life.
Primary disease
A primary disease is a disease that is due to a root cause of illness, as opposed to secondary disease, which is a sequela, or complication that is caused by the primary disease. For example, a common cold is a primary disease, where rhinitis is a possible secondary disease, or sequela. A doctor must determine what primary disease, a cold or bacterial infection, is causing a patient's secondary rhinitis when deciding whether or not to prescribe antibiotics.
Secondary disease
A secondary disease is a disease that is a sequela or complication of a prior, causal disease, which is referred to as the primary disease or simply the underlying cause (root cause). For example, a bacterial infection can be primary, wherein a healthy person is exposed to bacteria and becomes infected, or it can be secondary to a primary cause, that predisposes the body to infection. For example, a primary viral infection that weakens the immune system could lead to a secondary bacterial infection. Similarly, a primary burn that creates an open wound could provide an entry point for bacteria, and lead to a secondary bacterial infection.
Terminal disease
A terminal disease is one that is expected to have the inevitable result of death. Previously, AIDS was a terminal disease; it is now incurable, but can be managed indefinitely using medications.
Illness
The terms illness and sickness are both generally used as synonyms for disease; however, the term illness is occasionally used to refer specifically to the patient's personal experience of their disease. In this model, it is possible for a person to have a disease without being ill (to have an objectively definable, but asymptomatic, medical condition, such as a subclinical infection, or to have a clinically apparent physical impairment but not feel sick or distressed by it), and to be ill without being diseased (such as when a person perceives a normal experience as a medical condition, or medicalizes a non-disease situation in their life – for example, a person who feels unwell as a result of embarrassment, and who interprets those feelings as sickness rather than normal emotions). Symptoms of illness are often not directly the result of infection, but a collection of evolved responses – sickness behavior by the body – that helps clear infection and promote recovery. Such aspects of illness can include lethargy, depression, loss of appetite, sleepiness, hyperalgesia, and inability to concentrate.
Disorder
A disorder is a functional abnormality or disturbance that may or may not show specific signs and symptoms. Medical disorders can be categorized into mental disorders, physical disorders, genetic disorders, emotional and behavioral disorders, and functional disorders. The term disorder is often considered more value-neutral and less stigmatizing than the terms disease or illness, and therefore is preferred terminology in some circumstances. In mental health, the term mental disorder is used as a way of acknowledging the complex interaction of biological, social, and psychological factors in psychiatric conditions; however, the term disorder is also used in many other areas of medicine, primarily to identify physical disorders that are not caused by infectious organisms, such as metabolic disorders.
Medical condition or health condition
A medical condition or health condition is a broad concept that includes all diseases, lesions, disorders, or nonpathologic condition that normally receives medical treatment, such as pregnancy or childbirth. While the term medical condition generally includes mental illnesses, in some contexts the term is used specifically to denote any illness, injury, or disease except for mental illnesses. The Diagnostic and Statistical Manual of Mental Disorders (DSM), the widely used psychiatric manual that defines all mental disorders, uses the term general medical condition to refer to all diseases, illnesses, and injuries except for mental disorders. This usage is also commonly seen in the psychiatric literature. Some health insurance policies also define a medical condition as any illness, injury, or disease except for psychiatric illnesses.
As it is more value-neutral than terms like disease, the term medical condition is sometimes preferred by people with health issues that they do not consider deleterious. However, by emphasizing the medical nature of the condition, this term is sometimes rejected, such as by proponents of the autism rights movement.
The term medical condition is also a synonym for medical state, in which case it describes an individual patient's current state from a medical standpoint. This usage appears in statements that describe a patient as being in critical condition, for example.
Morbidity
Morbidity (from Latin morbidus 'sick, unhealthy') is a diseased state, disability, or poor health due to any cause. The term may refer to the existence of any form of disease, or to the degree that the health condition affects the patient. Among severely ill patients, the level of morbidity is often measured by ICU scoring systems. Comorbidity, or co-existing disease, is the simultaneous presence of two or more medical conditions, such as schizophrenia and substance abuse.
In epidemiology and actuarial science, the term morbidity (also morbidity rate or morbidity frequency) can refer to either the incidence rate, the prevalence of a disease or medical condition, or the percentage of people who experience a given condition within a given timeframe (e.g., 20% of people will get influenza in a year). This measure of sickness is contrasted with the mortality rate of a condition, which is the proportion of people dying during a given time interval. Morbidity rates are used in actuarial professions, such as health insurance, life insurance, and long-term care insurance, to determine the premiums charged to customers. Morbidity rates help insurers predict the likelihood that an insured will contract or develop any number of specified diseases.
Pathosis or pathology
Pathosis (plural pathoses) is synonymous with disease. The word pathology also has this sense, in which it is commonly used by physicians in the medical literature, although some editors prefer to reserve pathology to its other senses. Sometimes a slight connotative shade causes preference for pathology or pathosis implying "some [as yet poorly analyzed] pathophysiologic process" rather than disease implying "a specific disease entity as defined by diagnostic criteria being already met". This is hard to quantify denotatively, but it explains why cognitive synonymy is not invariable.
Syndrome
A syndrome is the association of several signs and symptoms, or other characteristics that often occur together, regardless of whether the cause is known. Some syndromes such as Down syndrome are known to have only one cause (an extra chromosome at birth). Others such as Parkinsonian syndrome are known to have multiple possible causes. Acute coronary syndrome, for example, is not a single disease itself but is rather the manifestation of any of several diseases including myocardial infarction secondary to coronary artery disease. In yet other syndromes, however, the cause is unknown. A familiar syndrome name often remains in use even after an underlying cause has been found or when there are a number of different possible primary causes. Examples of the first-mentioned type are that Turner syndrome and DiGeorge syndrome are still often called by the "syndrome" name despite that they can also be viewed as disease entities and not solely as sets of signs and symptoms.
Predisease
Predisease is a subclinical or prodromal vanguard of a disease. Prediabetes and prehypertension are common examples. The nosology or epistemology of predisease is contentious, though, because there is seldom a bright line differentiating a legitimate concern for subclinical or premonitory status and the conflict of interest–driven over-medicalization (e.g., by pharmaceutical manufacturers) or de-medicalization (e.g., by medical and disability insurers). Identifying legitimate predisease can result in useful preventive measures, such as motivating the person to get a healthy amount of physical exercise, but labeling a healthy person with an unfounded notion of predisease can result in overtreatment, such as taking drugs that only help people with severe disease or paying for treatments with a poor benefit–cost ratio.
One review proposed three criteria for predisease:
a high risk for progression to disease making one "far more likely to develop" it than others are- for example, a pre-cancer will almost certainly turn into cancer over time
actionability for risk reduction – for example, removal of the precancerous tissue prevents it from turning into a potentially deadly cancer
benefit that outweighs the harm of any interventions taken – removing the precancerous tissue prevents cancer, and thus prevents a potential death from cancer.
=== Types by body system ===
Mental
Mental illness is a broad, generic label for a category of illnesses that may include affective or emotional instability, behavioral dysregulation, cognitive dysfunction or impairment. Specific illnesses known as mental illnesses include major depression, generalized anxiety disorders, schizophrenia, and attention deficit hyperactivity disorder, to name a few. Mental illness can be of biological (e.g., anatomical, chemical, or genetic) or psychological (e.g., trauma or conflict) origin. It can impair the affected person's ability to work or study and can harm interpersonal relationship.
Organic
An organic disease is one caused by a physical or physiological change to some tissue or organ of the body. The term sometimes excludes infections. It is commonly used in contrast with mental disorders. It includes emotional and behavioral disorders if they are due to changes to the physical structures or functioning of the body, such as after a stroke or a traumatic brain injury, but not if they are due to psychosocial issues.
=== Stages ===
In an infectious disease, the incubation period is the time between infection and the appearance of symptoms. The latency period is the time between infection and the ability of the disease to spread to another person, which may precede, follow, or be simultaneous with the appearance of symptoms. Some viruses also exhibit a dormant phase, called viral latency, in which the virus hides in the body in an inactive state. For example, varicella zoster virus causes chickenpox in the acute phase; after recovery from chickenpox, the virus may remain dormant in nerve cells for many years, and later cause herpes zoster (shingles).
Acute disease
An acute disease is a short-lived disease, like the common cold.
Chronic disease
A chronic disease is one that lasts for a long time, usually at least six months. During that time, it may be constantly present, or it may go into remission and periodically relapse. A chronic disease may be stable (does not get any worse) or it may be progressive (gets worse over time). Some chronic diseases can be permanently cured. Most chronic diseases can be beneficially treated, even if they cannot be permanently cured.
Clinical disease
One that has clinical consequences; in other words, the stage of the disease that produces the characteristic signs and symptoms of that disease. AIDS is the clinical disease stage of HIV infection.
Cure
A cure is the end of a medical condition or a treatment that is very likely to end it, while remission refers to the disappearance, possibly temporarily, of symptoms. Complete remission is the best possible outcome for incurable diseases.
Flare-up
A flare-up can refer to either the recurrence of symptoms or an onset of more severe symptoms.
Progressive disease
Progressive disease is a disease whose typical natural course is the worsening of the disease until death, serious debility, or organ failure occurs. Slowly progressive diseases are also chronic diseases; many are also degenerative diseases. The opposite of progressive disease is stable disease or static disease: a medical condition that exists, but does not get better or worse.
Refractory disease
A refractory disease is a disease that resists treatment, especially an individual case that resists treatment more than is normal for the specific disease in question.
Subclinical disease
Also called silent disease, silent stage, or asymptomatic disease. This is a stage in some diseases before the symptoms are first noted.
Terminal phase
If a person will die soon from a disease, regardless of whether that disease typically causes death, then the stage between the earlier disease process and active dying is the terminal phase.
Recovery
Recovery can refer to the repairing of physical processes (tissues, organs etc.) and the resumption of healthy functioning after damage causing processes have been cured.
=== Extent ===
Localized disease
A localized disease is one that affects only one part of the body, such as athlete's foot or an eye infection.
Disseminated disease
A disseminated disease has spread to other parts; with cancer, this is usually called metastatic disease.
Systemic disease
A systemic disease is a disease that affects the entire body, such as influenza or high blood pressure.
== Classification ==
Diseases may be classified by cause, pathogenesis (mechanism by which the disease is caused), or by symptoms. Alternatively, diseases may be classified according to the organ system involved, though this is often complicated since many diseases affect more than one organ.
A chief difficulty in nosology is that diseases often cannot be defined and classified clearly, especially when cause or pathogenesis are unknown. Thus diagnostic terms often only reflect a symptom or set of symptoms (syndrome).
Classical classification of human disease derives from the observational correlation between pathological analysis and clinical syndromes. Today it is preferred to classify them by their cause if it is known.
The most known and used classification of diseases is the World Health Organization's ICD. This is periodically updated. Currently, the last publication is the ICD-11.
== Causes ==
Diseases can be caused by any number of factors and may be acquired or congenital. Microorganisms, genetics, the environment or a combination of these can contribute to a diseased state.
Only some diseases such as influenza are contagious and commonly believed infectious. The microorganisms that cause these diseases are known as pathogens and include varieties of bacteria, viruses, protozoa, and fungi. Infectious diseases can be transmitted, e.g. by hand-to-mouth contact with infectious material on surfaces, by bites of insects or other carriers of the disease, and from contaminated water or food (often via fecal contamination), etc. Also, there are sexually transmitted diseases. In some cases, microorganisms that are not readily spread from person to person play a role, while other diseases can be prevented or ameliorated with appropriate nutrition or other lifestyle changes.
Some diseases, such as most (but not all) forms of cancer, heart disease, and mental disorders, are non-infectious diseases. Many non-infectious diseases have a partly or completely genetic basis (see genetic disorder) and may thus be transmitted from one generation to another.
Social determinants of health are the social conditions in which people live that determine their health. Illnesses are generally related to social, economic, political, and environmental circumstances. Social determinants of health have been recognized by several health organizations such as the Public Health Agency of Canada and the World Health Organization to greatly influence collective and personal well-being. The World Health Organization's Social Determinants Council also recognizes Social determinants of health in poverty.
When the cause of a disease is poorly understood, societies tend to mythologize the disease or use it as a metaphor or symbol of whatever that culture considers evil. For example, until the bacterial cause of tuberculosis was discovered in 1882, experts variously ascribed the disease to heredity, a sedentary lifestyle, depressed mood, and overindulgence in sex, rich food, or alcohol, all of which were social ills at the time.
When a disease is caused by a pathogenic organism (e.g., when malaria is caused by Plasmodium), one should not confuse the pathogen (the cause of the disease) with disease itself. For example, West Nile virus (the pathogen) causes West Nile fever (the disease). The misuse of basic definitions in epidemiology is frequent in scientific publications.
=== Types of causes ===
Airborne
An airborne disease is any disease that is caused by pathogens and transmitted through the air.
Foodborne
Foodborne illness or food poisoning is any illness resulting from the consumption of food contaminated with pathogenic bacteria, toxins, viruses, prions or parasites.
Infectious
Infectious diseases, also known as transmissible diseases or communicable diseases, comprise clinically evident illness (i.e., characteristic medical signs or symptoms of disease) resulting from the infection, presence and growth of pathogenic biological agents in an individual host organism. Included in this category are contagious diseases – an infection, such as influenza or the common cold, that commonly spreads from one person to another – and communicable diseases – a disease that can spread from one person to another, but does not necessarily spread through everyday contact.
Lifestyle
A lifestyle disease is any disease that appears to increase in frequency as countries become more industrialized and people live longer, especially if the risk factors include behavioral choices like a sedentary lifestyle or a diet high in unhealthful foods such as refined carbohydrates, trans fats, or alcoholic beverages.
Non-communicable
A non-communicable disease is a medical condition or disease that is non-transmissible. Non-communicable diseases cannot be spread directly from one person to another. Heart disease and cancer are examples of non-communicable diseases in humans.
== Prevention ==
Many diseases and disorders can be prevented through a variety of means. These include sanitation, proper nutrition, adequate exercise, vaccinations and other self-care and public health measures, such as obligatory face mask mandates.
== Treatments ==
Medical therapies or treatments are efforts to cure or improve a disease or other health problems. In the medical field, therapy is synonymous with the word treatment. Among psychologists, the term may refer specifically to psychotherapy or "talk therapy". Common treatments include medications, surgery, medical devices, and self-care. Treatments may be provided by an organized health care system, or informally, by the patient or family members.
Preventive healthcare is a way to avoid an injury, sickness, or disease in the first place. A treatment or cure is applied after a medical problem has already started. A treatment attempts to improve or remove a problem, but treatments may not produce permanent cures, especially in chronic diseases. Cures are a subset of treatments that reverse diseases completely or end medical problems permanently. Many diseases that cannot be completely cured are still treatable. Pain management (also called pain medicine) is that branch of medicine employing an interdisciplinary approach to the relief of pain and improvement in the quality of life of those living with pain.
Treatment for medical emergencies must be provided promptly, often through an emergency department or, in less critical situations, through an urgent care facility.
== Epidemiology ==
Epidemiology is the study of the factors that cause or encourage diseases. Some diseases are more common in certain geographic areas, among people with certain genetic or socioeconomic characteristics, or at different times of the year.
Epidemiology is considered a cornerstone methodology of public health research and is highly regarded in evidence-based medicine for identifying risk factors for diseases. In the study of communicable and non-communicable diseases, the work of epidemiologists ranges from outbreak investigation to study design, data collection, and analysis including the development of statistical models to test hypotheses and the documentation of results for submission to peer-reviewed journals. Epidemiologists also study the interaction of diseases in a population, a condition known as a syndemic. Epidemiologists rely on a number of other scientific disciplines such as biology (to better understand disease processes), biostatistics (the current raw information available), Geographic Information Science (to store data and map disease patterns) and social science disciplines (to better understand proximate and distal risk factors). Epidemiology can help identify causes as well as guide prevention efforts.
In studying diseases, epidemiology faces the challenge of defining them. Especially for poorly understood diseases, different groups might use significantly different definitions. Without an agreed-on definition, different researchers may report different numbers of cases and characteristics of the disease.
Some morbidity databases are compiled with data supplied by states and territories health authorities, at national levels or larger scale (such as European Hospital Morbidity Database (HMDB)) which may contain hospital discharge data by detailed diagnosis, age and sex. The European HMDB data was submitted by European countries to the World Health Organization Regional Office for Europe.
=== Burdens of disease ===
Disease burden is the impact of a health problem in an area measured by financial cost, mortality, morbidity, or other indicators.
There are several measures used to quantify the burden imposed by diseases on people. The years of potential life lost (YPLL) is a simple estimate of the number of years that a person's life was shortened due to a disease. For example, if a person dies at the age of 65 from a disease, and would probably have lived until age 80 without that disease, then that disease has caused a loss of 15 years of potential life. YPLL measurements do not account for how disabled a person is before dying, so the measurement treats a person who dies suddenly and a person who died at the same age after decades of illness as equivalent. In 2004, the World Health Organization calculated that 932 million years of potential life were lost to premature death.
The quality-adjusted life year (QALY) and disability-adjusted life year (DALY) metrics are similar but take into account whether the person was healthy after diagnosis. In addition to the number of years lost due to premature death, these measurements add part of the years lost to being sick. Unlike YPLL, these measurements show the burden imposed on people who are very sick, but who live a normal lifespan. A disease that has high morbidity, but low mortality, has a high DALY and a low YPLL. In 2004, the World Health Organization calculated that 1.5 billion disability-adjusted life years were lost to disease and injury. In the developed world, heart disease and stroke cause the most loss of life, but neuropsychiatric conditions like major depressive disorder cause the most years lost to being sick.
== Society and culture ==
How a society responds to diseases is the subject of medical sociology.
A condition may be considered a disease in some cultures or eras but not in others. For example, obesity was associated with prosperity and abundance, and this perception persists in many African regions, especially since the beginning of the HIV/AIDS. Epilepsy is considered a sign of spiritual gifts among the Hmong people.
Sickness confers the social legitimization of certain benefits, such as illness benefits, work avoidance, and being looked after by others. The person who is sick takes on a social role called the sick role. A person who responds to a dreaded disease, such as cancer, in a culturally acceptable fashion may be publicly and privately honored with higher social status. In return for these benefits, the sick person is obligated to seek treatment and work to become well once more. As a comparison, consider pregnancy, which is not interpreted as a disease or sickness, even if the mother and baby may both benefit from medical care.
Most religions grant exceptions from religious duties to people who are sick. For example, one whose life would be endangered by fasting on Yom Kippur or during the month of Ramadan is exempted from the requirement, or even forbidden from participating. People who are sick are also exempted from social duties. For example, ill health is the only socially acceptable reason for an American to refuse an invitation to the White House.
The identification of a condition as a disease, rather than as simply a variation of human structure or function, can have significant social or economic implications. The controversial recognition of diseases such as repetitive stress injury (RSI) and post-traumatic stress disorder (PTSD) has had a number of positive and negative effects on the financial and other responsibilities of governments, corporations, and institutions towards individuals, as well as on the individuals themselves. The social implication of viewing aging as a disease could be profound, though this classification is not yet widespread.
Lepers were people who were historically shunned because they had an infectious disease, and the term "leper" still evokes social stigma. Fear of disease can still be a widespread social phenomenon, though not all diseases evoke extreme social stigma.
Social standing and economic status affect health. Diseases of poverty are diseases that are associated with poverty and low social status; diseases of affluence are diseases that are associated with high social and economic status. Which diseases are associated with which states vary according to time, place, and technology. Some diseases, such as diabetes mellitus, may be associated with both poverty (poor food choices) and affluence (long lifespans and sedentary lifestyles), through different mechanisms. The term lifestyle diseases describes diseases associated with longevity and that are more common among older people. For example, cancer is far more common in societies in which most members live until they reach the age of 80 than in societies in which most members die before they reach the age of 50.
=== Language of disease ===
An illness narrative is a way of organizing a medical experience into a coherent story that illustrates the sick individual's personal experience.
People use metaphors to make sense of their experiences with disease. The metaphors move disease from an objective thing that exists to an affective experience. The most popular metaphors draw on military concepts: Disease is an enemy that must be feared, fought, battled, and routed. The patient or the healthcare provider is a warrior, rather than a passive victim or bystander. The agents of communicable diseases are invaders; non-communicable diseases constitute internal insurrection or civil war. Because the threat is urgent, perhaps a matter of life and death, unthinkably radical, even oppressive, measures are society's and the patient's moral duty as they courageously mobilize to struggle against destruction. The War on Cancer is an example of this metaphorical use of language. This language is empowering to some patients, but leaves others feeling like they are failures.
Another class of metaphors describes the experience of illness as a journey: The person travels to or from a place of disease, and changes himself, discovers new information, or increases his experience along the way. He may travel "on the road to recovery" or make changes to "get on the right track" or choose "pathways". Some are explicitly immigration-themed: the patient has been exiled from the home territory of health to the land of the ill, changing identity and relationships in the process. This language is more common among British healthcare professionals than the language of physical aggression.
Some metaphors are disease-specific. Slavery is a common metaphor for addictions: The alcoholic is enslaved by drink, and the smoker is captive to nicotine. Some cancer patients treat the loss of their hair from chemotherapy as a metonymy or metaphor for all the losses caused by the disease.
Some diseases are used as metaphors for social ills: "Cancer" is a common description for anything that is endemic and destructive in society, such as poverty, injustice, or racism. AIDS was seen as a divine judgment for moral decadence, and only by purging itself from the "pollution" of the "invader" could society become healthy again. More recently, when AIDS seemed less threatening, this type of emotive language was applied to avian flu and type 2 diabetes mellitus. Authors in the 19th century commonly used tuberculosis as a symbol and a metaphor for transcendence. People with the disease were portrayed in literature as having risen above daily life to become ephemeral objects of spiritual or artistic achievement. In the 20th century, after its cause was better understood, the same disease became the emblem of poverty, squalor, and other social problems.
== See also ==
== References ==
== External links ==
"Man and Disease", BBC Radio 4 discussion with Anne Hardy, David Bradley & Chris Dye (In Our Time, 15 December 2002)
CTD The Comparative Toxicogenomics Database is a scientific resource connecting chemicals, genes, and human diseases.
Free online health-risk assessment by Your Disease Risk at Washington University in St. Louis
Health Topics A–Z, fact sheets about many common diseases at the Centers for Disease Control
Health Topics, MedlinePlus descriptions of most diseases, with access to current research articles.
NLM Comprehensive database from the US National Library of Medicine
OMIM Comprehensive information on genes that cause disease at Online Mendelian Inheritance in Man
Report: The global burden of disease from the World Health Organization (WHO), 2004
The Merck Manual containing detailed description of most diseases | Wikipedia/Diseases |
Epstein–Barr virus (EBV) latent membrane protein 2 (LMP2) are two viral proteins of the Epstein–Barr virus. LMP2A/LMP2B are transmembrane proteins that act to block tyrosine kinase signaling. LMP2A is a transmembrane protein that inhibits normal B-cell signal transduction by mimicking an activated B-cell receptor (BCR). The N-terminus domain of LMP2A is tyrosine phosphorylated and associates with Src family protein tyrosine kinases (PTKs) as well as spleen tyrosine kinase (Syk). PTKs and Syk are associated with BCR signal transduction.
== LMP2 gene structure and expression ==
Latent Membrane Protein 2 (LMP2) is a rightward transcribing gene. LMP2's transcript originates across the fused terminal repeats in sequences at opposite ends of the genome. 16–24 hours after infection, the genome circularizes and the open reading frame is created. 1.7 kb and 2.0 kb messages are created by alternative promoter usage and differ only in the sequences of the first exon. These messages are expressed in Epstein-Barr Virus transformed lymphoblastoid cell cultures. The ratio of these messages varies widely and unpredictably suggesting little co-ordinate control of promoter activity or mRNA abundance. Residues 497 (LMP2A) and 378 (LMP2B) are encoded by these two messages. These two iso forms of LMP2 only differ in that LMP2A contains an extra 119 residue N-terminal domain encoded in exon 1. LMP2B's first exon is non coding. Initiation of translation is presumed to occur at the first available [methionine] that is in-frame in exon two. Twelve membrane spanning segments ending with a short 28 residue COOH tail are common to both proteins in residue 379.
== LMP2A protein interactions ==
The 119 amino-terminal cytoplasmic domain of LMP2A has several motifs that mediate interactions between proteins, including eight tyrosine residues. Two motifs that are centered on Y74 and Y85 are spaced 7 residues apart to form an immunoreceptor tyrosine-based activation motif (ITAM) commonly found in Fc receptors and signal molecules of B-cell and T-cell receptors. Receptor docking with molecules containing cytoplasmic tyrosine kinases is governed by Phosphorylation of ITAM motifs. In lymphoblastoid cell cultures, Syk tyrosine kinases have been found in LMP2A immunoprecipitates following in vitro kinase reactions followed by Syk antibody reimunnoprecipitation. Affinity precipitation experiments have shown that Syk interacts with phosphorylated peptides corresponding to the LMP2A-ITAM complex. Residues for Syk binding have been discovered by inducing point mutations in Y74F and Y85F point. Tyrosine kinase LYN has also been detected in immunoprecipitates from transiently transfected B cells at residue Y112. Constitutive phosphorylation occurs on tyrosine, serine and threonine residues.
== LMP2A function ==
Epstein–Barr virus (EBV) establishes a lifelong latent infection in B lymphocytes. Viral LMP2A mRNA is frequently detected in peripheral blood B lymphocytes and the protein is often present in tumor biopsies from EBV malignancies. This suggests LMP2A plays an important role in viral latency, as well as in progression of EBV related diseases such as Burkitt's lymphoma, Nasopharyngeal carcinoma, and Hodgkin's lymphoma. Portis and Longnecker (2004) have found that LMP2A induces activation of B cell Ras pathway in vivo. Using down stream inhibitors of Ras signaling components, they demonstrated activation of PI3K/Akt pathway is involved in LMP2A mediated B cell survival and resistance to apoptosis Caldwell et al. (1998) demonstrated the ability of LMP2A to provide survival signals to B-cells in vivo where expression of an LMP2A transgene in mice disrupts with normal B-cell development. This results in BCR-negative cells being able to exit the bone marrow and survive in peripheral lymphoid organs. B-cells from LMP2A transgenic E line undergo immunoglobulin light chain rearrangements, but not heavy chain rearrangement. This indicates that LMP2A signaling bypasses the requirement for immunoglobulin recombination and allows immunoglobulin M-negative type cells to bypass apoptosis, allowing them to colonize peripheral lymphoid organs.
== LMP2B ==
Eight exons of LMP2 isoforms encode 12 membrane spanning segments that are connected by short hydrophilic loops and ends with a 27 amino acid cytoplasmic C-terminus domain. LMP2B, unlike LMP2A, does not contain the N-terminal 119 amino acid cytoplasmic signaling domain. Most LMP2 research is focused on LMP2A isoform due to its unique expression in latently infected B lymphocytes in situ. LMP2B protein function is unknown. There has not been a comprehensive phenotypic analysis of the LMP2B isoform because of its hydrophobic character. While the role of LMP2B in pathogenesis remains uncertain, homology studies comparing the LMP2 gene of EBV with Rhesus and Baboon Lymphocryptovirus, have revealed promoter regulatory elements, Epstein–Barr nuclear antigen-2 responsiveness, and the ability to make LMP2B transcripts are conserved. This implies that an unrecognized role for LMP2B in the EBV life cycle has yet to be determined.
== References == | Wikipedia/Epstein–Barr_virus_latent_membrane_protein_2 |
HHV Capsid Portal Protein, or HSV-1 UL-6 protein, is the protein which forms a cylindrical portal in the capsid of Herpes simplex virus (HSV-1). The protein is commonly referred to as the HSV-1 UL-6 protein because it is the transcription product of Herpes gene UL-6.
The Herpes viral DNA enters and exits the capsid via the capsid portal. The capsid portal is formed by twelve copies of portal protein arranged as a ring; the proteins contain a leucine zipper sequence of amino acids which allow them to adhere to each other. Each icosahedral capsid contains a single portal, located in one vertex.
The portal is formed during initial capsid assembly and interacts with scaffolding proteins that construct the procapsid.
When the capsid is nearly complete, the viral DNA enters the capsid (i.e., the DNA is encapsidated) by a mechanism involving the portal and a DNA-binding protein complex similar to bacteriophage terminase. Multiple studies suggest an evolutionary relationship between Capsid Portal Protein and bacteriophage portal proteins.
When a virus infects a cell, it is necessary for the viral DNA to be released from the capsid. The Herpes virus DNA exits through the capsid portal.
The genetic sequence of HSV-1 gene UL-6 is conserved across the family Herpesviridae and this family of genes is known as the "Herpesvirus UL6-like" gene family. "UL-6" is nomenclature meaning that the protein is genetically encoded by the sixth (6th) open reading frame found in the viral genome segment named "Unique-Long (UL)".
== Studies ==
=== Dodecameric structure ===
Research performed in 2004 used electron microscopy to predict that UL-6 forms 11, 12, 13, and 14-unit polymers. The dodecameric form was found to be most likely.
Refinements to the electron microscopy in 2007 allowed finding that the portal is a twelve (12)-unit polymer present at one of the twelve capsid vertices instead of the UL-19 pentamer found at non-portal vertices.
=== Leucine zipper creates inter-protein adhesion ===
A study using deletion and mutation of the UL-6 amino acid sequence demonstrated the leucine residues in a predicted leucine zipper motif were required for formation of the dodecameric ring structure.
=== Early involvement in capsid assembly ===
Assembly of portal units is an initial step in constructing capsids of viral progeny. Capsids assembled in the absence of portals lack portals.
=== Interaction with capsid scaffolding protein ===
In 2003, gel eletrophoresis studies demonstrated that intact UL-6 portals associate in vitro with viral protein UL-26. This association is antagonized by that action of WAY-150138, a thiourea inhibitor of HHV encapsidation.
Further investigation during 2006 showed that assembly of capsid with portal depends on interaction of UL-6 with "scaffolding" protein UL-26.5, amino acids 143 through 151.
=== Interaction with terminase complex ===
UL-6 associates with a UL-15/UL-28 protein complex during capsid assembly. The UL-15/UL-28 is believed to bind with viral DNA and serve the same purpose as terminase by packing viral DNA into the capsid during capsid assembly.
=== Function during DNA egress ===
The DNA exits the capsid in a single linear segment. DNA exit may be controlled by UL-6 and dependent on temperature or environmental proteins.
== References == | Wikipedia/HHV_capsid_portal_protein |
Inflammation (from Latin: inflammatio) is part of the biological response of body tissues to harmful stimuli, such as pathogens, damaged cells, or irritants. The five cardinal signs are heat, pain, redness, swelling, and loss of function (Latin calor, dolor, rubor, tumor, and functio laesa).
Inflammation is a generic response, and therefore is considered a mechanism of innate immunity, whereas adaptive immunity is specific to each pathogen.
Inflammation is a protective response involving immune cells, blood vessels, and molecular mediators. The function of inflammation is to eliminate the initial cause of cell injury, clear out damaged cells and tissues, and initiate tissue repair. Too little inflammation could lead to progressive tissue destruction by the harmful stimulus (e.g. bacteria) and compromise the survival of the organism. However inflammation can also have negative effects. Too much inflammation, in the form of chronic inflammation, is associated with various diseases, such as hay fever, periodontal disease, atherosclerosis, and osteoarthritis.
Inflammation can be classified as acute or chronic. Acute inflammation is the initial response of the body to harmful stimuli, and is achieved by the increased movement of plasma and leukocytes (in particular granulocytes) from the blood into the injured tissues. A series of biochemical events propagates and matures the inflammatory response, involving the local vascular system, the immune system, and various cells in the injured tissue. Prolonged inflammation, known as chronic inflammation, leads to a progressive shift in the type of cells present at the site of inflammation, such as mononuclear cells, and involves simultaneous destruction and healing of the tissue.
Inflammation has also been classified as Type 1 and Type 2 based on the type of cytokines and helper T cells (Th1 and Th2) involved.
== Meaning ==
The earliest known reference for the term inflammation is around the early 15th century. The word root comes from Old French inflammation around the 14th century, which then comes from Latin inflammatio or inflammationem. Literally, the term relates to the word "flame", as the property of being "set on fire" or "to burn".
The term inflammation is not a synonym for infection. Infection describes the interaction between the action of microbial invasion and the reaction of the body's inflammatory response—the two components are considered together in discussion of infection, and the word is used to imply a microbial invasive cause for the observed inflammatory reaction. Inflammation, on the other hand, describes just the body's immunovascular response, regardless of cause. But, because the two are often correlated, words ending in the suffix -itis (which means inflammation) are sometimes informally described as referring to infection: for example, the word urethritis strictly means only "urethral inflammation", but clinical health care providers usually discuss urethritis as a urethral infection because urethral microbial invasion is the most common cause of urethritis. However, the inflammation–infection distinction is crucial in situations in pathology and medical diagnosis that involve inflammation that is not driven by microbial invasion, such as cases of atherosclerosis, trauma, ischemia, and autoimmune diseases (including type III hypersensitivity).
== Causes ==
== Types ==
=== Acute ===
Acute inflammation is a short-term process, usually appearing within a few minutes or hours and begins to cease upon the removal of the injurious stimulus. It involves a coordinated and systemic mobilization response locally of various immune, endocrine and neurological mediators of acute inflammation. In a normal healthy response, it becomes activated, clears the pathogen and begins a repair process and then ceases.
Acute inflammation occurs immediately upon injury, lasting only a few days. Cytokines and chemokines promote the migration of neutrophils and macrophages to the site of inflammation. Pathogens, allergens, toxins, burns, and frostbite are some of the typical causes of acute inflammation. Toll-like receptors (TLRs) recognize microbial pathogens. Acute inflammation can be a defensive mechanism to protect tissues against injury. Inflammation lasting 2–6 weeks is designated subacute inflammation.
==== Cardinal signs ====
Inflammation is characterized by five cardinal signs, (the traditional names of which come from Latin):
Dolor (pain)
Calor (heat)
Rubor (redness)
Tumor (swelling)
Functio laesa (loss of function)
The first four (classical signs) were described by Celsus (c. 30 BC–38 AD).
Pain is due to the release of chemicals such as bradykinin and histamine that stimulate nerve endings. Acute inflammation of the lung (usually in response to pneumonia) does not cause pain unless the inflammation involves the parietal pleura, which does have pain-sensitive nerve endings. Heat and redness are due to increased blood flow at body core temperature to the inflamed site. Swelling is caused by accumulation of fluid.
===== Loss of function =====
The fifth sign, loss of function, is believed to have been added later by Galen, Thomas Sydenham or Rudolf Virchow. Examples of loss of function include pain that inhibits mobility, severe swelling that prevents movement, having a worse sense of smell during a cold, or having difficulty breathing when bronchitis is present. Loss of function has multiple causes.
==== Acute process ====
The process of acute inflammation is initiated by resident immune cells already present in the involved tissue, mainly resident macrophages, dendritic cells, histiocytes, Kupffer cells and mast cells. These cells possess surface receptors known as pattern recognition receptors (PRRs), which recognize (i.e., bind) two subclasses of molecules: pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs). PAMPs are compounds that are associated with various pathogens, but which are distinguishable from host molecules. DAMPs are compounds that are associated with host-related injury and cell damage.
At the onset of an infection, burn, or other injuries, these cells undergo activation (one of the PRRs recognize a PAMP or DAMP) and release inflammatory mediators responsible for the clinical signs of inflammation. Vasodilation and its resulting increased blood flow causes the redness (rubor) and increased heat (calor). Increased permeability of the blood vessels results in an exudation (leakage) of plasma proteins and fluid into the tissue (edema), which manifests itself as swelling (tumor). Some of the released mediators such as bradykinin increase the sensitivity to pain (hyperalgesia, dolor). The mediator molecules also alter the blood vessels to permit the migration of leukocytes, mainly neutrophils and macrophages, to flow out of the blood vessels (extravasation) and into the tissue. The neutrophils migrate along a chemotactic gradient created by the local cells to reach the site of injury. The loss of function (functio laesa) is probably the result of a neurological reflex in response to pain.
In addition to cell-derived mediators, several acellular biochemical cascade systems—consisting of preformed plasma proteins—act in parallel to initiate and propagate the inflammatory response. These include the complement system activated by bacteria and the coagulation and fibrinolysis systems activated by necrosis (e.g., burn, trauma).
Acute inflammation may be regarded as the first line of defense against injury. Acute inflammatory response requires constant stimulation to be sustained. Inflammatory mediators are short-lived and are quickly degraded in the tissue. Hence, acute inflammation begins to cease once the stimulus has been removed.
=== Chronic ===
Chronic inflammation is inflammation that lasts for months or years. Macrophages, lymphocytes, and plasma cells predominate in chronic inflammation, in contrast to the neutrophils that predominate in acute inflammation. Diabetes, cardiovascular disease, allergies, and chronic obstructive pulmonary disease are examples of diseases mediated by chronic inflammation. Obesity, smoking, stress and insufficient diet are some of the factors that promote chronic inflammation.
==== Cardinal signs ====
Common signs and symptoms that develop during chronic inflammation are:
Body pain, arthralgia, myalgia
Chronic fatigue and insomnia
Depression, anxiety and mood disorders
Gastrointestinal complications such as constipation, diarrhea, and acid reflux
Weight gain or loss
Frequent infections
== Vascular component ==
=== Vasodilation and increased permeability ===
As defined, acute inflammation is an immunovascular response to inflammatory stimuli, which can include infection or trauma. This means acute inflammation can be broadly divided into a vascular phase that occurs first, followed by a cellular phase involving immune cells (more specifically myeloid granulocytes in the acute setting). The vascular component of acute inflammation involves the movement of plasma fluid, containing important proteins such as fibrin and immunoglobulins (antibodies), into inflamed tissue.
Upon contact with PAMPs, tissue macrophages and mastocytes release vasoactive amines such as histamine and serotonin, as well as eicosanoids such as prostaglandin E2 and leukotriene B4 to remodel the local vasculature. Macrophages and endothelial cells release nitric oxide. These mediators vasodilate and permeabilize the blood vessels, which results in the net distribution of blood plasma from the vessel into the tissue space. The increased collection of fluid into the tissue causes it to swell (edema). This exuded tissue fluid contains various antimicrobial mediators from the plasma such as complement, lysozyme, antibodies, which can immediately deal damage to microbes, and opsonise the microbes in preparation for the cellular phase. If the inflammatory stimulus is a lacerating wound, exuded platelets, coagulants, plasmin and kinins can clot the wounded area using vitamin K-dependent mechanisms and provide haemostasis in the first instance. These clotting mediators also provide a structural staging framework at the inflammatory tissue site in the form of a fibrin lattice – as would construction scaffolding at a construction site – for the purpose of aiding phagocytic debridement and wound repair later on. Some of the exuded tissue fluid is also funneled by lymphatics to the regional lymph nodes, flushing bacteria along to start the recognition and attack phase of the adaptive immune system.
Acute inflammation is characterized by marked vascular changes, including vasodilation, increased permeability and increased blood flow, which are induced by the actions of various inflammatory mediators. Vasodilation occurs first at the arteriole level, progressing to the capillary level, and brings about a net increase in the amount of blood present, causing the redness and heat of inflammation. Increased permeability of the vessels results in the movement of plasma into the tissues, with resultant stasis due to the increase in the concentration of the cells within blood – a condition characterized by enlarged vessels packed with cells. Stasis allows leukocytes to marginate (move) along the endothelium, a process critical to their recruitment into the tissues. Normal flowing blood prevents this, as the shearing force along the periphery of the vessels moves cells in the blood into the middle of the vessel.
=== Plasma cascade systems ===
The complement system, when activated, creates a cascade of chemical reactions that promotes opsonization, chemotaxis, and agglutination, and produces the MAC.
The kinin system generates proteins capable of sustaining vasodilation and other physical inflammatory effects.
The coagulation system or clotting cascade, which forms a protective protein mesh over sites of injury.
The fibrinolysis system, which acts in opposition to the coagulation system, to counterbalance clotting and generate several other inflammatory mediators.
=== Plasma-derived mediators ===
* non-exhaustive list
== Cellular component ==
The cellular component involves leukocytes, which normally reside in blood and must move into the inflamed tissue via extravasation to aid in inflammation. Some act as phagocytes, ingesting bacteria, viruses, and cellular debris. Others release enzymatic granules that damage pathogenic invaders. Leukocytes also release inflammatory mediators that develop and maintain the inflammatory response. In general, acute inflammation is mediated by granulocytes, whereas chronic inflammation is mediated by mononuclear cells such as monocytes and lymphocytes.
=== Leukocyte extravasation ===
Various leukocytes, particularly neutrophils, are critically involved in the initiation and maintenance of inflammation. These cells must be able to move to the site of injury from their usual location in the blood, therefore mechanisms exist to recruit and direct leukocytes to the appropriate place. The process of leukocyte movement from the blood to the tissues through the blood vessels is known as extravasation and can be broadly divided up into a number of steps:
Leukocyte margination and endothelial adhesion: The white blood cells within the vessels which are generally centrally located move peripherally towards the walls of the vessels. Activated macrophages in the tissue release cytokines such as IL-1 and TNFα, which in turn leads to production of chemokines that bind to proteoglycans forming gradient in the inflamed tissue and along the endothelial wall. Inflammatory cytokines induce the immediate expression of P-selectin on endothelial cell surfaces and P-selectin binds weakly to carbohydrate ligands on the surface of leukocytes and causes them to "roll" along the endothelial surface as bonds are made and broken. Cytokines released from injured cells induce the expression of E-selectin on endothelial cells, which functions similarly to P-selectin. Cytokines also induce the expression of integrin ligands such as ICAM-1 and VCAM-1 on endothelial cells, which mediate the adhesion and further slow leukocytes down. These weakly bound leukocytes are free to detach if not activated by chemokines produced in injured tissue after signal transduction via respective G protein-coupled receptors that activates integrins on the leukocyte surface for firm adhesion. Such activation increases the affinity of bound integrin receptors for ICAM-1 and VCAM-1 on the endothelial cell surface, firmly binding the leukocytes to the endothelium.
Migration across the endothelium, known as transmigration, via the process of diapedesis: Chemokine gradients stimulate the adhered leukocytes to move between adjacent endothelial cells. The endothelial cells retract and the leukocytes pass through the basement membrane into the surrounding tissue using adhesion molecules such as ICAM-1.
Movement of leukocytes within the tissue via chemotaxis: Leukocytes reaching the tissue interstitium bind to extracellular matrix proteins via expressed integrins and CD44 to prevent them from leaving the site. A variety of molecules behave as chemoattractants, for example, C3a or C5a (the anaphylatoxins), and cause the leukocytes to move along a chemotactic gradient towards the source of inflammation.
=== Phagocytosis ===
Extravasated neutrophils in the cellular phase come into contact with microbes at the inflamed tissue. Phagocytes express cell-surface endocytic pattern recognition receptors (PRRs) that have affinity and efficacy against non-specific microbe-associated molecular patterns (PAMPs). Most PAMPs that bind to endocytic PRRs and initiate phagocytosis are cell wall components, including complex carbohydrates such as mannans and β-glucans, lipopolysaccharides (LPS), peptidoglycans, and surface proteins. Endocytic PRRs on phagocytes reflect these molecular patterns, with C-type lectin receptors binding to mannans and β-glucans, and scavenger receptors binding to LPS.
Upon endocytic PRR binding, actin-myosin cytoskeletal rearrangement adjacent to the plasma membrane occurs in a way that endocytoses the plasma membrane containing the PRR-PAMP complex, and the microbe. Phosphatidylinositol and Vps34-Vps15-Beclin1 signalling pathways have been implicated to traffic the endocytosed phagosome to intracellular lysosomes, where fusion of the phagosome and the lysosome produces a phagolysosome. The reactive oxygen species, superoxides and hypochlorite bleach within the phagolysosomes then kill microbes inside the phagocyte.
Phagocytic efficacy can be enhanced by opsonization. Plasma derived complement C3b and antibodies that exude into the inflamed tissue during the vascular phase bind to and coat the microbial antigens. As well as endocytic PRRs, phagocytes also express opsonin receptors Fc receptor and complement receptor 1 (CR1), which bind to antibodies and C3b, respectively. The co-stimulation of endocytic PRR and opsonin receptor increases the efficacy of the phagocytic process, enhancing the lysosomal elimination of the infective agent.
=== Cell-derived mediators ===
* non-exhaustive list
== Morphologic patterns ==
Specific patterns of acute and chronic inflammation are seen during particular situations that arise in the body, such as when inflammation occurs on an epithelial surface, or pyogenic bacteria are involved.
Granulomatous inflammation: Characterised by the formation of granulomas, they are the result of a limited but diverse number of diseases, which include among others tuberculosis, leprosy, sarcoidosis, and syphilis.
Fibrinous inflammation: Inflammation resulting in a large increase in vascular permeability allows fibrin to pass through the blood vessels. If an appropriate procoagulative stimulus is present, such as cancer cells, a fibrinous exudate is deposited. This is commonly seen in serous cavities, where the conversion of fibrinous exudate into a scar can occur between serous membranes, limiting their function. The deposit sometimes forms a pseudomembrane sheet. During inflammation of the intestine (pseudomembranous colitis), pseudomembranous tubes can be formed.
Purulent inflammation: Inflammation resulting in large amount of pus, which consists of neutrophils, dead cells, and fluid. Infection by pyogenic bacteria such as staphylococci is characteristic of this kind of inflammation. Large, localised collections of pus enclosed by surrounding tissues are called abscesses.
Serous inflammation: Characterised by the copious effusion of non-viscous serous fluid, commonly produced by mesothelial cells of serous membranes, but may be derived from blood plasma. Skin blisters exemplify this pattern of inflammation.
Ulcerative inflammation: Inflammation occurring near an epithelium can result in the necrotic loss of tissue from the surface, exposing lower layers. The subsequent excavation in the epithelium is known as an ulcer.
== Disorders ==
Inflammatory abnormalities are a large group of disorders that underlie a vast variety of human diseases. The immune system is often involved with inflammatory disorders, as demonstrated in both allergic reactions and some myopathies, with many immune system disorders resulting in abnormal inflammation. Non-immune diseases with causal origins in inflammatory processes include cancer, atherosclerosis, and ischemic heart disease.
Examples of disorders associated with inflammation include:
=== Atherosclerosis ===
Atherosclerosis, formerly considered a lipid storage disorder, is now understood as a chronic inflammatory condition involving the arterial walls. Research has established a fundamental role for inflammation in mediating all stages of atherosclerosis from initiation through progression and, ultimately, the thrombotic complications from it. These new findings reveal links between traditional risk factors like cholesterol levels and the underlying mechanisms of atherogenesis.
Clinical studies have shown that this emerging biology of inflammation in atherosclerosis applies directly to people. For instance, elevation in markers of inflammation predicts outcomes of people with acute coronary syndromes, independently of myocardial damage. In addition, low-grade chronic inflammation, as indicated by levels of the inflammatory marker C-reactive protein, prospectively defines risk of atherosclerotic complications, thus adding to prognostic information provided by traditional risk factors, such as LDL levels.
Moreover, certain treatments that reduce coronary risk also limit inflammation. Notably, lipid-lowering medications such as statins have shown anti-inflammatory effects, which may contribute to their efficacy beyond just lowering LDL levels. This emerging understanding of inflammation's role in atherosclerosis has had significant clinical implications, influencing both risk stratification and therapeutic strategies.
==== Emerging treatments ====
Recent developments in the treatment of atherosclerosis have focused on addressing inflammation directly. New anti-inflammatory drugs, such as monoclonal antibodies targeting IL-1β, have been studied in large clinical trials, showing promising results in reducing cardiovascular events. These drugs offer a potential new avenue for treatment, particularly for patients who do not respond adequately to statins. However, concerns about long-term safety and cost remain significant barriers to widespread adoption.
==== Connection to depression ====
Inflammatory processes can be triggered by negative cognition or their consequences, such as stress, violence, or deprivation. Negative cognition may therefore contribute to inflammation, which in turn can lead to depression. A 2019 meta-analysis found that chronic inflammation is associated with a 30% increased risk of developing major depressive disorder, supporting the link between inflammation and mental health.
=== Allergy ===
An allergic reaction, formally known as type 1 hypersensitivity, is the result of an inappropriate immune response triggering inflammation, vasodilation, and nerve irritation. A common example is hay fever, which is caused by a hypersensitive response by mast cells to allergens. Pre-sensitised mast cells respond by degranulating, releasing vasoactive chemicals such as histamine. These chemicals propagate an excessive inflammatory response characterised by blood vessel dilation, production of pro-inflammatory molecules, cytokine release, and recruitment of leukocytes. Severe inflammatory response may mature into a systemic response known as anaphylaxis.
