text stringlengths 26 3.6k | page_title stringlengths 1 71 | source stringclasses 1
value | token_count int64 10 512 | id stringlengths 2 8 | url stringlengths 31 117 | topic stringclasses 4
values | section stringlengths 4 49 ⌀ | sublist stringclasses 9
values |
|---|---|---|---|---|---|---|---|---|
Phages were discovered to be antibacterial agents and were used in the former Soviet Republic of Georgia (pioneered there by Giorgi Eliava with help from the co-discoverer of bacteriophages, Félix d'Hérelle) during the 1920s and 1930s for treating bacterial infections.
D'Herelle "quickly learned that bacteriophages are found wherever bacteria thrive: in sewers, in rivers that catch waste runoff from pipes, and in the stools of convalescent patients."
They had widespread use, including treatment of soldiers in the Red Army. However, they were abandoned for general use in the West for several reasons:
Antibiotics were discovered and marketed widely. They were easier to make, store, and prescribe.
Medical trials of phages were carried out, but a basic lack of understanding of phages raised questions about the validity of these trials.
Publication of research in the Soviet Union was mainly in the Russian or Georgian languages and for many years was not followed internationally.
The Soviet technology was widely discouraged and in some cases illegal due to the red scare. | Bacteriophage | Wikipedia | 221 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
The use of phages has continued since the end of the Cold War in Russia, Georgia, and elsewhere in Central and Eastern Europe. The first regulated, randomized, double-blind clinical trial was reported in the Journal of Wound Care in June 2009, which evaluated the safety and efficacy of a bacteriophage cocktail to treat infected venous ulcers of the leg in human patients. The FDA approved the study as a Phase I clinical trial. The study's results demonstrated the safety of therapeutic application of bacteriophages, but did not show efficacy. The authors explained that the use of certain chemicals that are part of standard wound care (e.g. lactoferrin or silver) may have interfered with bacteriophage viability. Shortly after that, another controlled clinical trial in Western Europe (treatment of ear infections caused by Pseudomonas aeruginosa) was reported in the journal Clinical Otolaryngology in August 2009. The study concludes that bacteriophage preparations were safe and effective for treatment of chronic ear infections in humans. Additionally, there have been numerous animal and other experimental clinical trials evaluating the efficacy of bacteriophages for various diseases, such as infected burns and wounds, and cystic fibrosis-associated lung infections, among others. On the other hand, phages of Inoviridae have been shown to complicate biofilms involved in pneumonia and cystic fibrosis and to shelter the bacteria from drugs meant to eradicate disease, thus promoting persistent infection.
Meanwhile, bacteriophage researchers have been developing engineered viruses to overcome antibiotic resistance, and engineering the phage genes responsible for coding enzymes that degrade the biofilm matrix, phage structural proteins, and the enzymes responsible for lysis of the bacterial cell wall. There have been results showing that T4 phages that are small in size and short-tailed can be helpful in detecting E. coli in the human body.
Therapeutic efficacy of a phage cocktail was evaluated in a mouse model with nasal infection of multi-drug-resistant (MDR) A. baumannii. Mice treated with the phage cocktail showed a 2.3-fold higher survival rate compared to those untreated at seven days post-infection. | Bacteriophage | Wikipedia | 465 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
In 2017, a 68-year-old diabetic patient with necrotizing pancreatitis complicated by a pseudocyst infected with MDR A. baumannii strains was being treated with a cocktail of Azithromycin, Rifampicin, and Colistin for 4 months without results and overall rapidly declining health.
Because discussion had begun of the clinical futility of further treatment, an Emergency Investigational New Drug (eIND) was filed as a last effort to at the very least gain valuable medical data from the situation, and approved, so he was subjected to phage therapy using a percutaneously (PC) injected cocktail containing nine different phages that had been identified as effective against the primary infection strain by rapid isolation and testing techniques (a process which took under a day). This proved effective for a very brief period, although the patient remained unresponsive and his health continued to worsen; soon isolates of a strain of A. baumannii were being collected from drainage of the cyst that showed resistance to this cocktail, and a second cocktail which was tested to be effective against this new strain was added, this time by intravenous (IV) injection as it had become clear that the infection was more pervasive than originally thought.
Once on the combination of the IV and PC therapy the patient's downward clinical trajectory reversed, and within two days he had awoken from his coma and become responsive. As his immune system began to function he had to be temporarily removed from the cocktail because his fever was spiking to over , but after two days the phage cocktails were re-introduced at levels he was able to tolerate. The original three-antibiotic cocktail was replaced by minocycline after the bacterial strain was found not to be resistant to this and he rapidly regained full lucidity, although he was not discharged from the hospital until roughly 145 days after phage therapy began. Towards the end of the therapy it was discovered that the bacteria had become resistant to both of the original phage cocktails, but they were continued because they seemed to be preventing minocycline resistance from developing in the bacterial samples collected so were having a useful synergistic effect.
Other | Bacteriophage | Wikipedia | 461 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
Food industry
Phages have increasingly been used to safen food products and to forestall spoilage bacteria. Since 2006, the United States Food and Drug Administration (FDA) and United States Department of Agriculture (USDA) have approved several bacteriophage products. LMP-102 (Intralytix) was approved for treating ready-to-eat (RTE) poultry and meat products. In that same year, the FDA approved LISTEX (developed and produced by Micreos) using bacteriophages on cheese to kill Listeria monocytogenes bacteria, in order to give them generally recognized as safe (GRAS) status. In July 2007, the same bacteriophage were approved for use on all food products. In 2011 USDA confirmed that LISTEX is a clean label processing aid and is included in USDA. Research in the field of food safety is continuing to see if lytic phages are a viable option to control other food-borne pathogens in various food products.
Water indicators
Bacteriophages, including those specific to Escherichia coli, have been employed as indicators of fecal contamination in water sources. Due to their shared structural and biological characteristics, coliphages can serve as proxies for viral fecal contamination and the presence of pathogenic viruses such as rotavirus, norovirus, and HAV. Research conducted on wastewater treatment systems has revealed significant disparities in the behavior of coliphages compared to fecal coliforms, demonstrating a distinct correlation with the recovery of pathogenic viruses at the treatment's conclusion. Establishing a secure discharge threshold, studies have determined that discharges below 3000 PFU/100 mL are considered safe in terms of limiting the release of pathogenic viruses.
Diagnostics
In 2011, the FDA cleared the first bacteriophage-based product for in vitro diagnostic use. The KeyPath MRSA/MSSA Blood Culture Test uses a cocktail of bacteriophage to detect Staphylococcus aureus in positive blood cultures and determine methicillin resistance or susceptibility. The test returns results in about five hours, compared to two to three days for standard microbial identification and susceptibility test methods. It was the first accelerated antibiotic-susceptibility test approved by the FDA. | Bacteriophage | Wikipedia | 476 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
Counteracting bioweapons and toxins
Government agencies in the West have for several years been looking to Georgia and the former Soviet Union for help with exploiting phages for counteracting bioweapons and toxins, such as anthrax and botulism. Developments are continuing among research groups in the U.S. Other uses include spray application in horticulture for protecting plants and vegetable produce from decay and the spread of bacterial disease. Other applications for bacteriophages are as biocides for environmental surfaces, e.g., in hospitals, and as preventative treatments for catheters and medical devices before use in clinical settings. The technology for phages to be applied to dry surfaces, e.g., uniforms, curtains, or even sutures for surgery now exists. Clinical trials reported in Clinical Otolaryngology show success in veterinary treatment of pet dogs with otitis.
Bacterium sensing and identification
The sensing of phage-triggered ion cascades (SEPTIC) bacterium sensing and identification method uses the ion emission and its dynamics during phage infection and offers high specificity and speed for detection.
Phage display
Phage display is a different use of phages involving a library of phages with a variable peptide linked to a surface protein. Each phage genome encodes the variant of the protein displayed on its surface (hence the name), providing a link between the peptide variant and its encoding gene. Variant phages from the library may be selected through their binding affinity to an immobilized molecule (e.g., botulism toxin) to neutralize it. The bound, selected phages can be multiplied by reinfecting a susceptible bacterial strain, thus allowing them to retrieve the peptides encoded in them for further study.
Antimicrobial drug discovery
Phage proteins often have antimicrobial activity and may serve as leads for peptidomimetics, i.e. drugs that mimic peptides. Phage-ligand technology makes use of phage proteins for various applications, such as binding of bacteria and bacterial components (e.g. endotoxin) and lysis of bacteria.
Basic research
Bacteriophages are important model organisms for studying principles of evolution and ecology.
Detriments | Bacteriophage | Wikipedia | 461 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
Dairy industry
Bacteriophages present in the environment can cause cheese to not ferment. In order to avoid this, mixed-strain starter cultures and culture rotation regimes can be used. Genetic engineering of culture microbes – especially Lactococcus lactis and Streptococcus thermophilus – have been studied for genetic analysis and modification to improve phage resistance. This has especially focused on plasmid and recombinant chromosomal modifications.
Some research has focused on the potential of bacteriophages as antimicrobial against foodborne pathogens and biofilm formation within the dairy industry. As the spread of antibiotic resistance is a main concern within the dairy industry, phages can serve as a promising alternative.
Replication
The life cycle of bacteriophages tends to be either a lytic cycle or a lysogenic cycle. In addition, some phages display pseudolysogenic behaviors.
With lytic phages such as the T4 phage, bacterial cells are broken open (lysed) and destroyed after immediate replication of the virion. As soon as the cell is destroyed, the phage progeny can find new hosts to infect. Lytic phages are more suitable for phage therapy. Some lytic phages undergo a phenomenon known as lysis inhibition, where completed phage progeny will not immediately lyse out of the cell if extracellular phage concentrations are high. This mechanism is not identical to that of the temperate phage going dormant and usually is temporary.
In contrast, the lysogenic cycle does not result in immediate lysing of the host cell. Those phages able to undergo lysogeny are known as temperate phages. Their viral genome will integrate with host DNA and replicate along with it, relatively harmlessly, or may even become established as a plasmid. The virus remains dormant until host conditions deteriorate, perhaps due to depletion of nutrients, then, the endogenous phages (known as prophages) become active. At this point they initiate the reproductive cycle, resulting in lysis of the host cell. As the lysogenic cycle allows the host cell to continue to survive and reproduce, the virus is replicated in all offspring of the cell. An example of a bacteriophage known to follow the lysogenic cycle and the lytic cycle is the phage lambda of E. coli. | Bacteriophage | Wikipedia | 501 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
Sometimes prophages may provide benefits to the host bacterium while they are dormant by adding new functions to the bacterial genome, in a phenomenon called lysogenic conversion. Examples are the conversion of harmless strains of Corynebacterium diphtheriae or Vibrio cholerae by bacteriophages to highly virulent ones that cause diphtheria or cholera, respectively. Strategies to combat certain bacterial infections by targeting these toxin-encoding prophages have been proposed.