=== Myopathies ===
Inflammatory myopathies are caused by the immune system inappropriately attacking components of muscle, leading to signs of muscle inflammation. They may occur in conjunction with other immune disorders, such as systemic sclerosis, and include dermatomyositis, polymyositis, and inclusion body myositis.
=== Leukocyte defects ===
Due to the central role of leukocytes in the development and propagation of inflammation, defects in leukocyte functionality often result in a decreased capacity for inflammatory defense with subsequent vulnerability to infection. Dysfunctional leukocytes may be unable to correctly bind to blood vessels due to surface receptor mutations, digest bacteria (Chédiak–Higashi syndrome), or produce microbicides (chronic granulomatous disease). In addition, diseases affecting the bone marrow may result in abnormal or few leukocytes.
=== Pharmacological ===
Certain drugs or exogenous chemical compounds are known to affect inflammation. Vitamin A deficiency, for example, causes an increase in inflammatory responses, and anti-inflammatory drugs work specifically by inhibiting the enzymes that produce inflammatory eicosanoids. Additionally, certain illicit drugs such as cocaine and ecstasy may exert some of their detrimental effects by activating transcription factors intimately involved with inflammation (e.g. NF-κB).
=== Cancer ===
Inflammation orchestrates the microenvironment around tumours, contributing to proliferation, survival and migration. Cancer cells use selectins, chemokines and their receptors for invasion, migration and metastasis. On the other hand, many cells of the immune system contribute to cancer immunology, suppressing cancer.
Molecular intersection between receptors of steroid hormones, which have important effects on cellular development, and transcription factors that play key roles in inflammation, such as NF-κB, may mediate some of the most critical effects of inflammatory stimuli on cancer cells. This capacity of a mediator of inflammation to influence the effects of steroid hormones in cells is very likely to affect carcinogenesis. On the other hand, due to the modular nature of many steroid hormone receptors, this interaction may offer ways to interfere with cancer progression, through targeting of a specific protein domain in a specific cell type. Such an approach may limit side effects that are unrelated to the tumor of interest, and may help preserve vital homeostatic functions and developmental processes in the organism.
There is some evidence from 2009 to suggest that cancer-related inflammation (CRI) may lead to accumulation of random genetic alterations in cancer cells.
==== Role in cancer ====
In 1863, Rudolf Virchow hypothesized that the origin of cancer was at sites of chronic inflammation. As of 2012, chronic inflammation was estimated to contribute to approximately 15% to 25% of human cancers.
==== Mediators and DNA damage in cancer ====
An inflammatory mediator is a messenger that acts on blood vessels and/or cells to promote an inflammatory response. Inflammatory mediators that contribute to neoplasia include prostaglandins, inflammatory cytokines such as IL-1β, TNF-α, IL-6 and IL-15 and chemokines such as IL-8 and GRO-alpha. These inflammatory mediators, and others, orchestrate an environment that fosters proliferation and survival.
Inflammation also causes DNA damages due to the induction of reactive oxygen species (ROS) by various intracellular inflammatory mediators. In addition, leukocytes and other phagocytic cells attracted to the site of inflammation induce DNA damages in proliferating cells through their generation of ROS and reactive nitrogen species (RNS). ROS and RNS are normally produced by these cells to fight infection. ROS, alone, cause more than 20 types of DNA damage. Oxidative DNA damages cause both mutations and epigenetic alterations. RNS also cause mutagenic DNA damages.
A normal cell may undergo carcinogenesis to become a cancer cell if it is frequently subjected to DNA damage during long periods of chronic inflammation. DNA damages may cause genetic mutations due to inaccurate repair. In addition, mistakes in the DNA repair process may cause epigenetic alterations. Mutations and epigenetic alterations that are replicated and provide a selective advantage during somatic cell proliferation may be carcinogenic.
Genome-wide analyses of human cancer tissues reveal that a single typical cancer cell may possess roughly 100 mutations in coding regions, 10–20 of which are "driver mutations" that contribute to cancer development. However, chronic inflammation also causes epigenetic changes such as DNA methylations, that are often more common than mutations. Typically, several hundreds to thousands of genes are methylated in a cancer cell (see DNA methylation in cancer). Sites of oxidative damage in chromatin can recruit complexes that contain DNA methyltransferases (DNMTs), a histone deacetylase (SIRT1), and a histone methyltransferase (EZH2), and thus induce DNA methylation. DNA methylation of a CpG island in a promoter region may cause silencing of its downstream gene (see CpG site and regulation of transcription in cancer). DNA repair genes, in particular, are frequently inactivated by methylation in various cancers (see hypermethylation of DNA repair genes in cancer). A 2018 report evaluated the relative importance of mutations and epigenetic alterations in progression to two different types of cancer. This report showed that epigenetic alterations were much more important than mutations in generating gastric cancers (associated with inflammation). However, mutations and epigenetic alterations were of roughly equal importance in generating esophageal squamous cell cancers (associated with tobacco chemicals and acetaldehyde, a product of alcohol metabolism).
=== HIV and AIDS ===
It has long been recognized that infection with HIV is characterized not only by development of profound immunodeficiency but also by sustained inflammation and immune activation. A substantial body of evidence implicates chronic inflammation as a critical driver of immune dysfunction, premature appearance of aging-related diseases, and immune deficiency. Many now regard HIV infection not only as an evolving virus-induced immunodeficiency, but also as chronic inflammatory disease. Even after the introduction of effective antiretroviral therapy (ART) and effective suppression of viremia in HIV-infected individuals, chronic inflammation persists. Animal studies also support the relationship between immune activation and progressive cellular immune deficiency: SIVsm infection of its natural nonhuman primate hosts, the sooty mangabey, causes high-level viral replication but limited evidence of disease. This lack of pathogenicity is accompanied by a lack of inflammation, immune activation and cellular proliferation. In sharp contrast, experimental SIVsm infection of rhesus macaque produces immune activation and AIDS-like disease with many parallels to human HIV infection.
Delineating how CD4 T cells are depleted and how chronic inflammation and immune activation are induced lies at the heart of understanding HIV pathogenesis—one of the top priorities for HIV research by the Office of AIDS Research, National Institutes of Health. Recent studies demonstrated that caspase-1-mediated pyroptosis, a highly inflammatory form of programmed cell death, drives CD4 T-cell depletion and inflammation by HIV. These are the two signature events that propel HIV disease progression to AIDS. Pyroptosis appears to create a pathogenic vicious cycle in which dying CD4 T cells and other immune cells (including macrophages and neutrophils) release inflammatory signals that recruit more cells into the infected lymphoid tissues to die. The feed-forward nature of this inflammatory response produces chronic inflammation and tissue injury. Identifying pyroptosis as the predominant mechanism that causes CD4 T-cell depletion and chronic inflammation, provides novel therapeutic opportunities, namely caspase-1 which controls the pyroptotic pathway. In this regard, pyroptosis of CD4 T cells and secretion of pro-inflammatory cytokines such as IL-1β and IL-18 can be blocked in HIV-infected human lymphoid tissues by addition of the caspase-1 inhibitor VX-765, which has already proven to be safe and well tolerated in phase II human clinical trials. These findings could propel development of an entirely new class of "anti-AIDS" therapies that act by targeting the host rather than the virus. Such agents would almost certainly be used in combination with ART. By promoting "tolerance" of the virus instead of suppressing its replication, VX-765 or related drugs may mimic the evolutionary solutions occurring in multiple monkey hosts (e.g. the sooty mangabey) infected with species-specific lentiviruses that have led to a lack of disease, no decline in CD4 T-cell counts, and no chronic inflammation.
=== Resolution ===
The inflammatory response must be actively terminated when no longer needed to prevent unnecessary "bystander" damage to tissues. Failure to do so results in chronic inflammation, and cellular destruction. Resolution of inflammation occurs by different mechanisms in different tissues.
Mechanisms that serve to terminate inflammation include:
Acute inflammation normally resolves by mechanisms that have remained somewhat elusive. Emerging evidence now suggests that an active, coordinated program of resolution initiates in the first few hours after an inflammatory response begins. After entering tissues, granulocytes promote the switch of arachidonic acid–derived prostaglandins and leukotrienes to lipoxins, which initiate the termination sequence. Neutrophil recruitment thus ceases and programmed death by apoptosis is engaged. These events coincide with the biosynthesis, from omega-3 polyunsaturated fatty acids, of resolvins and protectins, which critically shorten the period of neutrophil infiltration by initiating apoptosis. As a consequence, apoptotic neutrophils undergo phagocytosis by macrophages, leading to neutrophil clearance and release of anti-inflammatory and reparative cytokines such as transforming growth factor-β1. The anti-inflammatory program ends with the departure of macrophages through the lymphatics.
=== Connection to depression ===
There is evidence for a link between inflammation and depression. Inflammatory processes can be triggered by negative cognitions or their consequences, such as stress, violence, or deprivation. Thus, negative cognitions can cause inflammation that can, in turn, lead to depression.
In addition, there is increasing evidence that inflammation can cause depression because of the increase of cytokines, setting the brain into a "sickness mode".
Classical symptoms of being physically sick, such as lethargy, show a large overlap in behaviors that characterize depression. Levels of cytokines tend to increase sharply during the depressive episodes of people with bipolar disorder and drop off during remission. Furthermore, it has been shown in clinical trials that anti-inflammatory medicines taken in addition to antidepressants not only significantly improves symptoms but also increases the proportion of subjects positively responding to treatment.
Inflammations that lead to serious depression could be caused by common infections such as those caused by a virus, bacteria or even parasites.
=== Connection to delirium ===
There is evidence for a link between inflammation and delirium based on the results of a recent longitudinal study investigating CRP in COVID-19 patients.
== Systemic effects ==
An infectious organism can escape the confines of the immediate tissue via the circulatory system or lymphatic system, where it may spread to other parts of the body. If an organism is not contained by the actions of acute inflammation, it may gain access to the lymphatic system via nearby lymph vessels. An infection of the lymph vessels is known as lymphangitis, and infection of a lymph node is known as lymphadenitis. When lymph nodes cannot destroy all pathogens, the infection spreads further. A pathogen can gain access to the bloodstream through lymphatic drainage into the circulatory system.
When inflammation overwhelms the host, systemic inflammatory response syndrome is diagnosed. When it is due to infection, the term sepsis is applied, with the terms bacteremia being applied specifically for bacterial sepsis and viremia specifically to viral sepsis. Vasodilation and organ dysfunction are serious problems associated with widespread infection that may lead to septic shock and death.
=== Acute-phase proteins ===
Inflammation also is characterized by high systemic levels of acute-phase proteins. In acute inflammation, these proteins prove beneficial; however, in chronic inflammation, they can contribute to amyloidosis. These proteins include C-reactive protein, serum amyloid A, and serum amyloid P, which cause a range of systemic effects including:
=== Leukocyte numbers ===
Inflammation often affects the numbers of leukocytes present in the body:
Leukocytosis is often seen during inflammation induced by infection, where it results in a large increase in the amount of leukocytes in the blood, especially immature cells. Leukocyte numbers usually increase to between 15 000 and 20 000 cells per microliter, but extreme cases can see it approach 100 000 cells per microliter. Bacterial infection usually results in an increase of neutrophils, creating neutrophilia, whereas diseases such as asthma, hay fever, and parasite infestation result in an increase in eosinophils, creating eosinophilia.
Leukopenia can be induced by certain infections and diseases, including viral infection, Rickettsia infection, some protozoa, tuberculosis, and some cancers.
=== Interleukins and obesity ===
With the discovery of interleukins (IL), the concept of systemic inflammation developed. Although the processes involved are identical to tissue inflammation, systemic inflammation is not confined to a particular tissue but involves the endothelium and other organ systems.
Chronic inflammation is widely observed in obesity. Obese people commonly have many elevated markers of inflammation, including:
IL-6 (Interleukin-6)
Low-grade chronic inflammation is characterized by a two- to threefold increase in the systemic concentrations of cytokines such as TNF-α, IL-6, and CRP. Waist circumference correlates significantly with systemic inflammatory response.
Loss of white adipose tissue reduces levels of inflammation markers. As of 2017 the association of systemic inflammation with insulin resistance and type 2 diabetes, and with atherosclerosis was under preliminary research, although rigorous clinical trials had not been conducted to confirm such relationships.
C-reactive protein (CRP) is generated at a higher level in obese people, and may increase the risk for cardiovascular diseases.
== Outcomes ==
The outcome in a particular circumstance will be determined by the tissue in which the injury has occurred—and the injurious agent that is causing it. Here are the possible outcomes to inflammation:
ResolutionThe complete restoration of the inflamed tissue back to a normal status. Inflammatory measures such as vasodilation, chemical production, and leukocyte infiltration cease, and damaged parenchymal cells regenerate. Such is usually the outcome when limited or short-lived inflammation has occurred.
FibrosisLarge amounts of tissue destruction, or damage in tissues unable to regenerate, cannot be regenerated completely by the body. Fibrous scarring occurs in these areas of damage, forming a scar composed primarily of collagen. The scar will not contain any specialized structures, such as parenchymal cells, hence functional impairment may occur.
Abscess formationA cavity is formed containing pus, an opaque liquid containing dead white blood cells and bacteria with general debris from destroyed cells.
Chronic inflammationIn acute inflammation, if the injurious agent persists then chronic inflammation will ensue. This process, marked by inflammation lasting many days, months or even years, may lead to the formation of a chronic wound. Chronic inflammation is characterised by the dominating presence of macrophages in the injured tissue. These cells are powerful defensive agents of the body, but the toxins they release—including reactive oxygen species—are injurious to the organism's own tissues as well as invading agents. As a consequence, chronic inflammation is almost always accompanied by tissue destruction.
== Examples ==
Inflammation is usually indicated by adding the suffix "itis", as shown below. However, some conditions, such as asthma and pneumonia, do not follow this convention. More examples are available at List of types of inflammation.
== See also ==
== Notes ==
== References ==
== External links ==
Inflammation at the U.S. National Library of Medicine Medical Subject Headings (MeSH) | Wikipedia/Inflammatory_disease |
The family of vesiculovirus matrix proteins consists of several matrix proteins of the vesicular stomatitis virus, also known as VSIV or VSV. The matrix (M) protein of the virus causes many of the cytopathic effects of VSV, including an inhibition of host gene expression and the induction of cell rounding. It has been shown that M protein also induces apoptosis in the absence of other viral components. It is thought that the activation of apoptotic pathways causes the inhibition of host gene expression and cell rounding by M protein.
== Function ==
These proteins play a major role in assembly and budding of VSIV virions. Their main role is to aid virus assembly. They starts by shutting off host cell transcription by inhibiting mRNA nuclear export through direct interaction with the host RAE1-NUP98 complex. This inhibits interferon signaling and thus establishment of antiviral state in virus infected cells. In turn, this induces cell-rounding, cytoskeleton disorganization and apoptosis in infected cell. Enveloped viruses acquire their membrane by budding at a membrane of their host cell.
== Structure ==
The structure of these matrix proteins has revealed a single-globular domain with a new fold. The N-terminal part consists of a large five-stranded anti-parallel beta-sheet packed against two alpha-helices; the C-terminal part comprises a small two stranded anti-parallel beta-sheet and an alpha-helix.
== References == | Wikipedia/Vesiculovirus_matrix_proteins |
Viral matrix proteins are structural proteins linking the viral envelope with the virus core. They play a crucial role in virus assembly, and interact with the RNP complex as well as with the viral membrane. They are found in many enveloped viruses including paramyxoviruses, orthomyxoviruses, herpesviruses, retroviruses, filoviruses and other groups.
An example is the M1 protein of the influenza virus, showing affinity to the glycoproteins inserted in the host cell membrane on one side and affinity for the RNP complex molecules on the other side, which allows formation at the membrane of a complex made of the viral ribonucleoprotein at the inner side indirectly connected to the viral glycoproteins protruding from the membrane. This assembly complex will now bud out of the cell as new mature viruses.
Viral matrix proteins, like many other viral proteins, can exert different functions during the course of the infection. For example, in rhabdoviruses, binding of M proteins to nucleocapsids is accountable for the formation of its “bullet” shaped virions.
In herpesviruses, the viral matrix is usually called viral tegument and contains many proteins involved in viral entry, early gene expression and immune evasion.
== References ==
== See also ==
Retroviral matrix protein
Viral tegument | Wikipedia/Viral_matrix_protein |
Regulation of gene expression, or gene regulation, includes a wide range of mechanisms that are used by cells to increase or decrease the production of specific gene products (protein or RNA). Sophisticated programs of gene expression are widely observed in biology, for example to trigger developmental pathways, respond to environmental stimuli, or adapt to new food sources. Virtually any step of gene expression can be modulated, from transcriptional initiation, to RNA processing, and to the post-translational modification of a protein. Often, one gene regulator controls another, and so on, in a gene regulatory network.
Gene regulation is essential for viruses, prokaryotes and eukaryotes as it increases the versatility and adaptability of an organism by allowing the cell to express protein when needed. Although as early as 1951, Barbara McClintock showed interaction between two genetic loci, Activator (Ac) and Dissociator (Ds), in the color formation of maize seeds, the first discovery of a gene regulation system is widely considered to be the identification in 1961 of the lac operon, discovered by François Jacob and Jacques Monod, in which some enzymes involved in lactose metabolism are expressed by E. coli only in the presence of lactose and absence of glucose.
In multicellular organisms, gene regulation drives cellular differentiation and morphogenesis in the embryo, leading to the creation of different cell types that possess different gene expression profiles from the same genome sequence. Although this does not explain how gene regulation originated, evolutionary biologists include it as a partial explanation of how evolution works at a molecular level, and it is central to the science of evolutionary developmental biology ("evo-devo").
== Regulated stages of gene expression ==
Any step of gene expression may be modulated, from signaling to transcription to post-translational modification of a protein. The following is a list of stages where gene expression is regulated, where the most extensively utilized point is transcription initiation, the first stage in transcription:
Signal transduction
Chromatin, chromatin remodeling, chromatin domains
Transcription
Post-transcriptional modification
RNA transport
Translation
mRNA degradation
== Modification of DNA ==
In eukaryotes, the accessibility of large regions of DNA can depend on its chromatin structure, which can be altered as a result of histone modifications directed by DNA methylation, ncRNA, or DNA-binding protein. Hence these modifications may up or down regulate the expression of a gene. Some of these modifications that regulate gene expression are inheritable and are referred to as epigenetic regulation.
=== Structural ===
Transcription of DNA is dictated by its structure. In general, the density of its packing is indicative of the frequency of transcription. Octameric protein complexes called histones together with a segment of DNA wound around the eight histone proteins (together referred to as a nucleosome) are responsible for the amount of supercoiling of DNA, and these complexes can be temporarily modified by processes such as phosphorylation or more permanently modified by processes such as methylation. Such modifications are considered to be responsible for more or less permanent changes in gene expression levels.
=== Chemical ===
Methylation of DNA is a common method of gene silencing. DNA is typically methylated by methyltransferase enzymes on cytosine nucleotides in a CpG dinucleotide sequence (also called "CpG islands" when densely clustered). Analysis of the pattern of methylation in a given region of DNA (which can be a promoter) can be achieved through a method called bisulfite mapping. Methylated cytosine residues are unchanged by the treatment, whereas unmethylated ones are changed to uracil. The differences are analyzed by DNA sequencing or by methods developed to quantify SNPs, such as Pyrosequencing (Biotage) or MassArray (Sequenom), measuring the relative amounts of C/T at the CG dinucleotide. Abnormal methylation patterns are thought to be involved in oncogenesis.
Histone acetylation is also an important process in transcription. Histone acetyltransferase enzymes (HATs) such as CREB-binding protein also dissociate the DNA from the histone complex, allowing transcription to proceed. Often, DNA methylation and histone deacetylation work together in gene silencing. The combination of the two seems to be a signal for DNA to be packed more densely, lowering gene expression.
== Regulation of transcription ==
Regulation of transcription thus controls when transcription occurs and how much RNA is created. Transcription of a gene by RNA polymerase can be regulated by several mechanisms.
Specificity factors alter the specificity of RNA polymerase for a given promoter or set of promoters, making it more or less likely to bind to them (i.e., sigma factors used in prokaryotic transcription).
Repressors bind to the Operator, coding sequences on the DNA strand that are close to or overlapping the promoter region, impeding RNA polymerase's progress along the strand, thus impeding the expression of the gene. The image to the right demonstrates regulation by a repressor in the lac operon.
General transcription factors position RNA polymerase at the start of a protein-coding sequence and then release the polymerase to transcribe the mRNA.
Activators enhance the interaction between RNA polymerase and a particular promoter, encouraging the expression of the gene. Activators do this by increasing the attraction of RNA polymerase for the promoter, through interactions with subunits of the RNA polymerase or indirectly by changing the structure of the DNA.
Enhancers are sites on the DNA helix that are bound by activators in order to loop the DNA bringing a specific promoter to the initiation complex. Enhancers are much more common in eukaryotes than prokaryotes, where only a few examples exist (to date).
Silencers are regions of DNA sequences that, when bound by particular transcription factors, can silence expression of the gene.
== Regulation by RNA ==
RNA can be an important regulator of gene activity, e.g. by microRNA (miRNA), antisense-RNA, or long non-coding RNA (lncRNA). LncRNAs differ from mRNAs in the sense that they have specified subcellular locations and functions. They were first discovered to be located in the nucleus and chromatin, and the localizations and functions are highly diverse now. Some still reside in chromatin where they interact with proteins. While this lncRNA ultimately affects gene expression in neuronal disorders such as Parkinson, Huntington, and Alzheimer disease, others, such as, PNCTR(pyrimidine-rich non-coding transcriptors), play a role in lung cancer. Given their role in disease, lncRNAs are potential biomarkers and may be useful targets for drugs or gene therapy, although there are no approved drugs that target lncRNAs yet. The number of lncRNAs in the human genome remains poorly defined, but some estimates range from 16,000 to 100,000 lnc genes.
== Epigenetic gene regulation ==
Epigenetics refers to the modification of genes that is not changing the DNA or RNA sequence. Epigenetic modifications are also a key factor in influencing gene expression. They occur on genomic DNA and histones and their chemical modifications regulate gene expression in a more efficient manner. There are several modifications of DNA (usually methylation) and more than 100 modifications of RNA in mammalian cells.” Those modifications result in altered protein binding to DNA and a change in RNA stability and translation efficiency.
== Special cases in human biology and disease ==
=== Regulation of transcription in cancer ===
In vertebrates, the majority of gene promoters contain a CpG island with numerous CpG sites. When many of a gene's promoter CpG sites are methylated the gene becomes silenced. Colorectal cancers typically have 3 to 6 driver mutations and 33 to 66 hitchhiker or passenger mutations. However, transcriptional silencing may be of more importance than mutation in causing progression to cancer. For example, in colorectal cancers about 600 to 800 genes are transcriptionally silenced by CpG island methylation (see regulation of transcription in cancer). Transcriptional repression in cancer can also occur by other epigenetic mechanisms, such as altered expression of microRNAs. In breast cancer, transcriptional repression of BRCA1 may occur more frequently by over-expressed microRNA-182 than by hypermethylation of the BRCA1 promoter (see Low expression of BRCA1 in breast and ovarian cancers).
=== Regulation of transcription in addiction ===
One of the cardinal features of addiction is its persistence. The persistent behavioral changes appear to be due to long-lasting changes, resulting from epigenetic alterations affecting gene expression, within particular regions of the brain. Drugs of abuse cause three types of epigenetic alteration in the brain. These are (1) histone acetylations and histone methylations, (2) DNA methylation at CpG sites, and (3) epigenetic downregulation or upregulation of microRNAs. (See Epigenetics of cocaine addiction for some details.)
Chronic nicotine intake in mice alters brain cell epigenetic control of gene expression through acetylation of histones. This increases expression in the brain of the protein FosB, important in addiction. Cigarette addiction was also studied in about 16,000 humans, including never smokers, current smokers, and those who had quit smoking for up to 30 years. In blood cells, more than 18,000 CpG sites (of the roughly 450,000 analyzed CpG sites in the genome) had frequently altered methylation among current smokers. These CpG sites occurred in over 7,000 genes, or roughly a third of known human genes. The majority of the differentially methylated CpG sites returned to the level of never-smokers within five years of smoking cessation. However, 2,568 CpGs among 942 genes remained differentially methylated in former versus never smokers. Such remaining epigenetic changes can be viewed as “molecular scars” that may affect gene expression.
In rodent models, drugs of abuse, including cocaine, methamphetamine, alcohol and tobacco smoke products, all cause DNA damage in the brain. During repair of DNA damages some individual repair events can alter the methylation of DNA and/or the acetylations or methylations of histones at the sites of damage, and thus can contribute to leaving an epigenetic scar on chromatin.
Such epigenetic scars likely contribute to the persistent epigenetic changes found in addiction.
=== Regulation of transcription in learning and memory ===
In mammals, methylation of cytosine (see Figure) in DNA is a major regulatory mediator. Methylated cytosines primarily occur in dinucleotide sequences where cytosine is followed by a guanine, a CpG site. The total number of CpG sites in the human genome is approximately 28 million. and generally about 70% of all CpG sites have a methylated cytosine.
In a rat, a painful learning experience, contextual fear conditioning, can result in a life-long fearful memory after a single training event. Cytosine methylation is altered in the promoter regions of about 9.17% of all genes in the hippocampus neuron DNA of a rat that has been subjected to a brief fear conditioning experience. The hippocampus is where new memories are initially stored.
Methylation of CpGs in a promoter region of a gene represses transcription while methylation of CpGs in the body of a gene increases expression. TET enzymes play a central role in demethylation of methylated cytosines. Demethylation of CpGs in a gene promoter by TET enzyme activity increases transcription of the gene.
When contextual fear conditioning is applied to a rat, more than 5,000 differentially methylated regions (DMRs) (of 500 nucleotides each) occur in the rat hippocampus neural genome both one hour and 24 hours after the conditioning in the hippocampus. This causes about 500 genes to be up-regulated (often due to demethylation of CpG sites in a promoter region) and about 1,000 genes to be down-regulated (often due to newly formed 5-methylcytosine at CpG sites in a promoter region). The pattern of induced and repressed genes within neurons appears to provide a molecular basis for forming the first transient memory of this training event in the hippocampus of the rat brain.
== Post-transcriptional regulation ==
After the DNA is transcribed and mRNA is formed, there must be some sort of regulation on how much the mRNA is translated into proteins. Cells do this by modulating the capping, splicing, addition of a Poly(A) Tail, the sequence-specific nuclear export rates, and, in several contexts, sequestration of the RNA transcript. These processes occur in eukaryotes but not in prokaryotes. This modulation is a result of a protein or transcript that, in turn, is regulated and may have an affinity for certain sequences.
== Three prime untranslated regions and microRNAs ==
Three prime untranslated regions (3'-UTRs) of messenger RNAs (mRNAs) often contain regulatory sequences that post-transcriptionally influence gene expression. Such 3'-UTRs often contain both binding sites for microRNAs (miRNAs) as well as for regulatory proteins. By binding to specific sites within the 3'-UTR, miRNAs can decrease gene expression of various mRNAs by either inhibiting translation or directly causing degradation of the transcript. The 3'-UTR also may have silencer regions that bind repressor proteins that inhibit the expression of a mRNA.
The 3'-UTR often contains miRNA response elements (MREs). MREs are sequences to which miRNAs bind. These are prevalent motifs within 3'-UTRs. Among all regulatory motifs within the 3'-UTRs (e.g. including silencer regions), MREs make up about half of the motifs.
As of 2014, the miRBase web site, an archive of miRNA sequences and annotations, listed 28,645 entries in 233 biologic species. Of these, 1,881 miRNAs were in annotated human miRNA loci. miRNAs were predicted to have an average of about four hundred target mRNAs (affecting expression of several hundred genes). Freidman et al. estimate that >45,000 miRNA target sites within human mRNA 3'-UTRs are conserved above background levels, and >60% of human protein-coding genes have been under selective pressure to maintain pairing to miRNAs.
Direct experiments show that a single miRNA can reduce the stability of hundreds of unique mRNAs. Other experiments show that a single miRNA may repress the production of hundreds of proteins, but that this repression often is relatively mild (less than 2-fold).
The effects of miRNA dysregulation of gene expression seem to be important in cancer. For instance, in gastrointestinal cancers, a 2015 paper identified nine miRNAs as epigenetically altered and effective in down-regulating DNA repair enzymes.
The effects of miRNA dysregulation of gene expression also seem to be important in neuropsychiatric disorders, such as schizophrenia, bipolar disorder, major depressive disorder, Parkinson's disease, Alzheimer's disease and autism spectrum disorders.
== Regulation of translation ==
The translation of mRNA can also be controlled by a number of mechanisms, mostly at the level of initiation. Recruitment of the small ribosomal subunit can indeed be modulated by mRNA secondary structure, antisense RNA binding, or protein binding. In both prokaryotes and eukaryotes, a large number of RNA binding proteins exist, which often are directed to their target sequence by the secondary structure of the transcript, which may change depending on certain conditions, such as temperature or presence of a ligand (aptamer). Some transcripts act as ribozymes and self-regulate their expression.
== Examples of gene regulation ==
Enzyme induction is a process in which a molecule (e.g., a drug) induces (i.e., initiates or enhances) the expression of an enzyme.
The induction of heat shock proteins in the fruit fly Drosophila melanogaster.
The Lac operon is an interesting example of how gene expression can be regulated.
Viruses, despite having only a few genes, possess mechanisms to regulate their gene expression, typically into an early and late phase, using collinear systems regulated by anti-terminators (lambda phage) or splicing modulators (HIV).
Gal4 is a transcriptional activator that controls the expression of GAL1, GAL7, and GAL10 (all of which code for the metabolic of galactose in yeast). The GAL4/UAS system has been used in a variety of organisms across various phyla to study gene expression.
=== Developmental biology ===
A large number of studied regulatory systems come from developmental biology. Examples include:
The colinearity of the Hox gene cluster with their nested antero-posterior patterning
Pattern generation of the hand (digits - interdigits): the gradient of sonic hedgehog (secreted inducing factor) from the zone of polarizing activity in the limb, which creates a gradient of active Gli3, which activates Gremlin, which inhibits BMPs also secreted in the limb, results in the formation of an alternating pattern of activity as a result of this reaction–diffusion system.
Somitogenesis is the creation of segments (somites) from a uniform tissue (Pre-somitic Mesoderm). They are formed sequentially from anterior to posterior. This is achieved in amniotes possibly by means of two opposing gradients, Retinoic acid in the anterior (wavefront) and Wnt and Fgf in the posterior, coupled to an oscillating pattern (segmentation clock) composed of FGF + Notch and Wnt in antiphase.
Sex determination in the soma of a Drosophila requires the sensing of the ratio of autosomal genes to sex chromosome-encoded genes, which results in the production of sexless splicing factor in females, resulting in the female isoform of doublesex.
== Circuitry ==
=== Up-regulation and down-regulation ===
Up-regulation is a process which occurs within a cell triggered by a signal (originating internal or external to the cell), which results in increased expression of one or more genes and as a result the proteins encoded by those genes. Conversely, down-regulation is a process resulting in decreased gene and corresponding protein expression.
Up-regulation occurs, for example, when a cell is deficient in some kind of receptor. In this case, more receptor protein is synthesized and transported to the membrane of the cell and, thus, the sensitivity of the cell is brought back to normal, reestablishing homeostasis.
Down-regulation occurs, for example, when a cell is overstimulated by a neurotransmitter, hormone, or drug for a prolonged period of time, and the expression of the receptor protein is decreased in order to protect the cell (see also tachyphylaxis).
=== Inducible vs. repressible systems ===
Gene Regulation can be summarized by the response of the respective system:
Inducible systems - An inducible system is off unless there is the presence of some molecule (called an inducer) that allows for gene expression. The molecule is said to "induce expression". The manner by which this happens is dependent on the control mechanisms as well as differences between prokaryotic and eukaryotic cells.
Repressible systems - A repressible system is on except in the presence of some molecule (called a corepressor) that suppresses gene expression. The molecule is said to "repress expression". The manner by which this happens is dependent on the control mechanisms as well as differences between prokaryotic and eukaryotic cells.
The GAL4/UAS system is an example of both an inducible and repressible system. Gal4 binds an upstream activation sequence (UAS) to activate the transcription of the GAL1/GAL7/GAL10 cassette. On the other hand, a MIG1 response to the presence of glucose can inhibit GAL4 and therefore stop the expression of the GAL1/GAL7/GAL10 cassette.
=== Theoretical circuits ===
Repressor/Inducer: an activation of a sensor results in the change of expression of a gene
negative feedback: the gene product downregulates its own production directly or indirectly, which can result in
keeping transcript levels constant/proportional to a factor
inhibition of run-away reactions when coupled with a positive feedback loop
creating an oscillator by taking advantage in the time delay of transcription and translation, given that the mRNA and protein half-life is shorter
positive feedback: the gene product upregulates its own production directly or indirectly, which can result in
signal amplification
bistable switches when two genes inhibit each other and both have positive feedback
pattern generation
== Study methods ==
In general, most experiments investigating differential expression used whole cell extracts of RNA, called steady-state levels, to determine which genes changed and by how much. These are, however, not informative of where the regulation has occurred and may mask conflicting regulatory processes (see post-transcriptional regulation), but it is still the most commonly analysed (quantitative PCR and DNA microarray).
When studying gene expression, there are several methods to look at the various stages. In eukaryotes these include:
The local chromatin environment of the region can be determined by ChIP-chip analysis by pulling down RNA Polymerase II, Histone 3 modifications, Trithorax-group protein, Polycomb-group protein, or any other DNA-binding element to which a good antibody is available.
Epistatic interactions can be investigated by synthetic genetic array analysis
Due to post-transcriptional regulation, transcription rates and total RNA levels differ significantly. To measure the transcription rates nuclear run-on assays can be done and newer high-throughput methods are being developed, using thiol labelling instead of radioactivity.
Only 5% of the RNA polymerised in the nucleus exits, and not only introns, abortive products, and non-sense transcripts are degradated. Therefore, the differences in nuclear and cytoplasmic levels can be seen by separating the two fractions by gentle lysis.
Alternative splicing can be analysed with a splicing array or with a tiling array (see DNA microarray).
All in vivo RNA is complexed as RNPs. The quantity of transcripts bound to specific protein can be also analysed by RIP-Chip. For example, DCP2 will give an indication of sequestered protein; ribosome-bound gives and indication of transcripts active in transcription (although a more dated method, called polysome fractionation, is still popular in some labs)
Protein levels can be analysed by Mass spectrometry, which can be compared only to quantitative PCR data, as microarray data is relative and not absolute.
RNA and protein degradation rates are measured by means of transcription inhibitors (actinomycin D or α-Amanitin) or translation inhibitors (Cycloheximide), respectively.
== See also ==
Artificial transcription factors (small molecules that mimic transcription factor protein)
Cellular model
Conserved non-coding DNA sequence
Enhancer (genetics)
Gene structure
Spatiotemporal gene expression
Regulator gene glucosyltransferases (Rgg/SHP) systems
== Notes and references ==
== Bibliography ==
Latchman, David S. (2005). Gene regulation: a eukaryotic perspective. Psychology Press. ISBN 978-0-415-36510-9.
== External links ==
Plant Transcription Factor Database and Plant Transcriptional Regulation Data and Analysis Platform
Regulation of Gene Expression (MeSH) at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
ChIPBase An open database for decoding the transcriptional regulatory networks of non-coding RNAs and protein-coding genes from ChIP-seq data. | Wikipedia/Regulatory_protein |
Herpesvirus glycoprotein B is a viral glycoprotein that is involved in the viral cell entry of Herpes simplex virus (HSV). Herpesviruses have a lipid bilayer, called the envelope, which contains twelve surface glycoproteins. For infectivity to be attained, the double stranded DNA genome of HSV must enter the host cell through means of fusion of its envelope with the cellular membrane or via endocytosis. Other viral glycoproteins involved in the process of viral cell entry include gC, gB, gD, gH, and gL, but only gC, gB, gD, and gH are required for the fusion of the HSV's envelope with the cellular membrane. It can be noted that all herpesviruses have glycoproteins gB, gH, and gL.
== Structure ==
The herpesvirus glycoprotein B is a type-1 transmembrane protein with a signal sequence at its N terminus. The crystal structure of herpes simplex virus (HSV) type-1 and Epstein–Barr virus glycoprotein B ectodomains were solved as a trimer, revealing five structural domains (I-V). Domain I contains two internal fusion loops, thought to insert into the cellular membrane during virus-cell fusion. In HSV, domain II is hypothesized to interact with another herpesvirus glycoprotein, gH/gL, during the fusion process. Domain III consists of a structurally important elongated alpha helix, while domain IV is hypothesized to interact with cellular receptors. Finally, domain V acts in conjunction with domain I during protein-lipid interactions. In HSV, neutralizing monoclonal antibodies map to structural domains I, II, IV and V. Due to its unique structure, herpesvirus glycoprotein B (along with vesicular stomatitis virus glycoprotein G and baculovirus gp64) belongs to a new class of viral membrane fusion glycoproteins, class III.
== Function ==
The herpesvirus glycoprotein B is the most highly conserved of all surface glycoproteins and acts primarily as a fusion protein. The precise functions of gB and gH/gL are unknown but they are required for viral entry into the cell and constitute the core fusion machinery. The claim that gB is involved in fusion comes from the notable syncytial phenotype caused by certain mutations within the cytoplasmic domain of glycoprotein B, as well as its structural homology to other viral fusion proteins.
== References ==
== Further reading == | Wikipedia/Herpesvirus_glycoprotein_B |
E1 is one of two subunits of the envelope glycoprotein found in the hepatitis C virus. The other subunit is E2.
This protein is a type 1 transmembrane protein with a highly glycosylated N-terminal ectodomain and a C-terminal hydrophobic anchor. After being synthesized the E1 glycoproteins associates with the E2 glycoprotein as a noncovalent heterodimer.
== Structure ==
The E1 glycoprotein residues 192-383 in the genotype 1a H77 strain. After translation the E1 C-terminal transmembrane domains (TMDs) forms a hairpin of antiparallel a-helices. E1 is then cleaved by signal peptide peptidase at the endoplasmic reticulum and E1 is then made into a single long straight a-helix. What is known of the structure is from a crystal structure made in 2014. This crystal structure shows that it has two a-helixes and 3 B-sheets for both monomers; two disulfide bridges stabilize these two monomers. This means that E1 is more compact then its E2 counterpart. It has been shown that E1 can fold with a small amount of E2 protein present. In addition to this it was shown that E1 oxidation preceded E2 maturation. This means that E1 has a chaperone-like role for E2. Despite these finds there are many things still unknown about the structure of E1. The E1 protein is anchored to the membrane. Most of the time E1 remains in its unfolded conformation.
== Function ==
The E1 protein helps the virus attach to the membrane of the targeted cell. In other envelope virus the E1 protein has a similar role in helping the virus get into the cell. As a heterodimer with E2 it has been discovered that it is essential for HCV entry. When the heterodimer is formed the hepatitis C virus is then able to bind to the receptor of the cell. As a heterodimer the E1 protein alone with the E2 protein worked together to enter the cell. Also cleavage at the core-E1 junction is a prerequisite for SPP-catalyzed cleavage. This helps the virus relocate to the surface of lipid droplets. Once the virus gets to the surface of the lipid droplets it recruits the virus no-structural proteins and replication complex. The SP-catalyzed cleavage at the core-E1 junction is required for the formation of infectious particles and for the release of any HCV particles. Also E1 has no function with budding at the ER membrane. It also had no effect on the intracellular formation of capsid-containing particles. Instead when E1 was not allowed to form this tended to facilitate the budding process.
== Possible Vaccine ==
It has been shown that by blocking E1 we can prevent the formation of the envelope protein. There have been a number of studies trying to find the structure of E1. The hope for these vaccines is that they will be able to block the entry of Hepatitis C if they can block the formation of E1. If the virus cannot make the envelope protein then it will be unable to get into the host cells. The types of vaccines that would be used are synthetic peptide vaccines.
== References == | Wikipedia/Hepatitis_C_virus_envelope_glycoprotein_E1 |
The envelope (E) protein is the smallest and least well-characterized of the four major structural proteins found in coronavirus virions. It is an integral membrane protein less than 110 amino acid residues long; in SARS-CoV-2, the causative agent of Covid-19, the E protein is 75 residues long. Although it is not necessarily essential for viral replication, absence of the E protein may produce abnormally assembled viral capsids or reduced replication. E is a multifunctional protein and, in addition to its role as a structural protein in the viral capsid, it is thought to be involved in viral assembly, likely functions as a viroporin, and is involved in viral pathogenesis.
== Structure ==
The E protein consists of a short hydrophilic N-terminal region, a hydrophobic helical transmembrane domain, and a somewhat hydrophilic C-terminal region. In SARS-CoV and SARS-CoV-2, the C-terminal region contains a PDZ-binding motif (PBM). This feature appears to be conserved only in the alpha and beta coronavirus groups, but not gamma. In the beta and gamma groups, a conserved proline residue is found in the C-terminal region likely involved in targeting the protein to the Golgi.
The transmembrane helices of the E proteins of SARS-CoV and SARS-CoV-2 can oligomerize and have been shown in vitro to form pentameric structures with central pores that serve as cation-selective ion channels. Both viruses' E protein pentamers have been structurally characterized by nuclear magnetic resonance spectroscopy.
The membrane topology of the E protein has been studied in a number of coronaviruses with inconsistent results; the protein's orientation in the membrane may be variable. The balance of evidence suggests the most common orientation has the C-terminus oriented toward the cytoplasm. Studies of SARS-CoV-2 E protein are consistent with this orientation.
=== Post-translational modifications ===
In some, but not all, coronaviruses, the E protein is post-translationally modified by palmitoylation on conserved cysteine residues. In the SARS-CoV E protein, one glycosylation site has been observed, which may influence membrane topology; however, the functional significance of E glycosylation is unclear. Ubiquitination of SARS-CoV E has also been described, though its functional significance is also not known.
== Expression and localization ==
The E protein is expressed at high abundance in infected cells. However, only a small amount of the total E protein produced is found in assembled virions. E protein is localized to the endoplasmic reticulum, Golgi apparatus, and endoplasmic-reticulum–Golgi intermediate compartment (ERGIC), the intracellular compartment that gives rise to the coronavirus viral envelope.
== Function ==
=== Essentiality ===
Studies in different coronaviruses have reached different conclusions about whether E is essential to viral replication. In some coronaviruses, including MERS-CoV, E has been reported to be essential. In others, including mouse coronavirus and SARS-CoV, E is not essential, though its absence reduces viral titer, in some cases by introducing propagation defects or causing abnormal capsid morphology.
=== Virions and viral assembly ===
The E protein is found in assembled virions where it forms protein-protein interactions with the coronavirus membrane protein (M), the most abundant of the four structural proteins contained in the viral capsid. The interaction between E and M occurs through their respective C-termini on the cytoplasmic side of the membrane. In most coronaviruses, E and M are sufficient to form virus-like particles, though SARS-CoV has been reported to depend on N as well. There is good evidence that E is involved in inducing membrane curvature to create the typical spherical coronavirus virion. It is likely that E is involved in viral budding or scission, although its role in this process has not been well characterized.
=== Viroporin ===
In its pentameric state, E forms cation-selective ion channels and likely functions as a viroporin. NMR studies show that viroporin presents an open conformation at low pH or in the presence of calcium ions, while the closed conformation is favored at basic pH. The NMR structure shows a hydrophobic gate at leucine 28 in the middle of the pore. The passage of ions through the gate is thought to be facilitated by the polar residues at the C-terminus.
The cation leakage may disrupt ion homeostasis, alter membrane permeability, and modulate pH in the host cell, which may facilitate viral release.
The E protein's role as a viroporin appears to be involved in pathogenesis and may be related to activation of the inflammasome. In SARS-CoV, mutations that disrupt E's ion channel function result in attenuated pathogenesis in animal models despite little effect on viral growth.
=== Interactions with host proteins ===
Protein-protein interactions between E and proteins in the host cell are best described in SARS-CoV and occur via the C-terminal PDZ domain binding motif. The SARS-CoV E protein has been reported to interact with five host cell proteins: Bcl-xL, PALS1, syntenin, sodium/potassium (Na+/K+) ATPase α-1 subunit, and stomatin. The interaction with PALS1 may be related to pathogenesis via the resulting disruption in tight junctions. This interaction has also been identified in SARS-CoV-2.
== Evolution and conservation ==
The sequence of the E protein is not well conserved across coronavirus genera, with sequence identities reaching under 30%. In laboratory experiments on mouse hepatitis virus, substitution of E proteins from different coronaviruses, even from different groups, could produce viable viruses, suggesting that significant sequence diversity can be tolerated in functional E proteins. The SARS-CoV-2 E protein is very similar to that of SARS-CoV, with three substitutions and one deletion. A study of SARS-CoV-2 sequences suggests that the E protein is evolving relatively slowly compared to other structural proteins. The conserved nature of the envelope protein among SARS-CoV and SARS-CoV-2 variants has led it to be researched as a potential target for universal coronavirus vaccine development.
== References == | Wikipedia/Coronavirus_envelope_protein |
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity.
A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the genetic code specifies 20 standard amino acids; but in certain organisms the genetic code can include selenocysteine and—in certain archaea—pyrrolysine. Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification, which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. Some proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors. Proteins can work together to achieve a particular function, and they often associate to form stable protein complexes.
Once formed, proteins only exist for a certain period and are then degraded and recycled by the cell's machinery through the process of protein turnover. A protein's lifespan is measured in terms of its half-life and covers a wide range. They can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal or misfolded proteins are degraded more rapidly either due to being targeted for destruction or due to being unstable.
Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms and participate in virtually every process within cells. Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Some proteins have structural or mechanical functions, such as actin and myosin in muscle, and the cytoskeleton's scaffolding proteins that maintain cell shape. Other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized. Digestion breaks the proteins down for metabolic use.
== History and etymology ==
=== Discovery and early studies ===
Proteins have been studied and recognized since the 1700s by Antoine Fourcroy and others, who often collectively called them "albumins", or "albuminous materials" (Eiweisskörper, in German). Gluten, for example, was first separated from wheat in published research around 1747, and later determined to exist in many plants. In 1789, Antoine Fourcroy recognized three distinct varieties of animal proteins: albumin, fibrin, and gelatin. Vegetable (plant) proteins studied in the late 1700s and early 1800s included gluten, plant albumin, gliadin, and legumin.
Proteins were first described by the Dutch chemist Gerardus Johannes Mulder and named by the Swedish chemist Jöns Jacob Berzelius in 1838. Mulder carried out elemental analysis of common proteins and found that nearly all proteins had the same empirical formula, C400H620N100O120P1S1. He came to the erroneous conclusion that they might be composed of a single type of (very large) molecule. The term "protein" to describe these molecules was proposed by Mulder's associate Berzelius; protein is derived from the Greek word πρώτειος (proteios), meaning "primary", "in the lead", or "standing in front", + -in. Mulder went on to identify the products of protein degradation such as the amino acid leucine for which he found a (nearly correct) molecular weight of 131 Da.
Early nutritional scientists such as the German Carl von Voit believed that protein was the most important nutrient for maintaining the structure of the body, because it was generally believed that "flesh makes flesh." Around 1862, Karl Heinrich Ritthausen isolated the amino acid glutamic acid. Thomas Burr Osborne compiled a detailed review of the vegetable proteins at the Connecticut Agricultural Experiment Station. Osborne, alongside Lafayette Mendel, established several nutritionally essential amino acids in feeding experiments with laboratory rats. Diets lacking an essential amino acid stunts the rats' growth, consistent with Liebig's law of the minimum. The final essential amino acid to be discovered, threonine, was identified by William Cumming Rose.
The difficulty in purifying proteins impeded work by early protein biochemists. Proteins could be obtained in large quantities from blood, egg whites, and keratin, but individual proteins were unavailable. In the 1950s, the Armour Hot Dog Company purified 1 kg of bovine pancreatic ribonuclease A and made it freely available to scientists. This gesture helped ribonuclease A become a major target for biochemical study for the following decades.
=== Polypeptides ===
The understanding of proteins as polypeptides, or chains of amino acids, came through the work of Franz Hofmeister and Hermann Emil Fischer in 1902. The central role of proteins as enzymes in living organisms that catalyzed reactions was not fully appreciated until 1926, when James B. Sumner showed that the enzyme urease was in fact a protein.
Linus Pauling is credited with the successful prediction of regular protein secondary structures based on hydrogen bonding, an idea first put forth by William Astbury in 1933. Later work by Walter Kauzmann on denaturation, based partly on previous studies by Kaj Linderstrøm-Lang, contributed an understanding of protein folding and structure mediated by hydrophobic interactions.
The first protein to have its amino acid chain sequenced was insulin, by Frederick Sanger, in 1949. Sanger correctly determined the amino acid sequence of insulin, thus conclusively demonstrating that proteins consisted of linear polymers of amino acids rather than branched chains, colloids, or cyclols. He won the Nobel Prize for this achievement in 1958. Christian Anfinsen's studies of the oxidative folding process of ribonuclease A, for which he won the nobel prize in 1972, solidified the thermodynamic hypothesis of protein folding, according to which the folded form of a protein represents its free energy minimum.
=== Structure ===
With the development of X-ray crystallography, it became possible to determine protein structures as well as their sequences. The first protein structures to be solved were hemoglobin by Max Perutz and myoglobin by John Kendrew, in 1958. The use of computers and increasing computing power has supported the sequencing of complex proteins. In 1999, Roger Kornberg sequenced the highly complex structure of RNA polymerase using high intensity X-rays from synchrotrons.
Since then, cryo-electron microscopy (cryo-EM) of large macromolecular assemblies has been developed. Cryo-EM uses protein samples that are frozen rather than crystals, and beams of electrons rather than X-rays. It causes less damage to the sample, allowing scientists to obtain more information and analyze larger structures. Computational protein structure prediction of small protein structural domains has helped researchers to approach atomic-level resolution of protein structures.
As of April 2024, the Protein Data Bank contains 181,018 X-ray, 19,809 EM and 12,697 NMR protein structures.
== Classification ==
Proteins are primarily classified by sequence and structure, although other classifications are commonly used. Especially for enzymes the EC number system provides a functional classification scheme. Similarly, gene ontology classifies both genes and proteins by their biological and biochemical function, and by their intracellular location.
Sequence similarity is used to classify proteins both in terms of evolutionary and functional similarity. This may use either whole proteins or protein domains, especially in multi-domain proteins. Protein domains allow protein classification by a combination of sequence, structure and function, and they can be combined in many ways. In an early study of 170,000 proteins, about two-thirds were assigned at least one domain, with larger proteins containing more domains (e.g. proteins larger than 600 amino acids having an average of more than 5 domains).
== Biochemistry ==
Most proteins consist of linear polymers built from series of up to 20 L-α-amino acids. All proteinogenic amino acids have a common structure where an α-carbon is bonded to an amino group, a carboxyl group, and a variable side chain. Only proline differs from this basic structure as its side chain is cyclical, bonding to the amino group, limiting protein chain flexibility. The side chains of the standard amino acids have a variety of chemical structures and properties, and it is the combined effect of all amino acids that determines its three-dimensional structure and chemical reactivity.
The amino acids in a polypeptide chain are linked by peptide bonds between amino and carboxyl group. An individual amino acid in a chain is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone.: 19 The peptide bond has two resonance forms that confer some double-bond character to the backbone. The alpha carbons are roughly coplanar with the nitrogen and the carbonyl (C=O) group. The other two dihedral angles in the peptide bond determine the local shape assumed by the protein backbone. One conseqence of the N-C(O) double bond character is that proteins are somewhat rigid.: 31 A polypeptide chain ends with a free amino group, known as the N-terminus or amino terminus, and a free carboxyl group, known as the C-terminus or carboxy terminus. By convention, peptide sequences are written N-terminus to C-terminus, correlating with the order in which proteins are synthesized by ribosomes.
The words protein, polypeptide, and peptide are a little ambiguous and can overlap in meaning. Protein is generally used to refer to the complete biological molecule in a stable conformation, whereas peptide is generally reserved for a short amino acid oligomers often lacking a stable 3D structure. But the boundary between the two is not well defined and usually lies near 20–30 residues.
Proteins can interact with many types of molecules and ions, including with other proteins, with lipids, with carbohydrates, and with DNA.
=== Abundance in cells ===
A typical bacterial cell, e.g. E. coli and Staphylococcus aureus, is estimated to contain about 2 million proteins. Smaller bacteria, such as Mycoplasma or spirochetes contain fewer molecules, on the order of 50,000 to 1 million. By contrast, eukaryotic cells are larger and thus contain much more protein. For instance, yeast cells have been estimated to contain about 50 million proteins and human cells on the order of 1 to 3 billion. The concentration of individual protein copies ranges from a few molecules per cell up to 20 million. Not all genes coding proteins are expressed in most cells and their number depends on, for example, cell type and external stimuli. For instance, of the 20,000 or so proteins encoded by the human genome, only 6,000 are detected in lymphoblastoid cells. The most abundant protein in nature is thought to be RuBisCO, an enzyme that catalyzes the incorporation of carbon dioxide into organic matter in photosynthesis. Plants can consist of as much as 1% by weight of this enzyme.
== Synthesis ==
=== Biosynthesis ===
Proteins are assembled from amino acids using information encoded in genes. Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. The genetic code is a set of three-nucleotide sets called codons and each three-nucleotide combination designates an amino acid, for example AUG (adenine–uracil–guanine) is the code for methionine. Because DNA contains four nucleotides, the total number of possible codons is 64; hence, there is some redundancy in the genetic code, with some amino acids specified by more than one codon.: 1002–42 Genes encoded in DNA are first transcribed into pre-messenger RNA (mRNA) by proteins such as RNA polymerase. Most organisms then process the pre-mRNA (a primary transcript) using various forms of post-transcriptional modification to form the mature mRNA, which is then used as a template for protein synthesis by the ribosome. In prokaryotes the mRNA may either be used as soon as it is produced, or be bound by a ribosome after having moved away from the nucleoid. In contrast, eukaryotes make mRNA in the cell nucleus and then translocate it across the nuclear membrane into the cytoplasm, where protein synthesis then takes place. The rate of protein synthesis is higher in prokaryotes than eukaryotes and can reach up to 20 amino acids per second.
The process of synthesizing a protein from an mRNA template is known as translation. The mRNA is loaded onto the ribosome and is read three nucleotides at a time by matching each codon to its base pairing anticodon located on a transfer RNA molecule, which carries the amino acid corresponding to the codon it recognizes. The enzyme aminoacyl tRNA synthetase "charges" the tRNA molecules with the correct amino acids. The growing polypeptide is often termed the nascent chain. Proteins are always biosynthesized from N-terminus to C-terminus.: 1002–42
The size of a synthesized protein can be measured by the number of amino acids it contains and by its total molecular mass, which is normally reported in units of daltons (synonymous with atomic mass units), or the derivative unit kilodalton (kDa). The average size of a protein increases from Archaea to Bacteria to Eukaryote (283, 311, 438 residues and 31, 34, 49 kDa respectively) due to a bigger number of protein domains constituting proteins in higher organisms. For instance, yeast proteins are on average 466 amino acids long and 53 kDa in mass. The largest known proteins are the titins, a component of the muscle sarcomere, with a molecular mass of almost 3,000 kDa and a total length of almost 27,000 amino acids.
=== Chemical synthesis ===
Short proteins can be synthesized chemically by a family of peptide synthesis methods. These rely on organic synthesis techniques such as chemical ligation to produce peptides in high yield. Chemical synthesis allows for the introduction of non-natural amino acids into polypeptide chains, such as attachment of fluorescent probes to amino acid side chains. These methods are useful in laboratory biochemistry and cell biology, though generally not for commercial applications. Chemical synthesis is inefficient for polypeptides longer than about 300 amino acids, and the synthesized proteins may not readily assume their native tertiary structure. Most chemical synthesis methods proceed from C-terminus to N-terminus, opposite the biological reaction.
== Structure ==
Most proteins fold into unique 3D structures. The shape into which a protein naturally folds is known as its native conformation.: 36 Although many proteins can fold unassisted, simply through the chemical properties of their amino acids, others require the aid of molecular chaperones to fold into their native states.: 37 Biochemists often refer to four distinct aspects of a protein's structure:: 30–34
Primary structure: the amino acid sequence. A protein is a polyamide.
Secondary structure: regularly repeating local structures stabilized by hydrogen bonds. The most common examples are the α-helix, β-sheet and turns. Because secondary structures are local, many regions of distinct secondary structure can be present in the same protein molecule.
Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structures to one another. Tertiary structure is generally stabilized by nonlocal interactions, most commonly the formation of a hydrophobic core, but also through salt bridges, hydrogen bonds, disulfide bonds, and even post-translational modifications. The term "tertiary structure" is often used as synonymous with the term fold. The tertiary structure is what controls the basic function of the protein.
Quaternary structure: the structure formed by several protein molecules (polypeptide chains), usually called protein subunits in this context, which function as a single protein complex.
Quinary structure: the signatures of protein surface that organize the crowded cellular interior. Quinary structure is dependent on transient, yet essential, macromolecular interactions that occur inside living cells.
Proteins are not entirely rigid molecules. In addition to these levels of structure, proteins may shift between several related structures while they perform their functions. In the context of these functional rearrangements, these tertiary or quaternary structures are usually referred to as "conformations", and transitions between them are called conformational changes. Such changes are often induced by the binding of a substrate molecule to an enzyme's active site, or the physical region of the protein that participates in chemical catalysis. In solution, protein structures vary because of thermal vibration and collisions with other molecules.: 368–75
Proteins can be informally divided into three main classes, which correlate with typical tertiary structures: globular proteins, fibrous proteins, and membrane proteins. Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often structural, such as collagen, the major component of connective tissue, or keratin, the protein component of hair and nails. Membrane proteins often serve as receptors or provide channels for polar or charged molecules to pass through the cell membrane.: 165–85
A special case of intramolecular hydrogen bonds within proteins, poorly shielded from water attack and hence promoting their own dehydration, are called dehydrons.
=== Protein domains ===
Many proteins are composed of several protein domains, i.e. segments of a protein that fold into distinct structural units.: 134 Domains usually have specific functions, such as enzymatic activities (e.g. kinase) or they serve as binding modules.: 155–156
=== Sequence motif ===
Short amino acid sequences within proteins often act as recognition sites for other proteins. For instance, SH3 domains typically bind to short PxxP motifs (i.e. 2 prolines [P], separated by two unspecified amino acids [x], although the surrounding amino acids may determine the exact binding specificity). Many such motifs has been collected in the Eukaryotic Linear Motif (ELM) database.
== Cellular functions ==
Proteins are the chief actors within the cell, said to be carrying out the duties specified by the information encoded in genes. With the exception of certain types of RNA, most other biological molecules are relatively inert elements upon which proteins act. Proteins make up half the dry weight of an Escherichia coli cell, whereas other macromolecules such as DNA and RNA make up only 3% and 20%, respectively. The set of proteins expressed in a particular cell or cell type is known as its proteome.: 120
The chief characteristic of proteins that allows their diverse set of functions is their ability to bind other molecules specifically and tightly. The region of the protein responsible for binding another molecule is known as the binding site and is often a depression or "pocket" on the molecular surface. This binding ability is mediated by the tertiary structure of the protein, which defines the binding site pocket, and by the chemical properties of the surrounding amino acids' side chains. Protein binding can be extraordinarily tight and specific; for example, the ribonuclease inhibitor protein binds to human angiogenin with a sub-femtomolar dissociation constant (<10−15 M) but does not bind at all to its amphibian homolog onconase (> 1 M). Extremely minor chemical changes such as the addition of a single methyl group to a binding partner can sometimes suffice to nearly eliminate binding; for example, the aminoacyl tRNA synthetase specific to the amino acid valine discriminates against the very similar side chain of the amino acid isoleucine.
Proteins can bind to other proteins as well as to small-molecule substrates. When proteins bind specifically to other copies of the same molecule, they can oligomerize to form fibrils; this process occurs often in structural proteins that consist of globular monomers that self-associate to form rigid fibers. Protein–protein interactions regulate enzymatic activity, control progression through the cell cycle, and allow the assembly of large protein complexes that carry out many closely related reactions with a common biological function. Proteins can bind to, or be integrated into, cell membranes. The ability of binding partners to induce conformational changes in proteins allows the construction of enormously complex signaling networks.: 830–49
As interactions between proteins are reversible and depend heavily on the availability of different groups of partner proteins to form aggregates that are capable to carry out discrete sets of function, study of the interactions between specific proteins is a key to understand important aspects of cellular function, and ultimately the properties that distinguish particular cell types.
=== Enzymes ===
The best-known role of proteins in the cell is as enzymes, which catalyse chemical reactions. Enzymes are usually highly specific and accelerate only one or a few chemical reactions. Enzymes carry out most of the reactions involved in metabolism, as well as manipulating DNA in processes such as DNA replication, DNA repair, and transcription. Some enzymes act on other proteins to add or remove chemical groups in a process known as posttranslational modification. About 4,000 reactions are known to be catalysed by enzymes. The rate acceleration conferred by enzymatic catalysis is often enormous—as much as 1017-fold increase in rate over the uncatalysed reaction in the case of orotate decarboxylase (78 million years without the enzyme, 18 milliseconds with the enzyme).
The molecules bound and acted upon by enzymes are called substrates. Although enzymes can consist of hundreds of amino acids, it is usually only a small fraction of the residues that come in contact with the substrate, and an even smaller fraction—three to four residues on average—that are directly involved in catalysis. The region of the enzyme that binds the substrate and contains the catalytic residues is known as the active site.: 389
Dirigent proteins are members of a class of proteins that dictate the stereochemistry of a compound synthesized by other enzymes.
=== Cell signaling and ligand binding ===
Many proteins are involved in the process of cell signaling and signal transduction. Some proteins, such as insulin, are extracellular proteins that transmit a signal from the cell in which they were synthesized to other cells in distant tissues. Others are membrane proteins that act as receptors whose main function is to bind a signaling molecule and induce a biochemical response in the cell. Many receptors have a binding site exposed on the cell surface and an effector domain within the cell, which may have enzymatic activity or may undergo a conformational change detected by other proteins within the cell.: 251–81
Antibodies are protein components of an adaptive immune system whose main function is to bind antigens, or foreign substances in the body, and target them for destruction. Antibodies can be secreted into the extracellular environment or anchored in the membranes of specialized B cells known as plasma cells. Whereas enzymes are limited in their binding affinity for their substrates by the necessity of conducting their reaction, antibodies have no such constraints. An antibody's binding affinity to its target is extraordinarily high.: 275–50
Many ligand transport proteins bind particular small biomolecules and transport them to other locations in the body of a multicellular organism. These proteins must have a high binding affinity when their ligand is present in high concentrations, and release the ligand when it is present at low concentrations in the target tissues. The canonical example of a ligand-binding protein is haemoglobin, which transports oxygen from the lungs to other organs and tissues in all vertebrates and has close homologs in every biological kingdom.: 222–29 Lectins are sugar-binding proteins which are highly specific for their sugar moieties. Lectins typically play a role in biological recognition phenomena involving cells and proteins. Receptors and hormones are highly specific binding proteins.
Transmembrane proteins can serve as ligand transport proteins that alter the permeability of the cell membrane to small molecules and ions. The membrane alone has a hydrophobic core through which polar or charged molecules cannot diffuse. Membrane proteins contain internal channels that allow such molecules to enter and exit the cell. Many ion channel proteins are specialized to select for only a particular ion; for example, potassium and sodium channels often discriminate for only one of the two ions.: 232–34
=== Structural proteins ===
Structural proteins confer stiffness and rigidity to otherwise-fluid biological components. Most structural proteins are fibrous proteins; for example, collagen and elastin are critical components of connective tissue such as cartilage, and keratin is found in hard or filamentous structures such as hair, nails, feathers, hooves, and some animal shells.: 178–81 Some globular proteins can play structural functions, for example, actin and tubulin are globular and soluble as monomers, but polymerize to form long, stiff fibers that make up the cytoskeleton, which allows the cell to maintain its shape and size.: 490
Other proteins that serve structural functions are motor proteins such as myosin, kinesin, and dynein, which are capable of generating mechanical forces. These proteins are crucial for cellular motility of single celled organisms and the sperm of many multicellular organisms which reproduce sexually. They generate the forces exerted by contracting muscles: 258–64, 272 and play essential roles in intracellular transport.: 481, 490
== Methods of study ==
Methods commonly used to study protein structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance and mass spectrometry. The activities and structures of proteins may be examined in vitro, in vivo, and in silico. In vitro studies of purified proteins in controlled environments are useful for learning how a protein carries out its function: for example, enzyme kinetics studies explore the chemical mechanism of an enzyme's catalytic activity and its relative affinity for various possible substrate molecules. By contrast, in vivo experiments can provide information about the physiological role of a protein in the context of a cell or even a whole organism, and can often provide more information about protein behavior in different contexts. In silico studies use computational methods to study proteins.
=== Protein purification ===
Proteins may be purified from other cellular components using a variety of techniques such as ultracentrifugation, precipitation, electrophoresis, and chromatography;: 21–24 the advent of genetic engineering has made possible a number of methods to facilitate purification.
To perform in vitro analysis, a protein must be purified away from other cellular components. This process usually begins with cell lysis, in which a cell's membrane is disrupted and its internal contents released into a solution known as a crude lysate. The resulting mixture can be purified using ultracentrifugation, which fractionates the various cellular components into fractions containing soluble proteins; membrane lipids and proteins; cellular organelles, and nucleic acids. Precipitation by a method known as salting out can concentrate the proteins from this lysate. Various types of chromatography are then used to isolate the protein or proteins of interest based on properties such as molecular weight, net charge and binding affinity.: 21–24 The level of purification can be monitored using various types of gel electrophoresis if the desired protein's molecular weight and isoelectric point are known, by spectroscopy if the protein has distinguishable spectroscopic features, or by enzyme assays if the protein has enzymatic activity. Additionally, proteins can be isolated according to their charge using electrofocusing.
For natural proteins, a series of purification steps may be necessary to obtain protein sufficiently pure for laboratory applications. To simplify this process, genetic engineering is often used to add chemical features to proteins that make them easier to purify without affecting their structure or activity. Here, a "tag" consisting of a specific amino acid sequence, often a series of histidine residues (a "His-tag"), is attached to one terminus of the protein. As a result, when the lysate is passed over a chromatography column containing nickel, the histidine residues ligate the nickel and attach to the column while the untagged components of the lysate pass unimpeded. A number of tags have been developed to help researchers purify specific proteins from complex mixtures.
=== Cellular localization ===
The study of proteins in vivo is often concerned with the synthesis and localization of the protein within the cell. Although many intracellular proteins are synthesized in the cytoplasm and membrane-bound or secreted proteins in the endoplasmic reticulum, the specifics of how proteins are targeted to specific organelles or cellular structures is often unclear. A useful technique for assessing cellular localization uses genetic engineering to express in a cell a fusion protein or chimera consisting of the natural protein of interest linked to a "reporter" such as green fluorescent protein (GFP). The fused protein's position within the cell can then be cleanly and efficiently visualized using microscopy.
Other methods for elucidating the cellular location of proteins requires the use of known compartmental markers for regions such as the ER, the Golgi, lysosomes or vacuoles, mitochondria, chloroplasts, plasma membrane, etc. With the use of fluorescently tagged versions of these markers or of antibodies to known markers, it becomes much simpler to identify the localization of a protein of interest. For example, indirect immunofluorescence will allow for fluorescence colocalization and demonstration of location. Fluorescent dyes are used to label cellular compartments for a similar purpose.
Other possibilities exist, as well. For example, immunohistochemistry usually uses an antibody to one or more proteins of interest that are conjugated to enzymes yielding either luminescent or chromogenic signals that can be compared between samples, allowing for localization information. Another applicable technique is cofractionation in sucrose (or other material) gradients using isopycnic centrifugation. While this technique does not prove colocalization of a compartment of known density and the protein of interest, it indicates an increased likelihood.
Finally, the gold-standard method of cellular localization is immunoelectron microscopy. This technique uses an antibody to the protein of interest, along with classical electron microscopy techniques. The sample is prepared for normal electron microscopic examination, and then treated with an antibody to the protein of interest that is conjugated to an extremely electro-dense material, usually gold. This allows for the localization of both ultrastructural details as well as the protein of interest.
Through another genetic engineering application known as site-directed mutagenesis, researchers can alter the protein sequence and hence its structure, cellular localization, and susceptibility to regulation. This technique even allows the incorporation of unnatural amino acids into proteins, using modified tRNAs, and may allow the rational design of new proteins with novel properties.
=== Proteomics ===
The total complement of proteins present at a time in a cell or cell type is known as its proteome, and the study of such large-scale data sets defines the field of proteomics, named by analogy to the related field of genomics. Key experimental techniques in proteomics include 2D electrophoresis, which allows the separation of many proteins, mass spectrometry, which allows rapid high-throughput identification of proteins and sequencing of peptides (most often after in-gel digestion), protein microarrays, which allow the detection of the relative levels of the various proteins present in a cell, and two-hybrid screening, which allows the systematic exploration of protein–protein interactions. The total complement of biologically possible such interactions is known as the interactome. A systematic attempt to determine the structures of proteins representing every possible fold is known as structural genomics.
=== Structure determination ===
Discovering the tertiary structure of a protein, or the quaternary structure of its complexes, can provide important clues about how the protein performs its function and how it can be affected, i.e. in drug design. As proteins are too small to be seen under a light microscope, other methods have to be employed to determine their structure. Common experimental methods include X-ray crystallography and NMR spectroscopy, both of which can produce structural information at atomic resolution. However, NMR experiments are able to provide information from which a subset of distances between pairs of atoms can be estimated, and the final possible conformations for a protein are determined by solving a distance geometry problem. Dual polarisation interferometry is a quantitative analytical method for measuring the overall protein conformation and conformational changes due to interactions or other stimulus. Circular dichroism is another laboratory technique for determining internal β-sheet / α-helical composition of proteins. Cryoelectron microscopy is used to produce lower-resolution structural information about very large protein complexes, including assembled viruses;: 340–41 a variant known as electron crystallography can produce high-resolution information in some cases, especially for two-dimensional crystals of membrane proteins. Solved structures are usually deposited in the Protein Data Bank (PDB), a freely available resource from which structural data about thousands of proteins can be obtained in the form of Cartesian coordinates for each atom in the protein.
Many more gene sequences are known than protein structures. Further, the set of solved structures is biased toward proteins that can be easily subjected to the conditions required in X-ray crystallography, one of the major structure determination methods. In particular, globular proteins are comparatively easy to crystallize in preparation for X-ray crystallography. Membrane proteins and large protein complexes, by contrast, are difficult to crystallize and are underrepresented in the PDB. Structural genomics initiatives have attempted to remedy these deficiencies by systematically solving representative structures of major fold classes. Protein structure prediction methods attempt to provide a means of generating a plausible structure for proteins whose structures have not been experimentally determined.
=== Structure prediction ===
Complementary to the field of structural genomics, protein structure prediction develops efficient mathematical models of proteins to computationally predict the molecular formations in theory, instead of detecting structures with laboratory observation. The most successful type of structure prediction, known as homology modeling, relies on the existence of a "template" structure with sequence similarity to the protein being modeled; structural genomics' goal is to provide sufficient representation in solved structures to model most of those that remain. Although producing accurate models remains a challenge when only distantly related template structures are available, it has been suggested that sequence alignment is the bottleneck in this process, as quite accurate models can be produced if a "perfect" sequence alignment is known. Many structure prediction methods have served to inform the emerging field of protein engineering, in which novel protein folds have already been designed. Many proteins (in eukaryotes ~33%) contain large unstructured but biologically functional segments and can be classified as intrinsically disordered proteins. Predicting and analysing protein disorder is an important part of protein structure characterisation.
=== In silico simulation of dynamical processes ===
A more complex computational problem is the prediction of intermolecular interactions, such as in molecular docking, protein folding, protein–protein interaction and chemical reactivity. Mathematical models to simulate these dynamical processes involve molecular mechanics, in particular, molecular dynamics. In this regard, in silico simulations discovered the folding of small α-helical protein domains such as the villin headpiece, the HIV accessory protein and hybrid methods combining standard molecular dynamics with quantum mechanical mathematics have explored the electronic states of rhodopsins.
Beyond classical molecular dynamics, quantum dynamics methods allow the simulation of proteins in atomistic detail with an accurate description of quantum mechanical effects. Examples include the multi-layer multi-configuration time-dependent Hartree method and the hierarchical equations of motion approach, which have been applied to plant cryptochromes and bacteria light-harvesting complexes, respectively. Both quantum and classical mechanical simulations of biological-scale systems are extremely computationally demanding, so distributed computing initiatives such as the Folding@home project facilitate the molecular modeling by exploiting advances in GPU parallel processing and Monte Carlo techniques.
=== Chemical analysis ===
The total nitrogen content of organic matter is mainly formed by the amino groups in proteins. The Total Kjeldahl Nitrogen (TKN) is a measure of nitrogen widely used in the analysis of (waste) water, soil, food, feed and organic matter in general. As the name suggests, the Kjeldahl method is applied. More sensitive methods are available.
== Digestion ==
In the absence of catalysts, proteins are slow to hydrolyze. The breakdown of proteins to small peptides and amino acids (proteolysis) is a step in digestion; these breakdown products are then absorbed in the small intestine. The hydrolysis of proteins relies on enzymes called proteases or peptidases. Proteases, which are themselves proteins, come in several types according to the particular peptide bonds that they cleave as well as their tendency to cleave peptide bonds at the terminus of a protein (exopeptidases) vs peptide bonds at the interior of the protein (endopeptidases). Pepsin is an endopeptidase in the stomach. Subsequent to the stomach, the pancreas secretes other proteases to complete the hydrolysis, these include trypsin and chymotrypsin.
Protein hydrolysis is employed commercially as a means of producing amino acids from bulk sources of protein, such as blood meal, feathers, keratin. Such materials are treated with hot hydrochloric acid, which effects the hydrolysis of the peptide bonds.
== Mechanical properties ==
The mechanical properties of proteins are highly diverse and are often central to their biological function, as in the case of proteins like keratin and collagen. For instance, the ability of muscle tissue to continually expand and contract is directly tied to the elastic properties of their underlying protein makeup. Beyond fibrous proteins, the conformational dynamics of enzymes and the structure of biological membranes, among other biological functions, are governed by the mechanical properties of the proteins. Outside of their biological context, the unique mechanical properties of many proteins, along with their relative sustainability when compared to synthetic polymers, have made them desirable targets for next-generation materials design.
Young's modulus, E, is calculated as the axial stress σ over the resulting strain ε. It is a measure of the relative stiffness of a material. In the context of proteins, this stiffness often directly correlates to biological function. For example, collagen, found in connective tissue, bones, and cartilage, and keratin, found in nails, claws, and hair, have observed stiffnesses that are several orders of magnitude higher than that of elastin, which is though to give elasticity to structures such as blood vessels, pulmonary tissue, and bladder tissue, among others. In comparison to this, globular proteins, such as Bovine Serum Albumin, which float relatively freely in the cytosol and often function as enzymes (and thus undergoing frequent conformational changes) have comparably much lower Young's moduli.
The Young's modulus of a single protein can be found through molecular dynamics simulation. Using either atomistic force-fields, such as CHARMM or GROMOS, or coarse-grained forcefields like Martini, a single protein molecule can be stretched by a uniaxial force while the resulting extension is recorded in order to calculate the strain. Experimentally, methods such as atomic force microscopy can be used to obtain similar data. The internal dynamics of proteins involve subtle elastic and plastic deformations induced by viscoelastic forces, which can be probed by nano-rheology techniques. These estimates yield typical spring constants around k ≈ 100 pN/nm, equivalent to Yonung's moduli of E ≈ 100 MPa, and typical friction coefficients of γ ≈ 0.1 pN·s/nm, corresponding to viscosity of η ≈ 0.01 pN·s/nm2 = 107cP (that is, 107 more viscous than water).
At the macroscopic level, the Young's modulus of cross-linked protein networks can be obtained through more traditional mechanical testing. Experimentally observed values for a few proteins can be seen below.
== See also ==
== References ==
== Further reading ==
Textbooks
History
Tanford C, Reynolds JA (2001). Nature's Robots: A History of Proteins. Oxford New York: Oxford University Press, USA. ISBN 978-0-19-850466-5.
== External links ==
=== Databases and projects ===
NCBI Entrez Protein database
NCBI Protein Structure database
Human Protein Reference Database
Human Proteinpedia
Folding@Home (Stanford University) Archived 2012-09-08 at the Wayback Machine
Protein Databank in Europe (see also PDBeQuips, short articles and tutorials on interesting PDB structures)
Research Collaboratory for Structural Bioinformatics (see also Molecule of the Month Archived 2020-07-24 at the Wayback Machine, presenting short accounts on selected proteins from the PDB)
Proteopedia – Life in 3D: rotatable, zoomable 3D model with wiki annotations for every known protein molecular structure.
UniProt the Universal Protein Resource
=== Tutorials and educational websites ===
"An Introduction to Proteins" from HOPES (Huntington's Disease Outreach Project for Education at Stanford)
Proteins: Biogenesis to Degradation – The Virtual Library of Biochemistry and Cell Biology | Wikipedia/Structural_protein |
Epstein–Barr virus latent membrane protein 1 (LMP1) is an Epstein–Barr virus (EBV) protein that regulates its own expression and the expression of human genes. It has a molecular weight of approximately 63 kDa, and its expression induces many of the changes associated with EBV infections and activation of primary B cells. LMP1 is the best-documented oncoprotein of the EBV latent gene products, as it is expressed in most EBV-related human cancers such as the various malignant Epstein-Barr virus-associated lymphoproliferative diseases.
The structure of LMP1 consists of a short cytoplasmic terminal tail, six trans-membrane domains, and a long cytoplasmic C-terminus, which contains three activating domains: CTARt, CTAR2, and CTAR3. Each CTAR domain contains an amino acid sequence that serves as a recognition site for cellular adaptors to bind and trigger a series of signal transduction pathways that can lead to a change in gene expression.
LMP-1 is a functional homologue of tumor necrosis factor and mediates signaling through the nuclear factor-κB pathway, mimicking CD40 receptor signaling.
It is often found in the malignant Reed–Sternberg cells of Hodgkin lymphoma, the malignant B cells of EBV-associated B cell lymphatic cancers, and the malignant NK cells of NK/T cell lymphatic cancers.
== References == | Wikipedia/Epstein–Barr_virus_latent_membrane_protein_1 |
Infected cell protein 47 also ICP-47 or ICP47 is a protein encoded by the viruses such as Herpes simplex virus and Cytomegalovirus that allows them to evade the human immune system's CD8 T-cell response by interfering with an infected cell's ability to show viral epitopes to T cells. Its secondary structure shows three helices.
== Method of action ==
It works by inhibiting transfer of viral particles to the human TAP proteins and thus entry of viral peptides into the endoplasmic reticulum, which is supposed to bind them to MHC class I molecules for extracellular T-cell recognition so the viral component will trigger immune defense response as a foreign entity. However human or some animal TAP proteins differs in mice making rodents far less susceptible than humans to HSV.
== References == | Wikipedia/Infected_cell_protein_47 |
The M1 protein is a matrix protein of the influenza virus. It forms a coat inside the viral envelope. This is a bifunctional membrane/RNA-binding protein that mediates the encapsidation of nucleoprotein cores into the membrane envelope. It is therefore required that M1 binds both membrane and RNA simultaneously.
The M1 protein binds to the viral RNA. The binding is not specific to any RNA sequence, and is performed via a peptide sequence rich in basic amino acids.
It also has multiple regulatory functions, performed by interaction with the components of the host cell. The mechanisms regulated include a role in the export of the viral ribonucleoproteins from the host cell nucleus, inhibition of viral transcription, and a role in the virus assembly and budding. The protein was found to undergo phosphorylation in the host cell.
The M1 protein forms a layer under the patches of host cell membrane that are rich with the viral hemagglutinin, neuraminidase and M2 transmembrane proteins, and facilitates budding of the mature viruses.
M1 consists of two domains connected by a linker sequence. The N-terminal domain has a multi-helical structure that can be divided into two subdomains. The C-terminal domain also contains alpha-helical structure.
== See also ==
H5N1 genetic structure
== Sources and notes == | Wikipedia/M1_protein |
The p24 capsid protein is the most abundant HIV protein with each virus containing approximately 1,500 to 3,000 p24 molecules. It is the major structural protein within the capsid, and it is involved in maintaining the structural integrity of the virus and facilitating various stages of the viral life cycle, including viral entry into host cells and the release of new virus particles. Detection of p24 protein's antigen can be used to identify the presence of HIV in a person's blood and diagnose HIV/AIDS, however, more modern tests have taken their place. After approximately 50 days of infection, the p24 antigen is often cleared from the bloodstream entirely.
== Structure ==
P24 has a molecular weight of 24 kDa and is encoded by the gag gene. The structure of HIV capsid was determined by X-ray crystallography and cryo-electron microscopy. The p24 capsid protein consists of two domains: the N-terminal domain and the C-terminal domain connected by flexible inter-domain linkers. The N-terminal domain (NTD) is made up of 7 α-helices (H) and β-hairpin. The C-terminal domain (CTD) has 4 α-helices and an 11-residue unstructured region. The N-terminal domain (NTD) facilitates contacts within the hexamer, while the C-terminal domain (CTD) forms dimers that bind to adjacent hexamers. Each hexamer contains a size-selective pore surrounded by six positively charged arginine residues, and the pore is covered by a β-hairpin that can undergo conformational changes, which has both open and closed conformations. At the center of the hexamers lies an IP6 molecule which stabilizes the tertiary structure of the molecule. Additionally, the C-terminal domain includes a major homology region (MHR) spanning amino acids 153 to 172 with 20 highly conserved amino acids. Moreover, the N-terminal domain features a loop (amino acids 85–93) that interacts with the protein cyclophilin A (Cyp A).
== Function ==
P24 is a structural protein that plays a crucial role in the formation and stability of the viral capsid, which protects the viral RNA. p24 capsid protein's roles in the HIV replicative process are summarized as follows:
Fusion: HIV replication cycle begins when HIV fuses with the surface of the host cell. The capsid containing the virus’s genome and proteins then enters the cells.
Reverse transcription: The capsid ensures the secure transport of the viral genome and reverse-transcription machinery from the cytoplasm's periphery to transcriptionally active sites in the nucleus. It achieves this by shielding the viral genome from detection by restriction factors, while still allowing the necessary molecules to diffuse through the core, facilitating the process of reverse transcription.
Assembly: It is involved in the assembly of new virus particles, facilitating the proper organization of viral components.
Budding: P24 contributes to the viral budding process, ensuring the proper packaging and release of mature and infectious virus particles.
== p24 HIV capsid as a therapeutic target ==
=== New antiretroviral therapy ===
Cyclosporine, an immunosuppressant drug designed to prevent organ transplant rejection, has been shown to inhibit infection in HIV-1 positive people. Cyclosporine acts as a competitive inhibitor to the capsid protein’s association with CypA, a cellular protein. CypA has been shown to be important for HIV’s infectivity.
The HIV-1 p24 capsid protein plays crucial roles throughout the replication cycle, making it an attractive therapeutic target. Unlike the viral enzymes (protease, reverse transcriptase and integrase) that are currently targeted by small-molecule antiretroviral drugs, p24 capsid proteins operate through protein-protein interactions. Capsid inhibitors, such as Lenacapavir and GS-6207, interfere with the activities of the HIV capsid protein and underwent evaluation in phase-1 clinical trials as monotherapies. They demonstrated anti-viral activity against all subtypes with no cross-resistance with current antiretroviral drugs. These findings support therapies aimed at disrupting the functions of the HIV capsid protein.
=== Vaccine design ===
P24 can induce cellular immune responses and has been included in some vaccine strategies.
== Diagnosis ==
=== Fourth generation-HIV test ===
P24 is a target for the immune system, and antibodies against p24 are used in diagnostic tests to detect the presence of HIV antibodies. Fourth-generation HIV immunoassays detect viral p24 protein in the blood and patient antibodies against the virus. Previous generation tests relied on detecting patient antibodies alone; it takes about 3–4 weeks for the earliest antibodies to be detected. The p24 protein can be detected in a patient's blood as early as 2 weeks after infection, further reducing the window period necessary to accurately detect the HIV status of the patient.
== See also ==
HIV vaccine
== References ==
== Further reading ==
Wiznerowicz M. "TU vs pg of p24". Trono Lab – Laboratory of Virology and Genetics. École polytechnique fédérale de Lausanne (EPFL). Archived from the original on 9 March 2008.
"Frequently Asked Questions: Fourth Generation HIV Ab/Ag Combination Assays" (PDF). PA/ MidAtlantic AIDS Education and Training Center at the Health Federation of Philadelphia Last Revised. March 2013. Archived from the original (PDF) on 15 July 2015. | Wikipedia/P24_capsid_protein |
An oncogene is a gene that has the potential to cause cancer. In tumor cells, these genes are often mutated, or expressed at high levels.
Most normal cells undergo a preprogrammed rapid cell death (apoptosis) if critical functions are altered and then malfunction. Activated oncogenes can cause those cells designated for apoptosis to survive and proliferate instead. Most oncogenes began as proto-oncogenes: normal genes involved in cell growth and proliferation or inhibition of apoptosis. If, through mutation, normal genes promoting cellular growth are up-regulated (gain-of-function mutation), they predispose the cell to cancer and are termed oncogenes. Usually, multiple oncogenes, along with mutated apoptotic or tumor suppressor genes, act in concert to cause cancer. Since the 1970s, dozens of oncogenes have been identified in human cancer. Many cancer drugs target the proteins encoded by oncogenes. Oncogenes are a physically and functionally diverse set of genes, and as a result, their protein products have pleiotropic effects on a variety of intricate regulatory cascades within the cell.
Genes known as proto-oncogenes are those that normally encourage cell growth and division in order to generate new cells or sustain the viability of pre-existing cells. When overexpressed, proto-oncogenes can be inadvertently activated (turned on), which changes them to oncogenes.
There are numerous ways to activate (turn on) oncogenes in cells:
Gene changes or mutations: A person's genetic "coding" may differ in a way that causes an oncogene to always be activated. These types of gene changes can develop spontaneously throughout the course of a person's life or they might be inherited from a parent when a transcription error occurs during cell division.
Cells can frequently switch genes on or off via epigenetic mechanisms rather than actual genetic alterations. Alternately, different chemical compounds that can be linked to genetic material (DNA or RNA) may have an impact on which genes are active. An oncogene may sporadically become activated due to these epigenetic modifications.
Chromosomal rearrangement: Every living creature has chromosomes, which are substantial strands of DNA that contain the genes for a cell. A chromosome's DNA sequence may alter each time a cell divides. This could cause a gene to be located near to a proto-oncogene that acts as an "on" switch, keeping it active even when it shouldn't. The cell can develop irregularly with the aid of this new oncogene.
Gene duplication: If one cell has more copies of a gene than another, that cell may produce too much of a certain protein.
The first human oncogene (HRAS), a crucial finding in the field of cancer research, was discovered more than 40 years ago, and since then, the number of novel pathogenic oncogenes has increased steadily. The discovery of specific small-molecule inhibitors that specifically target the different oncogenic proteins and a comprehensive mechanistic analysis of the ways in which oncogenes dysregulate physiological signaling to cause different cancer types and developmental syndromes are potential future advances in the field of cancer research. Investigating the quickly expanding field of oncogene molecular research, the goal of this special issue was to generate practical translational indicators that could be able to meet clinical needs.
Genes that are considered crucial for cancer can be divided into two categories based on whether the harmful mutations in them result in function loss or gain. Gain-of-function mutations of proto-oncogenes drive cells to proliferate when they shouldn't, while loss-of-function mutations of tumor suppressor genes free cells from inhibitions that typically serve to control their numbers. The ability of the mutant genes, known as oncogenes, to steer a specific line of test cells toward malignant proliferation can occasionally be used to identify these later mutations, which have a dominating effect.
Many of them were initially found to induce cancer in animals when they are introduced through viral vector infection, which carries genetic information from a prior host cell. Another method for identifying oncogenes is to look for genes that are activated by mutations in human cancer cells or by chromosomal translocations that may indicate the presence of a gene that is crucial for cancer.
Cancer patients are generally categorized according to clinical parameters in order to tailor their cancer therapy. For example, the separation of patients with acute leukemia into those with lymphocytic leukemia and those with myelocytic leukemia is important, because the optimal treatment for each form is different. Even in a particular disease, the identification of patients with good and poor prognostic potential is helpful, since more aggressive therapy may be needed to achieve a cure in the poor prognostic group. Oncogenes are prognostic markers in certain human cancers. N-myc amplification is an independent determinant in predicting a poor outcome in childhood neuroblastoma. Those children with amplification of N-myc, regardless of stage, will have shortened survival. Thus, therapeutic efforts are concentrated on intensifying treatment in this poor prognostic group.
== History ==
The theory of oncogenes was foreshadowed by the German biologist Theodor Boveri in his 1914 book Zur Frage der Entstehung Maligner Tumoren (Concerning the Origin of Malignant Tumors) in which he predicted the existence of oncogenes (Teilungsfoerdernde Chromosomen) that become amplified (im permanenten Übergewicht) during tumor development.
Later on, the term "oncogene" was rediscovered in 1969 by National Cancer Institute scientists George Todaro and Robert Huebner.
The first confirmed oncogene was discovered in 1970 and was termed SRC (pronounced "sarc" as it is short for sarcoma). SRC was first discovered as an oncogene in a chicken retrovirus. Experiments performed by Dr. G. Steve Martin of the University of California, Berkeley demonstrated that SRC was indeed the gene of the virus that acted as an oncogene upon infection. The first nucleotide sequence of v-Src was sequenced in 1980 by A.P. Czernilofsky et al.
In 1976, Drs. Dominique Stéhelin, J. Michael Bishop and Harold E. Varmus of the University of California, San Francisco demonstrated that oncogenes were activated proto-oncogenes as is found in many organisms, including humans. Bishop and Varmus were awarded the Nobel Prize in Physiology or Medicine in 1989 for their discovery of the cellular origin of retroviral oncogenes.
Dr. Robert Weinberg is credited with discovering the first identified human oncogene in a human bladder cancer cell line. The molecular nature of the mutation leading to oncogenesis was subsequently isolated and characterized by the Spanish biochemist Mariano Barbacid and published in Nature in 1982. Dr. Barbacid spent the following months extending his research, eventually discovering that the oncogene was a mutated allele of HRAS and characterizing its activation mechanism.
The resultant protein encoded by an oncogene is termed oncoprotein. Oncogenes play an important role in the regulation or synthesis of proteins linked to tumorigenic cell growth. Some oncoproteins are accepted and used as tumor markers.
== Proto-oncogene ==
A proto-oncogene is a normal gene that could become an oncogene due to mutations or increased expression. Proto-oncogenes code for proteins that help to regulate the cell growth and differentiation. Proto-oncogenes are often involved in signal transduction and execution of mitogenic signals, usually through their protein products. Upon acquiring an activating mutation, a proto-oncogene becomes a tumor-inducing agent, an oncogene. Examples of proto-oncogenes include RAS, WNT, MYC, ERK, and TRK. The MYC gene is implicated in Burkitt's lymphoma, which starts when a chromosomal translocation moves an enhancer sequence within the vicinity of the MYC gene. The MYC gene codes for widely used transcription factors. When the enhancer sequence is wrongly placed, these transcription factors are produced at much higher rates. Another example of an oncogene is the Bcr-Abl gene found on the Philadelphia chromosome, a piece of genetic material seen in Chronic Myelogenous Leukemia caused by the translocation of pieces from chromosomes 9 and 22. Bcr-Abl codes for a tyrosine kinase, which is constitutively active, leading to uncontrolled cell proliferation. (More information about the Philadelphia Chromosome below)
=== Activation ===
The proto-oncogene can become an oncogene by a relatively small modification of its original function. There are three basic methods of activation:
A mutation within a proto-oncogene, or within a regulatory region (for example the promoter region), can cause a change in the protein structure, causing
an increase in protein (enzyme) activity
a loss of regulation
An increase in the amount of a certain protein (protein concentration), caused by
an increase of protein expression (through misregulation)
an increase of protein (mRNA) stability, prolonging its existence and thus its activity in the cell
gene duplication (one type of chromosome abnormality), resulting in an increased amount of protein in the cell
A chromosomal translocation (another type of chromosome abnormality)
There are 2 different types of chromosomal translocations that can occur:
translocation events which relocate a proto-oncogene to a new chromosomal site that leads to higher expression
translocation events that lead to a fusion between a proto-oncogene and a 2nd gene (this creates a fusion protein with increased cancerous/oncogenic activity)
the expression of a constitutively active hybrid protein. This type of mutation in a dividing stem cell in the bone marrow leads to adult leukemia
Philadelphia Chromosome is an example of this type of translocation event. This chromosome was discovered in 1960 by Peter Nowell and David Hungerford, and it is a fusion of parts of DNA from chromosome 22 and chromosome 9. The broken end of chromosome 22 contains the "BCR" gene, which fuses with a fragment of chromosome 9 that contains the "ABL1" gene. When these two chromosome fragments fuse the genes also fuse creating a new gene: "BCR-ABL". This fused gene encodes for a protein that displays high protein tyrosine kinase activity (this activity is due to the "ABL1" half of the protein). The unregulated expression of this protein activates other proteins that are involved in cell cycle and cell division which can cause a cell to grow and divide uncontrollably (the cell becomes cancerous). As a result, the Philadelphia Chromosome is associated with Chronic Myelogenous Leukemia (as mentioned before) as well as other forms of Leukemia.
The expression of oncogenes can be regulated by microRNAs (miRNAs), small RNAs 21-25 nucleotides in length that control gene expression by downregulating them. Mutations in such microRNAs (known as oncomirs) can lead to activation of oncogenes. Antisense messenger RNAs could theoretically be used to block the effects of oncogenes.
== Classification ==
There are several systems for classifying oncogenes, but there is not yet a widely accepted standard. They are sometimes grouped both spatially (moving from outside the cell inwards) and chronologically (parallelling the "normal" process of signal transduction). There are several categories that are commonly used:
Additional oncogenetic regulator properties include:
Growth factors are usually secreted by either specialized or non-specialized cells to induce cell proliferation in themselves, nearby cells, or distant cells. An oncogene may cause a cell to secrete growth factors even though it does not normally do so. It will thereby induce its own uncontrolled proliferation (autocrine loop), and proliferation of neighboring cells, possibly leading to tumor formation. It may also cause production of growth hormones in other parts of the body.
Receptor tyrosine kinases add phosphate groups to other proteins in order to turn them on or off. Receptor kinases add phosphate groups to receptor proteins at the surface of the cell (which receives protein signals from outside the cell and transmits them to the inside of the cell). Tyrosine kinases add phosphate groups to the amino acid tyrosine in the target protein. They can cause cancer by turning the receptor permanently on (constitutively), even without signals from outside the cell.
Ras is a small GTPase that hydrolyses GTP into GDP and phosphate. Ras is activated by growth factor signaling (i.e., EGF, TGFbeta) and acting as a binary switch (on/off) in growth signaling pathways. Downstream effectors of Ras include three mitogen-activated protein kinases Raf a MAP Kinase Kinase Kinase (MAPKKK), MEK a MAP Kinase Kinase (MAPKK), and ERK a MAP Kinase(MAPK), which in turn regulate genes that mediate cell proliferation.
== See also ==
Anticancer gene
Oncogenomics
Tumor suppressor gene
Oncovirus
Genetic predisposition
Quantitative trait locus
Genetic susceptibility
Oncometabolism
== References ==
== External links ==
Drosophila Oncogenes and Tumor Suppressors - The Interactive Fly | Wikipedia/Oncoprotein |
Varidnaviria is a realm of viruses that includes all DNA viruses that encode major capsid proteins that contain two vertical jelly roll folds. The major capsid proteins (MCP) form into pseudohexameric subunits of the viral capsid, which stores the viral deoxyribonucleic acid (DNA). The jelly roll folds are vertical, or perpendicular, to the surface of the capsid. Apart from the double jelly roll fold MCP (DJR-MCP), most viruses in the realm share many other characteristics, such as minor capsid proteins (mCP) that has one vertical jelly roll fold, an ATPase that packages viral DNA into the capsid, a DNA polymerase that replicates the viral genome, and capsids that are icosahedral in shape.
Varidnaviria was established in 2019 based on the shared characteristics of the viruses in the realm. There are two kingdoms in the realm: Abadenavirae, which contains all prokaryotic DJR-MCP viruses except tectiviruses, and Bamfordvirae which contains tectiviruses and all eukaryotic DJR-MCP viruses. The DJR-MCP of Varidnaviria is believed to share common ancestry with the DUF2961 family of proteins, which are widespread in cellular life and which are mainly involved in carbohydrate metabolism and binding. Up to 2025, the realm included viruses that have a vertical single jelly roll (SJR) fold in the MCP, but these viruses were moved to a separate realm, Singelaviria, after it was shown that the vertical SJR and DJR folds have separate evolutionary origins.