Attachment and penetration
Bacterial cells are protected by a cell wall of polysaccharides, which are important virulence factors protecting bacterial cells against both immune host defenses and antibiotics.
Host growth conditions also influence the ability of the phage to attach and invade them. As phage virions do not move independently, they must rely on random encounters with the correct receptors when in solution, such as blood, lymphatic circulation, irrigation, soil water, etc.
Myovirus bacteriophages use a hypodermic syringe-like motion to inject their genetic material into the cell. After contacting the appropriate receptor, the tail fibers flex to bring the base plate closer to the surface of the cell. This is known as reversible binding. Once attached completely, irreversible binding is initiated and the tail contracts, possibly with the help of ATP present in the tail, injecting genetic material through the bacterial membrane. The injection is accomplished through a sort of bending motion in the shaft by going to the side, contracting closer to the cell and pushing back up. Podoviruses lack an elongated tail sheath like that of a myovirus, so instead, they use their small, tooth-like tail fibers enzymatically to degrade a portion of the cell membrane before inserting their genetic material. | Bacteriophage | Wikipedia | 372 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
Synthesis of proteins and nucleic acid
Within minutes, bacterial ribosomes start translating viral mRNA into protein. For RNA-based phages, RNA replicase is synthesized early in the process. Proteins modify the bacterial RNA polymerase so it preferentially transcribes viral mRNA. The host's normal synthesis of proteins and nucleic acids is disrupted, and it is forced to manufacture viral products instead. These products go on to become part of new virions within the cell, helper proteins that contribute to the assemblage of new virions, or proteins involved in cell lysis. In 1972, Walter Fiers (University of Ghent, Belgium) was the first to establish the complete nucleotide sequence of a gene and in 1976, of the viral genome of bacteriophage MS2. Some dsDNA bacteriophages encode ribosomal proteins, which are thought to modulate protein translation during phage infection.
Virion assembly
In the case of the T4 phage, the construction of new virus particles involves the assistance of helper proteins that act catalytically during phage morphogenesis. The base plates are assembled first, with the tails being built upon them afterward. The head capsids, constructed separately, will spontaneously assemble with the tails. During assembly of the phage T4 virion, the morphogenetic 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 proteins produced during viral infection appears to be critical for normal phage T4 morphogenesis. The DNA is packed efficiently within the heads. The whole process takes about 15 minutes.
Early studies of bactioriophage T4 (1962-1964) provided an opportunity to gain understanding of virtually all of the genes that are essential for growth of the bacteriophage under laboratory conditions. These studies were made possible by the availability of two classes of conditional lethal mutants. One class of such mutants was referred to as amber mutants. The other class of conditional lethal mutants was referred to as temperature-sensitive mutants Studies of these two classes of mutants led to considerable insight into the functions and interactions of the proteins employed in the machinery of DNA replication, repair and recombination, and on how viruses are assembled from protein and nucleic acid components (molecular morphogenesis). | Bacteriophage | Wikipedia | 485 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
Release of virions
Phages may be released via cell lysis, by extrusion, or, in a few cases, by budding. Lysis, by tailed phages, is achieved by an enzyme called endolysin, which attacks and breaks down the cell wall peptidoglycan. An altogether different phage type, the filamentous phage, makes the host cell continually secrete new virus particles. Released virions are described as free, and, unless defective, are capable of infecting a new bacterium. Budding is associated with certain Mycoplasma phages. In contrast to virion release, phages displaying a lysogenic cycle do not kill the host and instead become long-term residents as prophages.
Communication
Research in 2017 revealed that the bacteriophage Φ3T makes a short viral protein that signals other bacteriophages to lie dormant instead of killing the host bacterium. Arbitrium is the name given to this protein by the researchers who discovered it. | Bacteriophage | Wikipedia | 215 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
Genome structure
Given the millions of different phages in the environment, phage genomes come in a variety of forms and sizes. RNA phages such as MS2 have the smallest genomes, with only a few kilobases. However, some DNA phages such as T4 may have large genomes with hundreds of genes; the size and shape of the capsid varies along with the size of the genome. The largest bacteriophage genomes reach a size of 735 kb.Bacteriophage genomes can be highly mosaic, i.e. the genome of many phage species appear to be composed of numerous individual modules. These modules may be found in other phage species in different arrangements. Mycobacteriophages, bacteriophages with mycobacterial hosts, have provided excellent examples of this mosaicism. In these mycobacteriophages, genetic assortment may be the result of repeated instances of site-specific recombination and illegitimate recombination (the result of phage genome acquisition of bacterial host genetic sequences). Evolutionary mechanisms shaping the genomes of bacterial viruses vary between different families and depend upon the type of the nucleic acid, characteristics of the virion structure, as well as the mode of the viral life cycle.
Some marine roseobacter phages contain deoxyuridine (dU) instead of deoxythymidine (dT) in their genomic DNA. There is some evidence that this unusual component is a mechanism to evade bacterial defense mechanisms such as restriction endonucleases and CRISPR/Cas systems which evolved to recognize and cleave sequences within invading phages, thereby inactivating them. Other phages have long been known to use unusual nucleotides. In 1963, Takahashi and Marmur identified a Bacillus phage that has dU substituting dT in its genome, and in 1977, Kirnos et al. identified a cyanophage containing 2-aminoadenine (Z) instead of adenine (A).
Systems biology
The field of systems biology investigates the complex networks of interactions within an organism, usually using computational tools and modeling. For example, a phage genome that enters into a bacterial host cell may express hundreds of phage proteins which will affect the expression of numerous host genes or the host's metabolism. All of these complex interactions can be described and simulated in computer models. | Bacteriophage | Wikipedia | 499 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
For instance, infection of Pseudomonas aeruginosa by the temperate phage PaP3 changed the expression of 38% (2160/5633) of its host's genes. Many of these effects are probably indirect, hence the challenge becomes to identify the direct interactions among bacteria and phage.
Several attempts have been made to map protein–protein interactions among phage and their host. For instance, bacteriophage lambda was found to interact with its host, E. coli, by dozens of interactions. Again, the significance of many of these interactions remains unclear, but these studies suggest that there most likely are several key interactions and many indirect interactions whose role remains uncharacterized.
Host resistance
Bacteriophages are a major threat to bacteria and prokaryotes have evolved numerous mechanisms to block infection or to block the replication of bacteriophages within host cells. The CRISPR system is one such mechanism as are retrons and the anti-toxin system encoded by them. The Thoeris defense system is known to deploy a unique strategy for bacterial antiphage resistance via NAD+ degradation.
Bacteriophage–host symbiosis
Temperate phages are bacteriophages that integrate their genetic material into the host as extrachromosomal episomes or as a prophage during a lysogenic cycle. Some temperate phages can confer fitness advantages to their host in numerous ways, including giving antibiotic resistance through the transfer or introduction of antibiotic resistance genes (ARGs), protecting hosts from phagocytosis, protecting hosts from secondary infection through superinfection exclusion, enhancing host pathogenicity, or enhancing bacterial metabolism or growth. Bacteriophage–host symbiosis may benefit bacteria by providing selective advantages while passively replicating the phage genome.
In the environment
Metagenomics has allowed the in-water detection of bacteriophages that was not possible previously.
Also, bacteriophages have been used in hydrological tracing and modelling in river systems, especially where surface water and groundwater interactions occur. The use of phages is preferred to the more conventional dye marker because they are significantly less absorbed when passing through ground waters and they are readily detected at very low concentrations. Non-polluted water may contain approximately 2×108 bacteriophages per ml. | Bacteriophage | Wikipedia | 484 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
Bacteriophages are thought to contribute extensively to horizontal gene transfer in natural environments, principally via transduction, but also via transformation. Metagenomics-based studies also have revealed that viromes from a variety of environments harbor antibiotic-resistance genes, including those that could confer multidrug resistance.
Recent findings have mapped the complex and intertwined arsenal of anti-phage defense tools in environmental bacteria.
In humans
Although phages do not infect humans, there are countless phage particles in the human body, given the extensive human microbiome. One's phage population has been called the human phageome, including the "healthy gut phageome" (HGP) and the "diseased human phageome" (DHP). The active phageome of a healthy human (i.e., actively replicating as opposed to nonreplicating, integrated prophage) has been estimated to comprise dozens to thousands of different viruses.
There is evidence that bacteriophages and bacteria interact in the human gut microbiome both antagonistically and beneficially.
Preliminary studies have indicated that common bacteriophages are found in 62% of healthy individuals on average, while their prevalence was reduced by 42% and 54% on average in patients with ulcerative colitis (UC) and Crohn's disease (CD). Abundance of phages may also decline in the elderly.
The most common phages in the human intestine, found worldwide, are crAssphages. CrAssphages are transmitted from mother to child soon after birth, and there is some evidence suggesting that they may be transmitted locally. Each person develops their own unique crAssphage clusters. CrAss-like phages also may be present in primates besides humans.
Commonly studied bacteriophages
Among the countless phages, only a few have been studied in detail, including some historically important phage that were discovered in the early days of microbial genetics. These, especially the T-phage, helped to discover important principles of gene structure and function. | Bacteriophage | Wikipedia | 432 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
186 phage
λ phage
Φ6 phage
Φ29 phage
ΦX174
Bacteriophage φCb5
G4 phage
M13 phage
MS2 phage (23–28 nm in size)
N4 phage
P1 phage
P2 phage
P4 phage
R17 phage
T2 phage
T4 phage (169 kbp genome, 200 nm long)
T7 phage
T12 phage
Bacteriophage databases and resources
Phagesdb
Phagescope | Bacteriophage | Wikipedia | 106 | 4185 | https://en.wikipedia.org/wiki/Bacteriophage | Biology and health sciences | Biology basics | Biology |
Bohrium is a synthetic chemical element; it has symbol Bh and atomic number 107. It is named after Danish physicist Niels Bohr. As a synthetic element, it can be created in particle accelerators but is not found in nature. All known isotopes of bohrium are highly radioactive; the most stable known isotope is 270Bh with a half-life of approximately 2.4 minutes, though the unconfirmed 278Bh may have a longer half-life of about 11.5 minutes.
In the periodic table, it is a d-block transactinide element. It is a member of the 7th period and belongs to the group 7 elements as the fifth member of the 6d series of transition metals. Chemistry experiments have confirmed that bohrium behaves as the heavier homologue to rhenium in group 7. The chemical properties of bohrium are characterized only partly, but they compare well with the chemistry of the other group 7 elements.