Marine viruses in the realm are highly abundant worldwide in the upper ocean and are important in marine ecology. Many animal viruses in Varidnaviria are associated with disease, including adenoviruses, poxviruses, and the African swine fever virus. Poxviruses have been prominent in the history of medicine, especially smallpox, caused by Variola virus. The first vaccine to be invented prevented smallpox, which later became the first disease eradicated. The realm includes a number of highly unusual viruses, including giant viruses that are much larger in size and contain a significantly greater number of genes than typical viruses, and virophages, which are viruses that are parasites of giant viruses.
== Etymology ==
The name "Varidnaviria" is a portmanteau of various DNA viruses and the suffix -viria, which is the suffix used for virus realms. Double-stranded DNA (dsDNA) viruses in the realm are often called non-tailed or tailless dsDNA viruses to distinguish them from the tailed dsDNA viruses of Duplodnaviria. Members of the realm are called varidnavirians.
== Characteristics ==
=== MCP, mCP, and ATPase ===
Most viruses in Varidnaviria contain a capsid that is made of major capsid proteins (MCPs) that contain vertical double jelly roll (DJR) folds. The major capsid proteins are named so because they are the primary proteins that the capsid is made of. A jelly roll fold is a type of folded structure in a protein in which eight antiparallel beta strands are organized into four antiparallel beta sheets in a layout resembling a jelly roll, also called a Swiss roll. Each beta strand is a specific sequence of amino acids, and these strands bond to their antiparallel strands via hydrogen bonds. A double jelly roll fold MCP is one that has two jelly roll folds in a single protein. Vertical folds are those that are perpendicular to the capsid surface, in contrast to horizontal folds that are parallel to the capsid surface.
During the process of assembling the viral capsid, MCPs self-assemble into hexagonal structures, called hexons, that contain three copies of the MCP. Hexons then bond to form the relatively flat triangular sides of the capsid, which is icosahedral in shape with 20 triangular faces and 12 vertices. All varidnavirians that encode a DJR-MCP that have been analyzed in high resolution also encode a minor capsid protein (mCP) that contains a single jelly roll fold. These mCPs assemble into pentagonal structures called pentons that contain five copies of the mCP and form the pentagonal vertices of the icosahedral capsid.
Most members of the realm also encode genome packaging ATPases of the FtsK-HerA superfamily. The ATPases in Varidnaviria are enzymes that package the viral DNA into the capsid during the process of assembling virions. FtsK-HerA is a family of proteins that contains a transmembrane domain with four membrane-spanning helices at the start of the protein's amino acid sequence, a central coiled-coil region, and an ATPase with a P-loop fold at the end of the protein's amino acid sequence. FtsK proteins are found in nearly all bacteria and HerA proteins in all archaea and some bacteria. The exact function of the ATPase for some viruses in Varidnaviria is unclear since morphological features, such as the circular, supercoiled genome of bacteriophage PM2, seemingly prohibit translocation by the ATPase of DNA from outside the capsid to the inside. The subset of the FtsK-HerA superfamily found in Varidnaviria is often called the A32 clade, named after the ATPase-encoding A32(R) gene of Vaccinia virus. The family Finnlakeviridae and the provisional Odin group lack the signature FtsK-HerA ATPase, as do adenoviruses, which instead encode their own ATPase that has the same role.
=== Other characteristics ===
Apart from the core morphogenetic triad of traits (the MCP, mCP, and ATPase), certain other characteristics are common or unique in various lineages within Varidnaviria, listed hereafter.
All members of Varidnaviria, except for the family Finnlakeviridae, have dsDNA genomes. Viruses in Finnlakeviridae instead have single-stranded DNA (ssDNA) genomes.
Many members of the realm encode a type B DNA polymerase, which copies the viral DNA, and often additional components of the DNA polymerase, such as superfamily 3 helicases, or replication initiation proteins in the case of the family Corticoviridae.
Many eukaryotic DJR-MCP viruses encode a capsid maturation protease that is involved in assembling the capsid.
Some members of the realm encode integrase, an enzyme that integrates the viral genome into the genome of the host.
In some unrelated lineages, the ancestral icosahedral shape of the capsid has been lost and replaced with other shapes. For example, ascoviruses have ovoid virions, and pandoraviruses have amphora-shaped virions. Poxviruses retain the DJR-MCP and use it to form intermediate virions, but mature virions are brick- or ovoid-shaped.
Some varidnavirians have special vertices in their icosahedral capsids for transporting the genome out of the capsid and for making virus factories.
== Phylogenetics ==
Varidnaviria may predate the last universal common ancestor (LUCA) of cellular life, and viruses in the realm may have been present in the LUCA. The DJR-MCP appears to share common ancestry with the GH172/DUF2961 family of proteins as they appear to be sister clades. DUF2961 proteins are widespread in both prokaryotes and eukaryotes and are mainly involved in carbohydrate metabolism and binding. They form trimers with a pseudohexagonal shape that resembles the capsomeres of viral DJR-MCPs. Other cellular proteins that appear to be distantly related to the DJR-MCP and DUF2961 proteins include peptide:N-glycosidase F (PNGase F) and peptidylglycine α-hydroxylating monooxygenase (PHM). The two jelly rolls shared by these proteins are likely the result of a gene duplication event of a cellular single jelly roll fold prior to the emergence of Varidnaviria, though it is possible that the DJR evolved independently via gene duplication in both the DUF2961 and Varidnaviria lineages.
In general, viruses in Varidnaviria do not share common descent with viruses in other realms. The main exception is the unclassified phylum Mirusviricota in the realm Duplodnaviria. Mirusviricots share some core replication and transcription-related genes with the varidnavirian phylum Nucleocytoviricota, including DNA polymerase B, RNA polymerase A, RNA polymerase B, and transcription factor TFIIS. Herpesviruses, also in Duplodnaviria, encode DNA polymerase B as well. It is proposed that this group of genes first emerged either in the ancestors of nucleocytoviricots or in the ancestors of mirusviricots and horizontally transferred to the other lineage. In both scenarios, herpesviruses lost most of them through reductive evolution. Despite the relation, mirusviricots and nucleocytoviricots belong to different realms because they have different MCPs, which are the defining characteristics of Duplodnaviria and Varidnaviria. The family Microviridae in Monodnaviria and various RNA viruses in Riboviria also encode MCPs that have jelly roll folds, but they are horizontal (parallel) to the capsid surface, in contrast to the jelly roll folds of Varidnaviria, which are vertical (perpendicular) to the capsid surface.
== Classification ==
Varidnaviria has two kingdoms: Abadenavirae and Bamfordvirae. Abadenavirae is monotypic down to the rank of phylum. This taxonomy can be visualized as follows:
Kingdom: Abadenavirae, which contains all prokaryotic DJR-MCP viruses except tectiviruses (Tectiliviricetes)
Phylum: Produgelaviricota
Kingdom: Bamfordvirae, which contains tectiviruses (Tectiliviricetes) and all eukaryotic DJR-MCP viruses
Nearly all varidnavirians belong to Group I: dsDNA viruses of the Baltimore classification system, which groups viruses together based on how they produce messenger RNA and is commonly used alongside virus taxonomy, which is based on evolutionary history. The exception is viruses of the family Finnlakeviridae in the kingdom Abadenavirae, which have ssDNA genomes and belong to Group II: ssDNA viruses in the Baltimore system. Realms are the highest level of taxonomy used for viruses and Varidnaviria is one of seven. The others are Adnaviria, Duplodnaviria, Monodnaviria, Riboviria, Ribozyviria, and Singelaviria.
== Interactions with hosts ==
=== Disease ===
Disease-causing viruses in Varidnaviria include adenoviruses, poxviruses, and the African swine fever virus (ASFV). Adenoviruses typically cause mild respiratory, gastrointestinal, and conjunctival illnesses, but occasionally cause more severe illnesses, such as hemorrhagic cystitis, hepatitis, and meningoencephalitis. Poxviruses infect many animals and typically cause non-specific symptoms paired with a characteristic rash that is called a pox. Poxviruses include Variola virus, which causes smallpox, and Vaccinia virus, which is used as the vaccine against smallpox. ASFV is usually asymptomatic in its natural reservoirs but causes a lethal hemorrhagic fever in domestic pigs that is a concern for agricultural production.
=== Endogenization ===
Many viruses in Varidnaviria encode the enzyme integrase and integrate their genome into the genome of their host. Polintons, which constitute the class Polintoviricetes, are apparently always endogenized in their hosts. This integration of viral DNA into the host's genome is a form of horizontal gene transfer between unrelated organisms, although polintons are typically transmitted vertically from parent to child. Endogenization is common among bacterial and archaeal DJR-MCP viruses.
==== Adapative immunity ====
A peculiar example of endogenization in Varidnaviria are virophages, satellite viruses that are dependent on giant virus infection to replicate and which are assigned to the class Virophaviricetes. Virophages replicate by hijacking the replication apparati of giant viruses, thereby suppressing the number of giant virus virions produced, which increases the likelihood of host survival. Some virophages are able to become endogenized, and this endogenization can be considered a form of adaptive immunity for the host against giant virus infection.
=== Viral shunt ===
Algal viruses of the family Phycodnaviridae play an important role in controlling algal blooms and, along with other marine viruses, contribute to a process called viral shunt, whereby organic material from killed organisms are "shunted" by viruses away from higher trophic levels and recycled for consumption by organisms at lower trophic levels. Bacteriophages in Varidnaviria are similarly a potential major cause of death among marine prokaryotes due to their large numbers. Autolykiviruses, a group of marine bacterial viruses, have broad host ranges that enable them to infect and kill many different bacteria species.
== History ==
Diseases caused by poxviruses have been known for much of recorded history. Smallpox in particular has been highly prominent in modern medicine. The first vaccine to be invented protected against smallpox, and smallpox would later become the first disease to be eradicated. Human adenoviruses were the first DJR-MCP viruses in Varidnaviria to have their MCPs analyzed. They stood out for having jelly roll folds that were perpendicular, rather than parallel, to the capsid surface. In 1999, the structure of the MCP of bacteriophage PRD1 was resolved, which showed that the DJR-MCP lineage included prokaryotic viruses.
Over time, the use of metagenomics has allowed for the identification of many viruses in the environment without identification of the host or with laboratory specimens. With the increased knowledge of the viruses of the realm, Varidnaviria was established in 2019 based on the shared traits of viruses in the realm. Metagenomic studies suggest that varidnavirians are the most common group of viruses in the upper oceans, where they make up 50–90% of detected viruses and may be more numerous than tailed dsDNA viruses of Duplodnaviria, the largest and most diverse lineage of viruses documented.
Up to 2025, Varidnaviria included viruses that have a single vertical jelly roll fold MCP (SJR-MCP) in the kingdom Helvetiavirae, now classified in the realm Singelaviria. It was believed at first that the DJR-MCP of Varidnaviria was the result of a gene fusion event of the SJR-MCPs of Singelaviria since singelavirians encode two SJR-MCPs that form homo- and heterodimers in capsomeres that resemble the capsomeres of DJR-MCPs. The discovery of cellular proteins that contain a DJR-fold, however, led to further research that showed that the DJR MCPs of Varidnaviria likely evolved from said cellular proteins independent from vertical SJR-MCP viruses. Because of this, the SJR-MCP-encoding viruses of Helvetiavirae were given their own realm, Singelaviria.
== See also ==
List of higher virus taxa
== Notes ==
== References ==
== Further reading ==
Ward, C. W. (1993). "Progress towards a higher taxonomy of viruses". Research in Virology. 144 (6): 419–53. doi:10.1016/S0923-2516(06)80059-2. PMC 7135741. PMID 8140287. | Wikipedia/Varidnaviria |
Agnoprotein is a protein expressed by some members of the polyomavirus family from a gene called the agnogene. Polyomaviruses in which it occurs include two human polyomaviruses associated with disease, BK virus and JC virus, as well as the simian polyomavirus SV40.
== Sequence and structure ==
Agnoprotein is typically quite short: examples from BK virus, JC virus, and SV40 are 62, 71, and 66 amino acid residues long, respectively. Among other known polyomavirus genomes with a predicted agnogene, the length of the resulting predicted protein varies considerably, from as short as 30 to as long as 154 residues. It contains a highly hydrophobic central amino acid sequence, a "bipartite" nuclear localization sequence at the N-terminus, and highly basic amino acids at both termini. Comparison of the sequences of different viral agnoproteins suggests sequence conservation toward the N-terminus with greater variability toward the C-terminus. Formation of amphipathic alpha helices under laboratory conditions has been demonstrated for part of the sequence believed to have a role in mediating dimerization and oligomerization of the protein. The BK, JC, and SV40 agnoproteins have all been experimentally demonstrated to be phosphorylated in vivo, which appears to improve both protein stability and viral propagation, but no other post-translational modifications have been detected.
== Expression ==
Agnoprotein is expressed from a region of the circular viral genome called the agnogene, an open reading frame contained in a region of the polyomavirus genome that codes for the viral capsid proteins and is known as the "late region" because it is expressed late in the cycle of viral infection and replication. The agnogene and its protein product received their name (from the Greek agnosis, "without knowledge") because the presence of the open reading frame and corresponding RNA was detected before the existence of the protein product was confirmed.
== Cellular localization ==
Agnoprotein is consistently detected in the cytoplasm of infected cells, with particularly high concentrations in the perinuclear space. It is also detectable in the cell nucleus; in the case of JC virus, nuclear-localized agnoprotein comprises 15–20% of the total agnoprotein expressed.
== Function ==
Agnoprotein is a regulatory protein required for efficient proliferation of the viruses in which it is present, although many polyomaviruses do not have the gene. Its functions are poorly characterized even in well-studied viruses. Null mutant viruses without agnoprotein are generally either incapable of proliferation or are vastly impaired; some such mutants can produce virions, but they may be deficient in exiting the host cell or lack appropriately packaged genetic material. Agnoprotein null mutants can successfully proliferate if agnoprotein is present in trans. Although the protein is not found in mature virions, there is some evidence that it can be secreted from infected cells, even before viral exit, and taken up by neighboring uninfected cells.
Agnoprotein has been associated with a number of processes in the viral life cycle, including transcription, replication, and encapsidation of the viral genome. It has also been suggested that agnoprotein functions as a viroporin – that is, a viral protein that alters membrane permeability to facilitate the virus particles' exit from the cell. In addition, effects on the behavior of the host cell itself have been observed, including impaired progression through the cell cycle and deficiencies in DNA repair.
Because it is highly basic, agnoprotein has been suspected to be a DNA-binding protein, but has not been shown to bind DNA. A large number of protein-protein interactions have been reported between agnoprotein and other proteins of both viral and host cell origin. Agnoprotein interacts with the viral proteins small tumor antigen and large tumor antigen as well as with the capsid protein VP1. Host cell proteins reported as binding partners for at least one virus species' agnoprotein include p53, Ku70, PP2A, YB-1, FEZ1, HP1α, α-SNAP, PCNA, and AP-3.
In some cases, the agnogene itself has functional significance, even if it cannot express agnoprotein. Deletion of the nucleotides in this region has been associated with a variant JC virus capable of infecting cell types not normally targeted by this virus. This variant has been associated with a disease recently described from case reports called JC virus encephalopathy, distinct from progressive multifocal leukoencephalopathy (PML), which has long been associated with JC in immunocompromised individuals.
== Evolution ==
Although agnoprotein is critical for proliferation in the polyomaviruses in which it occurs, its distribution among polyomaviruses whose genomes have been sequenced is patchy. It has been well studied in three viruses that infect mammalian hosts, including two human viruses – BK virus and JC virus – and the simian virus SV40; the BK, JC, and SV40 examples are by far the best-studied and have fairly high sequence conservation. Additional predicted agnogenes have been identified from the sequenced genomes of other polyomaviruses, and the predicted protein products vary considerably in length and have low sequence identity overall.
The distribution of agnoprotein among polyomaviruses has prompted speculation that there is little evolutionary selection pressure in favor of its presence. Among sequenced BK virus genomes, agnoprotein is the most variable viral protein in amino acid sequence. Differences in tissue tropism and in viral life cycle, particularly in viral exit from the host cell, have also been proposed as explanations for the presence or absence of agnoprotein in various human polyomaviruses.
== Avian polyomaviruses ==
A gene occurs in avian polyomaviruses in a similar genomic position and was originally annotated as an agnogene, but it has no detectable sequence similarity to the mammalian examples. The protein product of this gene has been detected in the capsids of mature virions, leading to its reclassification as VP4 to reflect its distinct role as a structural protein. However, it is still often referred to as "avian agnoprotein 1a".
== References == | Wikipedia/Agnoprotein |
A metalloproteinase, or metalloprotease, is any protease enzyme whose catalytic mechanism involves a metal. An example is ADAM12 which plays a significant role in the fusion of muscle cells during embryo development, in a process known as myogenesis.
Most metalloproteases require zinc, but some use cobalt. The metal ion is coordinated to the protein via three ligands. The ligands coordinating the metal ion can vary with histidine, glutamate, aspartate, lysine, and arginine. The fourth coordination position is taken up by a labile water molecule.
Treatment with chelating agents such as EDTA leads to complete inactivation. EDTA is a metal chelator that removes zinc, which is essential for activity. They are also inhibited by the chelator orthophenanthroline.
== Classification ==
There are two subgroups of metalloproteinases:
Exopeptidases, metalloexopeptidases (EC number: 3.4.17).
Endopeptidases, metalloendopeptidases (3.4.24). Well known metalloendopeptidases include ADAM proteins and matrix metalloproteinases, and M16 metalloproteinases such as Insulin Degrading Enzyme and Presequence Protease
In the MEROPS database peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In many instances, the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retained its function in protein recognition and binding.
Metalloproteases are the most diverse of the four main protease types, with more than 50 families classified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are histidine, glutamate, aspartate or lysine and at least one other residue is required for catalysis, which may play an electrophilic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases.
Metallopeptidases from family M48 are integral membrane proteins associated with the endoplasmic reticulum and Golgi, binding one zinc ion per subunit. These endopeptidases include CAAX prenyl protease 1, which proteolytically removes the C-terminal three residues of farnesylated proteins.
Metalloproteinase inhibitors are found in numerous marine organisms, including fish, cephalopods, mollusks, algae and bacteria.
Members of the M50 metallopeptidase family include: mammalian sterol-regulatory element binding protein (SREBP) site 2 protease and Escherichia coli protease EcfE, stage IV sporulation protein FB.
== See also ==
Matrix metalloproteinase
The Proteolysis Map
== References ==
== External links ==
The MEROPS online database for peptidases and their inhibitors: Metallo Peptidases Archived 2017-04-04 at the Wayback Machine
Metalloproteases at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
Proteopedia: Metalloproteases | Wikipedia/Metalloproteinase |
Duplodnaviria is a realm of viruses that includes all double-stranded DNA viruses that encode the HK97 fold major capsid protein. The HK97 fold major capsid protein (HK97 MCP) is the primary component of the viral capsid, which stores the viral deoxyribonucleic acid (DNA). Viruses in the realm also share a number of other characteristics, such as an icosahedral capsid, an opening in the capsid called a portal, a protease enzyme that empties the inside of the capsid prior to DNA packaging, and a terminase enzyme that packages viral DNA into the capsid. There are three groups of viruses in the realm: caudoviruses, herpesviruses, and the putative group mirusviruses.
Caudoviruses are one of the most abundant group of viruses on Earth and are ubiquitous worldwide. They infect prokaryotes and are a major cause of death in them, which contributes to the recycling of organic material in a process called viral shunt. Caudoviruses have been used as model organisms to study biological processes and as a form of therapy to treat bacterial infections. Herpesviruses infect animals and are commonly associated with diseases such as herpes and chickenpox. Mirusviruses infect microscopic eukaryotes and are among the most common eukaryotic viruses in sunlit oceans. Many duplodnavirians are able to enter a latent state in which they persist in cells without forming virions. This is called the lysogenic cycle and contrasts with the lytic cycle, which produces virions.
Duplodnaviria likely predates the last universal common ancestor (LUCA) of cellular life and was present in the LUCA. Caudoviruses in particular were likely already diverse by the time the LUCA emerged. Mirusviruses are related to viruses in the phylum Nucleocytoviricota in the realm Varidnaviria because they encode the core replication- and transcription-related proteins found in nucleocytoviruses. It is unclear, however, which realm these genes originate from. In any case, herpesviruses appear to have lost most of these genes through reductive evolution. Outside of the realm, an HK97-like fold is only found in encapsulins, which form nanocompartments in prokaryotes and are likely derived from duplodnaviruses.
== Classification ==
Duplodnaviria contains one kingdom, which is divided into two phyla that contain two lineages of viruses in the realm: caudoviruses and herpesviruses. This taxonomy can be visualized as follows:
Realm: Duplodnaviria
Kingdom: Heunggongvirae
Phylum: Peploviricota
Class: Herviviricetes
Order: Herpesvirales – herpesviruses, which infect animals (eukaryotes)
Phylum: Uroviricota
Class: Caudoviricetes – caudoviruses, also called head-tail viruses and tailed viruses, which infect archaea and bacteria (prokaryotes)
The realm also contains mirusviruses, which have not been assigned to any taxon officially but which constitute the putative phylum Mirusviricota. As all viruses in the realm are double-stranded DNA (dsDNA) viruses, the realm belongs to Group I: dsDNA viruses of Baltimore classification, a classification system based on a virus's manner of messenger RNA (mRNA) production that is often used alongside standard virus taxonomy, which is based on evolutionary history. Realms are the highest level of taxonomy used for viruses and Duplodnaviria is one of seven. The others are Adnaviria, Monodnaviria, Riboviria, Ribozyviria, Singelaviria, and Varidnaviria.
== Core characteristics ==
All viruses in Duplodnaviria contain an icosahedral capsid that is composed of a major capsid protein (MCP) that contains a unique folded structure, called the HK97 fold, named after the folded structure of the MCP of the bacterial virus HK97. The conserved elements of the HK97 fold, found in all duplodnavirians, are the axial (A) domain, the peripheral (P) domain, the extended (E) loop, and the N-terminal (N) arm. Many MCPs contain additional elements, such as the insertion (I) domain, which is grafted onto the A-domain, and the glycine-rich (G) loop, found in bacteriophage HK97's MCP. Other hallmark traits among viruses in the realm involve the structure and assembly of capsids and include a portal protein that forms the opening of the capsid, a protease that empties the capsid before viral DNA is packaged, and a terminase enzyme that packages viral DNA into the capsid. In herpesviruses, their proteases are often referred to as assemblins.
After HK97 MCPs have been synthesized by the host cell's ribosomes, the viral capsid is assembled from them with the proteins bonding to each other. The first product of capsid assembly is a procapsid, also called prohead for caudoviruses. Procapsids are roughly spherical, lumpy, and thick. Assembly of procapsids is driven by scaffold proteins that guide the geometric construction of the procapsid. In the absence of such proteins, the delta domain of the MCP, which faces toward the inside of the capsid, acts as a scaffold protein. A cylindrical opening the capsid, the portal, that serves as the entrance and exit for viral DNA is created with portal proteins at one of the 12 vertices of the capsid. After capsid assembly, scaffold proteins are removed from the inside of the capsid by the capsid maturation protease, which may be part of the scaffolding. Scaffold proteins may be removed intact or after the protease breaks them down in a process called proteolysis, either of which leaves the inside of the procapsid empty.
At the same time as capsid assembly, replication of viral DNA occurs, and long molecules of DNA containing numerous copies of the viral genome, called concatemers, are created. The enzyme terminase, made of two subunits (large and small), finds the viral DNA inside of the cell via the small subunit, cuts the concatemers, and creates the endings (termini) of the genomes. Terminase recognizes a packaging signal in the genome and cuts the nucleic acid, creating a free end that it binds to. The terminase, now bound to the concatemer, attaches itself to the capsid portal and begins translocating the DNA from outside the capsid to the inside, using energy generated from ATP hydrolysis by its large subunit. As more DNA is inserted into the capsid, the capsid expands in size, becomes thinner, and its surface becomes flatter and more angular. Once the genome is completely inside, terminase cuts the concatemer again, completing packaging. Terminase then detaches itself from the portal and proceeds to repeat this process until all genomes in the concatemer have been packaged into capsids.
For caudoviruses, the capsid is called the "head" of the complete virus particle and the rest of the virion is called the "tail". Caudoviruses sometimes have decoration proteins that attach to the capsid's surface to reinforance its structure. The tail, which is used for attaching to cells and injecting viral DNA into them, is assembled separately from the capsid and attached at the portal after DNA packaging. Caudoviruses have three types of tails and are informally referred to by which type of tail they have: short, non-contractile tails (podoviruses), long, contractile tails (myoviruses), and long, non-contractile, flexible tails (siphoviruses). After the virion is fully assembled, it leaves the cell. Caudoviruses leave the cell via rupturing of the cell membrane (lysis), which causes cell death. Herpesviruses leave via exocytosis after obtaining an envelope that covers the capsid from cellular vesicles from the Golgi apparatus.
== Distribution ==
Caudoviruses are one of the most abundant groups of viruses on Earth and are the most numerous viruses in prokaryotes. They can be found in a wide variety of environments, including geothermal, hypersaline, soil, marine, and moderate ecosystems, as well as in the human body. In certain environments, however, they may be outnumbered by other viruses, such as tectiliviricetes in marine environments and ssDNA viruses in offshore sediments. Archaeal caudoviruses transfer biomes recurrently via host-switching, including transfering between anoxic, hypersaline, and marine environments. Archaeal caudoviruses adapted to hypersaline environments become inactivated when removed from the environment but reactivate when reintroduced, indicating that they depend on high salinity.
Mirusviruses have been identified in most major lineages of eukaryotes, both unicellular and multicellular, including eukaryotes in saltwater, freshwater, soil, as well as in parasites of animals and plants. They commonly infect marine eukaryotic plankton and are among the most abundant eukaryotic viruses in sunlit oceans. They are especially common in the euphotic subsurface layer where chlorophyll concentrations are high. Different mirusviruses are found in different regions; for example, some are found exclusively in the Arctic Ocean. At Lake Biwa in Japan, a freshwater lake, they are among the most abundant viruses in the epilimnion zone of the lake during seasonal algal blooms and are also present in the hypolimnion zone. Most can be described as specific to either the epilimnion, where their presence tended to be transient, or the hypolimnion, where their presence was more persistent.
== Phylogenetics ==
The main scaffold of the HK97 fold MCP appears to have been created from a DUF1884 protein family domain that was inserted into a strand-helix-strand-strand (SHS2) fold protein related to the dodecin protein family. The emergence of duplodnavirians likely came before the last universal common ancestor (LUCA) of cellular life existed, and viruses in the realm likely infected the LUCA. Caudoviruses in particular likely had already diversified and obtained their three morphological types by the time the LUCA emerged. Outside of Duplodnaviria, an HK97-like fold is only found in encapsulins, proteins that form a type of prokaryotic nanocompartment that encapsulates a variety of cargo proteins related to the oxidative stress response. Encapsulins assemble into icosahedrons like the capsids of duplodnaviruses, but the HK97 MCP in viruses is much more divergent and widespread than encapsulins, which form a narrow monophyletic clade. As such, it is more likely that encapsulins are derived from viruses than vice versa. Archaea of the phylum Thermoproteota (formerly Crenarchaeota), however, contain encapsulins but are not known to be infected by caudoviruses, so the relation between encapsulins and Duplodnaviria remains unresolved.
The ATPase subunit of Duplodnaviria terminases that generates energy for packaging viral DNA has the same general structural design of the P-loop fold as the packaging ATPases of viruses in the realm Varidnaviria but are otherwise not directly related to each other. While viruses in Duplodnaviria make use of the HK97 fold for their major capsid proteins, the major capsid proteins of viruses in Varidnaviria instead are marked by double vertical jelly roll folds. The duplodnavirian ATPase likely represents an ancient acquisition shortly after the ancestors of duplodnavirians obtained capsids. The ATPase is distantly related to superfamily 2 helicases and contains an additional RNAse H-fold nuclease domain. Exaptation of this protein involved significant change to the protein, including fusion of the ATPase and nuclease domains.
Mirusviruses contain the hallmark structural genes of Duplodnaviria but also encode the replication and transcription (i.e. "informational") proteins of the Varidnaviria phylum Nucleocytoviricota, indicative of some form of evolutionary relationship between the two groups of viruses. Three possible scenarios have been proposed: a nucleocytovirus had its structural genes replaced with those of Duplodnaviria, the ancestors of mirusviruses inherited their informational proteins the ancestors of nucleocytoviruses, or vice versa. In the third scenario, the ancestors of caudoviruses may have had the informational genes, but they may have been replaced with another group of genes in the caudovirus lineage. The transfer of such genes to varidnavirians may explain the evolutionary leap from "simple" varidnavirians to highly complex nucleocytoviruses. In any case, herpesviruses are thought to have lost most of the informational genes through reductive evolution.
Mirusviruses have been found to integrate their genomes in their hosts and form episomes. Their episomal and integrate forms resemble the episomal and endogenous latent forms of herpesviruses. Furthermore, mirusviruses and herpesviruses have a tower domain inserted in the A subdomain of the HK97 fold that projects away from the surface of assembled capsids. The tower domain of mirusviruses is smaller than the tower domain of herpesviruses. Additionally, animals emerged after unicellular eukaryotes. For these reasons, mirusviruses may more closely resemble the ancestral state of eukaryotic duplodnavirians than herpesviruses, which would have underone reductive evolution and specialized to infecting animal cells. Although mirusviruses likely emerged before herpesviruses, their exact point of origin is unknown.
== Interactions with hosts ==
=== Latency ===
Viruses in Duplodnaviria have two different types of replication cycles: the lytic cycle, whereby infection leads directly to virion formation and exit from the host cell, and the lysogenic cycle, whereby a latent infection retains the viral DNA inside of the host cell without virion formation, either as an episome or via integration into the host cell's DNA, with the possibility of converting to the lytic cycle in the future. Viruses that can replicate through the lysogenic cycle are called temperate or lysogenic viruses. Caudoviruses vary in their temperateness, whereas all herpesviruses are temperate and able to avoid detection by the host's immune system and cause lifelong infections. Mirusviruses also appear to be capable of a lysogenic life cycle as they, like herpesviruses, are able to integrate their genome into the host cell's genome and form extra-chromosomal episomes.
=== Disease ===
Herpesviruses are associated with a wide range of diseases in their hosts, including a respiratory tract illness in chickens, a respiratory and reproductive illness in cattle, and tumors in sea turtles. In humans, herpesviruses usually cause various epithelial diseases such as herpes simplex, chickenpox, shingles, and Kaposi's sarcoma. Initial infection causes acute symptoms and leads to lifelong infection via latency. Herpesviruses may emerge from their latency to cause illnesses, which may have severe symptoms such as encephalitis and pneumonia.
=== Viral shunt ===
Caudoviruses are ubiquitous worldwide and are a major cause of death among prokaryotes. Infection may lead to cell death via lysis, the rupturing of the cell membrane. As a result of lysis, organic material from the killed prokaryotes is released into the environment, contributing to a process called viral shunt. Caudoviruses shunt nutrients from organic material away from higher trophic levels so that they can be consumed by organisms in lower trophic levels, which has the effects of recycling nutrients and promoting increased diversity among marine life.
== History ==
Caudoviruses were discovered independently by Frederick Twort in 1915 and Félix d'Hérelle in 1917, and they have been the focus of much research since then. Some have been used as model organisms to study various biological processes. For example, bacteriophage lambda has been used to study gene regulation and the lytic and lysogenic cycles. d'Hérelle envisioned bacteriophages as a way to treat bacterial infections and he first used caudoviruses to treat bacterial infections in 1919. Phage therapy was subsequently used extensively to treat bacterial infections in animals and humans. In the 1940s, phage therapy fell out of use due to the invention of penicillin and other antibiotics, but the emergence of drug-resistant bacteria and a decline in the number of novel antibiotics being invented has sparked renewed interest in using lytic caudoviruses to treat bacterial infections. In the late 1990s, HK97 became the first bacteriophage to have its capsid structure solved.
Diseases in humans caused by herpesviruses have been recognized for much of recorded history, and person-to-person transmission of the herpes simplex virus, the first herpesvirus discovered, was first recognized in 1893 by Émile Vidal. Over time, caudoviruses and herpesviruses were increasingly found to share many characteristics, and their genetic relation was formalized with the establishment of Duplodnaviria in 2019. Caudoviruses were originally classified into three families based on their morphology: Podoviridae, which have short, non-contractile tails; Myoviridae, which have long, contractile tails; and Siphoviridae, which have long, non-contractile, flexible tails. Since the early 2000s, genetic analysis has revealed a high level of diversity among caudoviruses, and the traditional system of morphology-based classification has been replaced with genetics-based classification starting in the late 2010s.
The first possible identification of a mirusvirus was made in thraustochytrids in 1972, but they couldn't be studied further due to the limitations of the methods used at that time. They were officially discovered in 2023 via metagenomic analysis of saltwater biome samples taken from Tara expedition sampling locations throughout the world. A year later, a genetically distinct group of mirusviruses were found in Lake Biwa in Japan, a freshwater lake, and metagenomic testing identified them in most major lineages of eukaryotes. Mirusvirus virions have not been isolated yet, but based on the proteins encoded by them, they are predicted to form capsids resembling those of caudoviruses and herpesviruses.
=== Etymology ===
The name Duplodnaviria is a portmanteau of duplo, the Latin word for double, dna, from deoxyribonucleic acid (DNA), which refers to all members of the realm having double-stranded DNA genomes, and -viria, which is the suffix used for virus realms. Duplodnaviria is monotypic with only one kingdom, Heunggongvirae, so both the realm and kingdom have the same definition. Heunggongvirae takes the first part of its name from Cantonese 香港 [Hēunggóng], meaning and approximately pronounced "Hong Kong", which is a reference to bacteriophage HK97 (Hong Kong 97), the namesake of the HK97 fold, and the suffix -virae, which is the suffix used for virus kingdoms.
== See also ==
List of higher virus taxa
== References ==
== Further reading ==
Ward CW (1993). "Progress towards a higher taxonomy of viruses". Research in Virology. 144 (6): 419–53. doi:10.1016/S0923-2516(06)80059-2. PMC 7135741. PMID 8140287. | Wikipedia/Duplodnaviria |
Infected cell protein 34.5 (ICP-34.5, ICP34.5) is a protein expressed by the γ34.5 gene in viruses such as herpes simplex virus; it blocks a cellular stress response to viral infection. It shares the C-terminal regulatory domain (InterPro: IPR019523) with protein phosphatase 1 subunit 15A/B.
When a cell is infected with a virus, protein kinase R is activated by the virus' double-stranded DNA,. Protein kinase R then phosphorylates a protein called eukaryotic initiation factor-2A (eIF-2A), which inactivates eIF-2A. EIF-2A is required for translation so by shutting down eIF-2A, the cell prevents the virus from hijacking its own protein-making machinery. Viruses in turn evolved ICP34.5 to defeat the defense; it activates protein phosphatase-1A which dephosphorylates eIF-2A, allowing translation to occur again. A herpesvirus lacking the γ34.5 gene will not be able to replicate in normal cells because it cannot make proteins.
The ICP34.5 deletion is useful for the construction of oncolytic herpes viruses, as cancer cells do not restrict replication as strongly.
== See also ==
Viral nonstructural protein
== References == | Wikipedia/Infected_cell_protein_34.5 |
Nonstructural protein 2 (NS2) is a viral protein found in the hepatitis C virus. It is also produced by influenza viruses, and is alternatively known as the nuclear export protein (NEP).
== Role in Hepatitis C virus ==
NS2 is one of seven nonstructural proteins in HCV, with each being encoded near the carboxy-terminal end of the positive-strand RNA virus. Once translated it is 217 amino acids in length and has a molecular weight of approximately 23 kDa. NS2 possesses a hydrophobic amino-terminal subdomain as well as a carboxy-terminal cytoplasmic domain, with the amino-terminal subdomain containing up to three putative transmembrane segments.
NS2 proteins are post-translationally processed by the HPV-encoded cysteine protease NS2-3, which is formed by residues 94-217 of NS2 itself as well as residues 1-181 of nonstructural protein 3 (NS3). The NS2-3 autoprotease acts by making a single cleavage between the junction of NS2 and NS3. While the NS2 protein itself is unnecessary for replication of the HCV virus (as demonstrated by HPV replicons that were able to self-replicate after removal of the entire C to NS2 coding region), this cleavage of the NS2/NS3 junction is critical.
Despite being dispensable in the replication of HCV, NS2 does play an important role in the production of new HCV particles. Multiple studies have shown that the full NS2 RNA sequence (and thus protein) is necessary for viral assembly. While it is somewhat uncertain as to why this is, one group demonstrated that viral particle production in HPV chimeras was most efficient when the chimeric fusions were conducted directly downstream of the first transmembrane domain of NS2. This discovery implies that the first transmembrane segment of NS2’s hydrophobic amino-terminal subdomain physically interacts with upstream structural components of the HPV sequence. Its structure is indeed highly conserved between HCV genotypes, with a flexible helix in residues 3-11 and an alpha helix in residues 12-21. A subsequent implication is that the carboxy-terminal domain – which is also home to the proteasome region of NS2 – are not important in particle production. This theory is corroborated by evidence that mutations in the NS2 protease region do not effect virus production.
Additional research shows that NS2 is involved in HPV particle production. It has been determined that the substitution of one highly conserved NS2 residue, Ser-168, with either Alanine or Glycine results in impaired virus production but not impaired RNA replication. Impairment or elimination of particle production was determined via the number of infectious HPV particles released by transfected cells post-genome mutation. This result further demonstrates that NS2 is critical for viral assembly but not viral RNA replication (which is, however, influenced by cleavage of the NS2/NS3 junction as discussed previously). Furthermore, that same study theorized that the mutation of Ser-168 affects viral assembly in terms of release: assembled NS2 mutants were unable to exit the cell (and were thus not infectious), suggesting that NS2’s importance lies in the very late stages of assembly.
== Role in the inhibition of apoptosis ==
NS2 is an inhibitor of liver cell apoptosis. The viral protein interacts with CIDE-B, a liver-specific pro-apoptotic protein whose carboxy-terminal killing domain induces cell death activity. The binding specificity is strong enough to counteract CIDE-B’s induced release of mitochondrial cytochrome c, as demonstrated by single deletion mutations that result in a loss of interference. This activity has been interpreted as an important strategy for the survival of HCV in host cells.
== See also ==
NS1 influenza protein
== References == | Wikipedia/Hepatitis_C_virus_nonstructural_protein_2 |
A viral structural protein is a viral protein that is a structural component of the mature virus.
Examples include the SARS coronavirus 3a and 7a accessory proteins.
== Bacteriophage T4 structural proteins ==
During assembly of the bacteriophage (phage) T4 virion, the structural proteins encoded by the phage genes interact with each other in a characteristic sequence. Maintaining an appropriate balance in the amounts of each of these structural proteins produced during viral infection appears to be critical for normal phage T4 morphogenesis. Phage T4 encoded proteins that determine virion structure include major structural components, minor structural components and non-structural proteins that catalyze specific steps in the morphogenesis sequence. Phage T4 morphogenesis is divided into three independent pathways: the head, the tail and the long tail fibres as detailed by Yap and Rossman.
== See also ==
Viral nonstructural protein
== References == | Wikipedia/Viral_structural_protein |
The NS1 influenza protein (NS1) is a viral nonstructural protein encoded by the NS gene segments of type A, B and C influenza viruses. Also encoded by this segment is the nuclear export protein (NEP), formerly referred to as NS2 protein, which mediates the export of influenza virus ribonucleoprotein (RNP) complexes from the nucleus into the cytoplasm, where they are assembled.
== Characteristics ==
The NS1 of influenza A virus is a 26,000 Dalton protein. It prevents polyadenylation of cellular mRNAs to circumvent antiviral responses of the host, e.g., maturation and translation of interferon mRNAs. NS1 might also inhibit splicing of pre-mRNA by binding to a stem-bulge region in U6 small nuclear RNA (snRNA). In addition, NS1 is probably able to suppress the interferon response in the virus-infected cell leading to unimpaired virus production.
NS1 also binds dsRNA. Binding assays with NS1 protein mutants established that the RNA-binding domain of the NS1 protein is required for binding to dsRNA as well as for binding to polyA and U6 snRNA. In addition, dsRNA competed with U6 snRNA for binding to the NS1 protein, a result consistent with both RNAs sharing the same binding site on the protein. As a consequence of its binding to dsRNA, the NS1 protein blocks the activation of the dsRNA-activated protein kinase (PKR) in vitro. This kinase phosphorylates the alpha subunit of eukaryotic translation initiation factor 2 (elF-2 alpha), leading to a decrease in the rate of initiation of translation. In the absence of NS1, this pathway is inhibited during anti-viral response to halt all protein translation – thus stopping the synthesis of viral proteins; however, the influenza virus' NS1 protein is an agent that circumvents host defenses to allows viral gene transcription to occur.
The NS1 protein can be divided into an N terminal (RNA binding) domain and C terminal (effector domain). The RNA binding domain is able to target RIG-I, and therefore prevent the activation of induction of interferon responses. At the effector domain, it interacts and inhibits cleavage and polyadenylation specificity factor (CPSF30). CPSF30 is part of processing pathway for cellular mRNAs, and its inhibition leads to inability of the cellular mRNA to be exported outside the nucleus for translation, thereby hindering the ability of host cell to produce Interferon-stimulated genes.
== Avian ==
The NS1 protein of the highly pathogenic avian H5N1 viruses circulating in poultry and waterfowl in Southeast Asia is currently believed to be responsible for the enhanced virulence of the strain. H5N1 NS1 is characterized by a single amino acid change at position 92. By changing the amino acid from glutamic acid to aspartic acid, researchers were able to annul the effect of the H5N1 NS1. This single amino acid change in the NS1 gene greatly increased the pathogenicity of the H5N1 influenza virus. However, the effect of residue 92 on the function of H5N1 NS1 appears to be questionable as noted by Nature Medicine editors: The above paper originally reported that H5N1 viruses are resistant to interferon in the SJPL cell line. The editors wish to alert our readers about three facts that may affect this conclusion. First, Ngunjiri et al. have recently found that aliquots of the SJPL cell line obtained from the American Type Culture Collection were heavily contaminated with mycoplasma. Although the mycoplasma status of the cells used in the original paper is unknown, it is not possible to rule out that they were contaminated. Second, SJPL cells were originally reported to be of porcine origin, but a recent analysis has indicated that they are of simian origin. Third, Ngunjiri et al. have found H5N1 viruses to be sensitive to interferons in all cell lines tested from multiple species.
== Pathogenicity ==
The fact that NS1 is involved in the pathogenicity of influenza A viruses makes it a good target to attenuate these viruses. Several studies demonstrated that influenza viruses with partial deletions in NS1 proteins are attenuated and do not cause disease, but induce a protective immune response in different species including mice, pigs, horses, birds and macaques. Although it had been known for more than a decade that influenza viruses with partial deletions in NS1 proteins were attenuated, all but one NS1 truncation variants of influenza A viruses were generated by in vitro mutagenesis. Wang et al. later demonstrated that the naturally truncated variant had propensity to generate new variants when passaged in ovo. Remarkably, the new variants were excellent live-attenuated influenza vaccine candidates. The ability to attenuate influenza viruses by truncation of the NS1 protein presents a novel approach in design and development of the next generation live-attenuated influenza vaccines for both poultry and humans.
== See also ==
H5N1 genetic structure
== References ==
== External links ==
NCBI Flu Genome Database | Wikipedia/NS1_influenza_protein |
The Early 35 kDa protein, or P35 in short, is a baculoviral protein that inhibits apoptosis in the cells infected by the virus. Although baculoviruses infect only invertebrates in nature, ectopic expression of P35 in vertebrate animals and cells also results in inhibition of apoptosis, thus indicating a universal mechanism. P35 has been shown to be a caspase inhibitor with a very wide spectrum of activity both in regard to inhibited caspase types and to species in which the mechanism is conserved.
== Species distribution ==
P35 has been found in different strains of the nuclear polyhedrosis virus, a species of baculovirus that infects insects. Two orthologs of P35 that have been studied in detail are the ones from the Autographa californica multicapsid nuclear polyhedrosis virus (AcMNPV) and from the Bombyx mori nuclear polyhedrosis virus (BmNPV). The P35 ortholog from AcMNPV was found to block apoptosis in mammalian cells much more efficiently as compared to the ortholog from BmNPV.
== Function ==
The P35 protein inhibits apoptosis by acting as a competitive, irreversible inhibitor of caspases. P35 first serves as a caspase substrate and is cleaved between the amino acids D87 and G88, i.e. after the sequence DQMD in P35 from AcMNPV and after the sequence DKID in P35 from BmNPV, resulting in two polypeptide products of about 10 kDa and 25 kDa in size. The cleavage site is situated in a solvent-exposed loop that extends from the protein's beta sheet core, thus ensuring good accessibility to the caspase. However, unlike other caspase substrate proteins, the fragments of P35 do not dissociate from the caspase after cleavage. Instead, the N-terminal, 10 kDa cleavage fragment remains bound to the caspase by a covalent, stable thioester bond between the cleavage residue D87 of P35 and the cysteine residue at the active site of the caspase.
While the formation of a thioester intermediate between the aspartate of the substrate's recognition site and the cysteine of the caspase's active site is a normal event in caspase-mediated protein cleavage, the resulting bond is normally quickly hydrolysed so that the cleaved products can detach. In the case of P35, however, the caspase-substrate complex remains stable. Cleavage of P35 triggers rapid conformational changes that reposition its N-terminus, which is normally buried in the protein's beta-sheet core, to the caspase's active site. As a consequence of this rearrangement, the N-terminal P35 residues C2 and V3 interact with the caspase's active site to displace water and prevent the hydrolysis reaction. The P35 residue C2 competes with the caspase's active site cysteine residue for binding of the P35 residue D87, keeping the reaction trapped in an equilibrium state.
== Interactions ==
In insect cells, P35 inhibits an enzyme called Sf caspase-1, which was identified as a structural and functional ortholog of human CASP3 (CPP32) and CASP7 (MCH3). Studies using purified human caspases in vitro found that the protein is able to also inhibit several of these, including CASP1, CASP3, CASP6, CASP7, CASP8, and CASP10.
== Clinical significance ==
Since baculoviridae infect only insects and not humans, the function of P35 in the immune evasion of infected cells is not clinically relevant. However, P35 has been considered as a potential tool in gene therapy to suppress apoptosis where it is not wanted, such as in the protection of transplanted tissue from immune rejection or in the killing of bystander cells in cancer therapy; such methods are still far from clinical application though.
== History and discovery ==
The role of P35 in the inhibition of apoptosis was first described by Rollie J. Clem in the research group of Lois K. Miller at the Department of Genetics at the University of Georgia in 1991. Four years later, in 1995, the reason for apoptosis inhibition by P35 was identified as its ability to bind and inhibit caspases (then still called ICE homologs) by Nancy J. Bump and co-workers at the BASF Bioresearch Corporation in Worcester, Massachusetts. The mechanism of caspase inhibition was discovered by Guozhou Xu in the team of Hao Wu at the Department of Biochemistry at Weill Cornell Medical College in 2001.
== References == | Wikipedia/Early_35_kDa_protein |
The classification of viral proteins as early proteins or late proteins depends on their relationship with genome replication. While many viruses (such as HIV)[1] are described as expressing early and late proteins, this definition of these terms is commonly reserved for class I DNA viruses. (HIV has two stages of protein expression but these are not as a result of two stages of transcription surrounding replication but by the production of the Rev protein which is required for the export of the transcripts of the second set of proteins transcribed form the cell nucleus.)
Early proteins are those produced following entry into the host cell but prior to replication. The expression of early genes, commonly encoding non-structural proteins, initiates replication of the genome and expression of late genes.
In some, simpler viruses, this pattern of expression is clearly defined, while in those with more complex genomes, such as the herpesviruses, these expression periods overlap.
== Examples ==
An example of early gene expression is the expression of the small, middle and large T antigen encoded by the polyomavirus. The middle T antigen is not required for replication and it acts to enhance transcription by binding host proteins which interact with the late promoter. On the other hand, the large T antigen is required and it acts to initiate replication directly. It binds the viral origin of replication and recruits DNA polymerase and s/s DNA-binding protein such that once its concentration is great enough it blocks the transcription of early genes and initiates genome replication. It also acts to cause the entry of the host cell into S phase.
=== Bacteriophage T4 ===
Bacteriophage T4 is a virus that infects the bacterium E. coli. Bacteriophage T4 genes are conventionally classified as early function genes or late function genes based on the time period in which their protein products are expressed during the course of bacteriophage infection. In general, the early proteins produced by early function genes act catalytically to promote bacteriophage genome specific DNA replication and repair as well as to facilitate modification of the host nucleotide pool to accommodate these functions. The late function genes code for late proteins that are involved in morphogenesis of the bacteriophage virion, particularly non-enzymatic proteins that comprise the structural components of the virus itself, but also some catalytic proteins that facilitate this morphogenetic assembly process.
== References == | Wikipedia/Early_protein |
The Matrix-2 (M2) protein is a proton-selective viroporin, integral in the viral envelope of the influenza A virus. The channel itself is a homotetramer (consists of four identical M2 units), where the units are helices stabilized by two disulfide bonds, and is activated by low pH. The M2 protein is encoded on the seventh RNA segment together with the M1 protein. Proton conductance by the M2 protein in influenza A is essential for viral replication.
Influenza B and C viruses encode proteins with similar function dubbed "BM2" and "CM2" respectively. They share little similarity with M2 at the sequence level, despite a similar overall structure and mechanism.
== Structure ==
In influenza A virus, M2 protein unit consists of three protein segments comprising 97 amino acid residues: (i) an extracellular N-terminal domain (residues 1–23); (ii) a transmembrane segment (TMS) (residues 24–46); (iii) an intracellular C-terminal domain (residues 47–97). The TMS forms the pore of the ion channel. The important residues are the imidazole of His37 (pH sensor) and the indole of Trp41 (gate). This domain is the target of the anti influenza drugs, amantadine and its ethyl derivative rimantadine, and probably also the methyl derivative of rimantadine, adapromine. The first 17 residues of the M2 cytoplasmic tail form a highly conserved amphipathic helix.
The amphipathic helix residues (46–62) within the cytoplasmic tail play role in virus budding and assembly. The influenza virus utilizes these amphipathic helices in M2 to alter membrane curvature at the budding neck of the virus in a cholesterol dependent manner. The residues 70–77 of cytoplasmic tail are important for binding to M1 and for the efficient production of infectious virus particles. This region also contains a caveolin binding domain (CBD). The C-terminal end of the channel extends into a loop (residues 47–50) that connects the trans membrane domain to the C-terminal amphipathic helix. (46–62). Two different high-resolution structures of truncated forms of M2 have been reported: the crystal structure of a mutated form of the M2 transmembrane region (residues 22–46), as well as a longer version of the protein (residues 18–60) containing the transmembrane region and a segment of the C-terminal domain as studied by nuclear magnetic resonance (NMR).
The two structures also suggest different binding sites for the adamantane class of anti-influenza drugs. According to the low pH crystal structure a single molecule of amantadine binds in the middle of the pore, surrounded by residues Val27, Ala30, Ser31 and Gly34. In contrast, the NMR structure showed four rimantadine molecules bind to the lipid facing outer surface of the pore, interacting with residues Asp44 and Arg45. However, a recent solid state NMR spectroscopy structure shows that the M2 channel has two binding sites for amantadine, one high affinity site is in the N terminal lumen, and a second low affinity site on the C terminal protein surface.
== Proton conductance and selectivity ==
The M2 ion channel of both influenza A is highly selective for protons. The channel is activated by low pH and has a low conductance. Histidine residues at position 37 (His37) are responsible for this proton selectivity and pH modulation. When His37 is replaced with glycine, alanine, glutamic acid, serine or threonine, the proton selective activity is lost and the mutant can transport Na+ and K+ ions also. When imidazole buffer is added to cells expressing mutant proteins, the ion selectivity is partially rescued.
Acharya et al. suggested that the conduction mechanism involves the exchange of protons between the His37 imidazole moieties of M2 and waters confined to the M2 bundle interior. Water molecules within the pore form hydrogen-bonded networks or 'water wires' from the channel entrance to His37. Pore-lining carbonyl groups are well situated to stabilize hydronium ions via second-shell interactions involving bridging water molecules. A collective switch of hydrogen bond orientations may contribute to the directionality of proton flux as His37 is dynamically protonated and deprotonated in the conduction cycle. The His37 residues form a box-like structure, bounded on either side by water clusters with well-ordered oxygen atoms near by. The conformation of the protein, which is intermediate between structures previously solved at higher and lower pH, suggests a mechanism by which conformational changes might facilitate asymmetric diffusion through the channel in the presence of a proton gradient. Moreover, protons diffusing through the channel need not be localized to a single His37 imidazole, but instead may be delocalized over the entire His-box and associated water clusters.
== Function ==
The M2 channel protein is an essential component of the viral envelope because of its ability to form a highly selective, pH-regulated, proton-conducting channel. The M2 proton channel maintains pH across the viral envelope during cell entry and across the trans-Golgi membrane of infected cells during viral maturation. As virus enters the host cell by receptor-mediated endocytosis, endosomal acidification occurs. This low pH activates the M2 channel, which brings protons into the virion core. Acidification of virus interior leads to weakening of electrostatic interaction and leads to dissociation between M1 and viral ribonucleoprotein (RNP) complexes. Subsequent membrane fusion releases the uncoated RNPs into the cytoplasm which is imported to the nucleus to start viral replication.
After its synthesis within the infected host cell, M2 is inserted into the endoplasmic reticulum (ER) and transported to the cell surface via trans-Golgi network (TGN). Within the acidic TGN, M2 transports H+ ions out of the lumen, and maintains hemagglutinin (HA) metastable configuration. At its TGN localization, M2 protein's ion channel activity has been shown to effectively activate the NLRP3 inflammasome pathway.
Other important functions of M2 are its role in formation of filamentous strains of influenza, membrane scission and the release of the budding virion. M2 stabilizes the virus budding site, and mutations of M2 that prevent its binding to M1 can impair filament formation at the site of budding.
=== Transport reaction ===
The generalized transport reaction catalyzed by the M2 channel is:
H+ (out) ⇌ H+ (in)
== Inhibition and resistance ==
The anti-influenza virus drug, amantadine, is a specific blocker of the M2 H+ channel. The drug binds in and occludes the central pore. In the presence of amantadine, viral uncoating and disassembly is incomplete. Mutations conferring resistance to adamantane drugs, including amantadine and rimantadine, occur in the transmembrane region and are widespread. The large majority of resistant viruses carry the S31N mutation. Resistance to adamantanes among circulating influenza A viruses varies by region but has globally increased significantly since the early 2000s. The US CDC has released information stating that most circulating strains are now resistant to the two drugs available, and as of June 2021, their use is not recommended.
== Influenza B and C M2 proteins ==
Influenza B and C viruses encode virion proteins with similar proton-transducing function dubbed "BM2" and "CM2" respectively. They share little similarity with M2 at the sequence level, despite a similar overall structure and mechanism.
=== BM2 ===
The M2 protein of influenza B is 109 residue long, homo-tetramer and is a functional homolog of influenza A protein. There is almost no sequence homology between influenza AM2 and BM2 except for the HXXXW sequence motif in the TMS that is essential for channel function. Its proton conductance pH profile is similar to that of AM2. However, the BM2 channel activity is higher than that of AM2, and the BM2 activity is completely insensitive to amantadine and rimantadine. The structure of the influenza B channel at resolutions of 1.4–1.5 Å, published in 2020, revealed that the channel opening mechanism is different from that of the influenza A channel.
=== CM2 ===
CM2 may play a role in genome packaging in virions. CM2 adjusts intracellular pH, and is able to replace influenza A M2 in this capacity.
== See also ==
H5N1 genetic structure
== References ==
== External links ==
M2+protein,+Influenza+A+virus at the U.S. National Library of Medicine Medical Subject Headings (MeSH) | Wikipedia/M2_protein |
B13R (sometimes called SPI-2) is a protein expressed by vaccinia virus.
Vaccinia virus is member of Orthopoxvirus family. These viruses contain approximately 200 genes in their genome. About one third of the genome is not necessary for the viral replication itself. These viral products interfere with the host immune response. SPI-2 is one of these immunomodulatory factors.
SPI-2 is a nonglycosylated peptide with size of 38,5 kDa. It is expressed in an early phase of infection. The initiation site for transcription was identified about 72 nucleotides upstream from the open reading frame. The translated protein stays in the cytoplasm of the host cell. SPI-2 shares 92% of its amino acid sequence with the cowpox virus modifier of the cytokine response – known as crmA.
SPI-2 belongs in superfamily of the inhibitors of serine proteases (serpins). Serpins are the most broadly distributed family of inhibitors of proteases. They were identified in all multicellular eukaryotic organisms. In mammals serpins are secreted in plasma where they serve as inhibitors of proteases involved in blood coagulation, inflammation and complement activation.
SPI-2 inhibits processing of an inactive precursor of interleukin-1β (pro-IL-1β) to active form of this cytokine. It does so by binding to caspase 1 (or ICE – interleukin-1 converting enzyme) which is under normal circumstances activated by the formation of inflammasome. SPI-2 expression also inhibits the apoptotic pathway activated by Fas-ligand and TNFα.
Deletion of SPI-2 leads to virus attenuation in vivo (observed in mice model after intranasal infection) but without any remarkable influence on the host immune response. That was one of the reasons this gene was targeted during search for more safe and efficient vaccine against smallpox. It was shown that immunization with vaccinia virus with deleted SPI-2 and 1 and coexpressing IFNγ leads to strong attenuation but without decreasing host immune response. Host reaction was comparable to that on MVA virus (modified virus Ankara) which serves as a smallpox vaccine nowadays. The Copenhagen strain of vaccinia virus only has a truncated version of this protein.
Vaccinia virus encodes two more serpin - SPI-1 and SPI-3. SPI-1 influences the host range and SPI-3 stops infected cells from fusing together.
== References == | Wikipedia/B13R_(virus_protein) |
Envelope glycoprotein GP120 (or gp120) is a glycoprotein exposed on the surface of the HIV envelope. It was discovered by Professors Tun-Hou Lee and Myron "Max" Essex of the Harvard School of Public Health in 1984. The 120 in its name comes from its molecular weight of 120 kDa. Gp120 is essential for virus entry into cells as it plays a vital role in attachment to specific cell surface receptors. These receptors are DC-SIGN, Heparan Sulfate Proteoglycan and a specific interaction with the CD4 receptor, particularly on helper T-cells. Binding to CD4 induces the start of a cascade of conformational changes in gp120 and gp41 that lead to the fusion of the viral membrane with the host cell membrane. Binding to CD4 is mainly electrostatic although there are van der Waals interactions and hydrogen bonds.
Gp120 is coded by the HIV env gene, which is around 2.5 kb long and codes for around 850 amino acids. The primary env product is the protein gp160, which gets cleaved to gp120 (~480 amino acids) and gp41 (~345 amino acids) in the endoplasmatic reticulum by the cellular protease furin. The crystal structure of core gp120 shows an organization with an outer domain, an inner domain with respect to its termini and a bridging sheet. Gp120 is anchored to the viral membrane, or envelope, via non-covalent bonds with the transmembrane glycoprotein, gp41. Three gp120s and gp41s combine in a trimer of heterodimers to form the envelope spike, which mediates attachment to and entry into the host cell.
== Variability ==
Since gp120 plays a vital role in the ability of HIV-1 to enter CD4+ cells, its evolution is of particular interest. Many neutralizing antibodies bind to sites located in variable regions of gp120, so mutations in these regions will be selected for strongly. The diversity of env has been shown to increase by 1-2% per year in HIV-1 group M and the variable units are notable for rapid changes in amino acid sequence length. Increases in gp120 variability result in significantly elevated levels of viral replication, indicating an increase in viral fitness in individuals infected by diverse HIV-1 variants. Further studies have shown that variability in potential N-linked glycosylation sites (PNGSs) also result in increased viral fitness. PNGSs allow for the binding of long-chain carbohydrates to the high variability regions of gp120, so the authors hypothesize that the number of PNGSs in env might affect the fitness of the virus by providing more or less sensitivity to neutralizing antibodies. The presence of large carbohydrate chains extending from gp120 might obscure possible antibody binding sites.
The boundaries of the potential to add and eliminate PNGSs are naively explored by growing viral populations following each new infection. While the transmitting host has developed a neutralizing antibody response to gp120, the newly infected host lacks immune recognition of the virus. Sequence data shows that initial viral variants in an immunologically naïve host have few glycosylation sites and shorter exposed variable loops. This may facilitate viral ability to bind host cell receptors. As the host immune system develops antibodies against gp120, immune pressures seem to select for increased glycosylation, particularly on the exposed variable loops of gp120. Consequently, insertions in env, which confer more PNGSs on gp120 may be more tolerated by the virus as higher glycan density promotes the viral ability to evade antibodies and thus promotes higher viral fitness. In considering how much PNGS density could theoretically change, there may be an upper bound to PNGS number due to its inhibition of gp120 folding, but if the PNGS number decreases substantially, then the virus is too easily detected by neutralizing antibodies. Therefore, a stabilizing selection balance between low and high glycan densities is likely established. A lower number of bulky glycans improves viral replication efficiency and higher number on the exposed loops aids host immune evasion via disguise.
The relationship between gp120 and neutralizing antibodies is an example of Red Queen evolutionary dynamics. Continuing evolutionary adaptation is required for the viral envelope protein to maintain fitness relative to the continuing evolutionary adaptations of the host immune neutralizing antibodies, and vice versa, forming a coevolving system.
== Vaccine target ==
Since CD4 receptor binding is the most obvious step in HIV infection, gp120 was among the first targets of HIV vaccine research. Efforts to develop HIV vaccines targeting gp120, however, have been hampered by the chemical and structural properties of gp120, which make it difficult for antibodies to bind to it. gp120 can also easily be shed from the surface of the virus and captured by T cells due to its loose binding with gp41. A conserved region in the gp120 glycoprotein that is involved in the metastable attachment of gp120 to CD4 has been identified and targeting of invariant region has been achieved with a broadly neutralising antibody, IgG1-b12.
NIH research published in Science reports the isolation of 3 antibodies that neutralize 90% of HIV-1 strains at the CD4bs region of gp120, potentially offering a therapeutic and vaccine strategy. [1] However, most antibodies that bind the CDbs region of gp120 do not neutralize HIV, and rare ones that do such as IgG1-b12 have unusual properties such as asymmetry of the Fab arms or in their positioning. Unless a gp120-based vaccine can be designed to elicit antibodies with strongly neutralizing antiviral properties, there is concern that breakthrough infection leading to humoral production of high levels of non-neutralizing antibodies targeting the CD4 binding site of gp120 is associated with faster disease progression to AIDS.
== Competition ==
The protein gp120 is necessary during the initial binding of HIV to its target cell. Consequently, anything which binds to gp120 or its targets can physically block gp120 from binding to a cell. Only one such agent, Maraviroc, which binds the co-receptor CCR5 is currently licensed and in clinical use. No agent targeting gp120's main first cellular interaction partner, CD4, is currently licensed since interfering with such a central molecule of the immune system can cause toxic side effects, such as the anti-CD4 monoclonal antibody OKT4. Targeting gp120 itself has proven extremely difficult due to its high degree of variability and shielding. Fostemsavir (BMS-663068) is a methyl phosphate prodrug of the small molecule inhibitor BMS-626529, which prevents viral entry by binding to the viral envelope gp120 and interfering with virus attachment to the host CD4 receptor.
== HIV dementia ==
The HIV viral protein gp120 induces apoptosis of neuronal cells by inhibiting levels of furin and tissue plasminogen activator, enzymes responsible for converting pBDNF to mBDNF. gp120 induces mitochondrial-death proteins like caspases which may influence the upregulation of the death receptor Fas leading to apoptosis of neuronal cells, gp120 induces oxidative stress in the neuronal cells, and it is also known to activate STAT1 and induce interleukins IL-6 and IL-8 secretion in neuronal cells.
== See also ==
HIV envelope gene
HIV entry to the cell
gp41
CD4
CCR5
Entry inhibitor
Structure and genome of HIV
== References ==
== Further reading ==
== External links ==
https://web.archive.org/web/20060219135317/http://www.aidsmap.com/en/docs/4406022B-85D7-4A9B-B700-91336CBB6B18.asp
http://www.mcld.co.uk/hiv/?q=gp120 Archived 2008-06-24 at the Wayback Machine
http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000777
Vashistha, H.; Husain, M.; Kumar, D.; Singhal, P. C. (2009). "Tubular Cell HIV-1 gp120 Expression Induces Caspase 8 Activation and Apoptosis". Renal Failure. 31 (4): 303–312. doi:10.1080/08860220902780101. PMID 19462280. S2CID 205593494. | Wikipedia/Envelope_glycoprotein_GP120 |
Nef (Negative Regulatory Factor) is a small 27-35 kDa myristoylated protein encoded by primate lentiviruses. These include Human Immunodeficiency Viruses (HIV-1 and HIV-2) and Simian Immunodeficiency Virus (SIV). Nef localizes primarily to the cytoplasm but also partially to the Plasma membrane (PM) and is one of many pathogen-expressed proteins, known as virulence factors, which function to manipulate the host's cellular machinery and thus allow infection, survival or replication of the pathogen. Nef stands for "Negative Factor" and although it is often considered indispensable for HIV-1 replication, in infected hosts the viral protein markedly elevates viral titers.
== Function ==
The expression of Nef early in the viral life cycle ensures T-cell activation and the establishment of a persistent state of infection, two basic attributes of HIV infection. Viral expression of Nef induces numerous changes within the infected cell including the modulation of protein cell surface expression, cytoskeletal remodeling, and signal transduction. Since the activation state of the infected cell plays an important role in the success rate of HIV-1 infection, it is important that resting T-cells be primed to respond to T-cell receptor (TCR) stimuli. HIV-1 Nef lowers the threshold for activation of CD4+ lymphocytes, but is not sufficient to cause activation in the absence of exogenous stimuli.
By down regulating cell surface expression of CD4 and Lck, Nef creates a narrow TCR response which likely optimizes HIV-1 viral production and generates a susceptible population of cells to further infect. Nef retargets kinase-active Lck away from the plasma membrane to early and recycling endosomes (RE) as well as the Trans-Golgi network (TGN). RE/TGN associated Lck sub-populations in Nef expressing cells are in the catalytically active conformation and thus signaling competent. While TCR signaling takes place at the plasma membrane (PM), activation of the Ras-GTPase takes place in intracellular compartments including the Golgi apparatus. Nef induced enrichment of active Lck in these compartments results in an increase of localized RAS activity and enhanced activation of Erk kinase and the production of Interleukin-2 (IL-2). Since IL-2 is known to activate the growth, proliferation, and differentiation of T-cells to become effector T-cells; this is a self-serving effect that creates a new population of cells which HIV-1 is able to infect. Self-activation of the infected cell by IL-2 also stimulates the cell to become an effector cell and initiate the machinery which HIV-1 relies upon for its own proliferation.
To further evade the host immune response, Nef down-regulates the cell surface and total expression of the negative immune modulator CTLA-4 by targeting the protein for lysosomal degradation. In contrast to CD28 which activates T-cells, CTLA-4 is essentially an “off-switch” which would inhibit the viral production if it were activated. Lentiviruses such as HIV-1 have acquired proteins such as Nef which perform a wide array of functions including the identification of CTLA-4 before it reaches the PM and tagging it for degradation. Nef is also known to phosphorylate and inactivate Bad, a proapoptotic member of the Bcl-2 family thus protecting the infected cells from apoptosis.
Cytoskeletal remodeling is thought to reduce TCR signaling during early infection and is also modulated to some degree by Nef. Actin remodeling is generally modulated by the actin severing factor cofilin. Nef is able to associate with the cellular kinase PAK2 which phosphorylates and inactivates cofilin and interferes with early TCR signaling.
== Clinical significance ==
The Sydney blood bank cohort (SBBC) were a group of eight patients who were asymptomatic many years after initial infection by transfusion from an infected blood donor. Later analyses showed that the virus strain was a Nef-deleted variant.
== Vaccine ==
A Nef-deleted virus vaccine has not been tried in humans although it was successfully tested in Rhesus macaques.
== See also ==
HIV structure and genome
== References ==
== Further reading ==
== External links ==
Michael Smith. "HIV protein hides infected cells from immune system". MedPageToday.com. Retrieved 2008-09-26. | Wikipedia/Nef_(protein) |
Minor capsid protein VP2 and minor capsid protein VP3 are viral proteins that are components of the polyomavirus capsid. Polyomavirus capsids are composed of three proteins; the major component is major capsid protein VP1, which self-assembles into pentamers that in turn self-assemble into enclosed icosahedral structures. The minor components are VP2 and VP3, which bind in the interior of the capsid.
== Gene expression ==
All three capsid proteins are expressed from alternative start sites on a single transcript of the "late region" of the circular viral chromosome (so named because it is transcribed late in the process of viral infection). The VP3 start site is in frame downstream from that of VP2; in consequence VP3's sequence is identical to the C-terminal portion of VP2, which has an additional N-terminal extension. In at least some polyomaviruses, the VP2 N-terminus is myristoylated. Some members of the polyomavirus family, such as Merkel cell polyomavirus, do not appear to encode or express VP3, though VP2 is present.
== Structure and interactions ==
Both VP2 and VP3 are primarily intrinsically unstructured proteins; they have DNA-binding domains and a nuclear localization signal at their C-terminal ends. Both VP2 and VP3 bind to the interior of VP1 pentamers in the assembled capsid. It is generally believed that the stoichiometry of this interaction is one molecule of VP2 or VP3 to each VP1 pentamer, though higher ratios have sometimes been reported, possibly indicating that pentamers can accommodate associations with two minor proteins.
== Function ==
VP2 and VP3 are thought to be involved in facilitating viral entry into the host cell, either by mediating associations with and exit from the endoplasmic reticulum or by facilitating the entry of the viral genome into the cell nucleus. However, the precise mechanism of their involvement is unclear, and may vary among polyomaviruses. In most studies, viral propagation is either reduced or abrogated in the absence of one or both proteins, but the apparent mechanisms vary; for example, in JC virus both VP2 and VP3 seem to be essential for packaging the viral chromosome into the capsid, while absence of these proteins in SV40 prevents successful entry into new host cells, with variable effects on packaging reported. In Merkel cell polyomavirus, the effect of VP2 appears to vary depending on the cell type of the infected cell. In murine polyomavirus the minor proteins have been reported to induce apoptosis in the infected cell, and in SV40 they have been identified as viroporins.
== See also ==
Viral structural protein
== References == | Wikipedia/Minor_capsid_proteins_VP2_and_VP3 |
The membrane (M) protein (previously called E1, sometimes also matrix protein) is an integral membrane protein that is the most abundant of the four major structural proteins found in coronaviruses. The M protein organizes the assembly of coronavirus virions through protein-protein interactions with other M protein molecules as well as with the other three structural proteins, the envelope (E), spike (S), and nucleocapsid (N) proteins.
== Structure ==
The M protein is a transmembrane protein with three transmembrane domains and is around 230 amino acid residues long. In SARS-CoV-2, the causative agent of COVID-19, the M protein is 222 residues long. Its membrane topology orients the C-terminus toward the cytosolic face of the membrane and thus into the interior of the virion. It has a short N-terminal segment and a larger C-terminal domain. Although the protein sequence is not well conserved across all coronavirus groups, there is a conserved amphipathic region near the C-terminal end of the third transmembrane segment.
M functions as a homodimer. Studies of the M protein in multiple coronaviruses by cryo-electron microscopy have identified two distinct functional protein conformations, thought to have different roles in forming protein-protein interactions with other structural proteins. M protein of SARS-CoV-2 is homologous to the prokaryotic sugar transport protein SemiSWEET.
=== Post-translational modifications ===
M is a glycoprotein whose glycosylation varies according to coronavirus subgroup; N-linked glycosylation is typically found in the alpha and gamma groups while O-linked glycosylation is typically found in the beta group. There are some exceptions; for example, in SARS-CoV, a betacoronavirus, the M protein has one N-glycosylation site. Glycosylation state does not appear to have a measurable effect on viral growth. No other post-translational modifications have been described for the M protein.
== Expression and localization ==
The gene encoding the M protein is located toward the 3' end of the virus's positive-sense RNA genome, along with the genes for the other three structural proteins and various virus-specific accessory proteins. M is translated by membrane-bound polysomes to be inserted into the endoplasmic reticulum (ER) and trafficked to the endoplasmic reticulum-Golgi intermediate compartment (ERGIC), the intracellular compartment that gives rise to the coronavirus viral envelope, or to the Golgi apparatus. The exact localization is dependent on the specific virus protein. Investigations of the subcellular localization of the MERS-CoV M protein found C-terminal sequence signals associated with trafficking to the Golgi.
== Function ==
The M protein is the most abundant protein in coronavirus virions. It is essential for viral replication.
=== Viral assembly ===
The primary function of the M protein is organizing assembly of new virions. It is involved in establishing viral shape and morphology. Individual M molecules interact with each other to form the viral envelope and may be able to exclude host cell proteins from the viral membrane. Studies of the SARS-CoV M protein suggest that M-M interactions involve both the N- and C-termini. Coronaviruses are moderately pleomorphic and conformational variations of M appear to be associated with virion size.
M forms protein-protein interactions with all three other major structural proteins. M is necessary but not sufficient for viral assembly; M and the E protein expressed together are reportedly sufficient to form virus-like particles, though some reports vary depending on experimental conditions and the specific virus studied. In some reports M appears to be capable of inducing membrane curvature, though others report M alone is insufficient for this and E is required. Although the E protein is not necessarily essential, it appears to be required for normal viral morphology and may be responsible for establishing curvature or initiating viral budding. M also appears to have functional roles in the later stages of viral maturation, secretion, and budding.
Incorporation of the spike protein (S) - which is required for assembly of infectious virions - is reported to occur though M interactions and may depend on specific conformations of M. The conserved amphipathic region C-terminal to the third transmembrane segment is important for spike interactions. Interactions with M appear to be required for correct subcellular localization of S at the viral budding site. M interacts directly with the nucleocapsid (N) protein without requiring the presence of RNA. This interaction appears to occur primarily through both proteins' C-termini.
=== Interactions with the immune system ===
The M protein in MERS-CoV, SARS-CoV, and SARS-CoV-2 has been described as an antagonist of interferon response.
The M protein is immunogenic and has been reported to be a determinant of humoral immunity. Cytotoxic T cell responses to M have been described. Antibodies to epitopes found in the M protein have been identified in patients recovered from severe acute respiratory syndrome (SARS).
Other recent research has identified that SAS-COV-2 membrane protein when treated on human PBMC's causes a significant increase in pro inflammatory mediators such as TNF and IL-6. The effects of exogenous SARS-COV-2 membrane protein challenge in mice was also studied. In these studies, exogenous membrane protein treated intra nasally caused a significant increase in pulmonary inflammation in mice leading to histological changes within the lungs.
=== Host cell entry ===
It has been reported that human coronavirus NL63 relies on the M protein as well as the S protein to mediate host cell interactions preceding viral entry. M is thought to bind heparan sulfate proteoglycans exposed on the cell surface.
== Evolution and conservation ==
A study of SARS-CoV-2 sequences collected during the COVID-19 pandemic found that missense mutations in the M gene were relatively uncommon and suggested it was under purifying selection. Similar results have been described for broader population genetics analyses over a wider range of related viruses, finding that the sequences of M and several non-structural proteins in the coronavirus genome are most subject to evolutionary constraints.
== References == | Wikipedia/Coronavirus_membrane_protein |
Nonstructural protein 5B (NS5B) is a viral protein found in the hepatitis C virus (HCV). It is an RNA-dependent RNA polymerase, having the key function of replicating HCV's viral RNA by using the viral positive RNA strand as a template to catalyze the polymerization of ribonucleoside triphosphates (rNTP) during RNA replication. Several crystal structures of NS5B polymerase in several crystalline forms have been determined based on the same consensus sequence BK (HCV-BK, genotype 1). The structure can be represented by a right hand shape with fingers, palm, and thumb. The encircled active site, unique to NS5B, is contained within the palm structure of the protein. Recent studies on NS5B protein genotype 1b strain J4's (HC-J4) structure indicate a presence of an active site where possible control of nucleotide binding occurs and initiation of de-novo RNA synthesis. De-novo adds necessary primers for initiation of RNA replication.
== Drugs targeting NS5B ==
Several drugs are either on the market or in various stages of research target NS5B as a means to prevent further viral RNA replication and thus treat or cure HCV. They are often used in combination with NS5A inhibitors.
Beclabuvir, currently in clinical trials.
Dasabuvir (Viekira Pak), non-nucleoside/nucleotide analog, approved by FDA in December 2014 (only in combination with ombitasvir, paritaprevir, and ritonavir).
Deleobuvir, development terminated.
Filibuvir, development terminated.
Radalbuvir, currently in clinical trials.
Setrobuvir, development terminated.
Sofosbuvir (Sovaldi; Harvoni (combination with ledipasvir)): nucleotide analog, approved by the FDA in December 2013.
== References == | Wikipedia/Hepatitis_C_virus_nonstructural_protein_5B |
Ebola viral protein 24 (eVP24) is considered a multifunctional secondary matrix protein present in viral particles. The broad roles eVP24 performs involve the formation of fully functional and infectious viral particles, promotion of filamentous nucleocapsid formation, mediation of host responses to infection, and suppression of the host innate immune system. It has been noted that eVP24 function can overlap with that of two other viral proteins; eVP40 matrix protein which functions in virus budding, and eVP35 which is also associated with immune suppression.
== History ==
=== Research ===
The first recorded human outbreak of Ebola virus disease was in 1976 and since then, there has been considerable effort to define the progression of the disease and the virus responsible. The history of Ebola virus characterization is rather short as most research on the mechanisms employed by the virus have occurred in the last two decades. This is due to the intensive biohazard containment required for laboratory studies of the virus and the difficulty in obtaining samples for study, particularly in common outbreak regions. The isolation of viral cDNAs has allowed research into viral gene products to progress. The genome of the Ebola virus was found to encode seven proteins: glycoprotein; nucleoprotein; matrix proteins, VP40 and VP24; nonstructural proteins, VP30 and VP35; and viral polymerase. The functions of the viral proteins remained the last to be well investigated. In particular, eVP24 remained the least studied for some time.
=== Characterization ===
eVP24 was initially described as a matrix protein that had similar properties and functions of eVP40. eVP24 was found to have characteristics of typical viral matrix proteins, such as a strong association with lipid bilayers and the ability to oligomerize to form tetramers. Like eVP40, eVP24 was found to be essential in virion assembly and budding. Later research indicated that the expression of eVP24 was required to switch from viral transcription and replication to virion assembly. A new role for eVP24 was found when its expression was monitored in rodent species where changes in eVP24 seemed to be responsible for enhancing virulence, indicating that adaption of Ebola in animal models occurs through mutations in eVP24. Additionally, eVP24 inhibits interferon signaling by competitively binding to karyopherins which blocks phosphorylated STAT1 nuclear import. In 2014, it was found that this mechanism interferes with the cells response to viral infection, which suppressed the innate immune response, allowing the virus to proliferate in the body.
== Function ==
eVP24 disrupts the signaling pathway of STAT1. The STAT1 protein is phosphorylated by interferons in response to viral infection causing it to express a non-classical nuclear localization signal and bind to the importin protein karyopherin-α (KPNA). Once bound to KPNA, STAT1 is transported to the nucleus where it stimulates gene transcription in response to viral infection.
Classical nuclear localization signals are bound by arms 2-4 or by 6-8 of KPNA while non-classical nuclear localization signals are bound by KPNA 1, 5 and 6 in arms 8-10 allowing non classical signals to be transported at the same time as classical signals, providing faster signaling of certain signals.
The eVP24 protein operates by binding to KPNA preventing the binding of STAT1. As a result, STAT1 is not able to elicit an immune response, however nuclear import is able to proceed as normal which may be important for viral replication. This means that eVP24 prevents the activation of an immune response against the Ebola virus without sacrificing its ability to have viral components transported to the nucleus or the target cell.
eVP24 provides Ebola with an advantages over other viruses which disrupt STAT1 because unlike most other viruses, eVP24 uses mimicry of the STAT1 protein. This makes it very unlikely for the host to develop an adaptation as mutations in KPNA which prevent eVP24 binding are also likely to prevent STAT1 signalling.
== Mechanism ==
eVP24 prevents the function of KPNA by binding in a region which overlaps with the binding region of STAT1. This is accomplished by the high binding affinity between KNPA and eVP24.
These proteins have very high complementarity in the binding interface, similar to the complementarity shown between antibodies and antigens. In addition, the binding interface is large; over 2000 angstroms squared of solvent accessible surface is buried by the binding. Overall binding takes place with very little conformational change in either protein.
There are three clusters of residues on eVP24 which form contacts to KPNA. These are located at residue positions 115 to 140, 184 to 186, and 201 to 207. Mutation of any single residue does not significantly reduce the binding of eVP24 to KPNA which demonstrates the robust mechanism of the viral protein.
KPNA proteins have 10 armadillo repeats each consisting of three alpha helices which determine their binding specificity, the second helix from ARM 9 and 10 form a hydrophobic core with helix 6 of eVP24 adding to the stability of the complex.
The binding sites for eVP24 and STAT1 have been shown to overlap. Mutation in any one of four residues in KPNA at positions 434, 474, 477 or 484 prevent binding to STAT1. Similarly, the mutations in residues 474, 477 or 484 of KPNA reduce the binding of eVP24. Additionally and critically, the binding of eVP24 does not prevent the binding of cargo proteins with classical nuclear localization signals as, like STAT1, eVP24 causes very little conformational changes in KPNA.
== Effects on symptom progression ==
eVP24 acts as an antagonist to PY-STAT1 on KPNA. With eVP24 being transported to the nucleus instead of STAT1, the interferon-stimulated genes IFN-α/IFN-β and IFN-γ are disrupted and the cell does not enter an antiviral state.
STAT1 has been shown to regulate the expression of certain immunoglobulins. More specifically, class switching from the predominant IgM to IgG2a was not present in STAT1-deficient cells. IgG2a plays a critical role in protection against pathogens and therefore without it, the cell is more susceptible to said pathogen.
STAT1 has also been shown to regulate cell death by the inhibition of anti-apoptotic proteins Bcl-2 and Bcl-xL. STAT1 also induces the expression of procaspases, which are important factors in apoptosis signaling. When nuclear transport of STAT1 is inhibited pro-apoptotic signalling is disrupted, leading to decreased cell death.
== Current and future research ==
The evasion of the host cell immune system is key in to the rapid replication and dispersion through the body by the Ebola virus. Current research is exploring how eVP24 enables this phenomenon to occur. The discovery of STAT1 nuclear import disruption by eVP24 binding to KPNA has already provided scientists with one mechanism for the inhibition of the immune response in the cell. Other current Ebola research is focused on developing treatments or vaccines against the virus. Early investigations into potential vaccines showed that in mice models, the highest levels of protection occurred after vaccination with viral-like particles expressing eVP24. However, at that time the role of eVP24 was still largely unknown. In the wake of the 2014 Ebola outbreak in West Africa, the largest and deadliest outbreak to date, there has been a considerable increase in research focused on developing a vaccine for Ebola.
== References == | Wikipedia/Ebola_viral_protein_24 |
The gag-onc fusion protein is a general term for a fusion protein formed from a group-specific antigen ('gag') gene and that of an oncogene ('onc'), a gene that plays a role in the development of a cancer. The name is also written as Gag-v-Onc, with "v" indicating that the Onc sequence resides in a viral genome. Onc is a generic placeholder for a given specific oncogene, such as C-jun. (In the case of a fusion with C-jun, the resulting "gag-jun" protein is known alternatively as p65).
== Background ==
Gag genes are part of a general architecture for retroviruses, viruses that replicate through reverse transcription, where the gag region of the genome encodes proteins that constitute the matrix, capsid and nucleocapsid of the mature virus particles. Like in HIV's replication cycle, these proteins are needed for viral budding from the host cell's plasma membrane, where the fully formed virions leave the cell to infect other cells.
== gag-v-onc ==
When a viral gene is introduced into the host cell and is sufficient to induce oncogenesis – the creation of cancerous cells – in the infected cell line, the gene is said to be a "viral transforming gene". When this type of gene is translated to a protein, the protein is called a "transforming protein". Note that since the viral oncogenes originated from a host genome, the transformation event is different from transduction, which describes the process of introducing non-native genes to a host organism via a viral infection.
=== Rous sarcoma virus ===
The Gag-v-Onc fusion protein from the Rous sarcoma virus illustrates the dual role that the fusion protein plays in the viral and host cellular life cycle. For example, the viral gene Src (as in "sarcoma") is not necessary for viral reproduction, but does affect virulence. Due to evidence of conserved homology between the v-Src gene and its host (animal) genomes, and its non-essential status for viral reproduction, the v-Src gene is likely to have been acquired from a host genome and altered by subsequent mutations. These subsequent mutations are responsible for the oncogenic capabilities of the virus, as the normal (host) version of the Src gene, c-Src promotes survival, angiogenesis, proliferation and invasion pathways. These native pathways are disrupted in the presence of the mutant Src gene (v-Src) such that oncogenesis becomes more likely for the infected host cells, since the v-Src gene is translated into a functionally distinct version of its host counterpart.
=== murine leukemia virus ===
In the case of the murine leukemia viruses, a species of viruses capable of causing cancer in murines (mice), the viral life cycle can also be responsible for oncogenesis through a Gag-v-Onc fusion protein called "Mo-MuLV(src)", which is a Gag-v-Src protein capable of inducing oncogenesis in living mice.
== See also ==
== External links ==
gag-onc+Fusion+Proteins at the U.S. National Library of Medicine Medical Subject Headings (MeSH)
http://www.ijbs.com/v06p0730.htm#headingA7
== References == | Wikipedia/Gag-onc_fusion_protein |
A late protein is a viral protein that is formed after replication of the virus. One example is VP4 from simian virus 40 (SV40).
== In Human papillomaviruses ==
In Human papillomavirus (HPV), two late proteins are involved in capsid formation: a major (L1) and a minor (L2) protein, in the approximate proportion 95:5%. L1 forms a pentameric assembly unit of the viral shell in a manner that closely resembles VP1 from polyomaviruses. Intermolecular disulphide bonding holds the L1 capsid proteins together. L1 capsid proteins can bind via its nuclear localisation signal (NLS) to karyopherins Kapbeta(2) and Kapbeta(3) and inhibit the Kapbeta(2) and Kapbeta(3) nuclear import pathways during the productive phase of the viral life cycle. Surface loops on L1 pentamers contain sites of sequence variation between HPV types. L2 minor capsid proteins enter the nucleus twice during infection: in the initial phase after virion disassembly, and in the productive phase when it assembles into replicated virions along with L1 major capsid proteins. L2 proteins contain two nuclear localisation signals (NLSs), one at the N-terminal (nNLS) and the other at the C-terminal (cNLS). L2 uses its NLSs to interact with a network of karyopherins in order to enter the nucleus via several import pathways. L2 from HPV types 11 and 16 was shown to interact with karyopherins Kapbeta(2) and Kapbeta(3). L2 capsid proteins can also interact with viral dsDNA, facilitating its release from the endocytic compartment after viral uncoating.
== See also ==
Early protein
== References == | Wikipedia/Late_protein |
Adenovirus E1B protein usually refers to one of two proteins transcribed from the E1B gene of the adenovirus: a 55kDa protein and a 19kDa protein. These two proteins are needed to block apoptosis in adenovirus-infected cells. E1B proteins work to prevent apoptosis that is induced by the small adenovirus E1A protein, which stabilizes p53, a tumor suppressor.
== Functions ==
=== E1B-19k ===
E1B-19k blocks a p53-independent apoptosis mechanism. Without E1B-19k, degradation of both cellular and viral DNA occurs, in addition to premature host cell death during the lytic cycle, thus limiting viral replication.
E1B-19k mimics MCL1, which is a cellular antiapoptotic protein. In infected cells, the expression of E1A results in the degradation of MCL-1, which normally binds the propaptotic protein, BAK. BAK activation induces apoptosis by cooligomerizing with another proapoptotic protein, BAX. Together, BAK and BAX form pores in the mitochondrial membrane, releasing apoptogenic proteins like cytochrome c. This and other proteins released from the mitochondria lead to activation of caspase-9 and caspase-3 and the resulting apoptotic program. However, in adenovirus-infected cells, activated BAK and BAX are sequestered by E1B-19k, preventing the pathway.
=== E1B-55k ===
E1B-55k blocks p53 from inhibiting cell cycling and stops it from inducing apoptosis. Observations show that E1b-55k inhibits activation by p53 by binding a repression domain to it, converting it from an activator to a repressor of p53-activated genes. This stabilizes p53 and causes a large increase in p53 concentration. Additionally, p53 bound to E1B-55k has an affinity for its binding site that is ten times higher than free p53. Presumably, this increased affinity and concentration of p53 turns the p53-E1B-55k complex into a powerful repressor.
E1B-55k also forms a complex with E4orf6, a viral protein. The E1B-55k/E4orf6 complex in infected cells assembles with other cellular proteins to form a ubiquitin ligase complex. Essentially, the E1B-55k/E4orf6 complex takes over the cellular ubiquitin ligase complexes and gives them viral substrate-recognition subunits. There are two known substrates for this ubiquitin ligases; p53 and the MRN complex. The MRN complex, if not bound by the E1B-55K/E4orf6 ubiquitin ligase, will treat the ends of the viral DNA like a double-stranded DNA break and the viral DNA becomes ligated into long concatemers of randomly assorted genomes.
Structural and bioinformatics studies have shown that E1B-55k, which is specific to mammalian mastadenoviruses, has evolved by exaptation from an LH3-like minor capsid protein encoded by atadenoviruses.
== See also ==
Oncolytic adenovirus
== References == | Wikipedia/Adenovirus_E1B_protein |
Nonstructural protein 5A (NS5A) is a zinc-binding and proline-rich hydrophilic phosphoprotein that plays a key role in Hepatitis C virus RNA replication. It appears to be a dimeric form without trans-membrane helices.
== Structure ==
NS5A is derived from a large polyprotein that is translated from the HCV genome, and undergoes post-translation processing by nonstructural protein 3 (NS3) viral protease. Despite no inherent enzymatic activity being attributed to NS5A, its function is mediated through interaction with other nonstructural (NS) viral and cellular proteins. NS5A has two phosphorylated forms: p56 and p58, which differ in the electrophoretic mobility. p56 is basally phosphorylated by host cellular protein kinase at the center and near the C terminus, whereas p58 is a form of hyper-phosphorylated NS5A at the center of the serine-rich region. Protein mass spectrometry identified several phosphorylated serine residues in this region including serine 225, 229, 232, and 235 responsible for NS5A hyper-phosphorylation. An array of phosphorylation-specific antibodies confirmed their phosphorylation in infected cells. It has been predicted that the N-terminal 30 aa of NS5A form an amphipathic α-helix with a highly preserved feature, which is essential to modulate the association between NS5A and ER membrane. The IFN-sensitivity determining region (ISDR) at the C-terminal of NS5A has been reported to perform strong trans-activating activities, suggesting that NS5A likely functions as a transcriptional activator.
NS5A has three structurally different domains: Domain I was demonstrated to be an alternative dimeric structure by crystallography, while domain II and III remained unfolded. Furthermore, the conformational flexibility of NS5A plays an important role in multiple HCV infection stages. It is also possible that NS5A is a critical component during HCV replication and subcellular localization, which may shed light on the poorly understood HCV life cycle. Additionally, NS5A has been shown to modulate the polymerase activity of NS5B, an RNA-dependent RNA polymerase (RdRp). Intriguingly, NS5A may be a RNA binding protein because it is able to bind to the 3’UTR of the plus and minus HCV RNA strands. Moreover, NS5A is a key mediator in regulating host cell function and activity upon HCV infection. Therefore, NS5A has been extensively studied in HCV research also due to its capability to regulate the interferon (IFN) response of the host cells. Because NS5A exerts functionally essential effects in regulation of viral replication, assembly and egress, it has been considered a potential drug target for antiviral therapeutic intervention. Indeed, small molecule drugs efficiently targeting NS5A displayed a much higher potency in controlling HCV infection than other drugs. Therefore, NS5A related researches would have important implications in single molecule drug design and pegIFN-free direct-acting antiviral (DAA) combination therapies.
== As a drug target ==
Many antiviral drugs target NS5A, e.g. to treat hepatitis C; they are often described as NS5A inhibitors, and they are often used in combination with NS5B inhibitors:
FDA-approved:
Ledipasvir, approved on October 10, 2014 in a fixed-dose combination (FDC) with sofosbuvir
Ombitasvir, approved on December 19, 2014 in a FDC with paritaprevir and ritonavir, co-packaged with dasabuvir
Daclatasvir, approved on July 24, 2015
Elbasvir, approved on January 28, 2016 in a FDC with grazoprevir
Velpatasvir, approved on June 28, 2016 in a FDC with sofosbuvir and on July 17, 2017 in a FDC with sofosbuvir and voxilaprevir
Pibrentasvir, approved on August 3, 2017 in a FDC with glecaprevir
Investigational drugs:
Odalasvir
Ravidasvir
Ruzasvir
Samatasvir
== Intragenic complementation ==
Multiple copies of a polypeptide encoded by a gene often can form an aggregate referred to as a multimer. When a multimer is formed from polypeptides produced by two different mutant alleles of a particular gene, the mixed multimer may exhibit greater functional activity than the unmixed multimers formed by each of the mutants alone. When a mixed multimer displays increased functionality relative to the unmixed multimers, the phenomenon is referred to as intragenic complementation.
NS5A protein is a multimer, a dimer in this case, and intragenic complementation of replication-defective NS5A alleles has been demonstrated by Fridell et al. On the bases of pairwise complementation tests between different NS5A mutant alleles, they identified three complementation groups that were considered to define three distinct and genetically separable functions of NS5A in RNA replication.
== See also ==
Discovery and development of NS5A inhibitors
== References == | Wikipedia/Hepatitis_C_virus_nonstructural_protein_5A |
Major capsid protein VP1 is a viral protein that is the main component of the polyomavirus capsid. VP1 monomers are generally around 350 amino acids long and are capable of self-assembly into an icosahedral structure consisting of 360 VP1 molecules organized into 72 pentamers. VP1 molecules possess a surface binding site that interacts with sialic acids attached to glycans, including some gangliosides, on the surfaces of cells to initiate the process of viral infection. The VP1 protein, along with capsid components VP2 and VP3, is expressed from the "late region" of the circular viral genome.
== Structure ==
VP1 is the major structural component of the polyomavirus icosahedral capsid, which has T=7 symmetry and a diameter of 40-45 nm. The capsid contains three proteins; VP1 is the primary component and forms a 360-unit outer capsid layer composed of 72 pentamers. The other two components, VP2 and VP3, have high sequence similarity to each other, with VP3 truncated at the N-terminus relative to VP2. VP2 and VP3 assemble inside the capsid in contact with VP1, with a stoichiometry of one VP2 or VP3 molecule to each pentamer.: 314 VP1 is capable of self-assembly into virus-like particles even in the absence of other viral components. This process requires bound calcium ions and the resulting particles are stabilized by, but do not require, inter-pentamer disulfide bonds.
The VP1 protein monomer is primarily composed of beta sheets folded into a jelly roll fold. Interactions between VP1 molecules within a pentamer involve extensive binding surfaces, mediated in part by interactions between edge beta-strands. The VP1 C-terminus is disordered and forms interactions between neighboring pentamers in the assembled capsid. The flexibility of the C-terminal arm will enable it to adopt different conformations in the six distinct interaction environments imposed by the symmetry of the icosahedral assembly. The C-terminus also contains a basic nuclear localization sequence,: 316 while the N-terminus - which is oriented toward the center of the assembled capsid - contains basic residues that facilitate non-sequence-specific interactions with DNA.
== Function and trafficking ==
The VP1 protein is responsible for initiating the process of infecting a cell by binding to sialic acids in glycans, including some gangliosides, on the cell surface. Canonically, VP1 interacts specifically with α(2,3)-linked and α(2,6)-linked sialic acids. In some cases additional factors are necessary conditions for viral entry; for example, JC virus requires the 5HT2A serotonin receptor for entry, although the specific mechanism of this requirement is unclear. Once attached to the cell surface, the virions enter the cell and are trafficked by a retrograde pathway to the endoplasmic reticulum. The exact mechanism of endocytosis varies depending on the virus, and some viruses use multiple mechanisms; caveolae-dependent mechanisms are common. The process by which polyomaviruses penetrate the membrane and exit the ER is not well understood, but conformational changes to VP1, possibly including reduction of its disulfide bonds, likely occur in the ER. For some polyomaviruses, VP1 has been detected reaching the nucleus along with the viral genome, though it is unclear how the genomic DNA disengages from VP1.