Introduction
History
Discovery
Two groups claimed discovery of the element. Evidence of bohrium was first reported in 1976 by a Soviet research team led by Yuri Oganessian, in which targets of bismuth-209 and lead-208 were bombarded with accelerated nuclei of chromium-54 and manganese-55, respectively. Two activities, one with a half-life of one to two milliseconds, and the other with an approximately five-second half-life, were seen. Since the ratio of the intensities of these two activities was constant throughout the experiment, it was proposed that the first was from the isotope bohrium-261 and that the second was from its daughter dubnium-257. Later, the dubnium isotope was corrected to dubnium-258, which indeed has a five-second half-life (dubnium-257 has a one-second half-life); however, the half-life observed for its parent is much shorter than the half-lives later observed in the definitive discovery of bohrium at Darmstadt in 1981. The IUPAC/IUPAP Transfermium Working Group (TWG) concluded that while dubnium-258 was probably seen in this experiment, the evidence for the production of its parent bohrium-262 was not convincing enough. | Bohrium | Wikipedia | 464 | 4194 | https://en.wikipedia.org/wiki/Bohrium | Physical sciences | Group 7 | Chemistry |
In 1981, a German research team led by Peter Armbruster and Gottfried Münzenberg at the GSI Helmholtz Centre for Heavy Ion Research (GSI Helmholtzzentrum für Schwerionenforschung) in Darmstadt bombarded a target of bismuth-209 with accelerated nuclei of chromium-54 to produce 5 atoms of the isotope bohrium-262:
+ → +
This discovery was further substantiated by their detailed measurements of the alpha decay chain of the produced bohrium atoms to previously known isotopes of fermium and californium. The IUPAC/IUPAP Transfermium Working Group (TWG) recognised the GSI collaboration as official discoverers in their 1992 report.
Proposed names
In September 1992, the German group suggested the name nielsbohrium with symbol Ns to honor the Danish physicist Niels Bohr. The Soviet scientists at the Joint Institute for Nuclear Research in Dubna, Russia had suggested this name be given to element 105 (which was finally called dubnium) and the German team wished to recognise both Bohr and the fact that the Dubna team had been the first to propose the cold fusion reaction, and simultaneously help to solve the controversial problem of the naming of element 105. The Dubna team agreed with the German group's naming proposal for element 107.
There was an element naming controversy as to what the elements from 104 to 106 were to be called; the IUPAC adopted unnilseptium (symbol Uns) as a temporary, systematic element name for this element. In 1994 a committee of IUPAC recommended that element 107 be named bohrium, not nielsbohrium, since there was no precedent for using a scientist's complete name in the naming of an element. This was opposed by the discoverers as there was some concern that the name might be confused with boron and in particular the distinguishing of the names of their respective oxyanions, bohrate and borate. The matter was handed to the Danish branch of IUPAC which, despite this, voted in favour of the name bohrium, and thus the name bohrium for element 107 was recognized internationally in 1997; the names of the respective oxyanions of boron and bohrium remain unchanged despite their homophony.
Isotopes | Bohrium | Wikipedia | 480 | 4194 | https://en.wikipedia.org/wiki/Bohrium | Physical sciences | Group 7 | Chemistry |
Bohrium has no stable or naturally occurring isotopes. Several radioactive isotopes have been synthesized in the laboratory, either by fusing two atoms or by observing the decay of heavier elements. Twelve different isotopes of bohrium have been reported with atomic masses 260–262, 264–267, 270–272, 274, and 278, one of which, bohrium-262, has a known metastable state. All of these but the unconfirmed 278Bh decay only through alpha decay, although some unknown bohrium isotopes are predicted to undergo spontaneous fission.
The lighter isotopes usually have shorter half-lives; half-lives of under 100 ms for 260Bh, 261Bh, 262Bh, and 262mBh were observed. 264Bh, 265Bh, 266Bh, and 271Bh are more stable at around 1 s, and 267Bh and 272Bh have half-lives of about 10 s. The heaviest isotopes are the most stable, with 270Bh and 274Bh having measured half-lives of about 2.4 min and 40 s respectively, and the even heavier unconfirmed isotope 278Bh appearing to have an even longer half-life of about 11.5 minutes.
The most proton-rich isotopes with masses 260, 261, and 262 were directly produced by cold fusion, those with mass 262 and 264 were reported in the decay chains of meitnerium and roentgenium, while the neutron-rich isotopes with masses 265, 266, 267 were created in irradiations of actinide targets. The five most neutron-rich ones with masses 270, 271, 272, 274, and 278 (unconfirmed) appear in the decay chains of 282Nh, 287Mc, 288Mc, 294Ts, and 290Fl respectively. The half-lives of bohrium isotopes range from about ten milliseconds for 262mBh to about one minute for 270Bh and 274Bh, extending to about 11.5 minutes for the unconfirmed 278Bh, which may have one of the longest half-lives among reported superheavy nuclides.
Predicted properties
Very few properties of bohrium or its compounds have been measured; this is due to its extremely limited and expensive production and the fact that bohrium (and its parents) decays very quickly. A few singular chemistry-related properties have been measured, but properties of bohrium metal remain unknown and only predictions are available. | Bohrium | Wikipedia | 499 | 4194 | https://en.wikipedia.org/wiki/Bohrium | Physical sciences | Group 7 | Chemistry |
Chemical
Bohrium is the fifth member of the 6d series of transition metals and the heaviest member of group 7 in the periodic table, below manganese, technetium and rhenium. All the members of the group readily portray their group oxidation state of +7 and the state becomes more stable as the group is descended. Thus bohrium is expected to form a stable +7 state. Technetium also shows a stable +4 state whilst rhenium exhibits stable +4 and +3 states. Bohrium may therefore show these lower states as well. The higher +7 oxidation state is more likely to exist in oxyanions, such as perbohrate, , analogous to the lighter permanganate, pertechnetate, and perrhenate. Nevertheless, bohrium(VII) is likely to be unstable in aqueous solution, and would probably be easily reduced to the more stable bohrium(IV).
The lighter group 7 elements are known to form volatile heptoxides M2O7 (M = Mn, Tc, Re), so bohrium should also form the volatile oxide Bh2O7. The oxide should dissolve in water to form perbohric acid, HBhO4.
Rhenium and technetium form a range of oxyhalides from the halogenation of the oxide. The chlorination of the oxide forms the oxychlorides MO3Cl, so BhO3Cl should be formed in this reaction. Fluorination results in MO3F and MO2F3 for the heavier elements in addition to the rhenium compounds ReOF5 and ReF7. Therefore, oxyfluoride formation for bohrium may help to indicate eka-rhenium properties. Since the oxychlorides are asymmetrical, and they should have increasingly large dipole moments going down the group, they should become less volatile in the order TcO3Cl > ReO3Cl > BhO3Cl: this was experimentally confirmed in 2000 by measuring the enthalpies of adsorption of these three compounds. The values are for TcO3Cl and ReO3Cl are −51 kJ/mol and −61 kJ/mol respectively; the experimental value for BhO3Cl is −77.8 kJ/mol, very close to the theoretically expected value of −78.5 kJ/mol. | Bohrium | Wikipedia | 509 | 4194 | https://en.wikipedia.org/wiki/Bohrium | Physical sciences | Group 7 | Chemistry |
Physical and atomic
Bohrium is expected to be a solid under normal conditions and assume a hexagonal close-packed crystal structure (c/a = 1.62), similar to its lighter congener rhenium. Early predictions by Fricke estimated its density at 37.1 g/cm3, but newer calculations predict a somewhat lower value of 26–27 g/cm3.
The atomic radius of bohrium is expected to be around 128 pm. Due to the relativistic stabilization of the 7s orbital and destabilization of the 6d orbital, the Bh+ ion is predicted to have an electron configuration of [Rn] 5f14 6d4 7s2, giving up a 6d electron instead of a 7s electron, which is the opposite of the behavior of its lighter homologues manganese and technetium. Rhenium, on the other hand, follows its heavier congener bohrium in giving up a 5d electron before a 6s electron, as relativistic effects have become significant by the sixth period, where they cause among other things the yellow color of gold and the low melting point of mercury. The Bh2+ ion is expected to have an electron configuration of [Rn] 5f14 6d3 7s2; in contrast, the Re2+ ion is expected to have a [Xe] 4f14 5d5 configuration, this time analogous to manganese and technetium. The ionic radius of hexacoordinate heptavalent bohrium is expected to be 58 pm (heptavalent manganese, technetium, and rhenium having values of 46, 57, and 53 pm respectively). Pentavalent bohrium should have a larger ionic radius of 83 pm.
Experimental chemistry
In 1995, the first report on attempted isolation of the element was unsuccessful, prompting new theoretical studies to investigate how best to investigate bohrium (using its lighter homologs technetium and rhenium for comparison) and removing unwanted contaminating elements such as the trivalent actinides, the group 5 elements, and polonium. | Bohrium | Wikipedia | 442 | 4194 | https://en.wikipedia.org/wiki/Bohrium | Physical sciences | Group 7 | Chemistry |
In 2000, it was confirmed that although relativistic effects are important, bohrium behaves like a typical group 7 element. A team at the Paul Scherrer Institute (PSI) conducted a chemistry reaction using six atoms of 267Bh produced in the reaction between 249Bk and 22Ne ions. The resulting atoms were thermalised and reacted with a HCl/O2 mixture to form a volatile oxychloride. The reaction also produced isotopes of its lighter homologues, technetium (as 108Tc) and rhenium (as 169Re). The isothermal adsorption curves were measured and gave strong evidence for the formation of a volatile oxychloride with properties similar to that of rhenium oxychloride. This placed bohrium as a typical member of group 7. The adsorption enthalpies of the oxychlorides of technetium, rhenium, and bohrium were measured in this experiment, agreeing very well with the theoretical predictions and implying a sequence of decreasing oxychloride volatility down group 7 of TcO3Cl > ReO3Cl > BhO3Cl.
2 Bh + 3 + 2 HCl → 2 +
The longer-lived heavy isotopes of bohrium, produced as the daughters of heavier elements, offer advantages for future radiochemical experiments. Although the heavy isotope 274Bh requires a rare and highly radioactive berkelium target for its production, the isotopes 272Bh, 271Bh, and 270Bh can be readily produced as daughters of more easily produced moscovium and nihonium isotopes. | Bohrium | Wikipedia | 333 | 4194 | https://en.wikipedia.org/wiki/Bohrium | Physical sciences | Group 7 | Chemistry |
Barnard's Star is a small red dwarf star in the constellation of Ophiuchus. At a distance of from Earth, it is the fourth-nearest-known individual star to the Sun after the three components of the Alpha Centauri system, and is the closest star in the northern celestial hemisphere. Its stellar mass is about 16% of the Sun's, and it has 19% of the Sun's diameter. Despite its proximity, the star has a dim apparent visual magnitude of +9.5 and is invisible to the unaided eye; it is much brighter in the infrared than in visible light.