All of the capsid proteins are expressed from the late region of the viral genome, so named because expression occurs only late in the infection process. VP1 has a nuclear localization sequence that enables import from the cytoplasm where it is synthesized by the host translation machinery to the cell nucleus where new virions are assembled. This nuclear import process, mediated by karyopherins, acts on assembled VP1 pentamers in complex with VP2 or VP3; oligomerization to form capsids occurs in the nucleus.: 316–17
== References == | Wikipedia/Major_capsid_protein_VP1 |
Spike (S) glycoprotein (sometimes also called spike protein, formerly known as E2) is the largest of the four major structural proteins found in coronaviruses. The spike protein assembles into trimers that form large structures, called spikes or peplomers, that project from the surface of the virion. The distinctive appearance of these spikes when visualized using negative stain transmission electron microscopy, "recalling the solar corona", gives the virus family its main name.
The function of the spike glycoprotein is to mediate viral entry into the host cell by first interacting with molecules on the exterior cell surface and then fusing the viral and cellular membranes. Spike glycoprotein is a class I fusion protein that contains two regions, known as S1 and S2, responsible for these two functions. The S1 region contains the receptor-binding domain that binds to receptors on the cell surface. Coronaviruses use a very diverse range of receptors; HCoV-NL63, SARS-CoV (which causes SARS) and SARS-CoV-2 (which causes COVID-19) all interact with angiotensin-converting enzyme 2 (ACE2). The S2 region contains the fusion peptide and other fusion infrastructure necessary for membrane fusion with the host cell, a required step for infection and viral replication. Spike glycoprotein determines the virus' host range (which organisms it can infect) and cell tropism (which cells or tissues it can infect within an organism).
Spike glycoprotein is highly immunogenic. Antibodies against spike glycoprotein are found in patients recovered from SARS and COVID-19. Neutralizing antibodies target epitopes on the receptor-binding domain. Most COVID-19 vaccine development efforts in response to the COVID-19 pandemic aim to activate the immune system against the spike protein.
== Structure ==
The spike protein is very large, often 1200 to 1400 amino acid residues long; it is 1273 residues in SARS-CoV-2. It is a single-pass transmembrane protein with a short C-terminal tail on the interior of the virus, a transmembrane helix, and a large N-terminal ectodomain exposed on the virus exterior.
Spike glycoprotein forms homotrimers in which three copies of the protein interact through their ectodomains. The trimer structures have been described as club- pear-, or petal-shaped. Each spike protein contains two regions known as S1 and S2, and in the assembled trimer the S1 regions at the N-terminal end form the portion of the protein furthest from the viral surface while the S2 regions form a flexible "stalk" containing most of the protein-protein interactions that hold the trimer in place.
=== S1 ===
The S1 region of the spike glycoprotein is responsible for interacting with receptor molecules on the surface of the host cell in the first step of viral entry. S1 contains two domains, called the N-terminal domain (NTD) and C-terminal domain (CTD), sometimes also known as the A and B domains. Depending on the coronavirus, either or both domains may be used as receptor-binding domains (RBD). Target receptors can be very diverse, including cell surface receptor proteins and sugars such as sialic acids as receptors or coreceptors. In general, the NTD binds sugar molecules while the CTD binds proteins, with the exception of mouse hepatitis virus which uses its NTD to interact with a protein receptor called CEACAM1. The NTD has a galectin-like protein fold, but binds sugar molecules somewhat differently than galectins. The observed binding of N-acetylneuraminic acid by the NTD and loss of that binding through mutation of the corresponding sugar binding pocket in emergent variants of concern has suggested a potential role for tranisent sugar-binding in the zoonosis of SARS-CoV-2, consistent with prior evolutionary proposals.
The CTD is responsible for the interactions of MERS-CoV with its receptor dipeptidyl peptidase-4, and those of SARS-CoV and SARS-CoV-2 with their receptor angiotensin-converting enzyme 2 (ACE2). The CTD of these viruses can be further divided into two subdomains, known as the core and the extended loop or receptor-binding motif (RBM), where most of the residues that directly contact the target receptor are located. There are subtle differences, mainly in the RBM, between the SARS-CoV and SARS-CoV-2 spike proteins' interactions with ACE2. Comparisons of spike proteins from multiple coronaviruses suggest that divergence in the RBM region can account for differences in target receptors, even when the core of the S1 CTD is structurally very similar.
Within coronavirus lineages, as well as across the four major coronavirus subgroups, the S1 region is less well conserved than S2, as befits its role in interacting with virus-specific host cell receptors. Within the S1 region, the NTD is more highly conserved than the CTD.
=== S2 ===
The S2 region of spike glycoprotein is responsible for membrane fusion between the viral envelope and the host cell, enabling entry of the virus' genome into the cell. The S2 region contains the fusion peptide, a stretch of mostly hydrophobic amino acids whose function is to enter and destabilize the host cell membrane. S2 also contains two heptad repeat subdomains known as HR1 and HR2, sometimes called the "fusion core" region. These subdomains undergo dramatic conformational changes during the fusion process to form a six-helix bundle, a characteristic feature of the class I fusion proteins. The S2 region is also considered to include the transmembrane helix and C-terminal tail located in the interior of the virion.
Relative to S1, the S2 region is very well conserved among coronaviruses.
=== Post-translational modifications ===
Spike glycoprotein is heavily glycosylated through N-linked glycosylation. Studies of the SARS-CoV-2 spike protein have also reported O-linked glycosylation in the S1 region. The C-terminal tail, located in the interior of the virion, is enriched in cysteine residues and is palmitoylated.
Spike proteins are activated through proteolytic cleavage. They are cleaved by host cell proteases at the S1-S2 boundary and later at what is known as the S2' site at the N-terminus of the fusion peptide. This cleavage may occur upon receptor binding, or the spike protein may be pre-cleaved such as by Furin at a furin cleavage site if one is present.
=== Conformational change ===
Like other class I fusion proteins, the spike protein undergoes a very large conformational change during the fusion process. Both the pre-fusion and post-fusion states of several coronaviruses, especially SARS-CoV-2, have been studied by cryo-electron microscopy. Functionally important protein dynamics have also been observed within the pre-fusion state, in which the relative orientations of some of the S1 regions relative to S2 in a trimer can vary. In the closed state, all three S1 regions are packed closely and the region that makes contact with host cell receptors is sterically inaccessible, while the open states have one or two S1 RBDs more accessible for receptor binding, in an open or "up" conformation.
== Expression and localization ==
The gene encoding the spike protein is located toward the 3' end of the virus's positive-sense RNA genome, along with the genes for the other three structural proteins and various virus-specific accessory proteins. Protein trafficking of spike proteins appears to depend on the coronavirus subgroup: when expressed in isolation without other viral proteins, spike proteins from betacoronaviruses are able to reach the cell surface, while those from alphacoronaviruses and gammacoronaviruses are retained intracellularly. In the presence of the M protein, spike protein trafficking is altered and instead is retained at the ERGIC, the site at which viral assembly occurs. In SARS-CoV-2, both the M and the E protein modulate spike protein trafficking through different mechanisms.
The spike protein is not required for viral assembly or the formation of virus-like particles; however, presence of spike may influence the size of the envelope. Incorporation of the spike protein into virions during assembly and budding is dependent on protein-protein interactions with the M protein through the C-terminal tail. Examination of virions using cryo-electron microscopy suggests that there are approximately 25 to 100 spike trimers per virion.
== Function ==
The spike protein is responsible for viral entry into the host cell, a required early step in viral replication. It is essential for replication. It performs this function in two steps, first binding to a receptor on the surface of the host cell through interactions with the S1 region, and then fusing the viral and cellular membranes through the action of the S2 region. The location of fusion varies depending on the specific coronavirus, with some able to enter at the plasma membrane and others entering from endosomes after endocytosis.
=== Attachment ===
The interaction of the receptor-binding domain in the S1 region with its target receptor on the cell surface initiates the process of viral entry. Different coronaviruses target different cell-surface receptors, sometimes using sugar molecules such as sialic acids, or forming protein-protein interactions with proteins exposed on the cell surface. Different coronaviruses vary widely in their target receptor, although some such as SARS-CoV-1 and HCoV-NL63 use the same receptor despite having widely divergent spike proteins (21% amino acid identity, and only 14% in the RBD). The presence of a target receptor that S1 can bind is a determinant of host range and cell tropism. Human serum albumin binds to the S1 region, competing with ACE2 and therefore restricting viral entry into cells.
=== Proteolytic cleavage ===
Proteolytic cleavage of the spike protein, sometimes known as "priming", is required for membrane fusion. Relative to other class I fusion proteins, this process is complex and requires two cleavages at different sites, one at the S1/S2 boundary and one at the S2' site to release the fusion peptide. Coronaviruses vary in which part of the viral life cycle these cleavages occur, particularly the S1/S2 cleavage. Many coronaviruses are cleaved at S1/S2 before viral exit from the virus-producing cell, by furin and other proprotein convertases; in SARS-CoV-2 a polybasic furin cleavage site is present at this position. Others may be cleaved by extracellular proteases such as elastase, by proteases located on the cell surface after receptor binding, or by proteases found in lysosomes after endocytosis. The specific proteases responsible for this cleavage depends on the virus, cell type, and local environment. In SARS-CoV, the serine protease TMPRSS2 is important for this process, with additional contributions from cysteine proteases cathepsin B and cathepsin L in endosomes. Trypsin and trypsin-like proteases have also been reported to contribute. In SARS-CoV-2, TMPRSS2 is the primary protease for S2' cleavage, and its presence is reported to be essential for viral infection, with cathepsin L protease being functional, but not essential.
=== Membrane fusion ===
Like other class I fusion proteins, the spike protein in its pre-fusion conformation is in a metastable state. A dramatic conformational change is triggered to induce the heptad repeats in the S2 region to refold into an extended six-helix bundle, causing the fusion peptide to interact with the cell membrane and bringing the viral and cell membranes into close proximity. Receptor binding and proteolytic cleavage (sometimes known as "priming") are required, but additional triggers for this conformational change vary depending on the coronavirus and local environment. In vitro studies of SARS-CoV suggest a dependence on calcium concentration. Unusually for coronaviruses, infectious bronchitis virus, which infects birds, can be triggered by low pH alone; for other coronaviruses, low pH is not itself a trigger but may be required for activity of proteases, which in turn are required for fusion. The location of membrane fusion—at the plasma membrane or in endosomes—may vary based on the availability of these triggers for conformational change. Fusion of the viral and cell membranes permits the entry of the virus' positive-sense RNA genome into the host cell cytosol, after which expression of viral proteins begins.
In addition to fusion of viral and host cell membranes, some coronavirus spike proteins can initiate membrane fusion between infected cells and neighboring cells, forming syncytia. This behavior can be observed in infected cells in cell culture. Syncytia have been observed in patient tissue samples from infections with SARS-CoV, MERS-CoV, and SARS-CoV-2, though some reports highlight a difference in syncytia formation between the SARS-CoV and SARS-CoV-2 spikes attributed to sequence differences near the S1/S2 cleavage site.
=== Immunogenicity ===
Because it is exposed on the surface of the virus, the spike protein is a major antigen to which neutralizing antibodies are developed. Its extensive glycosylation can serve as a glycan shield that hides epitopes from the immune system. Due to the outbreak of SARS and the COVID-19 pandemic, antibodies to SARS-CoV and SARS-CoV-2 spike proteins have been extensively studied. Antibodies to the SARS-CoV and SARS-CoV-2 spike proteins have been identified that target epitopes on the receptor-binding domain or interfere with the process of conformational change. The majority of antibodies from infected individuals target the receptor-binding domain. More recently antibodies targeting the S2 subunit of the spike protein have been reported with broad neutralization activities against variants.
== COVID-19 response ==
=== Vaccines ===
In response to the COVID-19 pandemic, a number of COVID-19 vaccines have been developed using a variety of technologies, including mRNA vaccines and viral vector vaccines. Most vaccine development has targeted the spike protein. Building on techniques previously used in vaccine research aimed at respiratory syncytial virus and SARS-CoV, many SARS-CoV-2 vaccine development efforts have used constructs that include mutations to stabilize the spike protein's pre-fusion conformation, facilitating development of antibodies against epitopes exposed in this conformation.
According to a study published in January 2023, markedly elevated levels of full-length spike protein unbound by antibodies were found in people who developed postvaccine myocarditis (vs. controls that remained healthy). However, these results do not alter the risk-benefit ratio favoring vaccination against COVID-19 to prevent severe clinical outcomes.
=== Monoclonal antibodies ===
Monoclonal antibodies that target the receptor-binding domain of the spike protein have been developed as COVID-19 treatments. As of July 8, 2021, three monoclonal antibody products had received Emergency Use Authorization in the United States: bamlanivimab/etesevimab, casirivimab/imdevimab, and sotrovimab. Bamlanivimab/etesevimab was not recommended in the United States due to the increase in SARS-CoV-2 variants that are less susceptible to these antibodies.
=== SARS-CoV-2 variants ===
Throughout the COVID-19 pandemic, the genome of SARS-CoV-2 viruses was sequenced many times, resulting in identification of thousands of distinct variants. Many of these possess mutations that change the amino acid sequence of the spike protein. In a World Health Organization analysis from July 2020, the spike (S) gene was the second most frequently mutated in the genome, after ORF1ab (which encodes most of the virus' nonstructural proteins). The evolution rate in the spike gene is higher than that observed in the genome overall. Analyses of SARS-CoV-2 genomes suggests that some sites in the spike protein sequence, particularly in the receptor-binding domain, are of evolutionary importance and are undergoing positive selection.
Spike protein mutations raise concern because they may affect infectivity or transmissibility, or facilitate immune escape. The mutation D614G has arisen independently in multiple viral lineages and become dominant among sequenced genomes; it may have advantages in infectivity and transmissibility possibly due to increasing the density of spikes on the viral surface, increasing the proportion of binding-competent conformations or improving stability, but it does not affect vaccines. The mutation N501Y is common to the Alpha, Beta, Gamma and Omicron Variants of SARS-CoV-2 and has contributed to enhanced infection and transmission, reduced vaccine efficacy, and the ability of SARS-CoV-2 to infect new rodent species. N501Y increases the affinity of spike for human ACE2 by around 10-fold, which could underlie some of fitness advantages conferred by this mutation even though the relationship between affinity and infectivity is complex. The mutation P681R alters the furin cleavage site, and has been responsible for increased infectivity, transmission and global impact of the SARS-CoV-2 Delta variant. Mutations at position E484, particularly E484K, have been associated with immune escape and reduced antibody binding.
The SARS-CoV-2 Omicron variant is notable for having an unusually high number of mutations in the spike protein. The SARS CoV-2 spike gene (S gene, S-gene) mutation 69–70del (Δ69-70) causes a TaqPath PCR test probe to not bind to its S gene target, leading to S gene target failure (SGTF) in SARS CoV-2 positive samples. This effect was used as a marker to monitor the propagation of the Alpha variant and the Omicron variant.
=== Additional Key Role in Illness ===
In 2021, Circulation Research and Salk had a new study that proves COVID-19 can be also a vascular disease, not only respiratory disease. The scientists created an “pseudovirus”, surrounded by SARS-CoV-2 spike proteins but without any actual virus. And pseudovirus resulted in damaging lungs and arteries of animal models. It shows SARS-CoV-2 spike protein alone can cause vascular disease and could explain some covid-19 patients who suffered from strokes, or other vascular problems in other parts of human body at the same time. The team replicated the process by removing replicating capabilities of virus and showed the same damaging effect on vascular cells again.
=== Misinformation ===
During the COVID-19 pandemic, anti-vaccination misinformation about COVID-19 circulated on social media platforms related to the spike protein's role in COVID-19 vaccines. Spike proteins were said to be dangerously "cytotoxic" and mRNA vaccines containing them therefore in themselves dangerous. Spike proteins are not cytotoxic or dangerous. Spike proteins were also said to be "shed" by vaccinated people, in an erroneous allusion to the phenomenon of vaccine-induced viral shedding, which is a rare effect of live-virus vaccines unlike those used for COVID-19. "Shedding" of spike proteins is not possible.
== Evolution, conservation and recombination ==
The class I fusion proteins, a group whose well-characterized examples include the coronavirus spike protein, influenza virus hemagglutinin, and HIV Gp41, are thought to be evolutionarily related. The S2 region of the spike protein responsible for membrane fusion is more highly conserved than the S1 region responsible for receptor interactions. The S1 region appears to have undergone significant diversifying selection.
Within the S1 region, the N-terminal domain (NTD) is more conserved than the C-terminal domain (CTD). The NTD's galectin-like protein fold suggests a relationship with structurally similar cellular proteins from which it may have evolved through gene capture from the host. It has been suggested that the CTD may have evolved from the NTD by gene duplication. The surface-exposed position of the CTD, vulnerable to the host immune system, may place this region under high selective pressure. Comparisons of the structures of different coronavirus CTDs suggests they may be under diversifying selection and in some cases, distantly related coronaviruses that use the same cell-surface receptor may do so through convergent evolution.
== References ==
== External links ==
Scudellari, Megan (28 July 2021). "How the coronavirus infects cells — and why Delta is so dangerous". Nature. Retrieved 15 August 2021.
Iwasa, Janet; Meyer, Miriah; Lex, Alexander; Rogers, Jen; Liu, Ann (Hui); Riggi, Margot. "Building a visual consensus model of the SARS-CoV-2 life cycle". Animation Lab. University of Utah. Retrieved 15 August 2021. | Wikipedia/Coronavirus_spike_protein |
Monodnaviria is a realm of viruses that includes all single-stranded DNA viruses that encode an endonuclease of the HUH superfamily that initiates rolling circle replication (RCR) of the circular viral genome. Viruses descended from such viruses are also included in the realm, including certain linear single-stranded DNA (ssDNA) viruses and circular double-stranded DNA (dsDNA) viruses. These atypical members typically replicate through means other than rolling circle replication.
Monodnaviria was established in 2019 and contains four kingdoms: Loebvirae, Sangervirae, Trapavirae, and Shotokuvirae. Viruses in the first three kingdoms infect prokaryotes, and viruses in Shotokuvirae infect eukaryotes and include the atypical members of the realm. Viruses in Monodnaviria appear to have come into existence independently multiple times from circular bacterial and archaeal plasmids that encode the HUH endonuclease. Eukaryotic viruses in the realm appear to have come into existence multiple times via genetic recombination events that merged deoxyribonucleic acid (DNA) from the aforementioned plasmids with capsid proteins of certain RNA viruses. Most identified ssDNA viruses belong to Monodnaviria.
The prototypic members of the realm are often called CRESS-DNA viruses. CRESS-DNA viruses are associated with a wide range of diseases, including diseases in economically important crops and a variety of diseases in animals. The atypical members of the realm include papillomaviruses and polyomaviruses, which are known to cause various cancers. Members of Monodnaviria are also known to frequently become integrated into the DNA of their hosts, and they experience a relatively high rate of genetic mutations and recombinations.
== Etymology ==
Monodnaviria is a portmanteau of mono, from Greek μόνος [mónos], which means single, DNA from deoxyribonucleic acid (DNA), which references single-stranded DNA, and the suffix -viria, which is the suffix used for virus realms. The prototypic members of Monodnaviria are often called CRESS-DNA, or CRESS DNA, viruses, which stands for "circular Rep-encoding ssDNA" viruses.
== Characteristics ==
=== Endonuclease-initiated replication ===
All prototypical viruses in Monodnaviria encode an endonuclease of the HUH superfamily. Endonucleases are enzymes that can cleave phosphodiester bonds within a polynucleotide chain. HUH, or HuH, endonucleases are endonucleases that contain a HUH motif made of two histidine residues separated by a bulky hydrophobic residue and a Y motif that contains one or two tyrosine residues. The HUH endonuclease of ssDNA viruses is often called the replication initiation protein, or simply Rep, because its cleavage of a specific site in the viral genome initiates replication.
Once the viral ssDNA is inside of the host cell, it is replicated by the host cell's DNA polymerase to produce a double-stranded form of the viral genome. Rep then recognizes a short sequence on the 3'-end ("three prime end") at the origin of replication. Upstream from the recognition site further away from the 3'-end, Rep binds to the DNA and nicks the positive-sense strand, which creates a nick site. In doing so, Rep binds to the 5'-end ("five prime end") via a tyrosine residue that covalently bonds to the phosphate backbone of DNA, which creates a phosphotyrosine molecule that connects Rep to the viral DNA. The 3'-end of the nicked strand remains as a free hydroxyl (-OH) end that acts as a signal for the host DNA polymerase to replicate the genome.
Replication commences at the 3'-OH end and is performed by extending the 3'-end of the positive strand using the negative strand as a template for DNA replication. During replication, the original nicked positive strand is gradually displaced by the newly replicated positive strand. After one cycle of replicating the genome, Rep may nick the positive strand a second time, doing so with a second tyrosine residue, or another Rep may nick the positive strand. After the positive strand is completely detached from the negative strand, the 3'-OH end bonds to the phosphotyrosine of the 5'-end, which creates a free circular ssDNA genome that usually is either converted into dsDNA for transcription or further replication or is packaged into newly constructed viral capsids. The replication process can be repeated numerous times on the same circular genome to produce many copies of the original viral genome. Strands displaced from the replication complex may contain multiple copies of the genome.
==== Atypical members ====
While the prototypical viruses in Monodnaviria have circular ssDNA genomes and replicate via rolling circle replication (RCR), some have linear ssDNA genomes with different replication methods, including the families Parvoviridae and Bidnaviridae, assigned to the phylum Cossaviricota of the kingdom Shotokuvirae. Parvoviruses use rolling hairpin replication, in which the ends of the genome have hairpin loops that repeatedly unfold and refold during replication to change the direction of DNA synthesis to move back and forth along the genome, which produces numerous copies of the genome in a continuous process. Individual genomes are then excised from this molecule by the HUH endonuclease. In place of the HUH endonuclease, bidnaviruses encode their own protein-primed DNA polymerase that replicates the genome, which is bipartite and packaged into two separate virions, instead of using the host cell's DNA polymerase for replication.
Additionally, some viruses in the realm are dsDNA viruses with circular genomes, including Polyomaviridae and Papillomaviridae, also assigned to the phylum Cossaviricota. Instead of replicating via RCR, these viruses use theta bidirectional DNA replication. This begins by unwinding the dsDNA at a site called the origin to separate the two DNA strands from each other. Two replication forks are established that move in opposite directions around the circular genome until they meet at the side opposite of the origin and replication is terminated. The replication method of anelloviruses, assigned to the phylum Commensaviricota, is unknown. Unlike typical CRESS-DNA viruses, which have positive-sense genomes, anelloviruses have negative-sense genomes.
=== Other characteristics ===
Apart from the aforementioned replication methods, ssDNA viruses in Monodnaviria share a number of other common characteristics. The capsids of ssDNA viruses, which store the viral DNA, are usually icosahedral in shape and composed of either one type of protein or, in the case of parvoviruses, multiple types of proteins. All ssDNA viruses that have had the structure of their capsid proteins analyzed in high resolution have been observed to contain a single jelly roll fold in their folded structure.
Nearly all families of ssDNA viruses have a positive-sense genome. The sole exception are viruses in the family Anelloviridae, which have a negative-sense genome. In any case, ssDNA viruses have their genomes converted to a dsDNA form prior to transcription, which creates the messenger RNA (mRNA) needed to produce viral proteins from translation by ribosomes. CRESS-DNA viruses also have similar genome structures, genome lengths, and gene compositions.
Lastly, ssDNA viruses have a relatively high rate of genetic recombinations and substitution mutations. Genetic recombination, or mixture, of ssDNA genomes can occur between closely related viruses when a gene is replicated and transcribed at the same time, which may cause the host cell's DNA polymerases to switch DNA templates (negative strands) during the process, which causes recombination. These recombinations usually occur in the negative strand and either outside of or at the peripheries of genes rather than toward the middle of genes.
The high substitution rate seen in ssDNA viruses is unusual since replication is performed primarily by the host cell's DNA polymerase, which contains proofreading mechanisms to prevent mutations. Substitutions in ssDNA viral genomes may occur because the viral DNA may become oxidatively damaged while the genome is inside the capsid. The prevalence of recombinations and substitutions among ssDNA viruses means that eukaryotic ssDNA viruses can emerge as threatening pathogens.
== Phylogenetics ==
Comparison of genomes and phylogenetic analyses of the HUH endonucleases, superfamily 3 helicases (S3H), and capsid proteins of viruses in Monodnaviria have shown that they have multiple, chimeric origins. HUH endonucleases of CRESS-DNA viruses are most similar to those found in small, RCR bacterial and archaeal plasmids, extra-chromosomal DNA molecules inside bacteria and archaea, and appear to have evolved from them at least three times. HUH endonucleases of prokaryotic CRESS-DNA viruses seem to have originated from plasmid endonucleases that lacked the S3H domain, whereas eukaryotic CRESS-DNA viruses evolved from ones that had S3H domains.
The capsid proteins of eukaryotic CRESS-DNA viruses are most closely related those of various animal and plant positive-sense RNA viruses, which belong to the realm Riboviria. Because of this, eukaryotic CRESS-DNA viruses appear to have emerged multiple times from recombination events that merged DNA from bacterial and archaeal plasmids with complementary DNA (cDNA) copies of positive-sense RNA viruses. CRESS-DNA viruses therefore represent a notable instance of convergent evolution, whereby organisms that are not directly related evolve the same or similar traits.
The atypical members of Monodnaviria have various origins:
Parvoviruses, which are linear ssDNA viruses, are likely to have evolved from CRESS-DNA viruses. The Rep of parvoviruses appears to have lost the joining activity used by the Rep of CRESS-DNA viruses to create circular genomes and instead remains covalently attached to the 5'-end of DNA strands during replication.
Circular dsDNA viruses in Monodnaviria appear to have evolved from ssDNA viruses, likely parvoviruses, through inactivation of the endonuclease's HUH domain. The HUH domain then became a DNA-binding domain. At the same time, these viruses' manner of replication changed from RCR to theta bidirectional replication. The capsid proteins of these circular dsDNA viruses are highly divergent, so it is unclear if they evolved from parvovirus capsid proteins or through other means.
Bidnaviruses, which are linear ssDNA viruses, appear to have been created as a result of a parvovirus genome becoming integrated into the genome of a polinton, a type of self-replicating genomic DNA molecule, which replaced the HUH endonuclease with a polinton's DNA polymerase.
Anelloviruses likely inherited their capsid protein from a circovirus or circovirus-like virus.
== Classification ==
Monodnaviria has four kingdoms: Loebvirae, Sangervirae, Shotokuvirae, and Trapavirae. Loebvirae is monotypic down to the rank of order, and Sangervirae is monotypic down to the rank of family. This taxonomy is described further as follows:
Kingdom: Loebvirae, which only infect bacteria, have filamentous or rod-shaped virions formed from an alpha-helical capsid protein, and encode a morphogenesis protein that is an ATPase of the FtsK-HerA superfamily
Phylum: Hofneiviricota
Class: Faserviricetes
Order: Tubulavirales
Kingdom: Sangervirae, which only infect bacteria, have a capsid protein that contains a single jelly roll fold, and have a pilot protein required for transferring DNA across the cell envelope. The endonuclease of Sangervirae may also be a unifying trait since it appears to be monophyletic.
Phylum: Phixviricota
Class: Malgrandaviricetes
Order: Petitvirales
Family: Microviridae
Kingdom: Shotokuvirae, which encode an endonuclease containing an endonuclease domain, or a derivative of one, at the start of the protein's amino acid sequence and a superfamily 3 helicase domain at the end of the protein's amino acid sequence. Shotokuvirae includes anelloviruses, assigned to its phylum Commensaviricota, and linear ssDNA viruses and circular dsDNA viruses, assigned to its phylum Cossaviricota, all of which are descended from CRESS-DNA viruses, assigned to the kingdom's phylum Cressdnaviricota.
Kingdom: Trapavirae, which only infect archaea and which have a viral envelope that contains a membrane fusion protein
Monodnaviria includes the vast majority of identified ssDNA viruses. ssDNA viruses are Group II in the Baltimore classification system, which groups viruses together based on how they produce mRNA and is often used alongside standard virus taxonomy, which is based on evolutionary history. Among ssDNA virus families, only two are not assigned to Monodnaviria: Finnlakeviridae and Spiraviridae. Finnlakeviridae is assigned to another realm, Varidnaviria, and Spiraviridae is unassigned to a realm. The dsDNA viruses in Monodnaviria are assigned to Group I in the Baltimore system. Realms are the highest level of taxonomy used for viruses and Monodnaviria is one of seven. The others are Adnaviria, Duplodnaviria, Riboviria, Ribozyviria, Singelaviria, and Varidnaviria.
== Interactions with hosts ==
=== Disease ===
The eukaryotic CRESS-DNA viruses are associated with a variety of diseases. Plant viruses in the families Geminiviridae and Nanoviridae infect economically important crops and cause significant damage to agricultural productivity. Animal viruses in Circoviridae are associated with many diseases, including respiratory illness, intestinal illness, and reproductive problems. Bacilladnaviruses, which primarily infect diatoms, are thought to have a significant role in controlling algal blooms.
The atypical members of the realm are also associated with many widely known diseases. Parvoviruses are most widely known for causing a lethal infection in canids as well as fifth disease in humans. Papillomaviruses and polyomaviruses are known to cause different types of cancers and other diseases. A polyomavirus is responsible for Merkel-cell carcinoma, and papillomaviruses cause various genital and other cancers as well as warts. Anelloviruses are part of the human virome but are not associated with disease, so they may be an example of a commensal relationship in which they are able to replicate in humans without affecting their host.
=== Endogenization ===
The Rep protein lacks homologues in cellular life, so it can be searched for within an organism's genome to identify if viral DNA has become endogenized as part of the organism's genome. Among eukaryotes, endogenization is most often observed in plants, but it is also observed in animals, fungi, and various protozoans. Endogenization can occur through several means such as the integrase or transpose enzymes or by exploiting the host cell's recombination machinery.
Most endogenized ssDNA viruses are in non-coding regions of the organism's genome, but sometimes the viral genes are expressed, and the Rep protein may be used by the organism. Because viral DNA can become a part of an organism's genome, this represents an example of horizontal gene transfer between unrelated organisms that can be used to study evolutionary history. By comparing related organisms, it is possible to estimate the approximate age of ssDNA viruses. For example, comparison of animal genomes has shown that circoviruses and parvoviruses first integrated into their hosts' genomes at least 40–50 million years ago.
== History ==
The earliest reference to a virus in Monodnaviria was made in a poem written in 752 by Japanese Empress Shotoku. The poem describes a yellowing or vein clearing disease of Eupatorium plants that was likely caused by a geminivirus. Centuries later, a circovirus infection that caused balding in birds was observed in Australia in 1888, which marked the first reference to ssDNA viruses in modern times. The first animal CRESS-DNA virus to be characterized was the porcine circovirus in 1974, and in 1977, the first genome of an ssDNA virus, the Bean golden mosaic virus, was detailed. Beginning in the 1970s, the families of related members in Monodnaviria began to be organized. Parvoviridae became the first ssDNA family recognized and additional families have been continually discovered since then.
In recent years, analyses of viral DNA in various contexts such as fecal matter and marine sediments have shown that ssDNA viruses are widespread throughout nature, and the increased knowledge of their diversity has helped to greater understand their evolutionary history. The relation between CRESS-DNA viruses was resolved from 2015 to 2017, which led to the establishment of Monodnaviria in 2019 based on their shared relation, including viruses descended from them. Despite appearing to have polyphyletic origins, the similar genome structure, genome length, and gene compositions of CRESS-DNA viruses provided the justification to unite them under a realm.
== See also ==
List of higher virus taxa
== Notes ==
== References ==
== Further reading ==
Ward, C. W. (1993). "Progress towards a higher taxonomy of viruses". Research in Virology. 144 (6): 419–53. doi:10.1016/S0923-2516(06)80059-2. PMC 7135741. PMID 8140287. | Wikipedia/Monodnaviria |
The nucleocapsid (N) protein is a protein that packages the positive-sense RNA genome of coronaviruses to form ribonucleoprotein structures enclosed within the viral capsid. The N protein is the most highly expressed of the four major coronavirus structural proteins. In addition to its interactions with RNA, N forms protein-protein interactions with the coronavirus membrane protein (M) during the process of viral assembly. N also has additional functions in manipulating the cell cycle of the host cell. The N protein is highly immunogenic and antibodies to N are found in patients recovered from SARS and COVID-19.
== History ==
COVID-19 was first identified in January 2020. A patient in the state of Washington was given a diagnosis of coronavirus infection on 20 January. A group of scientists based at the Centers for Disease Control and Prevention in Atlanta, Georgia isolated the virus from nasopharyngeal and oropharyngeal swabs and were able to characterize the genomic sequence, replication properties and cell culture tropism from the swabs. They made available the virus to the wider scientific community shortly thereafter "by depositing it into two virus reagent repositories".
== Structure ==
The N protein is composed of two main protein domains connected by an intrinsically disordered region (IDR) known as the linker region, with additional disordered segments at each terminus. A third small domain at the C-terminal tail appears to have an ordered alpha helical secondary structure and may be involved in the formation of higher-order oligomeric assemblies. In SARS-CoV, the causative agent of SARS, the N protein is 422 amino acid residues long and in SARS-CoV-2, the causative agent of COVID-19, it is 419 residues long.
Both the N-terminal and C-terminal domains are capable of binding RNA. The C-terminal domain forms a dimer that is likely to be the native functional state. Parts of the IDR, particularly a conserved sequence motif rich in serine and arginine residues (the SR-rich region), may also be implicated in dimer formation, though reports on this vary. Although higher-order oligomers formed through the C-terminal domain have been observed crystallographically, it is unclear if these structures have a physiological role.
The C-terminal dimer has been structurally characterized by X-ray crystallography for several coronaviruses and has a highly conserved structure. The N-terminal domain - sometimes known as the RNA-binding domain, though other parts of the protein also interact with RNA - has also been crystallized and has been studied by nuclear magnetic resonance spectroscopy in the presence of RNA.
=== Post-translational modifications ===
The N protein is post-translationally modified by phosphorylation at sites located in the IDR, particularly in the SR-rich region. SARS-CoV-2
nucleocapsid (N) protein is arginine methylated by protein arginine methyltransferase 1 (PRMT1) at residues R95 and R177. Type I PRMT inhibitor (MS023) or substitution of R95 or R177 with lysine inhibited interaction of N protein with the 5’-UTR of SARS-CoV-2 genomic RNA, a property required for viral packaging | doi: 10.1016/j.jbc.2021.100821 | PMID 34029587. In several coronaviruses, ADP-ribosylation of the N protein has also been reported. With unclear functional significance, the SARS-CoV N protein has been observed to be SUMOylated and the N proteins of several coronaviruses including SARS-CoV-2 have been observed to be proteolytically cleaved.
== Expression and localization ==
The N protein is the most highly expressed in host cells of the four major structural proteins. Like the other structural proteins, the gene encoding the N protein is located toward the 3' end of the genome.
N protein is localized primarily to the cytoplasm. In many coronaviruses, a population of N protein is localized to the nucleolus, thought to be associated with its effects on the cell cycle.
== Function ==
=== Genome packaging and viral assembly ===
The N protein binds to RNA to form ribonucleoprotein (RNP) structures for packaging the genome into the viral capsid. The RNP particles formed are roughly spherical and are organized in flexible helical structures inside the virus. Formation of RNPs is thought to involve allosteric interactions between RNA and multiple RNA-binding regions of the protein. Dimerization of N is important for assembly of RNPs. Encapsidation of the genome occurs through interactions between N and M. N is essential for viral assembly. N also serves as a chaperone protein for the formation of RNA structure in the genomic RNA.
=== Genomic and subgenomic RNA synthesis ===
Synthesis of genomic RNA appears to involve participation by the N protein. N is physically colocalized with the viral RNA-dependent RNA polymerase early in the replication cycle and forms interactions with non-structural protein 3, a component of the replicase-transcriptase complex. Although N appears to facilitate efficient replication of genomic RNA, it is not required for RNA transcription in all coronaviruses. In at least one coronavirus, transmissible gastroenteritis virus (TGEV), N is involved in template switching in the production of subgenomic mRNAs, a process that is a distinctive feature of viruses in the order Nidovirales.
=== Cell cycle effects ===
Coronaviruses manipulate the cell cycle of the host cell through various mechanisms. In several coronaviruses, including SARS-CoV, the N protein has been reported to cause cell cycle arrest in S phase through interactions with cyclin-CDK. In SARS-CoV, a cyclin box-binding region in the N protein can serve as a cyclin-CDK phosphorylation substrate. Trafficking of N to the nucleolus may also play a role in cell cycle effects. More broadly, N may be involved in reduction of host cell protein translation activity.
=== Immune system effects ===
The N protein is involved in viral pathogenesis via its effects on components of the immune system. In SARS-CoV, MERS-CoV, and SARS-CoV-2, N has been reported as suppressing interferon responses.
== Evolution and conservation ==
The sequences and structures of N proteins from different coronaviruses, particularly the C-terminal domains, appear to be well conserved. Similarities between the structure and topology of the N proteins of coronaviruses and arteriviruses suggest a common evolutionary origin and supports the classification of these two groups in the common order Nidovirales.
Examination of SARS-CoV-2 sequences collected during the COVID-19 pandemic found that missense mutations were most common in the central linker region of the protein, suggesting this relatively unstructured region is more tolerant of mutations than the structured domains. A separate study of SARS-CoV-2 sequences identified at least one site in the N protein under positive selection.
The N protein's properties of being well conserved, not appearing to recombine frequently, and producing a strong T-cell response have led to it being studied as a potential target for coronavirus vaccines. The vaccine candidate UB-612 is one such experimental vaccine that targets the N protein, along with other viral proteins, to attempt to induce broad immunity.
== References == | Wikipedia/Coronavirus_nucleocapsid_protein |
Cytomegalovirus (CMV) (from cyto- 'cell' via Greek κύτος kútos- 'container' + μέγας mégas 'big, megalo-' + -virus via Latin vīrus 'poison') is a genus of viruses in the order Herpesvirales, in the family Herpesviridae, in the subfamily Betaherpesvirinae. Humans and other primates serve as natural hosts. The 11 species in this genus include human betaherpesvirus 5 (HCMV, human cytomegalovirus, HHV-5), which is the species that infects humans. Diseases associated with HHV-5 include mononucleosis and pneumonia, and congenital CMV in infants can lead to deafness and ambulatory problems.
In the medical literature, most mentions of CMV without further specification refer implicitly to human CMV. Human CMV is the most studied of all cytomegaloviruses.
MX2/MXB protein was identified as a restriction factor for herpesviruses, which acts at a very early stage of the replication cycle and MX2/MXB restriction of herpesvirus requires GTPase activity.
== Taxonomy ==
Within the Herpesviridae, CMV belongs to the Betaherpesvirinae subfamily, which also includes the genera Muromegalovirus and Roseolovirus (human herpesvirus 6 and human herpesvirus 7). It is also related to other herpesviruses within the Alphaherpesvirinae subfamily, which includes herpes simplex viruses 1 and 2 and varicella-zoster virus, and the Gammaherpesvirinae subfamily, which includes Epstein–Barr virus and Kaposi's sarcoma-associated herpesvirus.
Several species of Cytomegalovirus have been identified and classified for different mammals. The most studied is Human cytomegalovirus (HCMV), which is also known as Human betaherpesvirus 5 (HHV-5). Other primate CMV species include Chimpanzee cytomegalovirus (CCMV) that infects chimpanzees and orangutans, and Simian cytomegalovirus (SCCMV) and Rhesus cytomegalovirus (RhCMV) that infect macaques; CCMV is known as both Panine beta herpesvirus 2 (PaHV-2) and Pongine betaherpesvirus 4 (PoHV-4). SCCMV is called cercopithecine betaherpesvirus 5 (CeHV-5) and RhCMV, Cercopithecine betaherpesvirus 8 (CeHV-8). A further two viruses found in the night monkey are tentatively placed in the genus Cytomegalovirus, and are called Herpesvirus aotus 1 and Herpesvirus aotus 3. Rodents also have viruses previously called cytomegaloviruses that are now reclassified under the genus Muromegalovirus; this genus contains Mouse cytomegalovirus (MCMV) is also known as Murid betaherpesvirus 1 (MuHV-1) and the closely related Murid betaherpesvirus 2 (MuHV-2) that is found in rats.
=== Species ===
The following 11 species are assigned to the genus in ICTV 2022:
== Structure ==
Viruses in Cytomegalovirus are enveloped, with icosahedral, spherical to pleomorphic, and round geometries, and T=16 symmetry. The diameter is around 150–200 nm. Genomes are linear and nonsegmented, around 200 kb in length.
== Genome ==
Herpesviruses have some of the largest genomes among human viruses, often encoding hundreds of proteins. For instance, the double‑stranded DNA (dsDNA) genome of wild-type HCMV strains has a size of around 235 kb and encodes at least 208 proteins. It is thus longer than all other human herpesviruses and one of the longest genomes of all human viruses in general. It has the characteristic herpesvirus class E genome architecture, consisting of two unique regions (unique long UL and unique short US), both flanked by a pair of inverted repeats (terminal/internal repeat long TRL/IRL and internal/terminal repeat short IRS/TRS). Both sets of repeats share a region of a few hundred bps, the so-called "a sequence"; the other regions of the repeats are sometimes referred to as "b sequence" and "c sequence".
== Life cycle ==
Viral replication is nuclear and lysogenic. Entry into the host cell is achieved by attachment of the viral glycoproteins to host receptors, which mediates endocytosis. Replication follows the dsDNA bidirectional replication model. DNA templated transcription, with some alternative splicing mechanism is the method of transcription. Translation takes place by leaky scanning. The virus exits the host cell by nuclear egress, and budding. Humans and monkeys serve as the natural hosts. Transmission routes are dependent on coming into contact with bodily fluids (such as saliva, urine, and genital secretions) from an infected individual.
All herpesviruses share a characteristic ability to remain latent within the body over long periods. Although they may be found throughout the body, CMV infections are frequently associated with the salivary glands in humans and other mammals.
== Genetic engineering ==
The CMV promoter is commonly included in vectors used in genetic engineering work conducted in mammalian cells, as it is a strong promoter and drives constitutive expression of genes under its control.
== History ==
Cytomegalovirus was first observed by German pathologist Hugo Ribbert in 1881 when he noticed enlarged cells with enlarged nuclei present in the cells of an infant. Years later, between 1956 and 1957, Thomas Huckle Weller together with Smith and Rowe independently isolated the virus, known thereafter as "cytomegalovirus". In 1990, the first draft of human cytomegalovirus genome was published, the biggest contiguous genome sequenced at that time.
== See also ==
CMV polyradiculomyelopathy
Human cytomegalovirus
== References ==
== External links ==
ICTV | Wikipedia/Cytomegalic_inclusion_disease |
Foot-and-mouth disease virus (FMDV) is a virus in the genus Aphthovirus that causes foot-and-mouth disease. As a member of the family Picornaviridae, FMDV is a positive-sense, single-stranded RNA virus. Like other members of the picornavirus family, FMDV is small and unenveloped, with an icosahedral capsid.
The virus causes foot-and-mouth disease, a highly contagious disease affecting cattle, pigs, sheep, goats, and other cloven-hoofed animals. Foot-and-mouth disease causes fever and the formation of vesicles (blisters) in infected animals, which form in the mouth and on the feet and teats. While the disease is usually nonfatal to adult livestock, survivors are left in a weakened state which impacts both meat and milk production, making outbreaks very costly and disruptive to agricultural production overall.
== Structure and genome ==
The virus particle (25-30 nm) has an icosahedral capsid made of protein, without envelope, containing a positive-sense (mRNA sense) single-stranded ribonucleic acid (RNA) genome.
== Replication ==
When the virus comes in contact with the membrane of a host cell, it binds to a receptor site and triggers a folding-in of the membrane. Once the virus is inside the host cell, the capsid dissolves, and the RNA gets replicated, and translated into viral proteins by the cell's ribosomes using a cap-independent mechanism driven by the internal ribosome entry site element.
The synthesis of viral proteins include 2A 'cleavage' during translation. They include proteases that inhibit the synthesis of normal cell proteins, and other proteins that interact with different components of the host cell. The infected cell ends up producing large quantities of viral RNA and capsid proteins, which are assembled to form new viruses. After assembly, the host cell lyses (bursts) and releases the new viruses.
=== Recombination ===
Recombination can occur within host cells during co-infections by different FMDV strains.
Recombination is common and a key feature of FMDV evolution.
== Serotypes ==
Foot-and-mouth disease virus occurs in seven major serotypes: O, A, C, SAT-1, SAT-2, SAT-3, and Asia-1. These serotypes show some regionality, and the O serotype is most common.
== See also ==
Animal viruses
== References == | Wikipedia/Foot-and-mouth_disease_virus |
Bidensovirus is a genus of single stranded DNA viruses that infect invertebrates. The species in this genus were originally classified in the family Parvoviridae (subfamily Densovirinae) but were moved to a new genus because of significant differences in the genomes.
== Taxonomy ==
There is one species in this genus currently recognised: Bombyx mori bidensovirus.
== Host ==
As the name suggests this virus infects Bombyx mori, the silkworm.
== Virology ==
The virions are icosahedral, non enveloped and ~25 nanometers in diameter. They contain two structural proteins.
The genome is bipartite, unique among ssDNA viruses, with two linear segments of ~6 and 6.5 kilobases (kb). These segments and the complementary strands are that are packaged separately giving rise to 4 different types of full particles.
Both segments have an ambisense organization, coding for a structural protein in one sense and the non-structural proteins on the complementary strand.
DNA1 (also known as VD1) — the larger segment of 6.5 kb — encodes the capsid protein VP1 (128 kDa — kilodaltons) on one strand and three non-structural proteins — NS1 of 14 kDa, NS2 of 37 kDa and NS3 of 55 kDa — on the complementary strand.
DNA2 (also known as VD2) — the smaller segment of 6 kb — encodes the capsid protein VP2 (133 kDa) on one strand and the non-structural protein NS4 (27 kDa) on the complementary strand.
The open reading frame 4 (VD1-ORF4) is 3318 nucleotides (bases) in length and encodes a predicted (3318/3 − 1 =) 1105 amino acid protein which has a conserved DNA polymerase motif. It appears to encode at least 2 other proteins including one of ~53 kDa that forms part of the virion.
== Evolution ==
Comprehensive analysis of bidnavirus genes has shown that these viruses have evolved from a parvovirus ancestor from which they inherit a jelly-roll capsid protein and a superfamily 3 helicase. It has been further suggested that the key event that led to the separation of the bidnaviruses from parvoviruses was the acquisition of the PolB gene. A likely scenario has been proposed under which the ancestral parvovirus genome was integrated into a large virus-derived DNA transposon of the Polinton/Maverick family (polintoviruses) resulting in the acquisition of the polintovirus PolB gene along with terminal inverted repeats. Bidnavirus genes for a minor structural protein (putative receptor-binding protein) and a potential novel antiviral defense modulator were derived from dsRNA viruses (Reoviridae) and dsDNA viruses (Baculoviridae), respectively.
== References ==
== External links ==
Bidensovirus ~ ViralZone page. The top image erraneously shows a monopartite genome, text and genome map are right (March 30, 2021). | Wikipedia/Bidnaviridae |
Phycodnaviridae is a family of large (100–560 kb) double-stranded DNA viruses that infect marine or freshwater eukaryotic algae. Viruses within this family have a similar morphology, with an icosahedral capsid (polyhedron with 20 faces). As of 2014, there were 33 species in this family, divided among 6 genera. This family belongs to a super-group of large viruses known as nucleocytoplasmic large DNA viruses. Evidence was published in 2014 suggesting that specific strains of Phycodnaviridae might infect humans rather than just algal species, as was previously believed. Most genera under this family enter the host cell by cell receptor endocytosis and replicate in the nucleus. Phycodnaviridae play important ecological roles by regulating the growth and productivity of their algal hosts. Algal species such Heterosigma akashiwo and the genus Chrysochromulina can form dense blooms which can be damaging to fisheries, resulting in losses in the aquaculture industry. Heterosigma akashiwo virus (HaV) has been suggested for use as a microbial agent to prevent the recurrence of toxic red tides produced by this algal species. Phycodnaviridae cause death and lysis of freshwater and marine algal species, liberating organic carbon, nitrogen and phosphorus into the water, providing nutrients for the microbial loop.
== Taxonomy ==
Group: double-stranded DNA
The taxonomy of this family was initially based on host range: chloroviruses infect chlorella-like green algae from freshwaters; whereas, members of the other five genera infect marine microalgae and a some species of brown macroalgae. This was subsequently confirmed by analysis of their B-family DNA polymerases, which indicated that members of the Phycodnaviridae are more closely related to one another, in comparison to other double stranded DNA viruses, forming a monophyletic group. The phycodnaviruses contain six genera: Coccolithovirus, Chlorovirus, Phaeovirus, Prasinovirus, Prymnesiovirus and Raphidovirus. The genera can be distinguished from one another by, for example, differences in life cycle and gene content.
== Structure ==
All six genera in the family Phycodnaviridae have similar virion structure and morphology. They are large virions that can range between 100 and 220 nm in diameter. They have a double-stranded DNA genome, and a protein core surrounded by a lipid bilayer and an icosahedral capsid. The capsid has 2, 3 and 5 fold axis of symmetry with 20 equilateral triangle faces composing of protein subunits. In all known members of the Phycodnaviridae the capsid is composed of ordered substructures with 20 trisymmetrons and 12 pentasymmetrons made up of donut-shaped trimeric capsomers, where each capsomer is made up of three monomers of the major capsid protein. If all the trimeric capsomers are identical in structure, the virion capsid contains 5040 copies of the major capsid protein in total with a triangulation number of 169. At the five-fold vertices there are 12 pentamer-capsomers consist of different proteins. The protein(s) that can be found below the axial channel of each pentamer may be responsible for digesting the host cell wall during viral infection. The species Phaeocystis puchetii virus from the genus Prymnesiovirus has the largest capsid structure in the Phycodnaviridae family.
The lipid bilayer membrane in phycodnaviruses is not well understood or researched. Some studies suggested that the membrane originates from the endoplasmic reticulum and may also be directly acquired from the host cell membrane during viral assembly. Although members of the family Phycodnaviridae are highly diverse, they share very conserved genes involved with virion morphology or structure.
Despite the similarity of the capsid structure of phycodnaviruses, recent experiments have identified morphological differences among members in this family. Emiliania huxleyi virus 86 (EhV-86), a coccolithovirus strain, differs from its algal virus counterparts in that its capsid is enveloped by a lipid membrane. In addition, recent 3D reconstruction experiments revealed that the chlorella virus PBCV-1 has a 250A-long cylindrical spike extending from one of its vertices. EhV-86 may also possess a spike or tail structure.
== Genome ==
Phycodnaviruses are known for their large double-stranded DNA genomes ranging from 100kb to over 550 kb with 40% to 50% GC content. Currently, complete genome sequences are available for several members of the family Phycodnaviridae (including six chloroviruses, two phaeoviruses, several prasinoviruses and a coccolithovirus) and there are also some partial sequences available for a different coccolithovirus.
The genome structures of phycodnaviruses have considerable variation. The chlorovirus PBCV-1 has a linear 330 kb genome with non-permuted double-stranded DNA that is covalently closed by hairpin termini. Similarly, the EsV-1 phaeovirus has a linear double-stranded DNA genome with inverted repeats that have almost perfect homology. These inverted repeats could facilitate effective circularization of the genome and for a period of time it has been suspected that EsV-1 has a circular genome. The EhV-86 coccolithovirus is suggested to have both linear and circular genomes at different phases during DNA packaging. PCR amplification reveals random A/T overhangs, detection of DNA ligases and endonucleases hinting that a linear genome may be packaged and circularizes during DNA replication. The phycodnaviruses have compact genomes for replication efficiency with approximately one gene per 900 to 1000 bp of genome sequences. The EsV-1 phaeovirus is an exception with 231 protein encoding genes, which means it has one gene per approximately 1450 bp. In spite of the compact genomes typically found in viruses, Phycodnaviridae genomes have repetitive regions usually near the terminal ends and certain tandem repeats located throughout the genome. It is suggested that these repetitive sequences may play a role in gene recombination that allows the virus to exchange genetic information with other viruses or the host cell.
== Phylogeny ==
Viruses belonging to Phycodnaviridae harbor double-stranded DNA genomes with sizes of several 100kbp, which together with other Megavirales (e.g. Iridoviridae, Pandoraviridae and Mimiviridae) are named nucleocytoplasmic large DNA viruses. Because of their large genome sizes and various proteins that are encoded, viruses of Phycodnaviridae are challenging the traditional concepts that viruses are small and simple "organisms at the edge of life". Phylogenetic analyses of core genes based on gene concatenation, individual phylogenies of the DNA polymerase, and the major capsid protein, indicate the close evolutionary relationships among members of Phycodnaviridae and between Phycodnaviridae and other families of nucleocytoplasmic large DNA viruses.
== Life cycle ==
=== Raphidovirus ===
In Raphidovirus (likely misspelled Rhaphidovirus), there is only one species, Heterosigma akashiwo virus (HaV), which infects the unicellular alga, Heterosigma akashiwo. H. akashiwo is a member of the class Raphidophyceae, a bloom forming species and is widely distributed in temperate and neritic waters. Several other types of viruses infecting H. akashiwo have been isolated and are not to be confused with HaV, such as the H. akashiwo RNA virus (HaRNAV). and H. akashiwo nuclear inclusion virus (HaNIV). As HaV was first isolated and characterized in 1997, information about the life cycle is limited.
HaV specifically infects H. akashiwo and does not infect other marine phytoplankton species tested. The mechanisms determining the virus-host specificity is not well understood. Tomaru et al. (2008) suggest that virus-host specificity maybe caused by unique interactions between a viral ligand and a host receptor. In a study by Nagaski et al., virus particles were found inside the host cytoplasm at 24 hours post-infection. The latent period or lysogenic cycle was estimated to be 30–33 h with an average burst size (number of viruses produced after lysis) of 770 per cell. Virus particles were found in the subsurface area and in the viroplasm area
=== Coccolithovirus ===
In 2009, MacKinder et al. elucidated the entry mechanism of the genera Coccolithovirus. Using confocal and electron microscopy, the researchers demonstrated that the virus strain EhV-86 uses a unique infection mechanism, which differs from other algal viruses, and shows a greater similarity to the entry and exit strategies seen in animal-like nucleocytoplasmic large double stranded DNA viruses (nucleocytoplasmic large DNA viruses). EhV-86 differs from its algal counterparts in that its capsid is enveloped by a lipid membrane. EhV-86 enters cells by endocytosis (the process by which food or liquid particles are taken into the cell by a vesicle), or direct fusion (the viral envelope fuses with the host membrane). EhV-86 entry by endocytosis results in an additional membrane coat surrounding the capsid encapsulated genome. Regardless of the mechanism of entry, the capsid enters the cytoplasm intact. After entering the cell, the viral capsid disassembles and the DNA is released into the host cytoplasm or directly into the nucleus. EhV-86 is unique to other phycodnaviruses as it encodes six RNA polymerase subunits. Neither PBCV-1 nor ESV-1, for example encodes RNA polymerase components. Viral RNA polymerase genes are not transcribed until at least 2 hours post infection (p.i). At 3–4 p.i, virions are assembled in the cytoplasm, with the help of ATPase (a DNA packaging protein) and transported to the plasma membrane where they are released from the host via a budding mechanism. In this budding mechanism, EhV-86 gains an outer membrane from the host membrane. Burst size ranges from 400 to 1000 particles per cell.
A cluster of sphingolipid-producing genes have been identified in EhV-86. Researchers have found that the production of viral sphingolipids produced during the lytic stage are involved in programmed cell death in coccolithophore populations. A high correlation was found between glycosphingolipid (GSL) production and caspase activity during the lytic stage in infected cells. Caspases are a family of protease enzymes involved in programmed cell death. The researchers also found that a critical concentration of GSLs (>0.06 mg/ml) is required to initiate cell lysis. Thus, the authors suggest that the production of GSLs to a critical concentration may be part of a timing mechanism for the lytic cycle. The authors also suggest that these biomolecules may be able to induce programmed cell death in other unaffected cells, thus serving as an algal bloom termination signal.
=== Phaeovirus ===
Coccolithoviruses and phaeoviruses have been described as having opposing life strategies. The coccolithovirus possesses an Acute life strategy characterized by high reproduction and mutation rates and greater dependency on dense host populations for transmission. Phaeoviruses possess a Persistent life strategy where infection may or may not cause disease, and the genome is passed from parent to offspring.
Phaeoviruses infect the Ectocarpales brown algae, which is an order of filamentous brown algae. One of the most studied phaeoviruses is Ectocarpus siliculosus virus, most commonly known as EsV-1. The EsV-1 virus only infects the single-celled gametes or spores of E. siliculosus. Vegetative cells are immune to infection, as they are protected by a rigid cell wall. Following infection, one copy of the viral DNA is incorporated into the host genome. The EsV-1 viral genome is then replicated and virions are assembled in the sporangia or gametangia of infected plants. Viruses are subsequently released via lysis of reproductive cells, stimulated by changes in environmental conditions, such as an increase in temperature. In healthy plants, environmental stimuli synchronize the release of gametes and zoospores into the surrounding water. Free virus particles can then re-infect free-swimming gametes or spores of healthy plants. Infected gametes or spores undergo mitosis, forming infected plants and all cells of the progeny plant contain viral DNA. However, viral particles are only produced in the reproductive cells of the algae, while viruses remain latent in vegetative cells. In infected sporophytes, cells undergo meiosis and produce haploid spores. The EsV genome is transmitted in a Mendelian manner, where half of the progeny contain viral DNA. Often algae from infected spores are indistinguishable from algae derived from healthy spores, but are partially or fully incapable of reproduction.
=== Chlorovirus ===
Chloroviruses are the only viruses characterized thus far that infect freshwater algae. The hosts of chloroviruses are zoochlorellae, which are endosymbiotic green algae commonly associated with hosts Paramecium bursaria, coelenterate Hydra viridis, or the heliozoan Acanthocystis turfacea. In the ciliate Paramecium bursaria, for example, the algae lives within the cells of the host, providing nutrients via photosynthesis. Living inside the cells of the ciliate offers protection for the algae, and a mode of transportation. Zoochlorellae are resistant to infection in their symbiotic state. When the relationship between the algae and host is disrupted, for example, through grazing by copepods, infection by chloroviruses is permitted.
The life cycle of the chlorovirus infecting Paramecium bursaria, known as PBCV-1 has been studied in detail . Cryo-electron microscopy and 3D reconstruction of the viral capsid shows that there is a long 'spike' structure which first contacts the cell wall and likely serves to puncture the cell wall of the host. The PBCV-1 virus is specific to its host and recognition is mediated by the interaction of virus surface proteins with algal surface carbohydrates. Following attachment of the virus to the host's cell wall, capsid-bound glycolytic enzymes break down the cell wall. The viral membrane likely fuses with the host membrane, allowing the viral DNA to enter the cytoplasm, leaving an empty capsid on the outside. As PBCV-1 lacks an RNA polymerase gene, the virus must use the host cell's machinery to produce viral RNA. Thus, the viral DNA quickly moves to the nucleus where early transcription is initiated 5–10 minutes post infection. Within minutes of infection, host chromosomal degradation occurs, inhibiting host transcription. At 20 minutes post infection, most of the mRNAs in the infected cell are viral mRNAs. The proteins translated from the early stage of transcription are involved in initiating viral DNA replication, occurring 60–90 minutes post infection. The second phase of proteins are translated in the cytoplasm and the assembly of virus capsids begins about 2–3 hours post infection. Mature virions are formed with the addition of newly replicated viral DNA from the host nucleus, likely facilitated by a virus encoded DNA packaging ATPase. About 5–6 hours following PBCV-1 infection, the cytoplasm is filled with virions and lysis occurs at 6–8 hours post infection releasing roughly 1000 particles per cell.
=== Prymnesiovirus ===
The genus Prymnesiovirus currently contains only one species, known as Chrysochromulina brevifilum virus PW1 (CbV-PW1). CbV-PW1 infects two species of marine phytoplankton, Chrysochromulina brevifilum and C. strobilus, belonging to the genus Chrysochromulina. According to the AlgaeBase database, there are currently 63 marine and freshwater species names in the genus, of which 48 are recognized as taxonomically acceptable names. Chrysochromulina is a particularly important genus as it can comprise more than 50% of the photosynthetic nanoplanktonic cells in the ocean.
Little is known about the life cycle of the virus infecting these flagellate-containing planktonic species, Chrysochromulina brevifilum and C. strobilus. Suttle and Chan (1995) were the first to isolate viruses which infect Prymnesiophytes or haptophytes. In this study, ultrathin sections of viruses within Chyrsochromulina brevifilum were prepared and viewed using transmission electron microscopy. Electron micrographs in the early stage of infection suggest that virus replication occurs in the cytoplasm within a viroplasm. A viroplasm is a localized area in the cytoplasm, or around the nucleus of the cell which serves as a 'viral replication factory'. The viroplasm contains components such as virus genetic material, host proteins and ribosomes necessary for replication. Virosomes are often surrounded by a membrane; the membrane surrounding the virosome contained in the infected cells in the study was found to consist of a fibrillar matrix. Virions are released from infected cells following disruption of the organelles and lysis of the host cell membrane. Suttle and Chan (1995) counted more than 320 viruses in an ultrathin section of an infection cell. Estimates for burst sizes range from 320 to 600 viruses per cell.
=== Prasinovirus ===
Members of the genus Prasinovirus infect small unicellular green algae in the order Mamiellales, commonly found in coastal marine waters. A species of the genus Prasinovirus is Micromonas pusilla virus SP1 (MpV-SP1), which was isolated from a water sample collected off of San Diego. The prasinovirus MpV-SP1 infects Micromonas pusilla which is a dominant photosynthetic marine picoeukaryote. and which infects Micromonas pusilla (UTEX 991, Plymouth 27). Common hosts of prasinoviruses include members from the genera Ostreococcus and Micromonas. Three potential species of Ostreococcus have been identified and differ based on their light requirements. One of the most widely studied prasinoviruses, strain OtV5 whose genome is fully sequenced infects Ostreococcus tauri, the smallest free-living eukaryotes currently known.
Prasinoviruses employ a nucleo-cytoplasmic replication strategy where virions adhere to the host-cell surface, followed by injection of DNA into the host cytoplasm. Researchers found that 'empty' OtV5 viruses, or viruses with only the capsid attached to the host membrane, were rarely seen at any stage of the infection, suggesting that virions detach from the host membrane after injection of their DNA. The authors also found that a high proportion of viruses did not attach to cells after inoculation and suggest that viral attachment may be a limiting step in the infection. The viral DNA is then replicated inside the nucleus by the host cell's machinery. Virus particles are assembled in the cytoplasm, usually occupying a space near the inner face of the nucleus. Due to the extremely small size of the algae cells, the average burst size was found to be 25 virus particles per cell.
Viral production without cell lysis has recently been observed in O. tauri cells. Thomas et al. (2011) found that in resistant host cells, the viral genome was replicated and viruses were released via a budding mechanism. This low rate of viral release through budding allows for prolonged survivability of the host and virus progeny, resulting in a stable co-existence.
== Encoded proteins ==
Ectocarpus siliculosus virus (EsV-1), belonging to the genus Phaeovirus, and Paramecium bursaria chlorella virus (PBCV-1), belonging to the genus Chlorovirus, are two well-studied viruses, whose genomes have been found to encode many proteins. These proteins function in virus stability, DNA synthesis, transcription, and other important interactions with the host.
=== Enzymes for glycosylation ===
PBCV-1 has a 54-kDa glycosylated major capsid protein, which comprises about 40% of total viral protein. Unlike most of the viral structural proteins which are glycosylated in the endoplasmic reticulum (ER) and Golgi apparatus by host-encoded glycosyltransferases, PBCV-1 glycosylates its major capsid protein independently by encoding most of the enzymes necessary for constructing the complex oligosaccharides, which then attach to the major capsid protein of PBCV-1 to form the glycoprotein. Therefore, the glycosylation of the major capsid protein of PBCV-1 happens independently of the ER and Golgi apparatus in host cells.
=== Ion channel proteins ===
The first known viral protein that functions as a potassium-selective ion channel was found in PBCV-1. The protein (called Kcv) consists of 94 amino acids and is encoded from a small open reading frame (ORF) (ORF A250R) in PBCV-1, which can produce potassium-selective and voltage-sensitive conductance in Xenopus oocytes. The supposed PBCV-1 protein has a short cytoplasmic N-terminus (12 amino acids) containing one consensus protein kinase C site and it has 2 transmembrane domains. The different amino acid sequences and lack of COOH-terminal cytoplasmic tail make the Kcv protein different from other potassium channels.
EsV-1 encodes a 124 codon ORF that has significant amino acid similarity to PBCV-1 Kcv (41% amino acid identity). However, the EsV-1 protein has a longer N-terminus (35 amino acids) containing two consensus protein kinase C sites and it has three transmembrane domains. It is unknown whether the EsV-1 protein can form a functional channel in heterologous cells. The EsV-1 genome also encodes several proteins with hydrophobic amino acid rich regions that resemble helical transmembrane domains. Among these proteins, the input domain of the supposed hybrid His-kinase 186 and the ORF 188 resemble ion channel proteins.
=== DNA replication-associated proteins ===
Both EsV-1 and PBCV-1 encode DNA polymerase which belong to the DNA polymerase-δ family, and they all contain a proof-reading 3'-5' exonuclease domain. Additionally, both PBCV-1 and EsV-1 encode a sliding clamp processivity factor protein (PCNA), which interacts with proteins involved in DNA replication as well as proteins involved in DNA repair and postreplicative processing (e.g. DNA methylases and DNA transposases).
Heteropentameric replication factor C (RFC) is a complex which is responsible for the ATP-dependent loading of PCNA onto DNA; EsV-1 encodes five proteins which can form a RFC complex. PBCV-1 encodes a single protein which resembles the found in the Archae RFC complex. PBCV-1 also encodes other proteins involved in DNA replication including an ATP-dependent DNA ligase, a type II DNA topoisomerase, and RNase H. Although both EsV-1 and PBCV-1 possess genes for essential elements of the eukaryotic replication system, neither have complete replicative genes, since they all lack genes for primase.
=== Transcription-associated proteins ===
Neither EsV-1 nor PBCV-1 encode a complete RNA polymerase, but they produce several transcription factor-like proteins to assist the host transcription system.
EsV-1 encodes two small polypeptides (ORF 193 and ORF 196) for transcriptional regulation; the proteins resemble the α/β/α domain of TFIID-18 subunit. The TFIID complex is necessary for transcription of eukaryotes, as it binds to the TATA box in the core promoter of the gene to initiate the assembly of RNA polymerase. Besides, polypeptides resemble to the SET, BTB/POZ (i.e. Broad Complex, Tramtrack, and Bric-a-brac/poxvirus and zinc finger) (ORF 40), and BAF60b (ORF 129) domains are also encoded by ESV-1 to regulate chromatin remodeling and transcription repression.
Four transcription factor-like proteins have been found in PBSV-1, including TFIIB (A107L), TFIID (A552R), TFIIS (A125L), and a VLTF-2 type transcription factor (A482R). In addition, PBCV-1 also encodes two enzymes involved in forming a mRNA cap structure, an RNA triphosphatase and a mRNA guanylyltransferase. The PBCV-1 enzymes are more closely related to yeast enzymes than to poxvirus multifunctional RNA capping enzymes according to its size, amino-acid sequence, and biochemical properties. PBCV-1 also encodes RNase III, which is involved in virus mRNAs processing.
=== Nucleotide metabolism-associated proteins ===
To supply deoxynucleotides for viral production in the low proliferating host cells, large DNA viruses possess genes to encode deoxynucleotide synthesis enzymes themselves. Thirteen nucleotide metabolic enzymes have been found in PBCV-1, two of which include dUTP pyrophosphatase and dCMP deaminase, which can produce dUMP (i.e. the substrate for thymidylate synthetase). In comparison, EsV-1 only encodes an ATPase (ORF 26) as well as both subunits of ribonucleotide reductase (ORF 128 and 180), which is a key enzyme in deoxynucleotide synthesis.
=== Other enzymes ===
Other enzymes such as methyltransferases, DNA restriction endonucleases, and integrase were also found in PBCV-1. PBCV-1 also encodes a 187-amino-acid protein that resembles the Cu-Zn SOD with all of the conserved amino acid residues for binding copper and zinc, which can decompose the rapid accumulated superoxide in host cells during infection, thereby benefiting virus replication.
== Ecological implications ==
=== Raphidovirus ===
Heterosigma akashiwo forms dense, harmful blooms in temperate and subarctic waters, occurring at densities up to 5 ×106 cells/ml. These algal blooms can be extremely harmful to aquatic life, causing mortality in wild and cultured fish, such as salmon, yellowtail and sea bream. The severity and duration of these blooms varies from year, and damage to aquaculture by H.akashiwo has been increasing. In 1989, a noxious algal bloom off the coast of New Zealand resulted in the loss of seventeen million New Zealand dollars worth of Chinook salmon. In 1995 and 1997 in Japanese coastal waters in Kagoshimo Bay, 1,090 million and 327 million Yen worth of fish were killed, respectively.
The HaV virus, infecting H. akashiwo has been shown to be a factor in bloom termination. Suttle et al. (1990) suggested that viral infection of algae could have a role in regulating population densities of phytoplankton communities, thus having significant roles in their dynamics in the oceans. Earlier studies, such as the study by Nagasaki et al. (1993), explored the dynamics between HaV and H. akashiwo. Algal samples were obtained in the middle or final stages of a red tide in Hiroshima Bay, Japan. Using transmission electron microscopy, Nagaski et al. identified the HaV virus in and around the nuclear area of H. akashiwo cells. Further support for the role of the HaV virus in bloom termination was provided by a study conducted by Nagaski et al. (1994). Nagaski et al. (1994) found that proportion of virus-containing cells increased quickly before termination of the red tide; no virus-containing cells were detected three days before termination of the red tide and the sample collected on the last day revealed a high frequency (11.5%) of virus-containing cells.
Further studies by Tarutani et al. (2000) also found an association between a decrease in cell density of H. akashiwo with an increase in the abundance of HaV. The researchers found that HaV not only plays in important role in controlling biomass, but also influences the clonal composition or characteristics of H. akashiwo cells. The researchers found that most isolates following bloom termination were resistant to HaV clonal isolates, while during bloom formation resistant cells were a minor component. The authors suggest that viral infection, during the bloom termination period influences the properties of dominant cells in H. akashiwo populations. Selective pressure exerted by the viruses in the later stage of infection may promote genetic diversity, allowing the H. akashiwo population to thrive after bloom termination.
As mentioned, H. akashiwo blooms are detrimental to fish populations in temperate and subarctic waters, and continue to pose serious threats for aquaculture. Nagasaki et al. (1999) examined the growth characteristics of HaV and suggested that HaV could be used as a microbial agent against H. akashiwo red tides. The advantages of using HaV is that it specifically infects H. akashiwo even when other microorganisms are present. Additionally, it has a high growth rate and can be produced at a low cost. Using HaV as a microbial agent is a promising solution for eliminating red tides to protect fisheries and marine life, but as the authors concluded, the effects of various HaV clones on H. akashiwo populations should be explored in greater detail before the virus is used for wide-scale applications.
=== Coccolithovirus ===
The coccolithovirus (EhV) infects the coccolithophore Emiliania huxleyi (E. huxleyi). Coccolithophores are marine haptophytes which are surrounded by microscopic plates made of calcium carbonate. They live in the upper layers of the world's oceans and represent the third most abundant group of phytoplankton, containing about 300 species. E. huxleyi is recognized as the most prominent and ecologically important of the coccolithophores. E. huxleyi has a global distribution from the tropics to subarctic waters and occasionally forms dense blooms which can cover 100,000s of square kilometers. These trillions of coccolithophores produced, then die and sink to the bottom of oceans, contributing to sediment formation, and are the biggest producers of calcite in the oceans. Thus, coccoliths have significant roles in global carbon fixation and the carbon cycle as well as sulfur cycling. Over time, coccolithophores have shaped geological features of our planet. For example, the White Cliffs of Dover are formed from white chalk, or calcium carbonate produced by coccolithophores over millions of years.
Coccolithophore blooms are typically not harmful to marine life in the ocean. As these organisms thrive in nutrient-poor conditions, the coccolithophores offer a source of nutrition for small fish and zooplankton. E. huxylei viruses (EhVs) have been shown to be linked to the termination of these blooms. The termination stage of the bloom is indicated by a color change in the water. When large amounts of coccoliths (carbonate shell surrounding E. huxylei) are shed from E. huxylei cells from cell death or lysis, the water turns white or turquoise. In areas of dense bloom termination, the white color is reflective and can be seen in satellite imagery. Wilson et al. (2002) used analytical flow cytometry to measure the abundance of viruses at different locations in and around the bloom area. The researchers found that the concentrations of viruses were higher inside the 'high reflectance area', suggesting that virus-induced lysis of E. huxleyi cells resulted in coccolith detachment. Other studies by Martinez et al. (2007) and Bratbak et al. (1993) found higher concentrations of EhV viruses as the E. huxleyi bloom declined, indicating that lytic viral infection was the main cause of bloom termination. EhV viruses therefore have important roles in regulating biomass production in marine environments and ecological succession. This regulation of coccolithophore populations by EhV viruses therefore has significant effects on biogeochemical cycles, particularly the carbon cycle.
=== Phaeovirus ===
One of the best-studied phaeoviruses, EsV-1, infects the small, filamentous brown algae E. siliculosus, which has a cosmopolitan distribution (found in most of the world's oceans). The Ectocarpales are closely related to the brown algal group, the Laminariales, which are the most economically important group of brown algae, having a wide range of applications in the cosmetics and food industry.
Muller et al. (1990) were one of the first to explore the causes of gametangium defects in E. siliculosus originating from New Zealand. The researchers identified reproductive cells of E. siliculosus filled with hexagonal particles which were then released into culture medium when the cells burst. Following release of these particles, sporophytes became infected, shown by pathological symptoms, suggesting that the particles are viruses. Such studies allowed for the evaluation of infection potential of E. siliculosus viruses. Using PCR amplification of a viral gene fragment, Muller et al. (2005) monitored levels of pathogen infection in Ectocarpus samples from the Gran Canaria Island, North Atlantic and southern Chile. The researchers found high levels of pathogen prevalence; 40–100% of Ectocarpus specimens contained viral DNA. Similar estimates have been given by Sengco et al. (1996) who estimated that at least 50% of Ectocarpus plants in the world contain viral DNA. This high frequency of viral infection among globally distributed Ectocarpus plants has ecological implications. Viral infection by EsV-1 in E. siliculosus plants, as mentioned, limits reproductive success of infected plants. Thus, the EsV-1 virus plays a key role in regulating populations of E. siliculosus, having further effects on local ecosystem dynamics.
=== Chlorovirus ===
Members of the genus Chlorovirus are found in freshwater sources around the world and infect the green algae symbionts zoochlorellae. There is a lack of information about the role chloroviruses play in freshwater ecology. Despite this, chloroviruses are found in native waters at 1–100 plaque-forming units (PFU)/ml and measurements as high as 100,000 PFU/ml of native water have been obtained. A plaque-forming unit is the number of particles capable of forming visible structures within a cell culture, known as plaques. Abundances of chloroviruses vary with season, with the highest abundances occurring in the spring. Chloroviruses, such as PBCV-1, play a role in regulating host populations of zoochlorella. As mentioned previously, infection of zoochlorella occurs only when the symbiotic relationship with its host is disrupted. Infection of the algae during this stage of host/algae independence will prevent the host and algae relationship from being restored, thus decreasing the survivability of the endosymbiotic hosts of the zoochlorellae, such as Paramecium bursaria. Thus, chloroviruses play in important role in freshwater ecosystems by not only regulating populations of their host, zoochlorellae, but also regulating, to an extent, populations of zoochlorellae hosts as well. Chloroviruses and viruses in general cause death and lysis of their hosts, releasing dissolved organic carbon, nitrogen and phosphorus into the water. These nutrients can then be taken up by bacteria, thus contributing to the microbial loop. Liberation of dissolved organic materials allows for bacterial growth, and bacteria are an important source of food for organisms in higher trophic levels. Consequently, chloroviruses have significant effects on carbon and nutrient flows, influencing freshwater ecosystem dynamics.
=== Prymnesiovirus ===
Prymnesiovirus, CbV-PW1, as mentioned infects the algal genus Chyrsochromulina. Chyrsochromulina, found in global fresh and marine waters, occasionally forms dense blooms which can produce harmful toxins, having negative effects on fisheries. A particularly toxic species called C. polylepis has caused enormous damage to commercial fisheries in Scandinavia. In 1988, this bloom caused a loss of 500 tons of caged fish, worth 5 million US. Given that Chyrsochromulina is a widespread species, and is of significant ecological importance, viral infection and lysis of genus members is likely to have significant impacts on biogeochemical cycles, such as nutrient recycling in aquatic environments. Suttle and Chan suggest that the presence of viruses should have a strong regulatory effect on Chyrsochromulina populations, thus preventing bloom formation or enabling bloom termination, explaining why persistent blooms are an unusual phenomenon in nature.
=== Prasinovirus ===
A commonly studied prasinovirus, OtV5, as mentioned, infects the smallest currently known eukaryote, Ostreococcus tauri. O. tauri is about 0.8 micrometers in diameter and is within the picosize fraction (0.2–2 micrometers). Picoeukaryotes, such as Ostreococcus tauri are widely distributed and contribute significantly to microbial biomass and total primary productivity. In oligotrophic environments, marine picophytoplankton account for up to 90% of the autotrophic biomass and thus are an important food source for nanoplanktonic and phagotrophic protists. As picoeukaryotes serve as the base for marine microbial food webs, they are intrinsic to the survival of higher trophic levels. Ostreococcus tauri has a rapid growth rate and dense blooms have been observed off the coasts of Long Island and California. Samples collected from Long Island bay were found to contain many virus-like particles, a likely cause for the decline of the bloom. Despite the large abundances of picoeukaryotes, these unicellular organisms are outnumbered by viruses by about ten to one. Viruses such as OtV5, play important roles in regulating phytoplankton populations, and through lysis of cells contribute to the recycling of nutrients back towards other microorganisms, otherwise known as the viral shunt.
As mentioned, the prasinovirus MpV-SP1 infects Micromonas pusilla which is a major component of the picophytoplankton of the world's oceans. M. pusilla lives from tropical to polar marine ecosystems. Cottrell & Suttle (1995) found that 2–10% of the M. pusilla population in an inshore environment was lysed per day, with an average of 4.4%. Higher estimates have been given by Evans et al. (2003), who suggest that M. pusilla viruses can lyse up to 25% of the Micromonas population per day. This suggests that viruses are responsible for a moderate amount of mortality in M. pusilla populations. On a larger scale, viral infection of M. pusilla is responsible for nutrient and energy recycling in aquatic food webs, which is yet to be quantified.
== Pathology ==
Until recently phycodnaviruses were believed to infect algal species exclusively. Recently, DNA homologous to Chlorovirus Acanthocystis turfacea virus 1 (ATCV-1) were isolated from human nasopharyngeal mucosal surfaces. The presence of ATCV-1 in the human microbiome was associated with diminished performance on cognitive assessments. Inoculation of ATCV-1 in experimental animals was associated with decreased performance in memory and sensory-motor gating, as well as altered expression of genes in the hippocampus related to synaptic plasticity, learning, memory formation, and the viral immune response.
== References ==
== Further reading ==
== External links ==
Viralzone: Phycodnaviridae
ICTV | Wikipedia/Phycodnaviridae |
Coronavirus disease 2019 (COVID-19, also known as SARS-2) is a contagious disease caused by the coronavirus SARS-CoV-2. In January 2020, the disease spread worldwide, resulting in the COVID-19 pandemic.
The symptoms of COVID‑19 can vary but often include fever, fatigue, cough, breathing difficulties, loss of smell, and loss of taste. Symptoms may begin one to fourteen days after exposure to the virus. At least a third of people who are infected do not develop noticeable symptoms. Of those who develop symptoms noticeable enough to be classified as patients, most (81%) develop mild to moderate symptoms (up to mild pneumonia), while 14% develop severe symptoms (dyspnea, hypoxia, or more than 50% lung involvement on imaging), and 5% develop critical symptoms (respiratory failure, shock, or multiorgan dysfunction). Older people have a higher risk of developing severe symptoms. Some complications result in death. Some people continue to experience a range of effects (long COVID) for months or years after infection, and damage to organs has been observed. Multi-year studies on the long-term effects are ongoing.
COVID‑19 transmission occurs when infectious particles are breathed in or come into contact with the eyes, nose, or mouth. The risk is highest when people are in close proximity, but small airborne particles containing the virus can remain suspended in the air and travel over longer distances, particularly indoors. Transmission can also occur when people touch their eyes, nose, or mouth after touching surfaces or objects that have been contaminated by the virus. People remain contagious for up to 20 days and can spread the virus even if they do not develop symptoms.
Testing methods for COVID-19 to detect the virus's nucleic acid include real-time reverse transcription polymerase chain reaction (RT‑PCR), transcription-mediated amplification, and reverse transcription loop-mediated isothermal amplification (RT‑LAMP) from a nasopharyngeal swab.
Several COVID-19 vaccines have been approved and distributed in various countries, many of which have initiated mass vaccination campaigns. Other preventive measures include physical or social distancing, quarantining, ventilation of indoor spaces, use of face masks or coverings in public, covering coughs and sneezes, hand washing, and keeping unwashed hands away from the face. While drugs have been developed to inhibit the virus, the primary treatment is still symptomatic, managing the disease through supportive care, isolation, and experimental measures.
The first known case was identified in Wuhan, China, in December 2019. Most scientists believe that the SARS-CoV-2 virus entered into human populations through natural zoonosis, similar to the SARS-CoV-1 and MERS-CoV outbreaks, and consistent with other pandemics in human history. Social and environmental factors including climate change, natural ecosystem destruction and wildlife trade increased the likelihood of such zoonotic spillover.
== Nomenclature ==
During the initial outbreak in Wuhan, the virus and disease were commonly referred to as "coronavirus" and "Wuhan coronavirus", with the disease sometimes called "Wuhan pneumonia". In the past, many diseases have been named after geographical locations, such as the Spanish flu, Middle East respiratory syndrome, and Zika virus. In January 2020, the World Health Organization (WHO) recommended 2019-nCoV and 2019-nCoV acute respiratory disease as interim names for the virus and disease per 2015 guidance and international guidelines against using geographical locations or groups of people in disease and virus names to prevent social stigma. The official names COVID‑19 and SARS-CoV-2 were issued by the WHO on 11 February 2020 with COVID-19 being shorthand for "coronavirus disease 2019". The WHO additionally uses "the COVID‑19 virus" and "the virus responsible for COVID‑19" in public communications.
== Symptoms and signs ==
=== Complications ===
Complications may include pneumonia, acute respiratory distress syndrome (ARDS), multi-organ failure, septic shock, and death. Cardiovascular complications may include heart failure, arrhythmias (including atrial fibrillation), heart inflammation, thrombosis, particularly venous thromboembolism, and endothelial cell injury and dysfunction. Approximately 20–30% of people who present with COVID‑19 have elevated liver enzymes, reflecting liver injury.
Neurologic manifestations include seizure, stroke, encephalitis, and Guillain–Barré syndrome (which includes loss of motor functions). Following the infection, children may develop paediatric multisystem inflammatory syndrome, which has symptoms similar to Kawasaki disease, which can be fatal. In very rare cases, acute encephalopathy can occur, and it can be considered in those who have been diagnosed with COVID‑19 and have an altered mental status.
According to the US Centers for Disease Control and Prevention, pregnant women are at increased risk of becoming seriously ill from COVID‑19. This is because pregnant women with COVID‑19 appear to be more likely to develop respiratory and obstetric complications that can lead to miscarriage, premature delivery and intrauterine growth restriction.
Fungal infections such as aspergillosis, candidiasis, cryptococcosis and mucormycosis have been recorded in people recovering from COVID‑19.
== Cause ==
COVID‑19 is caused by infection with a strain of coronavirus known as "severe acute respiratory syndrome coronavirus 2" (SARS-CoV-2).
=== Transmission ===
=== Virology ===
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel severe acute respiratory syndrome coronavirus. It was first isolated from three people with pneumonia connected to the cluster of acute respiratory illness cases in Wuhan. All structural features of the novel SARS-CoV-2 virus particle occur in related coronaviruses in nature, particularly in Rhinolophus sinicus (Chinese horseshoe bats).
Outside the human body, the virus is destroyed by household soap which bursts its protective bubble. Hospital disinfectants, alcohols, heat, povidone-iodine, and ultraviolet-C (UV-C) irradiation are also effective disinfection methods for surfaces.
SARS-CoV-2 is closely related to the original SARS-CoV. It is thought to have an animal (zoonotic) origin. Genetic analysis has revealed that the coronavirus genetically clusters with the genus Betacoronavirus, in subgenus Sarbecovirus (lineage B) together with two bat-derived strains. It is 96% identical at the whole genome level to other bat coronavirus samples (BatCov RaTG13). The structural proteins of SARS-CoV-2 include membrane glycoprotein (M), envelope protein (E), nucleocapsid protein (N), and the spike protein (S). The M protein of SARS-CoV-2 is about 98% similar to the M protein of bat SARS-CoV, maintains around 98% homology with pangolin SARS-CoV, and has 90% homology with the M protein of SARS-CoV; whereas, the similarity is only around 38% with the M protein of MERS-CoV.
=== SARS-CoV-2 variants ===
The many thousands of SARS-CoV-2 variants are grouped into either clades or lineages. The WHO, in collaboration with partners, expert networks, national authorities, institutions and researchers, have established nomenclature systems for naming and tracking SARS-CoV-2 genetic lineages by GISAID, Nextstrain and Pango. The expert group convened by the WHO recommended the labelling of variants using letters of the Greek alphabet, for example, Alpha, Beta, Delta, and Gamma, giving the justification that they "will be easier and more practical to discussed by non-scientific audiences". Nextstrain divides the variants into five clades (19A, 19B, 20A, 20B, and 20C), while GISAID divides them into seven (L, O, V, S, G, GH, and GR). The Pango tool groups variants into lineages, with many circulating lineages being classed under the B.1 lineage.
Several notable variants of SARS-CoV-2 emerged throughout 2020. Cluster 5 emerged among minks and mink farmers in Denmark. After strict quarantines and the slaughter of all the country's mink, the cluster was assessed to no longer be circulating among humans in Denmark as of 1 February 2021.
As of December 2021, there are five dominant variants of SARS-CoV-2 spreading among global populations: the Alpha variant (B.1.1.7, formerly called the UK variant), first found in London and Kent, the Beta variant (B.1.351, formerly called the South Africa variant), the Gamma variant (P.1, formerly called the Brazil variant), the Delta variant (B.1.617.2, formerly called the India variant), and the Omicron variant (B.1.1.529), which had spread to 57 countries as of 7 December.
On 19 December 2023, the WHO declared that another distinctive variant, JN.1, had emerged as a "variant of interest". Though the WHO expected an increase in cases globally, particularly for countries entering winter, the overall global health risk was considered low.
== Pathophysiology ==
The SARS-CoV-2 virus can infect a wide range of cells and systems of the body. COVID‑19 is most known for affecting the upper respiratory tract (sinuses, nose, and throat) and the lower respiratory tract (windpipe and lungs). The lungs are the organs most affected by COVID‑19 because the virus accesses host cells via the receptor for the enzyme angiotensin-converting enzyme 2 (ACE2), which is most abundant on the surface of type II alveolar cells of the lungs. The virus uses a special surface glycoprotein called a "spike" to connect to the ACE2 receptor and enter the host cell.
=== Respiratory tract ===
Following viral entry, COVID‑19 infects the ciliated epithelium of the nasopharynx and upper airways. Autopsies of people who died of COVID‑19 have found diffuse alveolar damage, and lymphocyte-containing inflammatory infiltrates within the lung.
From the CT scans of COVID-19 infected lungs, white patches were observed containing fluid known as ground-glass opacity (GGO) or simply ground glass. This tended to correlate with the clear jelly liquid found in lung autopsies of people who died of COVID-19. One possibility addressed in medical research is that hyuralonic acid (HA) could be the leading factor for this observation of the clear jelly liquid found in the lungs, in what could be hyuralonic storm, in conjunction with cytokine storm.
=== Nervous system ===
One common symptom, loss of smell, results from infection of the support cells of the olfactory epithelium, with subsequent damage to the olfactory neurons. The involvement of both the central and peripheral nervous system in COVID‑19 has been reported in many medical publications. It is clear that many people with COVID-19 exhibit neurological or mental health issues. The virus is not detected in the central nervous system (CNS) of the majority of people with COVID-19 who also have neurological issues. However, SARS-CoV-2 has been detected at low levels in the brains of those who have died from COVID‑19, but these results need to be confirmed. While virus has been detected in cerebrospinal fluid of autopsies, the exact mechanism by which it invades the CNS remains unclear and may first involve invasion of peripheral nerves given the low levels of ACE2 in the brain. The virus may also enter the bloodstream from the lungs and cross the blood–brain barrier to gain access to the CNS, possibly within an infected white blood cell.
Research conducted when Alpha was the dominant variant has suggested COVID-19 may cause brain damage. Later research showed that all variants studied (including Omicron) killed brain cells, but the exact cells killed varied by variant. It is unknown if such damage is temporary or permanent. Observed individuals infected with COVID-19 (most with mild cases) experienced an additional 0.2% to 2% of brain tissue lost in regions of the brain connected to the sense of smell compared with uninfected individuals, and the overall effect on the brain was equivalent on average to at least one extra year of normal ageing; infected individuals also scored lower on several cognitive tests. All effects were more pronounced among older ages.
=== Gastrointestinal tract ===
The virus also affects gastrointestinal organs as ACE2 is abundantly expressed in the glandular cells of gastric, duodenal and rectal epithelium as well as endothelial cells and enterocytes of the small intestine.
=== Cardiovascular system ===
The virus can cause acute myocardial injury and chronic damage to the cardiovascular system. An acute cardiac injury was found in 12% of infected people admitted to the hospital in Wuhan, China, and is more frequent in severe disease. Rates of cardiovascular symptoms are high, owing to the systemic inflammatory response and immune system disorders during disease progression, but acute myocardial injuries may also be related to ACE2 receptors in the heart. ACE2 receptors are highly expressed in the heart and are involved in heart function.
A high incidence of thrombosis and venous thromboembolism occurs in people transferred to intensive care units with COVID‑19 infections, and may be related to poor prognosis. Blood vessel dysfunction and clot formation (as suggested by high D-dimer levels caused by blood clots) may have a significant role in mortality, incidents of clots leading to pulmonary embolisms, and ischaemic events (strokes) within the brain found as complications leading to death in people infected with COVID‑19. Infection may initiate a chain of vasoconstrictive responses within the body, including pulmonary vasoconstriction – a possible mechanism in which oxygenation decreases during pneumonia. Furthermore, damage of arterioles and capillaries was found in brain tissue samples of people who died from COVID‑19.
COVID‑19 may also cause substantial structural changes to blood cells, sometimes persisting for months after hospital discharge. A low level of blood lymphocytess may result from the virus acting through ACE2-related entry into lymphocytes.
=== Kidneys ===
Another common cause of death is complications related to the kidneys. Early reports show that up to 30% of people hospitalised with COVID-19 both in China and in New York have experienced some injury to their kidneys, including some persons with no previous kidney problems.
=== Immunopathology ===
Although SARS-CoV-2 has a tropism for ACE2-expressing epithelial cells of the respiratory tract, people with severe COVID‑19 have symptoms of systemic hyperinflammation. Clinical laboratory findings of elevated IL‑2, IL‑6, IL‑7, as well as the following suggest an underlying immunopathology:
Granulocyte-macrophage colony-stimulating factor (GM‑CSF)
Interferon gamma-induced protein 10 (IP‑10)
Monocyte chemoattractant protein 1 (MCP1)
Macrophage inflammatory protein 1‑alpha (MIP‑1‑alpha)
Tumour necrosis factor (TNF‑α) indicative of cytokine release syndrome (CRS)
Interferon alpha plays a complex, Janus-faced role in the pathogenesis of COVID-19. Although it promotes the elimination of virus-infected cells, it also upregulates the expression of ACE-2, thereby facilitating the SARS-Cov2 virus to enter cells and to replicate. A competition of negative feedback loops (via protective effects of interferon alpha) and positive feedback loops (via upregulation of ACE-2) is assumed to determine the fate of people with COVID-19.
Additionally, people with COVID‑19 and acute respiratory distress syndrome (ARDS) have classical serum biomarkers of CRS, including elevated C-reactive protein (CRP), lactate dehydrogenase (LDH), D-dimer, and ferritin.
Systemic inflammation results in vasodilation, allowing inflammatory lymphocytic and monocytic infiltration of the lung and the heart. In particular, pathogenic GM-CSF-secreting T cells were shown to correlate with the recruitment of inflammatory IL-6-secreting monocytes and severe lung pathology in people with COVID‑19. Lymphocytic infiltrates have also been reported at autopsy.
=== Viral and host factors ===
==== Virus proteins ====
Multiple viral and host factors affect the pathogenesis of the virus. The S-protein, otherwise known as the spike protein, is the viral component that attaches to the host receptor via the ACE2 receptors. It includes two subunits: S1 and S2.
S1 determines the virus-host range and cellular tropism via the receptor-binding domain.
S2 mediates the membrane fusion of the virus to its potential cell host via the H1 and HR2, which are heptad repeat regions.
Studies have shown that S1 domain induced IgG and IgA antibody levels at a much higher capacity. It is the focus spike proteins expression that are involved in many effective COVID‑19 vaccines.
The M protein is the viral protein responsible for the transmembrane transport of nutrients. It is the cause of the bud release and the formation of the viral envelope. The N and E protein are accessory proteins that interfere with the host's immune response.
==== Host factors ====
Human angiotensin converting enzyme 2 (hACE2) is the host factor that SARS-CoV-2 virus targets causing COVID‑19. Theoretically, the usage of angiotensin receptor blockers (ARB) and ACE inhibitors upregulating ACE2 expression might increase morbidity with COVID‑19, though animal data suggest some potential protective effect of ARB; however no clinical studies have proven susceptibility or outcomes. Until further data is available, guidelines and recommendations for people with hypertension remain.
The effect of the virus on ACE2 cell surfaces leads to leukocytic infiltration, increased blood vessel permeability, alveolar wall permeability, as well as decreased secretion of lung surfactants. These effects cause the majority of the respiratory symptoms. However, the aggravation of local inflammation causes a cytokine storm eventually leading to a systemic inflammatory response syndrome.
Among healthy adults not exposed to SARS-CoV-2, about 35% have CD4+ T cells that recognise the SARS-CoV-2 S protein (particularly the S2 subunit) and about 50% react to other proteins of the virus, suggesting cross-reactivity from previous common colds caused by other coronaviruses.
It is unknown whether different persons use similar antibody genes in response to COVID‑19.
=== Host cytokine response ===
The severity of the inflammation can be attributed to the severity of what is known as the cytokine storm. Levels of interleukin 1B, interferon-gamma, interferon-inducible protein 10, and monocyte chemoattractant protein 1 were all associated with COVID‑19 disease severity. Treatment has been proposed to combat the cytokine storm as it remains to be one of the leading causes of morbidity and mortality in COVID‑19 disease.
A cytokine storm is due to an acute hyperinflammatory response that is responsible for clinical illness in an array of diseases but in COVID‑19, it is related to worse prognosis and increased fatality. The storm causes acute respiratory distress syndrome, blood clotting events such as strokes, myocardial infarction, encephalitis, acute kidney injury, and vasculitis. The production of IL-1, IL-2, IL-6, TNF-alpha, and interferon-gamma, all crucial components of normal immune responses, inadvertently become the causes of a cytokine storm. The cells of the central nervous system, the microglia, neurons, and astrocytes, are also involved in the release of pro-inflammatory cytokines affecting the nervous system, and effects of cytokine storms toward the CNS are not uncommon.
=== Pregnancy response ===
There are many unknowns for pregnant women during the COVID-19 pandemic. Given that they are prone to have complications and severe disease infection with other types of coronaviruses, they have been identified as a vulnerable group and advised to take supplementary preventive measures.
Physiological responses to pregnancy can include:
Immunological: The immunological response to COVID-19, like other viruses, depends on a working immune system. It adapts during pregnancy to allow the development of the foetus whose genetic load is only partially shared with their mother, leading to a different immunological reaction to infections during the course of pregnancy.