The star is named after Edward Emerson Barnard, an American astronomer who in 1916 measured its proper motion as 10.3 arcseconds per year relative to the Sun, the highest known for any star. The star had previously appeared on Harvard University photographic plates in 1888 and 1890.
Barnard's Star is among the most studied red dwarfs because of its proximity and favorable location for observation near the celestial equator. Historically, research on Barnard's Star has focused on measuring its stellar characteristics, its astrometry, and also refining the limits of possible extrasolar planets. Although Barnard's Star is ancient, it still experiences stellar flare events, one being observed in 1998.
Barnard's Star hosts at least one planet, Barnard's Star b, a close-orbiting sub-Earth discovered in 2024, with additional candidates suspected. Previously, it was subject to multiple claims of planets that were disproven.
Naming
In 2016, the International Astronomical Union organized a Working Group on Star Names (WGSN) to catalogue and standardize proper names for stars. The WGSN approved the name Barnard's Star for this star on 1 February 2017 and it is now included in the List of IAU-approved Star Names.
Description
Barnard's Star is a red dwarf of the dim spectral type M4 and is too faint to see without a telescope; its apparent magnitude is 9.5. | Barnard's Star | Wikipedia | 406 | 4196 | https://en.wikipedia.org/wiki/Barnard%27s%20Star | Physical sciences | Notable stars | Astronomy |
At 7–12 billion years of age, Barnard's Star is considerably older than the Sun, which is 4.5 billion years old, and it might be among the oldest stars in the Milky Way galaxy. Barnard's Star has lost a great deal of rotational energy; the periodic slight changes in its brightness indicate that it rotates once in 130 days (the Sun rotates in 25). Given its age, Barnard's Star was long assumed to be quiescent in terms of stellar activity. In 1998, astronomers observed an intense stellar flare, showing that Barnard's Star is a flare star. Barnard's Star has the variable star designation V2500 Ophiuchi. In 2003, Barnard's Star presented the first detectable change in the radial velocity of a star caused by its motion. Further variability in the radial velocity of Barnard's Star was attributed to its stellar activity.
The proper motion of Barnard's Star corresponds to a relative lateral speed of 90km/s. The 10.3 arcseconds it travels in a year amount to a quarter of a degree in a human lifetime, roughly half the angular diameter of the full Moon.
The radial velocity of Barnard's Star is , as measured from the blueshift due to its motion toward the Sun. Combined with its proper motion and distance, this gives a "space velocity" (actual speed relative to the Sun) of . Barnard's Star will make its closest approach to the Sun around 11,800 CE, when it will approach to within about 3.75 light-years.
Proxima Centauri is the closest star to the Sun at a position currently 4.24 light-years distant from it. However, despite Barnard's Star's even closer pass to the Sun in 11,800 CE, it will still not then be the nearest star, since by that time Proxima Centauri will have moved to a yet-nearer proximity to the Sun. At the time of the star's closest pass by the Sun, Barnard's Star will still be too dim to be seen with the naked eye, since its apparent magnitude will only have increased by one magnitude to about 8.5 by then, still being 2.5 magnitudes short of visibility to the naked eye. | Barnard's Star | Wikipedia | 466 | 4196 | https://en.wikipedia.org/wiki/Barnard%27s%20Star | Physical sciences | Notable stars | Astronomy |
Barnard's Star has a mass of about 0.16 solar masses (), and a radius about 0.2 times that of the Sun. Thus, although Barnard's Star has roughly 150 times the mass of Jupiter (), its radius is only roughly 2 times larger, due to its much higher density. Its effective temperature is about 3,220 kelvin, and it has a luminosity of only 0.0034 solar luminosities. Barnard's Star is so faint that if it were at the same distance from Earth as the Sun is, it would appear only 100 times brighter than a full moon, comparable to the brightness of the Sun at 80 astronomical units.
Barnard's Star has 10–32% of the solar metallicity. Metallicity is the proportion of stellar mass made up of elements heavier than helium and helps classify stars relative to the galactic population. Barnard's Star seems to be typical of the old, red dwarf population II stars, yet these are also generally metal-poor halo stars. While sub-solar, Barnard's Star's metallicity is higher than that of a halo star and is in keeping with the low end of the metal-rich disk star range; this, plus its high space motion, have led to the designation "intermediate population II star", between a halo and disk star. However, some recently published scientific papers have given much higher estimates for the metallicity of the star, very close to the Sun's level, between 75 and 125% of the solar metallicity.
Planetary system
In August 2024, by using data from ESPRESSO spectrograph of the Very Large Telescope, the existence of an exoplanet with a minimum mass of and orbital period of 3.15 days was confirmed. This constituted the first convincing evidence for a planet orbiting Barnard's Star. Additionally, three other candidate low-mass planets were proposed in this study. All of these planets orbit closer to the star than the habitable zone. The confirmed planet is designated Barnard's Star b (or Barnard b), a re-use of the designation originally used for the refuted super-Earth candidate. | Barnard's Star | Wikipedia | 439 | 4196 | https://en.wikipedia.org/wiki/Barnard%27s%20Star | Physical sciences | Notable stars | Astronomy |
Previous planetary claims
Barnard's Star has been subject to multiple claims of planets that were later disproven. From the early 1960s to the early 1970s, Peter van de Kamp argued that planets orbited Barnard's Star. His specific claims of large gas giants were refuted in the mid-1970s after much debate. In November 2018, a candidate super-Earth planetary companion was reported to orbit Barnard's Star. It was believed to have a minimum mass of and orbit at . However, work presented in July 2021 refuted the existence of this planet.
Astrometric planetary claims
For a decade from 1963 to about 1973, a substantial number of astronomers accepted a claim by Peter van de Kamp that he had detected, by using astrometry, a perturbation in the proper motion of Barnard's Star consistent with its having one or more planets comparable in mass with Jupiter. Van de Kamp had been observing the star from 1938, attempting, with colleagues at the Sproul Observatory at Swarthmore College, to find minuscule variations of one micrometre in its position on photographic plates consistent with orbital perturbations that would indicate a planetary companion; this involved as many as ten people averaging their results in looking at plates, to avoid systemic individual errors.
Van de Kamp's initial suggestion was a planet having about at a distance of 4.4AU in a slightly eccentric orbit, and these measurements were apparently refined in a 1969 paper. Later that year, Van de Kamp suggested that there were two planets of 1.1 and .
Other astronomers subsequently repeated Van de Kamp's measurements, and two papers in 1973 undermined the claim of a planet or planets. George Gatewood and Heinrich Eichhorn, at a different observatory and using newer plate measuring techniques, failed to verify the planetary companion. Another paper published by John L. Hershey four months earlier, also using the Swarthmore observatory, found that changes in the astrometric field of various stars correlated to the timing of adjustments and modifications that had been carried out on the refractor telescope's objective lens; the claimed planet was attributed to an artifact of maintenance and upgrade work. The affair has been discussed as part of a broader scientific review. | Barnard's Star | Wikipedia | 452 | 4196 | https://en.wikipedia.org/wiki/Barnard%27s%20Star | Physical sciences | Notable stars | Astronomy |
Van de Kamp never acknowledged any error and published a further claim of two planets' existence as late as 1982; he died in 1995. Wulff Heintz, Van de Kamp's successor at Swarthmore and an expert on double stars, questioned his findings and began publishing criticisms from 1976 onwards. The two men were reported to have become estranged because of this.
Refuted 2018 planetary claim
In November 2018, an international team of astronomers announced the detection by radial velocity of a candidate super-Earth orbiting in relatively close proximity to Barnard's Star. Led by Ignasi Ribas of Spain their work, conducted over two decades of observation, provided strong evidence of the planet's existence. However, the existence of the planet was refuted in 2021, when the radial velocity signal was found to originate from long-term activity on the star itself, related to its rotation. Further studies in the following years confirmed this result.
Dubbed Barnard's Star b, the planet was thought to be near the stellar system's snow line, which is an ideal spot for the icy accretion of proto-planetary material. It was thought to orbit at 0.4AU every 233 days and had a proposed minimum mass of . The planet would have most likely been frigid, with an estimated surface temperature of about , and lie outside Barnard Star's presumed habitable zone. Direct imaging of the planet and its tell-tale light signature would have been possible in the decade after its discovery. Further faint and unaccounted-for perturbations in the system suggested there may be a second planetary companion even farther out.
Refining planetary boundaries
For the more than four decades between van de Kamp's rejected claim and the eventual announcement of a planet candidate, Barnard's Star was carefully studied and the mass and orbital boundaries for possible planets were slowly tightened. M dwarfs such as Barnard's Star are more easily studied than larger stars in this regard because their lower masses render perturbations more obvious. | Barnard's Star | Wikipedia | 408 | 4196 | https://en.wikipedia.org/wiki/Barnard%27s%20Star | Physical sciences | Notable stars | Astronomy |
Null results for planetary companions continued throughout the 1980s and 1990s, including interferometric work with the Hubble Space Telescope in 1999. Gatewood was able to show in 1995 that planets with were impossible around Barnard's Star, in a paper which helped refine the negative certainty regarding planetary objects in general. In 1999, the Hubble work further excluded planetary companions of with an orbital period of less than 1,000 days (Jupiter's orbital period is 4,332 days), while Kuerster determined in 2003 that within the habitable zone around Barnard's Star, planets are not possible with an "M sin i" value greater than 7.5 times the mass of the Earth (), or with a mass greater than 3.1 times the mass of Neptune (much lower than van de Kamp's smallest suggested value).
In 2013, a research paper was published that further refined planet mass boundaries for the star. Using radial velocity measurements, taken over a period of 25 years, from the Lick and Keck Observatories and applying Monte Carlo analysis for both circular and eccentric orbits, upper masses for planets out to 1,000-day orbits were determined. Planets above two Earth masses in orbits of less than 10 days were excluded, and planets of more than ten Earth masses out to a two-year orbit were also confidently ruled out. It was also discovered that the habitable zone of the star seemed to be devoid of roughly Earth-mass planets or larger, save for face-on orbits.
Even though this research greatly restricted the possible properties of planets around Barnard's Star, it did not rule them out completely as terrestrial planets were always going to be difficult to detect. NASA's Space Interferometry Mission, which was to begin searching for extrasolar Earth-like planets, was reported to have chosen Barnard's Star as an early search target, however the mission was shut down in 2010. ESA's similar Darwin interferometry mission had the same goal, but was stripped of funding in 2007. | Barnard's Star | Wikipedia | 413 | 4196 | https://en.wikipedia.org/wiki/Barnard%27s%20Star | Physical sciences | Notable stars | Astronomy |
The analysis of radial velocities that eventually led to the announcement of a candidate super-Earth orbiting Barnard's Star was also used to set more precise upper mass limits for possible planets, up to and within the habitable zone: a maximum of up to the inner edge and on the outer edge of the optimistic habitable zone, corresponding to orbital periods of up to 10 and 40 days respectively. Therefore, it appears that Barnard's Star indeed does not host Earth-mass planets or larger, in hot and temperate orbits, unlike other M-dwarf stars that commonly have these types of planets in close-in orbits.
Stellar flares
1998
In 1998 a stellar flare on Barnard's Star was detected based on changes in the spectral emissions on 17 July during an unrelated search for variations in the proper motion. Four years passed before the flare was fully analyzed, at which point it was suggested that the flare's temperature was 8,000K, more than twice the normal temperature of the star. Given the essentially random nature of flares, Diane Paulson, one of the authors of that study, noted that "the star would be fantastic for amateurs to observe".
The flare was surprising because intense stellar activity is not expected in stars of such age. Flares are not completely understood, but are believed to be caused by strong magnetic fields, which suppress plasma convection and lead to sudden outbursts: strong magnetic fields occur in rapidly rotating stars, while old stars tend to rotate slowly. For Barnard's Star to undergo an event of such magnitude is thus presumed to be a rarity. Research on the star's periodicity, or changes in stellar activity over a given timescale, also suggest it ought to be quiescent; 1998 research showed weak evidence for periodic variation in the star's brightness, noting only one possible starspot over 130 days.
Stellar activity of this sort has created interest in using Barnard's Star as a proxy to understand similar stars. It is hoped that photometric studies of its X-ray and UV emissions will shed light on the large population of old M dwarfs in the galaxy. Such research has astrobiological implications: given that the habitable zones of M dwarfs are close to the star, any planet located therein would be strongly affected by solar flares, stellar winds, and plasma ejection events. | Barnard's Star | Wikipedia | 475 | 4196 | https://en.wikipedia.org/wiki/Barnard%27s%20Star | Physical sciences | Notable stars | Astronomy |
2019
In 2019, two additional ultraviolet stellar flares were detected, each with far-ultraviolet energy of 3×1022 joules, together with one X-ray stellar flare with energy 1.6×1022 joules. The flare rate observed to date is enough to cause loss of 87 Earth atmospheres per billion years through thermal processes and ≈3 Earth atmospheres per billion years through ion loss processes on Barnard's Star b.
Environment
Barnard's Star shares much the same neighborhood as the Sun. The neighbors of Barnard's Star are generally of red dwarf size, the smallest and most common star type. Its closest neighbor is currently the red dwarf Ross 154, at a distance of 1.66 parsecs (5.41 light-years). The Sun (5.98 light-years) and Alpha Centauri (6.47 light-years) are, respectively, the next closest systems. From Barnard's Star, the Sun would appear on the diametrically opposite side of the sky at coordinates RA=, Dec=, in the westernmost part of the constellation Monoceros. The absolute magnitude of the Sun is 4.83, and at a distance of 1.834 parsecs, it would be a first-magnitude star, as Pollux is from the Earth.
Proposed exploration
Project Daedalus
Barnard's Star was studied as part of Project Daedalus. Undertaken between 1973 and 1978, the study suggested that rapid, uncrewed travel to another star system was possible with existing or near-future technology. Barnard's Star was chosen as a target partly because it was believed to have planets.
The theoretical model suggested that a nuclear pulse rocket employing nuclear fusion (specifically, electron bombardment of deuterium and helium-3) and accelerating for four years could achieve a velocity of 12% of the speed of light. The star could then be reached in 50 years, within a human lifetime. Along with detailed investigation of the star and any companions, the interstellar medium would be examined and baseline astrometric readings performed. | Barnard's Star | Wikipedia | 419 | 4196 | https://en.wikipedia.org/wiki/Barnard%27s%20Star | Physical sciences | Notable stars | Astronomy |
The initial Project Daedalus model sparked further theoretical research. In 1980, Robert Freitas suggested a more ambitious plan: a self-replicating spacecraft intended to search for and make contact with extraterrestrial life. Built and launched in Jupiter's orbit, it would reach Barnard's Star in 47 years under parameters similar to those of the original Project Daedalus. Once at the star, it would begin automated self-replication, constructing a factory, initially to manufacture exploratory probes and eventually to create a copy of the original spacecraft after 1,000 years. | Barnard's Star | Wikipedia | 119 | 4196 | https://en.wikipedia.org/wiki/Barnard%27s%20Star | Physical sciences | Notable stars | Astronomy |
Boötes ( ) is a constellation in the northern sky, located between 0° and +60° declination, and 13 and 16 hours of right ascension on the celestial sphere. The name comes from , which comes from 'herdsman' or 'plowman' (literally, 'ox-driver'; from boûs 'cow').
One of the 48 constellations described by the 2nd-century astronomer Ptolemy, Boötes is now one of the 88 modern constellations. It contains the fourth-brightest star in the night sky, the orange giant Arcturus. Epsilon Boötis, or Izar, is a colourful multiple star popular with amateur astronomers. Boötes is home to many other bright stars, including eight above the fourth magnitude and an additional 21 above the fifth magnitude, making a total of 29 stars easily visible to the naked eye.
History and mythology
In ancient Babylon, the stars of Boötes were known as SHU.PA. They were apparently depicted as the god Enlil, who was the leader of the Babylonian pantheon and special patron of farmers. Boötes may have been represented by the animal foreleg constellation in ancient Egypt, resembling that of an ox sufficiently to have been originally proposed as the "foreleg of ox" by Berio.
Homer mentions Boötes in the Odyssey as a celestial reference for navigation, describing it as "late-setting" or "slow to set". Exactly whom Boötes is supposed to represent in Greek mythology is not clear. According to one version, he was a son of Demeter, Philomenus, twin brother of Plutus, a plowman who drove the oxen in the constellation Ursa Major. This agrees with the constellation's name. The ancient Greeks saw the asterism now called the "Big Dipper" or "Plough" as a cart with oxen. Some myths say that Boötes invented the plow and was memorialized for his ingenuity as a constellation. | Boötes | Wikipedia | 400 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Another myth associated with Boötes by Hyginus is that of Icarius, who was schooled as a grape farmer and winemaker by Dionysus. Icarius made wine so strong that those who drank it appeared poisoned, which caused shepherds to avenge their supposedly poisoned friends by killing Icarius. Maera, Icarius' dog, brought his daughter Erigone to her father's body, whereupon both she and the dog died by suicide. Zeus then chose to honor all three by placing them in the sky as constellations: Icarius as Boötes, Erigone as Virgo, and Maera as Canis Major or Canis Minor.
Following another reading, the constellation is identified with Arcas and also referred to as Arcas and Arcturus, son of Zeus and Callisto. Arcas was brought up by his maternal grandfather Lycaon, to whom one day Zeus went and had a meal. To verify that the guest was really the king of the gods, Lycaon killed his grandson and prepared a meal made from his flesh. Zeus noticed and became very angry, transforming Lycaon into a wolf and giving life back to his son. In the meantime Callisto had been transformed into a she-bear by Zeus's wife Hera, who was angry at Zeus's infidelity. This is corroborated by the Greek name for Boötes, Arctophylax, which means "Bear Watcher".
Callisto, in the form of a bear was almost killed by her son, who was out hunting. Zeus rescued her, taking her into the sky where she became Ursa Major, "the Great Bear". Arcturus, the name of the constellation's brightest star, comes from the Greek word meaning "guardian of the bear". Sometimes Arcturus is depicted as leading the hunting dogs of nearby Canes Venatici and driving the bears of Ursa Major and Ursa Minor. | Boötes | Wikipedia | 407 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Several former constellations were formed from stars now included in Boötes. Quadrans Muralis, the Quadrant, was a constellation created near Beta Boötis from faint stars. It was designated in 1795 by Jérôme Lalande, an astronomer who used a quadrant to perform detailed astronometric measurements. Lalande worked with Nicole-Reine Lepaute and others to predict the 1758 return of Halley's Comet. Quadrans Muralis was formed from the stars of eastern Boötes, western Hercules and Draco. It was originally called Le Mural by Jean Fortin in his 1795 Atlas Céleste; it was not given the name Quadrans Muralis until Johann Bode's 1801 Uranographia. The constellation was quite faint, with its brightest stars reaching the 5th magnitude. Mons Maenalus, representing the Maenalus mountains, was created by Johannes Hevelius in 1687 at the foot of the constellation's figure. The mountain was named for the son of Lycaon, Maenalus. The mountain, one of Diana's hunting grounds, was also holy to Pan.
Non-Western astronomy
The stars of Boötes were incorporated into many different Chinese constellations. Arcturus was part of the most prominent of these, variously designated as the celestial king's throne (Tian Wang) or the Blue Dragon's horn (Daijiao); the name Daijiao, meaning "great horn", is more common. Arcturus was given such importance in Chinese celestial mythology because of its status marking the beginning of the lunar calendar, as well as its status as the brightest star in the northern night sky.
Two constellations flanked Daijiao: Yousheti to the right and Zuosheti to the left; they represented companions that orchestrated the seasons. Zuosheti was formed from modern Zeta, Omicron and Pi Boötis, while Yousheti was formed from modern Eta, Tau and Upsilon Boötis. Dixi, the Emperor's ceremonial banquet mat, was north of Arcturus, consisting of the stars 12, 11 and 9 Boötis. Another northern constellation was Qigong, the Seven Dukes, which mostly straddled the Boötes-Hercules border. It included either Delta Boötis or Beta Boötis as its terminus. | Boötes | Wikipedia | 469 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
The other Chinese constellations made up of the stars of Boötes existed in the modern constellation's north; they are all representations of weapons. Tianqiang, the spear, was formed from Iota, Kappa and Theta Boötis; Genghe, variously representing a lance or shield, was formed from Epsilon, Rho and Sigma Boötis.
There were also two weapons made up of a singular star. Xuange, the halberd, was represented by Lambda Boötis, and Zhaoyao, either the sword or the spear, was represented by Gamma Boötis.
Two Chinese constellations have an uncertain placement in Boötes. Kangchi, the lake, was placed south of Arcturus, though its specific location is disputed. It may have been placed entirely in Boötes, on either side of the Boötes-Virgo border, or on either side of the Virgo-Libra border. The constellation Zhouding, a bronze tripod-mounted container used for food, was sometimes cited as the stars 1, 2 and 6 Boötis. However, it has also been associated with three stars in Coma Berenices.
Boötes is also known to Native American cultures. In Yup'ik language, Boötes is Taluyaq, literally "fish trap," and the funnel-shaped part of the fish trap is known as Ilulirat.