Respiratory: Many factors can make pregnant women more vulnerable to hard respiratory infections. One of them is the total reduction of the lungs' capacity and inability to clear secretions.
Coagulation: During pregnancy, there are higher levels of circulating coagulation factors, and the pathogenesis of SARS-CoV-2 infection can be implicated. The thromboembolic events with associated mortality are a risk for pregnant women.
However, from the evidence base, it is difficult to conclude whether pregnant women are at increased risk of grave consequences of this virus.
In addition to the above, other clinical studies have proved that SARS-CoV-2 can affect the period of pregnancy in different ways. On the one hand, there is little evidence of its impact up to 12 weeks gestation. On the other hand, COVID-19 infection may cause increased rates of unfavourable outcomes in the course of the pregnancy. Some examples of these could be foetal growth restriction, preterm birth, and perinatal mortality, which refers to the foetal death past 22 or 28 completed weeks of pregnancy as well as the death among live-born children up to seven completed days of life. For preterm birth, a 2023 review indicates that there appears to be a correlation with COVID-19.
Unvaccinated women in later stages of pregnancy with COVID-19 are more likely than other people to need very intensive care. Babies born to mothers with COVID-19 are more likely to have breathing problems. Pregnant women are strongly encouraged to get vaccinated.
== Diagnosis ==
COVID‑19 can provisionally be diagnosed on the basis of symptoms and confirmed using reverse transcription polymerase chain reaction (RT-PCR) or other nucleic acid testing of infected secretions. Along with laboratory testing, chest CT scans may be helpful to diagnose COVID‑19 in individuals with a high clinical suspicion of infection. Detection of a past infection is possible with serological tests, which detect antibodies produced by the body in response to the infection.
=== Viral testing ===
The standard methods of testing for presence of SARS-CoV-2 are nucleic acid tests, which detects the presence of viral RNA fragments. As these tests detect RNA but not infectious virus, its "ability to determine duration of infectivity of patients is limited". The test is typically done on respiratory samples obtained by a nasopharyngeal swab; however, a nasal swab or sputum sample may also be used. Results are generally available within hours. The WHO has published several testing protocols for the disease.
Several laboratories and companies have developed serological tests, which detect antibodies produced by the body in response to infection. Some have been evaluated by Public Health England and approved for use in the UK.
The University of Oxford's CEBM has pointed to mounting evidence that "a good proportion of 'new' mild cases and people re-testing positives after quarantine or discharge from hospital are not infectious, but are simply clearing harmless virus particles which their immune system has efficiently dealt with" and have called for "an international effort to standardize and periodically calibrate testing" In September 2020, the UK government issued "guidance for procedures to be implemented in laboratories to provide assurance of positive SARS-CoV-2 RNA results during periods of low prevalence, when there is a reduction in the predictive value of positive test results".
=== Imaging ===
Chest CT scans may be helpful to diagnose COVID‑19 in individuals with a high clinical suspicion of infection but are not recommended for routine screening. Bilateral multilobar ground-glass opacities with a peripheral, asymmetric, and posterior distribution are common in early infection. Subpleural dominance, crazy paving (lobular septal thickening with variable alveolar filling), and consolidation may appear as the disease progresses. Characteristic imaging features on chest radiographs and computed tomography (CT) of people who are symptomatic include asymmetric peripheral ground-glass opacities without pleural effusions.
Many groups have created COVID‑19 datasets that include imagery such as the Italian Radiological Society which has compiled an international online database of imaging findings for confirmed cases. Due to overlap with other infections such as adenovirus, imaging without confirmation by rRT-PCR is of limited specificity in identifying COVID‑19. A large study in China compared chest CT results to PCR and demonstrated that though imaging is less specific for the infection, it is faster and more sensitive.
=== Coding ===
In late 2019, the WHO assigned emergency ICD-10 disease codes U07.1 for deaths from lab-confirmed SARS-CoV-2 infection and U07.2 for deaths from clinically or epidemiologically diagnosed COVID‑19 without lab-confirmed SARS-CoV-2 infection.
=== Pathology ===
The main pathological findings at autopsy are:
Macroscopy: pericarditis, lung consolidation and pulmonary oedema
Lung findings:
Minor serous exudation, minor fibrin exudation
Pulmonary oedema, pneumocyte hyperplasia, large atypical pneumocytes, interstitial inflammation with lymphocytic infiltration and multinucleated giant cell formation
Diffuse alveolar damage (DAD) with diffuse alveolar exudates. DAD is the cause of acute respiratory distress syndrome (ARDS) and severe hypoxaemia.
Organisation of exudates in alveolar cavities and pulmonary interstitial fibrosis
Plasmocytosis in bronchoalveolar lavage (BAL)
Blood and vessels: disseminated intravascular coagulation (DIC); leukoerythroblastic reaction, endotheliitis, hemophagocytosis
Heart: cardiac muscle cell necrosis
Liver: microvesicular steatosis
Nose: shedding of olfactory epithelium
Brain: infarction
Kidneys: acute tubular damage.
Spleen: white pulp depletion.
== Prevention ==
Preventive measures to reduce the chances of infection include getting vaccinated, staying at home, wearing a mask in public, avoiding crowded places, keeping distance from others, ventilating indoor spaces, managing potential exposure durations, washing hands with soap and water often and for at least twenty seconds, practising good respiratory hygiene, and avoiding touching the eyes, nose, or mouth with unwashed hands.
Those diagnosed with COVID‑19 or who believe they may be infected are advised by the CDC to stay home except to get medical care, call ahead before visiting a healthcare provider, wear a face mask before entering the healthcare provider's office and when in any room or vehicle with another person, cover coughs and sneezes with a tissue, regularly wash hands with soap and water and avoid sharing personal household items.
The first COVID‑19 vaccine was granted regulatory approval on 2 December 2020 by the UK medicines regulator MHRA. It was evaluated for emergency use authorisation (EUA) status by the US FDA, and in several other countries. Initially, the US National Institutes of Health guidelines do not recommend any medication for prevention of COVID‑19, before or after exposure to the SARS-CoV-2 virus, outside the setting of a clinical trial. Without a vaccine, other prophylactic measures, or effective treatments, a key part of managing COVID‑19 is trying to decrease and delay the epidemic peak, known as "flattening the curve". This is done by slowing the infection rate to decrease the risk of health services being overwhelmed, allowing for better treatment of active cases, and delaying additional cases until effective treatments or a vaccine become available.
=== Vaccine ===
=== Face masks and respiratory hygiene ===
=== Indoor ventilation and avoiding crowded indoor spaces ===
The CDC states that avoiding crowded indoor spaces reduces the risk of COVID-19 infection. When indoors, increasing the rate of air change, decreasing recirculation of air and increasing the use of outdoor air can reduce transmission. The WHO recommends ventilation and air filtration in public spaces to help clear out infectious aerosols.
Exhaled respiratory particles can build-up within enclosed spaces with inadequate ventilation. The risk of COVID‑19 infection increases especially in spaces where people engage in physical exertion or raise their voice (e.g., exercising, shouting, singing) as this increases exhalation of respiratory droplets. Prolonged exposure to these conditions, typically more than 15 minutes, leads to higher risk of infection.
Displacement ventilation with large natural inlets can move stale air directly to the exhaust in laminar flow while significantly reducing the concentration of droplets and particles. Passive ventilation reduces energy consumption and maintenance costs but may lack controllability and heat recovery. Displacement ventilation can also be achieved mechanically with higher energy and maintenance costs. The use of large ducts and openings helps to prevent mixing in closed environments. Recirculation and mixing should be avoided because recirculation prevents dilution of harmful particles and redistributes possibly contaminated air, and mixing increases the concentration and range of infectious particles and keeps larger particles in the air.
=== Hand-washing and hygiene ===
Thorough hand hygiene after any cough or sneeze is required. The WHO also recommends that individuals wash hands often with soap and water for at least 20 seconds, especially after going to the toilet or when hands are visibly dirty, before eating and after blowing one's nose. When soap and water are not available, the CDC recommends using an alcohol-based hand sanitiser with at least 60% alcohol. For areas where commercial hand sanitisers are not readily available, the WHO provides two formulations for local production. In these formulations, the antimicrobial activity arises from ethanol or isopropanol. Hydrogen peroxide is used to help eliminate bacterial spores in the alcohol; it is "not an active substance for hand antisepsis". Glycerol is added as a humectant.
=== Social distancing ===
Social distancing (also known as physical distancing) includes infection control actions intended to slow the spread of the disease by minimising close contact between individuals. Methods include quarantines; travel restrictions; and the closing of schools, workplaces, stadiums, theatres, or shopping centres. Individuals may apply social distancing methods by staying at home, limiting travel, avoiding crowded areas, using no-contact greetings, and physically distancing themselves from others.
In 2020, outbreaks occurred in prisons due to crowding and an inability to enforce adequate social distancing. In the United States, the prisoner population is ageing and many of them are at high risk for poor outcomes from COVID‑19 due to high rates of coexisting heart and lung disease, and poor access to high-quality healthcare.
=== Surface cleaning ===
After being expelled from the body, coronaviruses can survive on surfaces for hours to days. If a person touches the dirty surface, they may deposit the virus at the eyes, nose, or mouth where it can enter the body and cause infection. Evidence indicates that contact with infected surfaces is not the main driver of COVID‑19, leading to recommendations for optimised disinfection procedures to avoid issues such as the increase of antimicrobial resistance through the use of inappropriate cleaning products and processes. Deep cleaning and other surface sanitation has been criticised as hygiene theatre, giving a false sense of security against something primarily spread through the air.
The amount of time that the virus can survive depends significantly on the type of surface, the temperature, and the humidity. Coronaviruses die very quickly when exposed to the UV light in sunlight. Like other enveloped viruses, SARS-CoV-2 survives longest when the temperature is at room temperature or lower, and when the relative humidity is low (<50%).
On many surfaces, including glass, some types of plastic, stainless steel, and skin, the virus can remain infective for several days indoors at room temperature, or even about a week under ideal conditions. On some surfaces, including cotton fabric and copper, the virus usually dies after a few hours. The virus dies faster on porous surfaces than on non-porous surfaces due to capillary action within pores and faster aerosol droplet evaporation. However, of the many surfaces tested, two with the longest survival times are N95 respirator masks and surgical masks, both of which are considered porous surfaces.
The CDC says that in most situations, cleaning surfaces with soap or detergent, not disinfecting, is enough to reduce risk of transmission. The CDC recommends that if a COVID‑19 case is suspected or confirmed at a facility such as an office or day care, all areas such as offices, bathrooms, common areas, shared electronic equipment like tablets, touch screens, keyboards, remote controls, and ATMs used by the ill persons should be disinfected. Surfaces may be decontaminated with the following:
62–71% ethanol
50–100% isopropanol
0.1% sodium hypochlorite
0.5% hydrogen peroxide
0.2–7.5% povidone-iodine
50–200 ppm hypochlorous acid
Other solutions, such as benzalkonium chloride and chlorhexidine gluconate, are less effective. Ultraviolet germicidal irradiation may also be used, although popular devices require 5–10 min exposure and may deteriorate some materials over time. A datasheet listing the authorised substances to disinfection in the food industry (including suspension or surface tested, kind of surface, use dilution, disinfectant and inoculum volumes) can be seen in the supplementary material of a 2021 Foods article.
=== Self-isolation ===
Self-isolation at home has been recommended for those diagnosed with COVID‑19 and those who suspect they have been infected. Health agencies have issued detailed instructions for proper self-isolation. Many governments have mandated or recommended self-quarantine for entire populations. The strongest self-quarantine instructions have been issued to those in high-risk groups. Those who may have been exposed to someone with COVID‑19 and those who have recently travelled to a country or region with the widespread transmission have been advised to self-quarantine for 14 days from the time of last possible exposure.
=== International travel-related control measures ===
A 2021 Cochrane rapid review found that based upon low-certainty evidence, international travel-related control measures such as restricting cross-border travel may help to contain the spread of COVID‑19. Additionally, symptom/exposure-based screening measures at borders may miss many positive cases. While test-based border screening measures may be more effective, it could also miss many positive cases if only conducted upon arrival without follow-up. The review concluded that a minimum 10-day quarantine may be beneficial in preventing the spread of COVID‑19 and may be more effective if combined with an additional control measure like border screening.
== Treatment ==
== Prognosis and risk factors ==
The severity of COVID‑19 varies. The disease may take a mild course with few or no symptoms, resembling other common upper respiratory diseases such as the common cold. In 3–4% of cases (7.4% for those over age 65) symptoms are severe enough to cause hospitalisation. Mild cases typically recover within two weeks, while those with severe or critical diseases may take three to six weeks to recover. Among those who have died, the time from symptom onset to death has ranged from two to eight weeks. The Italian Istituto Superiore di Sanità reported that the median time between the onset of symptoms and death was twelve days, with seven being hospitalised. However, people transferred to an ICU had a median time of ten days between hospitalisation and death. Abnormal sodium levels during hospitalisation with COVID-19 are associated with poor prognoses: high sodium with a greater risk of death, and low sodium with an increased chance of needing ventilator support. Prolonged prothrombin time and elevated C-reactive protein levels on admission to the hospital are associated with severe course of COVID‑19 and with a transfer to ICU.
Some early studies suggest 10% to 20% of people with COVID‑19 will experience symptoms lasting longer than a month. A majority of those who were admitted to hospital with severe disease report long-term problems including fatigue and shortness of breath. On 30 October 2020, WHO chief Tedros Adhanom warned that "to a significant number of people, the COVID virus poses a range of serious long-term effects". He has described the vast spectrum of COVID‑19 symptoms that fluctuate over time as "really concerning". They range from fatigue, a cough and shortness of breath, to inflammation and injury of major organs – including the lungs and heart, and also neurological and psychologic effects. Symptoms often overlap and can affect any system in the body. Infected people have reported cyclical bouts of fatigue, headaches, months of complete exhaustion, mood swings, and other symptoms. Tedros therefore concluded that a strategy of achieving herd immunity by infection, rather than vaccination, is "morally unconscionable and unfeasible".
In terms of hospital readmissions about 9% of 106,000 individuals had to return for hospital treatment within two months of discharge. The average to readmit was eight days since first hospital visit. There are several risk factors that have been identified as being a cause of multiple admissions to a hospital facility. Among these are advanced age (above 65 years of age) and presence of a chronic condition such as diabetes, COPD, heart failure or chronic kidney disease.
According to scientific reviews smokers are more likely to require intensive care or die compared to non-smokers. Acting on the same ACE2 pulmonary receptors affected by smoking, air pollution has been correlated with the disease. Short-term and chronic exposure to air pollution seems to enhance morbidity and mortality from COVID‑19. Pre-existing heart and lung diseases and also obesity, especially in conjunction with fatty liver disease, contributes to an increased health risk of COVID‑19.
It is also assumed that those that are immunocompromised are at higher risk of getting severely sick from SARS-CoV-2. One research study that looked into the COVID‑19 infections in hospitalised kidney transplant recipients found a mortality rate of 11%.
Men with untreated hypogonadism were 2.4 times more likely than men with eugonadism to be hospitalised if they contracted COVID-19; Hypogonad men treated with testosterone were less likely to be hospitalised for COVID-19 than men who were not treated for hypogonadism.
=== Genetic risk factors ===
Genetics plays an important role in the ability to fight off Covid. For instance, those that do not produce detectable type I interferons or produce auto-antibodies against these may get much sicker from COVID‑19. Genetic screening is able to detect interferon effector genes. Some genetic variants are risk factors in specific populations. For instance, an allele of the DOCK2 gene (dedicator of cytokinesis 2 gene) is a common risk factor in Asian populations but much less common in Europe. The mutation leads to lower expression of DOCK2 especially in younger people with severe COVID-19 infections. In fact, many other genes and genetic variants have been found that determine the outcome of SARS-CoV-2 infections.
=== Children ===
While very young children have experienced lower rates of infection, older children have a rate of infection that is similar to the population as a whole. Children are likely to have milder symptoms and are at lower risk of severe disease than adults. The CDC reports that in the US roughly a third of hospitalised children were admitted to the ICU, while a European multinational study of hospitalised children from June 2020, found that about 8% of children admitted to a hospital needed intensive care. Four of the 582 children (0.7%) in the European study died, but the actual mortality rate may be "substantially lower" since milder cases that did not seek medical help were not included in the study.
=== Long-term effects ===
Around 10% to 30% of non-hospitalised people with COVID-19 go on to develop long COVID. For those that do need hospitalisation, the incidence of long-term effects is over 50%. Long COVID is an often severe multisystem disease with a large set of symptoms. There are likely various, possibly coinciding, causes. Organ damage from the acute infection can explain a part of the symptoms, but long COVID is also observed in people where organ damage seems to be absent.
By a variety of mechanisms, the lungs are the organs most affected in COVID‑19. In people requiring hospital admission, up to 98% of CT scans performed show lung abnormalities after 28 days of illness even if they had clinically improved. People with advanced age, severe disease, prolonged ICU stays, or who smoke are more likely to have long-lasting effects, including pulmonary fibrosis. Overall, approximately one-third of those investigated after four weeks will have findings of pulmonary fibrosis or reduced lung function as measured by DLCO, even in asymptomatic people, but with the suggestion of continuing improvement with the passing of more time. After severe disease, lung function can take anywhere from three months to a year or more to return to previous levels.
The risks of cognitive deficit, dementia, psychotic disorders, and epilepsy or seizures persists at an increased level two years after infection.
=== Immunity ===
The immune response by humans to SARS-CoV-2 virus occurs as a combination of the cell-mediated immunity and antibody production, just as with most other infections. B cells interact with T cells and begin dividing before selection into the plasma cell, partly on the basis of their affinity for antigen. Since SARS-CoV-2 has been in the human population only since December 2019, it remains unknown if the immunity is long-lasting in people who recover from the disease. The presence of neutralising antibodies in blood strongly correlates with protection from infection, but the level of neutralising antibody declines with time. Those with asymptomatic or mild disease had undetectable levels of neutralising antibody two months after infection. In another study, the level of neutralising antibodies fell four-fold one to four months after the onset of symptoms. However, the lack of antibodies in the blood does not mean antibodies will not be rapidly produced upon reexposure to SARS-CoV-2. Memory B cells specific for the spike and nucleocapsid proteins of SARS-CoV-2 last for at least six months after the appearance of symptoms.
As of August 2021, reinfection with COVID‑19 was possible but uncommon. The first case of reinfection was documented in August 2020. A systematic review found 17 cases of confirmed reinfection in medical literature as of May 2021. With the Omicron variant, as of 2022, reinfections have become common, albeit it is unclear how common. COVID-19 reinfections are thought to likely be less severe than primary infections, especially if one was previously infected by the same variant.
== Mortality ==
Several measures are commonly used to quantify mortality. These numbers vary by region and over time and are influenced by the volume of testing, healthcare system quality, treatment options, time since the initial outbreak, and population characteristics such as age, sex, and overall health.
The mortality rate reflects the number of deaths within a specific demographic group divided by the population of that demographic group. Consequently, the mortality rate reflects the prevalence as well as the severity of the disease within a given population. Mortality rates are highly correlated to age, with relatively low rates for young people and relatively high rates among the elderly. In fact, one relevant factor of mortality rates is the age structure of the countries' populations. For example, the case fatality rate for COVID‑19 is lower in India than in the US since India's younger population represents a larger percentage than in the US.
=== Case fatality rate ===
The case fatality rate (CFR) reflects the number of deaths divided by the number of diagnosed cases within a given time interval. Based on Johns Hopkins University statistics, the global death-to-case ratio is 1.02% (6,881,955/676,609,955) as of 10 March 2023. The number varies by region.
=== Infection fatality rate ===
A key metric in gauging the severity of COVID‑19 is the infection fatality rate (IFR), also referred to as the infection fatality ratio or infection fatality risk. This metric is calculated by dividing the total number of deaths from the disease by the total number of infected individuals; hence, in contrast to the CFR, the IFR incorporates asymptomatic and undiagnosed infections as well as reported cases.
==== Estimates ====
A December 2020 systematic review and meta-analysis estimated that population IFR during the first wave of the pandemic was about 0.5% to 1% in many locations (including France, Netherlands, New Zealand, and Portugal), 1% to 2% in other locations (Australia, England, Lithuania, and Spain), and exceeded 2% in Italy. That study also found that most of these differences in IFR reflected corresponding differences in the age composition of the population and age-specific infection rates; in particular, the metaregression estimate of IFR is very low for children and younger adults (e.g., 0.002% at age 10 and 0.01% at age 25) but increases progressively to 0.4% at age 55, 1.4% at age 65, 4.6% at age 75, and 15% at age 85. These results were also highlighted in a December 2020 report issued by the WHO.
An analysis of those IFR rates indicates that COVID‑19 is hazardous not only for the elderly but also for middle-aged adults, for whom the infection fatality rate of COVID-19 is two orders of magnitude greater than the annualised risk of a fatal automobile accident and far more dangerous than seasonal influenza.
==== Earlier estimates of IFR ====
At an early stage of the pandemic, the World Health Organization reported estimates of IFR between 0.3% and 1%. On 2 July, The WHO's chief scientist reported that the average IFR estimate presented at a two-day WHO expert forum was about 0.6%. In August, the WHO found that studies incorporating data from broad serology testing in Europe showed IFR estimates converging at approximately 0.5–1%. Firm lower limits of IFRs have been established in a number of locations such as New York City and Bergamo in Italy since the IFR cannot be less than the population fatality rate. (After sufficient time however, people can get reinfected). As of 10 July, in New York City, with a population of 8.4 million, 23,377 individuals (18,758 confirmed and 4,619 probable) have died with COVID‑19 (0.3% of the population). Antibody testing in New York City suggested an IFR of ≈0.9%, and ≈1.4%. In Bergamo province, 0.6% of the population has died. In September 2020, the U.S. Centers for Disease Control and Prevention (CDC) reported preliminary estimates of age-specific IFRs for public health planning purposes.
=== Sex differences ===
COVID‑19 case fatality rates are higher among men than women in most countries. However, in a few countries like India, Nepal, Vietnam, and Slovenia the fatality cases are higher in women than men. Globally, men are more likely to be admitted to the ICU and more likely to die. One meta-analysis found that globally, men were more likely to get COVID‑19 than women; there were approximately 55 men and 45 women per 100 infections (CI: 51.43–56.58).
The Chinese Center for Disease Control and Prevention reported the death rate was 2.8% for men and 1.7% for women. Later reviews in June 2020 indicated that there is no significant difference in susceptibility or in CFR between genders. One review acknowledges the different mortality rates in Chinese men, suggesting that it may be attributable to lifestyle choices such as smoking and drinking alcohol rather than genetic factors. Smoking, which in some countries like China is mainly a male activity, is a habit that contributes to increasing significantly the case fatality rates among men. Sex-based immunological differences, lesser prevalence of smoking in women and men developing co-morbid conditions such as hypertension at a younger age than women could have contributed to the higher mortality in men. In Europe as of February 2020, 57% of the infected people were men and 72% of those died with COVID‑19 were men. As of April 2020, the US government is not tracking sex-related data of COVID‑19 infections. Research has shown that viral illnesses like Ebola, HIV, influenza and SARS affect men and women differently.
=== Ethnic differences ===
In the US, a greater proportion of deaths due to COVID‑19 have occurred among African Americans and other minority groups. Structural factors that prevent them from practising social distancing include their concentration in crowded substandard housing and in "essential" occupations such as retail grocery workers, public transit employees, health-care workers and custodial staff. Greater prevalence of lacking health insurance and care of underlying conditions such as diabetes, hypertension, and heart disease also increase their risk of death. Similar issues affect Native American and Latino communities. On the one hand, in the Dominican Republic there is a clear example of both gender and ethnic inequality. In this Latin American territory, there is great inequality and precariousness that especially affects Dominican women, with greater emphasis on those of Haitian descent. According to a US health policy non-profit, 34% of American Indian and Alaska Native People (AIAN) non-elderly adults are at risk of serious illness compared to 21% of white non-elderly adults. The source attributes it to disproportionately high rates of many health conditions that may put them at higher risk as well as living conditions like lack of access to clean water.
Leaders have called for efforts to research and address the disparities. In the UK, a greater proportion of deaths due to COVID‑19 have occurred in those of a Black, Asian, and other ethnic minority background. More severe impacts upon patients including the relative incidence of the necessity of hospitalisation requirements, and vulnerability to the disease has been associated via DNA analysis to be expressed in genetic variants at chromosomal region 3, features that are associated with European Neanderthal heritage. That structure imposes greater risks that those affected will develop a more severe form of the disease. The findings are from Professor Svante Pääbo and researchers he leads at the Max Planck Institute for Evolutionary Anthropology and the Karolinska Institutet. This admixture of modern human and Neanderthal genes is estimated to have occurred roughly between 50,000 and 60,000 years ago in Southern Europe.
=== Comorbidities ===
Biological factors (immune response) and the general behaviour (habits) can strongly determine the consequences of COVID‑19. Most of those who die of COVID‑19 have pre-existing (underlying) conditions, including hypertension, diabetes mellitus, and cardiovascular disease. According to March data from the United States, 89% of those hospitalised had preexisting conditions. The Italian Istituto Superiore di Sanità reported that out of 8.8% of deaths where medical charts were available, 96.1% of people had at least one comorbidity with the average person having 3.4 diseases. According to this report the most common comorbidities are hypertension (66% of deaths), type 2 diabetes (29.8% of deaths), ischaemic heart disease (27.6% of deaths), atrial fibrillation (23.1% of deaths) and chronic renal failure (20.2% of deaths).
Most critical respiratory comorbidities according to the US Centers for Disease Control and Prevention (CDC), are: moderate or severe asthma, pre-existing COPD, pulmonary fibrosis, cystic fibrosis. Evidence stemming from meta-analysis of several smaller research papers also suggests that smoking can be associated with worse outcomes. When someone with existing respiratory problems is infected with COVID‑19, they might be at greater risk for severe symptoms. COVID‑19 also poses a greater risk to people who misuse opioids and amphetamines, insofar as their drug use may have caused lung damage.
In August 2020, the CDC issued a caution that tuberculosis (TB) infections could increase the risk of severe illness or death. The WHO recommended that people with respiratory symptoms be screened for both diseases, as testing positive for COVID‑19 could not rule out co-infections. Some projections have estimated that reduced TB detection due to the pandemic could result in 6.3 million additional TB cases and 1.4 million TB-related deaths by 2025.
== History ==
The virus is thought to be of natural animal origin, most likely through spillover infection. A joint-study conducted in early 2021 by the People's Republic of China and the World Health Organization indicated that the virus descended from a coronavirus that infects wild bats, and likely spread to humans through an intermediary wildlife host. There are several theories about where the index case originated and investigations into the origin of the pandemic are ongoing. According to articles published in July 2022 in Science, virus transmission into humans occurred through two spillover events in November 2019 and was likely due to live wildlife trade on the Huanan wet market in the city of Wuhan (Hubei, China). Doubts about the conclusions have mostly centered on the precise site of spillover. Earlier phylogenetics estimated that SARS-CoV-2 arose in October or November 2019. A phylogenetic algorithm analysis suggested that the virus may have been circulating in Guangdong before Wuhan.
Most scientists believe the virus spilled into human populations through natural zoonosis, similar to the SARS-CoV-1 and MERS-CoV outbreaks, and consistent with other pandemics in human history. According to the Intergovernmental Panel on Climate Change several social and environmental factors including climate change, natural ecosystem destruction and wildlife trade increased the likelihood of such zoonotic spillover. One study made with the support of the European Union found climate change increased the likelihood of the pandemic by influencing distribution of bat species.
Available evidence suggests that the SARS-CoV-2 virus was originally harboured by bats, and spread to humans multiple times from infected wild animals at the Huanan Seafood Market in Wuhan in December 2019. A minority of scientists and some members of the U.S intelligence community believe the virus may have been unintentionally leaked from a laboratory such as the Wuhan Institute of Virology. The US intelligence community has mixed views on the issue, but overall agrees with the scientific consensus that the virus was not developed as a biological weapon and is unlikely to have been genetically engineered. There is no evidence SARS-CoV-2 existed in any laboratory prior to the pandemic.
The first confirmed human infections were in Wuhan. A study of the first 41 cases of confirmed COVID‑19, published in January 2020 in The Lancet, reported the earliest date of onset of symptoms as 1 December 2019. Official publications from the WHO reported the earliest onset of symptoms as 8 December 2019. Human-to-human transmission was confirmed by the WHO and Chinese authorities by 20 January 2020. According to official Chinese sources, these were mostly linked to the Huanan Seafood Wholesale Market, which also sold live animals. In May 2020, George Gao, the director of the CDC, said animal samples collected from the seafood market had tested negative for the virus, indicating that the market was the site of an early superspreading event, but that it was not the site of the initial outbreak. Traces of the virus have been found in wastewater samples that were collected in Milan and Turin, Italy, on 18 December 2019.
By December 2019, the spread of infection was almost entirely driven by human-to-human transmission. The number of COVID-19 cases in Hubei gradually increased, reaching sixty by 20 December, and at least 266 by 31 December. On 24 December, Wuhan Central Hospital sent a bronchoalveolar lavage fluid (BAL) sample from an unresolved clinical case to sequencing company Vision Medicals. On 27 and 28 December, Vision Medicals informed the Wuhan Central Hospital and the Chinese CDC of the results of the test, showing a new coronavirus. A pneumonia cluster of unknown cause was observed on 26 December and treated by the doctor Zhang Jixian in Hubei Provincial Hospital, who informed the Wuhan Jianghan CDC on 27 December. On 30 December, a test report addressed to Wuhan Central Hospital, from company CapitalBio Medlab, stated an erroneous positive result for SARS, causing a group of doctors at Wuhan Central Hospital to alert their colleagues and relevant hospital authorities of the result. The Wuhan Municipal Health Commission issued a notice to various medical institutions on "the treatment of pneumonia of unknown cause" that same evening. Eight of these doctors, including Li Wenliang (punished on 3 January), were later admonished by the police for spreading false rumours and another, Ai Fen, was reprimanded by her superiors for raising the alarm.
The Wuhan Municipal Health Commission made the first public announcement of a pneumonia outbreak of unknown cause on 31 December, confirming 27 cases – enough to trigger an investigation.
During the early stages of the outbreak, the number of cases doubled approximately every seven and a half days. In early and mid-January 2020, the virus spread to other Chinese provinces, helped by the Chinese New Year migration and Wuhan being a transport hub and major rail interchange. On 20 January, China reported nearly 140 new cases in one day, including two people in Beijing and one in Shenzhen. Later official data shows 6,174 people had already developed symptoms by then, and more may have been infected. A report in The Lancet on 24 January indicated human transmission, strongly recommended personal protective equipment for health workers, and said testing for the virus was essential due to its "pandemic potential". On 30 January, the WHO declared COVID-19 a Public Health Emergency of International Concern. By this time, the outbreak spread by a factor of 100 to 200 times.
Italy had its first confirmed cases on 31 January 2020, two tourists from China. Italy overtook China as the country with the most deaths on 19 March 2020. By 26 March the United States had overtaken China and Italy with the highest number of confirmed cases in the world. Research on coronavirus genomes indicates the majority of COVID-19 cases in New York came from European travellers, rather than directly from China or any other Asian country. Retesting of prior samples found a person in France who had the virus on 27 December 2019, and a person in the United States who died from the disease on 6 February 2020.
RT-PCR testing of untreated wastewater samples from Brazil and Italy have suggested detection of SARS-CoV-2 as early as November and December 2019, respectively, but the methods of such sewage studies have not been optimised, many have not been peer-reviewed, details are often missing, and there is a risk of false positives due to contamination or if only one gene target is detected. A September 2020 review journal article said, "The possibility that the COVID‑19 infection had already spread to Europe at the end of last year is now indicated by abundant, even if partially circumstantial, evidence", including pneumonia case numbers and radiology in France and Italy in November and December.
As of 1 October 2021, Reuters reported that it had estimated the worldwide total number of deaths due to COVID‑19 to have exceeded five million.
The Public Health Emergency of International Concern for COVID-19 ended on 5 May 2023. By this time, everyday life in most countries had returned to how it was before the pandemic.
== Misinformation ==
After the initial outbreak of COVID‑19, misinformation and disinformation regarding the origin, scale, prevention, treatment, and other aspects of the disease rapidly spread online.
In September 2020, the US Centers for Disease Control and Prevention (CDC) published preliminary estimates of the risk of death by age groups in the United States, but those estimates were widely misreported and misunderstood.
== Other species ==
Humans appear to be capable of spreading the virus to some other animals, a type of disease transmission referred to as zooanthroponosis.
Some pets, especially cats and ferrets, can catch this virus from infected humans. Symptoms in cats include respiratory (such as a cough) and digestive symptoms. Cats can spread the virus to other cats, and may be able to spread the virus to humans, but cat-to-human transmission of SARS-CoV-2 has not been proven. Compared to cats, dogs are less susceptible to this infection. Behaviours which increase the risk of transmission include kissing, licking, and petting the animal.
The virus does not appear to be able to infect pigs, ducks, or chickens at all. Mice, rats, and rabbits, if they can be infected at all, are unlikely to be involved in spreading the virus.
Tigers and lions in zoos have become infected as a result of contact with infected humans. As expected, monkeys and great ape species such as orangutans can also be infected with the COVID‑19 virus.
Minks, which are in the same family as ferrets, have been infected. Minks may be asymptomatic, and can also spread the virus to humans. Multiple countries have identified infected animals in mink farms. Denmark, a major producer of mink pelts, ordered the slaughter of all minks over fears of viral mutations, following an outbreak referred to as Cluster 5. A vaccine for mink and other animals is being researched.
== Research ==
International research on vaccines and medicines in COVID‑19 is underway by government organisations, academic groups, and industry researchers. The CDC has classified it to require a BSL3 grade laboratory. There has been a great deal of COVID‑19 research, involving accelerated research processes and publishing shortcuts to meet the global demand.
As of December 2020, hundreds of clinical trials have been undertaken, with research happening on every continent except Antarctica. As of November 2020, more than 200 possible treatments have been studied in humans.
=== Transmission and prevention research ===
Modelling research has been conducted with several objectives, including predictions of the dynamics of transmission, diagnosis and prognosis of infection, estimation of the impact of interventions, or allocation of resources. Modelling studies are mostly based on compartmental models in epidemiology, estimating the number of infected people over time under given conditions. Several other types of models have been developed and used during the COVID‑19 pandemic including computational fluid dynamics models to study the flow physics of COVID‑19, retrofits of crowd movement models to study occupant exposure, mobility-data based models to investigate transmission, or the use of macroeconomic models to assess the economic impact of the pandemic.
=== Treatment-related research ===
Repurposed antiviral drugs make up most of the research into COVID‑19 treatments. Other candidates in trials include vasodilators, corticosteroids, immune therapies, lipoic acid, bevacizumab, and recombinant angiotensin-converting enzyme 2.
In March 2020, the World Health Organization (WHO) initiated the Solidarity trial to assess the treatment effects of some promising drugs:
An experimental drug called remdesivir
Anti-malarial drugs chloroquine and hydroxychloroquine
Two anti-HIV drugs, lopinavir/ritonavir and interferon-beta
More than 300 active clinical trials are underway as of April 2020.
Research on the antimalarial drugs hydroxychloroquine and chloroquine showed that they were ineffective at best, and that they may reduce the antiviral activity of remdesivir. By May 2020, France, Italy, and Belgium had banned the use of hydroxychloroquine as a COVID‑19 treatment.
In June, initial results from the randomised RECOVERY Trial in the United Kingdom showed that dexamethasone reduced mortality by one third for people who are critically ill on ventilators and one fifth for those receiving supplemental oxygen. Because this is a well-tested and widely available treatment, it was welcomed by the WHO, which is in the process of updating treatment guidelines to include dexamethasone and other steroids. Based on those preliminary results, dexamethasone treatment has been recommended by the NIH for peoples with COVID‑19 who are mechanically ventilated or who require supplemental oxygen but not in people with COVID‑19 who do not require supplemental oxygen.
In September 2020, the WHO released updated guidance on using corticosteroids for COVID‑19. The WHO recommends systemic corticosteroids rather than no systemic corticosteroids for the treatment of people with severe and critical COVID‑19 (strong recommendation, based on moderate certainty evidence). The WHO suggests not to use corticosteroids in the treatment of people with non-severe COVID‑19 (conditional recommendation, based on low certainty evidence). The updated guidance was based on a meta-analysis of clinical trials of people critically ill with COVID‑19.
In September 2020, the European Medicines Agency (EMA) endorsed the use of dexamethasone in adults and adolescents from twelve years of age and weighing at least 40 kilograms (88 lb) who require supplemental oxygen therapy. Dexamethasone can be taken by mouth or given as an injection or infusion (drip) into a vein.
In November 2020, the US Food and Drug Administration (FDA) issued an emergency use authorisation for the investigational monoclonal antibody therapy bamlanivimab for the treatment of mild-to-moderate COVID‑19. Bamlanivimab is authorised for people with positive results of direct SARS-CoV-2 viral testing who are twelve years of age and older weighing at least 40 kilograms (88 lb), and who are at high risk for progressing to severe COVID‑19 or hospitalisation. This includes those who are 65 years of age or older, or who have chronic medical conditions.
In February 2021, the FDA issued an emergency use authorisation (EUA) for bamlanivimab and etesevimab administered together for the treatment of mild to moderate COVID‑19 in people twelve years of age or older weighing at least 40 kilograms (88 lb) who test positive for SARS‑CoV‑2 and who are at high risk for progressing to severe COVID‑19. The authorised use includes treatment for those who are 65 years of age or older or who have certain chronic medical conditions.
In April 2021, the FDA revoked the emergency use authorisation (EUA) that allowed for the investigational monoclonal antibody therapy bamlanivimab, when administered alone, to be used for the treatment of mild-to-moderate COVID‑19 in adults and certain paediatric patients.
==== Cytokine storm ====
A cytokine storm can be a complication in the later stages of severe COVID‑19. A cytokine storm is a potentially deadly immune reaction where a large amount of pro-inflammatory cytokines and chemokines are released too quickly. A cytokine storm can lead to ARDS and multiple organ failure. Data collected from Jin Yin-tan Hospital in Wuhan, China indicates that people who had more severe responses to COVID‑19 had greater amounts of pro-inflammatory cytokines and chemokines in their system than people who had milder responses. These high levels of pro-inflammatory cytokines and chemokines indicate presence of a cytokine storm.
Tocilizumab has been included in treatment guidelines by China's National Health Commission after a small study was completed. It is undergoing a Phase II non-randomised trial at the national level in Italy after showing positive results in people with severe disease. Combined with a serum ferritin blood test to identify a cytokine storm (also called cytokine storm syndrome, not to be confused with cytokine release syndrome), it is meant to counter such developments, which are thought to be the cause of death in some affected people. The interleukin-6 receptor (IL-6R) antagonist was approved by the FDA to undergo a Phase III clinical trial assessing its effectiveness on COVID‑19 based on retrospective case studies for the treatment of steroid-refractory cytokine release syndrome induced by a different cause, CAR T cell therapy, in 2017. There is no randomised, controlled evidence that tocilizumab is an efficacious treatment for CRS. Prophylactic tocilizumab has been shown to increase serum IL-6 levels by saturating the IL-6R, driving IL-6 across the blood–brain barrier, and exacerbating neurotoxicity while having no effect on the incidence of CRS.
Lenzilumab, an anti-GM-CSF monoclonal antibody, is protective in murine models for CAR T cell-induced CRS and neurotoxicity and is a viable therapeutic option due to the observed increase of pathogenic GM-CSF secreting T cells in hospitalised patients with COVID‑19.
==== Passive antibodies ====
Transferring purified and concentrated antibodies produced by the immune systems of those who have recovered from COVID‑19 to people who need them is being investigated as a non-vaccine method of passive immunisation. Viral neutralisation is the anticipated mechanism of action by which passive antibody therapy can mediate defence against SARS-CoV-2. The spike protein of SARS-CoV-2 is the primary target for neutralising antibodies. As of 8 August 2020, eight neutralising antibodies targeting the spike protein of SARS-CoV-2 have entered clinical studies. It has been proposed that selection of broad-neutralising antibodies against SARS-CoV-2 and SARS-CoV might be useful for treating not only COVID‑19 but also future SARS-related CoV infections. Other mechanisms, however, such as antibody-dependant cellular cytotoxicity or phagocytosis, may be possible. Other forms of passive antibody therapy, for example, using manufactured monoclonal antibodies, are in development.
The use of passive antibodies to treat people with active COVID‑19 is also being studied. This involves the production of convalescent serum, which consists of the liquid portion of the blood from people who recovered from the infection and contains antibodies specific to this virus, which is then administered to active patients. This strategy was tried for SARS with inconclusive results. An updated Cochrane review in May 2023 found high certainty evidence that, for the treatment of people with moderate to severe COVID‑19, convalescent plasma did not reduce mortality or bring about symptom improvement. There continues to be uncertainty about the safety of convalescent plasma administration to people with COVID‑19 and differing outcomes measured in different studies limits their use in determining efficacy.
=== Bioethics ===
Since the outbreak of the COVID‑19 pandemic, scholars have explored the bioethics, normative economics, and political theories of healthcare policies related to the public health crisis. Academics have pointed to the moral distress of healthcare workers, ethics of distributing scarce healthcare resources such as ventilators, and the global justice of vaccine diplomacies. The socio-economic inequalities between genders, races, groups with disabilities, communities, regions, countries, and continents have also drawn attention in academia and the general public.
== See also ==
Coronavirus diseases, a group of closely related syndromes
Disease X, a WHO term
Law of declining virulence – Disproved hypothesis of epidemiologist Theobald Smith
Theory of virulence – Theory by biologist Paul W. Ewald
== References ==
== Further reading ==
== External links ==
=== Health agencies ===
Coronavirus disease (COVID‑19) Facts by the World Health Organization (WHO)
Coronavirus (COVID‑19) by the UK National Health Service (NHS)
Coronavirus 2019 (COVID-19) by the US Centers for Disease Control and Prevention (CDC)
=== Directories ===
Coronavirus Resource Center at the Center for Inquiry
COVID‑19 Information on FireMountain.net Archived 13 January 2022 at the Wayback Machine
COVID‑19 Resource Directory on OpenMD
=== Medical journals ===
BMJ's Coronavirus (covid‑19) Hub by the BMJ
Coronavirus (Covid‑19) by The New England Journal of Medicine
Coronavirus (COVID‑19) Research Highlights by Springer Nature
Coronavirus Disease 2019 (COVID‑19) by JAMA
COVID‑19 Resource Centre by The Lancet
Covid‑19: Novel Coronavirus Archived 24 September 2020 at the Wayback Machine by Wiley Publishing
Novel Coronavirus Information Center by Elsevier
=== Treatment guidelines ===
"Bouncing Back From COVID-19: Your Guide to Restoring Movement" (PDF). Johns Hopkins Medicine.
"Coronavirus Disease 2019 (COVID-19) Treatment Guidelines" (PDF). National Institutes of Health.
"Guidelines on the Treatment and Management of Patients with COVID-19". Infectious Diseases Society of America.
"JHMI Clinical Recommendations for Available Pharmacologic Therapies for COVID-19" (PDF). Johns Hopkins Medicine.
NHS England and NHS Improvement. National Guidance for post-COVID syndrome assessment clinics (Report).
World Health Organization (2022). Therapeutics and COVID-19: living guideline, 14 January 2022 (Report). hdl:10665/351006. WHO/2019-nCoV/therapeutics/2022.1. | Wikipedia/Coronavirus_disease_2019 |
Autographivirales is an order of viruses in the class Caudoviricetes. Bacteria serve as natural hosts. The order has 4 families, 2 subfamilies unassigned to a family, and a large number of genera unassigned to a family.
== History ==
Since the 1990s, the term "T7 supergroup" has been coined for the expanding group of bacteriophages related to coliphage T7, as members of the family Podoviridae. Enterobacteriaceae phages SP6 and K1-5 were the first to be considered as an estranged subgroup of the "T7 supergroup". Pseudomonas phage phiKMV also shared commonalities at the genome organizational level. As such, based on the available morphological and proteomic data, this clade of viruses was established as a subfamily of the family Podoviridae. The subfamily was later raised to the level of family in 2019. In 2025, the family Autographiviridae was elevated to the rank of order under the name Autographivirales.
== Applications ==
=== Therapeutic Antibiotic Use ===
Some experiments suggest that Autographivirales bacteriophages show promise in regulating and stifling the growth of infectious bacteria, like Klebsiella pneumoniae, in humans. Infectious bacteria like K. pneumoniae have increasingly become more resistant to traditional antibiotics. Some bacteria are even resistant to multiple antibiotics and antibacterial drugs. This problem prompted researchers to look towards other possible regulators of bacterial growth, like Autographivirales bacteriophages. This type of treatment is referred to as phage therapy. Phage therapy is effective against drug-resistant bacteria because bacteriophages are naturally inclined to infect and kill specific bacteria.
For the past two decades, studying phage therapy has grown in popularity with major research centers opening up in the United States, Poland, Georgia, and Belgium. In turn, many biotechnology companies have shifted their focus to phage therapy, with some like Armata Pharmaceuticals completely dedicating themselves to combating the problem of antibiotic resistance.
Autographivirales has also been used in combination with existing antibiotics to effective results. A recent study showed that Autographivirales combined with antibiotic medication Tigecycline can effectively combat skin and soft tissue infections associated with Acinetobacter baumannii, a bacterium that previously showed resistance to multiple drugs.
However, phage therapy does pose some potential drawbacks. Antibiotics work by targeting a key part bacterial structure or by impeding a bacterial metabolic function. Because many bacteria have similar metabolic processes and physical structures, an antibiotic could be effective against many different bacteria. Phages on the other hand are much more specific to a single bacteria. This means that scientists would have to put in more work to perfect a phage therapy that only works against one bacteria. Also, some clinical studies involving phage therapy have resulted in low to moderate efficacy rates and in a huge variation of results for different patients.
Autographivirales and other lytic phages lyse host bacteria through a process that begins with adsorption. Once Autographivirales is adsorbed on the cell surface of the host bacteria, the enzyme located in its tail structure can penetrate the host bacteria's peptidoglycan layer and inner membrane, where it releases genetic material into the interior of the bacteria. When the phage genetic material is integrated with the bacterial host genes, it will replicate to form a new progeny phage with bacteriolytic ability. The infected bacteria are finally lysed and the progeny phages released post-lysis continue to proliferate and lyse surrounding host bacteria.
=== Autographivirales in Phage Cocktail Formulation ===
“Phage cocktails” are a form of phage therapy that involves employing at least two phages to target a single bacterial strain, creating a form of therapy with greater ‘depth.’ Phage cocktails are an effective substitute for antibiotics as they create a broader host range and delay the development of phage resistance in bacteria. Phage cocktails are most commonly used to combat infections caused by Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli.
Clinical practices have employed phage cocktails to prevent bacterial biofilm formation, which is one of the greatest challenges in the healthcare industry. A recent study showed that formulated phage cocktails that included Autographivirales under the now-abolished family classification Podoviridae, effectively reduced the growth of Klebsiella pneumoniae.
== Etymology ==
The name of this order, termed Autographivirales, refers to the “auto-graphein” or “self-transcribing” phages which encode their own (single subunit) RNA polymerase, a common characteristic among its members.
== Structure ==
Viruses in Autographivirales are non-enveloped, with icosahedral and Head-tail geometries, and T=7 symmetry. The diameter is around 60 nm. Genomes are linear, around 40-42kb in length.
== Life cycle ==
Viral replication is cytoplasmic. DNA templated transcription is the method of transcription. The virus exits the host cell by lysis, and holin/endolysin/spanin proteins. Bacteria serve as the natural host. Transmission routes are passive diffusion.
== Basis for taxonomy ==
The former family of Podoviridae, which contained many of the viruses that are now classified under Autographivirales, was defined based on morphology and the presence of short noncontractile tails. The Podoviridae family, along with Myoviridae and Siphoviridae families, were abolished for being polyphyletic, meaning that viruses under a single family derived from more than one common ancestor and are thus not suitable for placing in the same taxa. However, these terms (Podoviridae, Myoviridae, and Siphoviridae) are still used to refer to the distinct morphological features of certain bacteriophages.
== Taxonomy ==
The order contains the following families:
Autonotataviridae
Autoscriptoviridae
Autosignataviridae
Autotranscriptaviridae
The order contains the following subfamilies that are unassigned to a family:
Dunnvirinae
Sechaudvirinae
The following genera are unassigned to a subfamily and family:
== References ==
== External links ==
Viralzone: Autographiviridae
ICTV | Wikipedia/Autographiviridae |
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