Characteristics
Boötes is a constellation bordered by Virgo to the south, Coma Berenices and Canes Venatici to the west, Ursa Major to the northwest, Draco to the northeast, and Hercules, Corona Borealis and Serpens Caput to the east. The three-letter abbreviation for the constellation, as adopted by the International Astronomical Union in 1922, is "Boo". The official constellation boundaries, as set by Belgian astronomer Eugène Delporte in 1930, are defined by a polygon of 16 segments. In the equatorial coordinate system, the right ascension coordinates of these borders lie between and , while the declination coordinates stretch from +7.36° to +55.1°. Covering 907 square degrees, Boötes culminates at midnight around 2 May and ranks 13th in area. | Boötes | Wikipedia | 445 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Colloquially, its pattern of stars has been likened to a kite or ice cream cone. However, depictions of Boötes have varied historically. Aratus described him circling the north pole, herding the two bears. Later ancient Greek depictions, described by Ptolemy, have him holding the reins of his hunting dogs (Canes Venatici) in his left hand, with a spear, club, or staff in his right hand. After Hevelius introduced Mons Maenalus in 1681, Boötes was often depicted standing on the Peloponnese mountain. By 1801, when Johann Bode published his Uranographia, Boötes had acquired a sickle, which was also held in his left hand.
The placement of Arcturus has also been mutable through the centuries. Traditionally, Arcturus lay between his thighs, as Ptolemy depicted him. However, Germanicus Caesar deviated from this tradition by placing Arcturus "where his garment is fastened by a knot".
Features
Stars
In his Uranometria, Johann Bayer used the Greek letters alpha through to omega and then A to k to label what he saw as the most prominent 35 stars in the constellation, with subsequent astronomers splitting Kappa, Mu, Nu and Pi as two stars each. Nu is also the same star as Psi Herculis. John Flamsteed numbered 54 stars for the constellation.
Located 36.7 light-years from Earth, Arcturus, or Alpha Boötis, is the brightest star in Boötes and the fourth-brightest star in the sky at an apparent magnitude of −0.05; It is also the brightest star north of the celestial equator, just shading out Vega and Capella. Its name comes from the Greek for "bear-keeper". An orange giant of spectral class K1.5III, Arcturus is an ageing star that has exhausted its core supply of hydrogen and cooled and expanded to a diameter of 27 solar diameters, equivalent to approximately 32 million kilometers. Though its mass is approximately one solar mass (), Arcturus shines with 133 times the luminosity of the Sun (). | Boötes | Wikipedia | 434 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Bayer located Arcturus above the Herdman's left knee in his Uranometria. Nearby Eta Boötis, or Muphrid, is the uppermost star denoting the left leg. It is a 2.68-magnitude star 37 light-years distant with a spectral class of G0IV, indicating it has just exhausted its core hydrogen and is beginning to expand and cool. It is 9 times as luminous as the Sun and has 2.7 times its diameter. Analysis of its spectrum reveals that it is a spectroscopic binary. Muphrid and Arcturus lie only 3.3 light-years away from each other. Viewed from Arcturus, Muphrid would have a visual magnitude of −2½, while Arcturus would be around visual magnitude −4½ when seen from Muphrid.
Marking the herdsman's head is Beta Boötis, or Nekkar, a yellow giant of magnitude 3.5 and spectral type G8IIIa. Like Arcturus, it has expanded and cooled off the main sequence—likely to have lived most of its stellar life as a blue-white B-type main sequence star. Its common name comes from the Arabic phrase for "ox-driver". It is 219 light-years away and has a luminosity of .
Located 86 light-years distant, Gamma Boötis, or Seginus, is a white giant star of spectral class A7III, with a luminosity 34 times and diameter 3.5 times that of the Sun. It is a Delta Scuti variable, ranging between magnitudes 3.02 and 3.07 every 7 hours. These stars are short period (six hours at most) pulsating stars that have been used as standard candles and as subjects to study asteroseismology.
Delta Boötis is a wide double star with a primary of magnitude 3.5 and a secondary of magnitude 7.8. The primary is a yellow giant that has cooled and expanded to 10.4 times the diameter of the Sun. Of spectral class G8IV, it is around 121 light-years away, while the secondary is a yellow main sequence star of spectral type G0V. The two are thought to take 120,000 years to orbit each other. | Boötes | Wikipedia | 465 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Mu Boötis, known as Alkalurops, is a triple star popular with amateur astronomers. It has an overall magnitude of 4.3 and is 121 light-years away. Its name is from the Arabic phrase for "club" or "staff". The primary appears to be of magnitude 4.3 and is blue-white. The secondary appears to be of magnitude 6.5, but is actually a close double star itself with a primary of magnitude 7.0 and a secondary of magnitude 7.6. The secondary and tertiary stars have an orbital period of 260 years. The primary has an absolute magnitude of 2.6 and is of spectral class F0. The secondary and tertiary stars are separated by 2 arcseconds; the primary and secondary are separated by 109.1 arcseconds at an angle of 171 degrees.
Nu Boötis is an optical double star. The primary is an orange giant of magnitude 5.0 and the secondary is a white star of magnitude 5.0. The primary is 870 light-years away and the secondary is 430 light-years.
Epsilon Boötis, also known as Izar or Pulcherrima, is a close triple star popular with amateur astronomers and the most prominent binary star in Boötes. The primary is a yellow- or orange-hued magnitude 2.5 giant star, the secondary is a magnitude 4.6 blue-hued main-sequence star, and the tertiary is a magnitude 12.0 star. The system is 210 light-years away. The name "Izar" comes from the Arabic word for "girdle" or "loincloth", referring to its location in the constellation. The name "Pulcherrima" comes from the Latin phrase for "most beautiful", referring to its contrasting colors in a telescope. The primary and secondary stars are separated by 2.9 arcseconds at an angle of 341 degrees; the primary's spectral class is K0 and it has a luminosity of . To the naked eye, Izar has a magnitude of 2.37. | Boötes | Wikipedia | 427 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Nearby Rho and Sigma Boötis denote the herdsman's waist. Rho is an orange giant of spectral type K3III located around 160 light-years from Earth. It is ever so slightly variable, wavering by 0.003 of a magnitude from its average of 3.57. Sigma, a yellow-white main-sequence star of spectral type F3V, is suspected of varying in brightness from 4.45 to 4.49. It is around 52 light-years distant.
Traditionally known as Aulād al Dhiʼbah (أولاد الضباع – aulād al dhiʼb), "the Whelps of the Hyenas", Theta, Iota, Kappa and Lambda Boötis (or Xuange) are a small group of stars in the far north of the constellation. The magnitude 4.05 Theta Boötis has a spectral type of F7 and an absolute magnitude of 3.8. Iota Boötis is a triple star with a primary of magnitude 4.8 and spectral class of A7, a secondary of magnitude 7.5, and a tertiary of magnitude 12.6. The primary is 97 light-years away. The primary and secondary stars are separated by 38.5 arcseconds, at an angle of 33 degrees. The primary and tertiary stars are separated by 86.7 arcseconds at an angle of 194 degrees. Both the primary and tertiary appear white in a telescope, but the secondary appears yellow-hued.
Kappa Boötis is another wide double star. The primary is 155 light-years away and has a magnitude of 4.5. The secondary is 196 light-years away and has a magnitude of 6.6. The two components are separated by 13.4 arcseconds, at an angle of 236 degrees. The primary, with spectral class A7, appears white and the secondary appears bluish. | Boötes | Wikipedia | 395 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
An apparent magnitude 4.18 type A0p star, Lambda Boötis is the prototype of a class of chemically peculiar stars, only some of which pulsate as Delta Scuti-type stars. The distinction between the Lambda Boötis stars as a class of stars with peculiar spectra, and the Delta Scuti stars whose class describes pulsation in low-overtone pressure modes, is an important one. While many Lambda Boötis stars pulsate and are Delta Scuti stars, not many Delta Scuti stars have Lambda Boötis peculiarities, since the Lambda Boötis stars are a much rarer class whose members can be found both inside and outside the Delta Scuti instability strip. Lambda Boötis stars are dwarf stars that can be either spectral class A or F. Like BL Boötis-type stars they are metal-poor. Scientists have had difficulty explaining the characteristics of Lambda Boötis stars, partly because only around 60 confirmed members exist, but also due to heterogeneity in the literature. Lambda has an absolute magnitude of 1.8.
There are two dimmer F-type stars, magnitude 4.83 12 Boötis, class F8; and magnitude 4.93 45 Boötis, class F5. Xi Boötis is a G8 yellow dwarf of magnitude 4.55, and absolute magnitude is 5.5. Two dimmer G-type stars are magnitude 4.86 31 Boötis, class G8, and magnitude 4.76 44 Boötis, class G0.
Of apparent magnitude 4.06, Upsilon Boötis has a spectral class of K5 and an absolute magnitude of −0.3. Dimmer than Upsilon Boötis is magnitude 4.54 Phi Boötis, with a spectral class of K2 and an absolute magnitude of −0.1. Just slightly dimmer than Phi at magnitude 4.60 is O Boötis, which, like Izar, has a spectral class of K0. O Boötis has an absolute magnitude of 0.2. The other four dim stars are magnitude 4.91 6 Boötis, class K4; magnitude 4.86 20 Boötis, class K3; magnitude 4.81 Omega Boötis, class K4; and magnitude 4.83 A Boötis, class K1. | Boötes | Wikipedia | 468 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
There is one bright B-class star in Boötes; magnitude 4.93 Pi1 Boötis, also called Alazal. It has a spectral class of B9 and is 40 parsecs from Earth. There is also one M-type star, magnitude 4.81 34 Boötis. It is of class gM0.
Multiple stars
Besides Pulcherrima and Alkalurops, there are several other binary stars in Boötes:
Xi Boötis is a quadruple star popular with amateur astronomers. The primary is a yellow star of magnitude 4.7 and the secondary is an orange star of magnitude 6.8. The system is 22 light-years away and has an orbital period of 150 years. The primary and secondary have a separation of 6.7 arcseconds at an angle of 319 degrees. The tertiary is a magnitude 12.6 star (though it may be observed to be brighter) and the quaternary is a magnitude 13.6 star.
Pi Boötis is a close triple star. The primary is a blue-white star of magnitude 4.9, the secondary is a blue-white star of magnitude 5.8, and the tertiary is a star of magnitude 10.4. The primary and secondary components are separated by 5.6 arcseconds at an angle of 108 degrees; the primary and tertiary components are separated by 128 arcseconds at an angle of 128 degrees.
Zeta Boötis is a triple star that consists of a physical binary pair with an optical companion. Lying 205 light-years away from Earth, The physical pair has a period of 123.3 years and consists of a magnitude 4.5 and a magnitude 4.6 star. The two components are separated by 1.0 arcseconds at an angle of 303 degrees. The optical companion is of magnitude 10.9, separated by 99.3 arcseconds at an angle of 259 degrees. 44 Boötis is an eclipsing variable star. The primary is of variable magnitude and the secondary is of magnitude 6.2; they have an orbital period of 225 years. The components are separated by 1.0 arcsecond at an angle of 40 degrees. | Boötes | Wikipedia | 446 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
44 Boötis (i Boötis) is a double variable star 42 light-years away. It has an overall magnitude of 4.8 and appears yellow to the naked eye. The primary is of magnitude 5.3 and the secondary is of magnitude 6.1; their orbital period is 220 years. The secondary is itself an eclipsing variable star with a range of 0.6 magnitudes; its orbital period is 6.4 hours. It is a W Ursae Majoris variable that ranges in magnitude from a minimum of 7.1 to a maximum of 6.5 every 0.27 days. Both stars are G-type stars. Another eclipsing binary star is ZZ Boötis, which has two F2-type components of almost equal mass, and ranges in magnitude from a minimum of 6.79 to a maximum of 7.44 over a period of 5.0 days.
Variable stars
Two of the brighter Mira-type variable stars in the constellation are R and S Boötis. Both are red giants that range greatly in magnitude—from 6.2 to 13.1 over 223.4 days, and 7.8 to 13.8 over a period of 270.7 days, respectively. Also red giants, V and W Boötis are semi-regular variable stars that range in magnitude from 7.0 to 12.0 over a period of 258 days, and magnitude 4.7 to 5.4 over 450 days, respectively.
BL Boötis is the prototype of its class of pulsating variable stars, the anomalous Cepheids. These stars are somewhat similar to Cepheid variables, but they do not have the same relationship between their period and luminosity. Their periods are similar to RRAB variables; however, they are far brighter than these stars. BL Boötis is a member of the cluster NGC 5466. Anomalous Cepheids are metal poor and have masses not much larger than the Sun's, on average, . BL Boötis type stars are a subtype of RR Lyrae variables.
T Boötis was a nova observed in April 1860 at a magnitude of 9.7. It has never been observed since, but that does not preclude the possibility of it being a highly irregular variable star or a recurrent nova.
Stars with planetary systems | Boötes | Wikipedia | 479 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Extrasolar planets have been discovered encircling ten stars in Boötes as of 2012. Tau Boötis is orbited by a large planet, discovered in 1999. The host star itself is a magnitude 4.5 star of type F7V, 15.6 parsecs from Earth. It has a mass of and a radius of 1.331 solar radii (); a companion, GJ527B, orbits at a distance of 240 AU. Tau Boötis b, the sole planet discovered in the system, orbits at a distance of 0.046 AU every 3.31 days. Discovered through radial velocity measurements, it has a mass of 5.95 Jupiter masses (). This makes it a hot Jupiter. The host star and planet are tidally locked, meaning that the planet's orbit and the star's particularly high rotation are synchronized. Furthermore, a slight variability in the host star's light may be caused by magnetic interactions with the planet. Carbon monoxide is present in the planet's atmosphere. Tau Boötis b does not transit its star, rather, its orbit is inclined 46 degrees.
Like Tau Boötis b, HAT-P-4b is also a hot Jupiter. It is noted for orbiting a particularly metal-rich host star and being of low density. Discovered in 2007, HAT-P-4 b has a mass of and a radius of . It orbits every 3.05 days at a distance of 0.04 AU. HAT-P-4, the host star, is an F-type star of magnitude 11.2, 310 parsecs from Earth. It is larger than the Sun, with a mass of and a radius of .
Boötes is also home to multiple-planet systems. HD 128311 is the host star for a two-planet system, consisting of HD 128311 b and HD 128311 c, discovered in 2002 and 2005, respectively. HD 128311 b is the smaller planet, with a mass of ; it was discovered through radial velocity observations. It orbits at almost the same distance as Earth, at 1.099 AU; however, its orbital period is significantly longer at 448.6 days. | Boötes | Wikipedia | 451 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
The larger of the two, HD 128311 c, has a mass of and was discovered in the same manner. It orbits every 919 days inclined at 50°, and is 1.76 AU from the host star. The host star, HD 128311, is a K0V-type star located 16.6 parsecs from Earth. It is smaller than the Sun, with a mass of and a radius of ; it also appears below the threshold of naked-eye visibility at an apparent magnitude of 7.51.
There are several single-planet systems in Boötes. HD 132406 is a Sun-like star of spectral type G0V with an apparent magnitude of 8.45, 231.5 light-years from Earth. It has a mass of and a radius of . The star is orbited by a gas giant, HD 132406 b, discovered in 2007. HD 132406 orbits 1.98 AU from its host star with a period of 974 days and has a mass of . The planet was discovered by the radial velocity method.
WASP-23 is a star with one orbiting planet, WASP-23 b. The planet, discovered by the transit method in 2010, orbits every 2.944 days very close to its Sun, at 0.0376 AU. It is smaller than Jupiter, at and . Its star is a K1V-type star of apparent magnitude 12.7, far below naked-eye visibility, and smaller than the Sun at and .
HD 131496 is also encircled by one planet, HD 131496 b. The star is of type K0 and is located 110 parsecs from Earth; it appears at a visual magnitude of 7.96. It is significantly larger than the Sun, with a mass of and a radius of 4.6 solar radii. Its one planet, discovered in 2011 by the radial velocity method, has a mass of ; its radius is as yet undetermined. HD 131496 b orbits at a distance of 2.09 AU with a period of 883 days. | Boötes | Wikipedia | 427 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Another single planetary system in Boötes is the HD 132563 system, a triple star system. The parent star, technically HD 132563B, is a star of magnitude 9.47, 96 parsecs from Earth. It is almost exactly the size of the Sun, with the same radius and a mass only 1% greater. Its planet, HD 132563B b, was discovered in 2011 by the radial velocity method. , it orbits 2.62 AU from its star with a period of 1544 days. Its orbit is somewhat elliptical, with an eccentricity of 0.22. HD 132563B b is one of very few planets found in triple star systems; it orbits the isolated member of the system, which is separated from the other components, a spectroscopic binary, by 400 AU.
Also discovered through the radial velocity method, albeit a year earlier, is HD 136418 b, a two-Jupiter-mass planet that orbits the star HD 136418 at a distance of 1.32 AU with a period of 464.3 days. Its host star is a magnitude 7.88 G5-type star, 98.2 parsecs from Earth. It has a radius of and a mass of .
WASP-14 b is one of the most massive and dense exoplanets known, with a mass of and a radius of . Discovered via the transit method, it orbits 0.036 AU from its host star with a period of 2.24 days. WASP-14 b has a density of 4.6 grams per cubic centimeter, making it one of the densest exoplanets known. Its host star, WASP-14, is an F5V-type star of magnitude 9.75, 160 parsecs from Earth. It has a radius of and a mass of . It also has a very high proportion of lithium.
Deep-sky objects | Boötes | Wikipedia | 390 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Boötes is in a part of the celestial sphere facing away from the plane of our home Milky Way galaxy, and so does not have open clusters or nebulae. Instead, it has one bright globular cluster and many faint galaxies. The globular cluster NGC 5466 has an overall magnitude of 9.1 and a diameter of 11 arcminutes. It is a very loose globular cluster with fairly few stars and may appear as a rich, concentrated open cluster in a telescope. NGC 5466 is classified as a Shapley–Sawyer Concentration Class 12 cluster, reflecting its sparsity. Its fairly large diameter means that it has a low surface brightness, so it appears far dimmer than the catalogued magnitude of 9.1 and requires a large amateur telescope to view. Only approximately 12 stars are resolved by an amateur instrument.
Boötes has two bright galaxies. NGC 5248 (Caldwell 45) is a type Sc galaxy (a variety of spiral galaxy) of magnitude 10.2. It measures 6.5 by 4.9 arcminutes. Fifty million light-years from Earth, NGC 5248 is a member of the Virgo Cluster of galaxies; it has dim outer arms and obvious H II regions, dust lanes and young star clusters. NGC 5676 is another type Sc galaxy of magnitude 10.9. It measures 3.9 by 2.0 arcminutes. Other galaxies include NGC 5008, a type Sc emission-line galaxy, NGC 5548, a type S Seyfert galaxy, NGC 5653, a type S HII galaxy, NGC 5778 (also classified as NGC 5825), a type E galaxy that is the brightest of its cluster, NGC 5886, and NGC 5888, a type SBb galaxy. NGC 5698 is a barred spiral galaxy, notable for being the host of the 2005 supernova SN 2005bc, which peaked at magnitude 15.3.
Further away lies the 250-million-light-year-diameter Boötes void, a huge space largely empty of galaxies. Discovered by Robert Kirshner and colleagues in 1981, it is roughly 700 million light-years from Earth. Beyond it and within the bounds of the constellation, lie two superclusters at around 830 million and 1 billion light-years distant.
The Hercules–Corona Borealis Great Wall, the largest-known structure in the Universe, covers a significant part of Boötes.
Meteor showers | Boötes | Wikipedia | 504 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Boötes is home to the Quadrantid meteor shower, the most prolific annual meteor shower. It was discovered in January 1835 and named in 1864 by Alexander Herschel. The radiant is located in northern Boötes near Kappa Boötis, in its namesake former constellation of Quadrans Muralis. Quadrantid meteors are dim, but have a peak visible hourly rate of approximately 100 per hour on January 3–4. The zenithal hourly rate of the Quadrantids is approximately 130 meteors per hour at their peak; it is also a very narrow shower.
The Quadrantids are notoriously difficult to observe because of a low radiant and often inclement weather. The parent body of the meteor shower has been disputed for decades; however, Peter Jenniskens has proposed 2003 EH1, a minor planet, as the parent. 2003 EH1 may be linked to C/1490 Y1, a comet previously thought to be a potential parent body for the Quadrantids.
2003 EH1 is a short-period comet of the Jupiter family; 500 years ago, it experienced a catastrophic breakup event. It is now dormant. The Quadrantids had notable displays in 1982, 1985 and 2004. Meteors from this shower often appear to have a blue hue and travel at a moderate speed of 41.5–43 kilometers per second.
On April 28, 1984, a remarkable outburst of the normally placid Alpha Bootids was observed by visual observer Frank Witte from 00:00 to 2:30 UTC. In a 6 cm telescope, he observed 433 meteors in a field of view near Arcturus with a diameter of less than 1°. Peter Jenniskens comments that this outburst resembled a "typical dust trail crossing". The Alpha Bootids normally begin on April 14, peaking on April 27 and 28, and finishing on May 12. Its meteors are slow-moving, with a velocity of 20.9 kilometers per second. They may be related to Comet 73P/Schwassmann–Wachmann 3, but this connection is only theorized. | Boötes | Wikipedia | 419 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
The June Bootids, also known as the Iota Draconids, is a meteor shower associated with the comet 7P/Pons–Winnecke, first recognized on May 27, 1916, by William F. Denning. The shower, with its slow meteors, was not observed prior to 1916 because Earth did not cross the comet's dust trail until Jupiter perturbed Pons–Winnecke's orbit, causing it to come within of Earth's orbit the first year the June Bootids were observed.
In 1982, E. A. Reznikov discovered that the 1916 outburst was caused by material released from the comet in 1819. Another outburst of the June Bootids was not observed until 1998, because Comet Pons–Winnecke's orbit was not in a favorable position. However, on June 27, 1998, an outburst of meteors radiating from Boötes, later confirmed to be associated with Pons-Winnecke, was observed. They were incredibly long-lived, with trails of the brightest meteors lasting several seconds at times. Many fireballs, green-hued trails, and even some meteors that cast shadows were observed throughout the outburst, which had a maximum zenithal hourly rate of 200–300 meteors per hour.
Two Russian astronomers determined in 2002 that material ejected from the comet in 1825 was responsible for the 1998 outburst. Ejecta from the comet dating to 1819, 1825 and 1830 was predicted to enter Earth's atmosphere on June 23, 2004. The predictions of a shower less spectacular than the 1998 showing were borne out in a display that had a maximum zenithal hourly rate of 16–20 meteors per hour that night. The June Bootids are not expected to have another outburst in the next 50 years.
Typically, only 1–2 dim, very slow meteors are visible per hour; the average June Bootid has a magnitude of 5.0. It is related to the Alpha Draconids and the Bootids-Draconids. The shower lasts from June 27 to July 5, with a peak on the night of June 28. The June Bootids are classified as a class III shower (variable), and has an average entry velocity of 18 kilometers per second. Its radiant is located 7 degrees north of Beta Boötis. | Boötes | Wikipedia | 472 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
The Beta Bootids is a weak shower that begins on January 5, peaks on January 16, and ends on January 18. Its meteors travel at 43 km/s. The January Bootids is a short, young meteor shower that begins on January 9, peaks from January 16 to January 18, and ends on January 18.
The Phi Bootids is another weak shower radiating from Boötes. It begins on April 16, peaks on April 30 and May 1, and ends on May 12. Its meteors are slow-moving, with a velocity of 15.1 km/s. They were discovered in 2006. The shower's peak hourly rate can be as high as six meteors per hour. Though named for a star in Boötes, the Phi Bootid radiant has moved into Hercules. The meteor stream is associated with three different asteroids: 1620 Geographos, 2062 Aten and 1978 CA.
The Lambda Bootids, part of the Bootid-Coronae Borealid Complex, are a weak annual shower with moderately fast meteors; 41.75 km/s. The complex includes the Lambda Bootids, as well as the Theta Coronae Borealids and Xi Coronae Borealids. All of the Bootid-Coronae Borealid showers are Jupiter family comet showers; the streams in the complex have highly inclined orbits.
There are several minor showers in Boötes, some of whose existence is yet to be verified. The Rho Bootids radiate from near the namesake star, and were hypothesized in 2010. The average Rho Bootid has an entry velocity of 43 km/s. It peaks in November and lasts for three days.
The Rho Bootid shower is part of the SMA complex, a group of meteor showers related to the Taurids, which is in turn linked to the comet 2P/Encke. However, the link to the Taurid shower remains unconfirmed and may be a chance correlation. Another such shower is the Gamma Bootids, which were hypothesized in 2006. Gamma Bootids have an entry velocity of 50.3 km/s. The Nu Bootids, hypothesized in 2012, have faster meteors, with an entry velocity of 62.8 km/s. | Boötes | Wikipedia | 467 | 4200 | https://en.wikipedia.org/wiki/Bo%C3%B6tes | Physical sciences | Other | Astronomy |
Bipedalism is a form of terrestrial locomotion where an animal moves by means of its two rear (or lower) limbs or legs. An animal or machine that usually moves in a bipedal manner is known as a biped , meaning 'two feet' (from Latin bis 'double' and pes 'foot'). Types of bipedal movement include walking or running (a bipedal gait) and hopping.
Several groups of modern species are habitual bipeds whose normal method of locomotion is two-legged. In the Triassic period some groups of archosaurs (a group that includes crocodiles and dinosaurs) developed bipedalism; among the dinosaurs, all the early forms and many later groups were habitual or exclusive bipeds; the birds are members of a clade of exclusively bipedal dinosaurs, the theropods. Within mammals, habitual bipedalism has evolved multiple times, with the macropods, kangaroo rats and mice, springhare, hopping mice, pangolins and hominin apes (australopithecines, including humans) as well as various other extinct groups evolving the trait independently.
A larger number of modern species intermittently or briefly use a bipedal gait. Several lizard species move bipedally when running, usually to escape from threats. Many primate and bear species will adopt a bipedal gait in order to reach food or explore their environment, though there are a few cases where they walk on their hind limbs only. Several arboreal primate species, such as gibbons and indriids, exclusively walk on two legs during the brief periods they spend on the ground. Many animals rear up on their hind legs while fighting or copulating. Some animals commonly stand on their hind legs to reach food, keep watch, threaten a competitor or predator, or pose in courtship, but do not move bipedally.
Etymology
The word is derived from the Latin words bi(s) 'two' and ped- 'foot', as contrasted with quadruped 'four feet'. | Bipedalism | Wikipedia | 426 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Advantages
Limited and exclusive bipedalism can offer a species several advantages. Bipedalism raises the head; this allows a greater field of vision with improved detection of distant dangers or resources, access to deeper water for wading animals and allows the animals to reach higher food sources with their mouths. While upright, non-locomotory limbs become free for other uses, including manipulation (in primates and rodents), flight (in birds), digging (in the giant pangolin), combat (in bears, great apes and the large monitor lizard) or camouflage.
The maximum bipedal speed appears slower than the maximum speed of quadrupedal movement with a flexible backbone – both the ostrich and the red kangaroo can reach speeds of , while the cheetah can exceed . Even though bipedalism is slower at first, over long distances, it has allowed humans to outrun most other animals according to the endurance running hypothesis. Bipedality in kangaroo rats has been hypothesized to improve locomotor performance, which could aid in escaping from predators.
Facultative and obligate bipedalism
Zoologists often label behaviors, including bipedalism, as "facultative" (i.e. optional) or "obligate" (the animal has no reasonable alternative). Even this distinction is not completely clear-cut — for example, humans other than infants normally walk and run in biped fashion, but almost all can crawl on hands and knees when necessary. There are even reports of humans who normally walk on all fours with their feet but not their knees on the ground, but these cases are a result of conditions such as Uner Tan syndrome — very rare genetic neurological disorders rather than normal behavior. Even if one ignores exceptions caused by some kind of injury or illness, there are many unclear cases, including the fact that "normal" humans can crawl on hands and knees. This article therefore avoids the terms "facultative" and "obligate", and focuses on the range of styles of locomotion normally used by various groups of animals. Normal humans may be considered "obligate" bipeds because the alternatives are very uncomfortable and usually only resorted to when walking is impossible. | Bipedalism | Wikipedia | 463 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Movement
There are a number of states of movement commonly associated with bipedalism.
Standing. Staying still on both legs. In most bipeds this is an active process, requiring constant adjustment of balance.
Walking. One foot in front of another, with at least one foot on the ground at any time.
Running. One foot in front of another, with periods where both feet are off the ground.
Jumping/hopping. Moving by a series of jumps with both feet moving together.
Bipedal animals
The great majority of living terrestrial vertebrates are quadrupeds, with bipedalism exhibited by only a handful of living groups. Humans, gibbons and large birds walk by raising one foot at a time. On the other hand, most macropods, smaller birds, lemurs and bipedal rodents move by hopping on both legs simultaneously. Tree kangaroos are able to walk or hop, most commonly alternating feet when moving arboreally and hopping on both feet simultaneously when on the ground.
Extant reptiles
Many species of lizards become bipedal during high-speed, sprint locomotion, including the world's fastest lizard, the spiny-tailed iguana (genus Ctenosaura).
Early reptiles and lizards
The first known biped is the bolosaurid Eudibamus whose fossils date from 290 million years ago. Its long hind-legs, short forelegs, and distinctive joints all suggest bipedalism. The species became extinct in the early Permian.
Archosaurs (includes crocodilians and dinosaurs)
Birds
All birds are bipeds, as is the case for all theropod dinosaurs. However, hoatzin chicks have claws on their wings which they use for climbing.
Other archosaurs
Bipedalism evolved more than once in archosaurs, the group that includes both dinosaurs and crocodilians. All dinosaurs are thought to be descended from a fully bipedal ancestor, perhaps similar to Eoraptor. | Bipedalism | Wikipedia | 409 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Dinosaurs diverged from their archosaur ancestors approximately 230 million years ago during the Middle to Late Triassic period, roughly 20 million years after the Permian-Triassic extinction event wiped out an estimated 95 percent of all life on Earth. Radiometric dating of fossils from the early dinosaur genus Eoraptor establishes its presence in the fossil record at this time. Paleontologists suspect Eoraptor resembles the common ancestor of all dinosaurs; if this is true, its traits suggest that the first dinosaurs were small, bipedal predators. The discovery of primitive, dinosaur-like ornithodirans such as Marasuchus and Lagerpeton in Argentinian Middle Triassic strata supports this view; analysis of recovered fossils suggests that these animals were indeed small, bipedal predators.
Bipedal movement also re-evolved in a number of other dinosaur lineages such as the iguanodonts. Some extinct members of Pseudosuchia, a sister group to the avemetatarsalians (the group including dinosaurs and relatives), also evolved bipedal forms – a poposauroid from the Triassic, Effigia okeeffeae, is thought to have been bipedal. Pterosaurs were previously thought to have been bipedal, but recent trackways have all shown quadrupedal locomotion.
Mammals
A number of groups of extant mammals have independently evolved bipedalism as their main form of locomotion - for example humans, ground pangolins, the extinct giant ground sloths, numerous species of jumping rodents and macropods. Humans, as their bipedalism has been extensively studied, are documented in the next section. Macropods are believed to have evolved bipedal hopping only once in their evolution, at some time no later than 45 million years ago. | Bipedalism | Wikipedia | 370 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Bipedal movement is less common among mammals, most of which are quadrupedal. All primates possess some bipedal ability, though most species primarily use quadrupedal locomotion on land. Primates aside, the macropods (kangaroos, wallabies and their relatives), kangaroo rats and mice, hopping mice and springhare move bipedally by hopping. Very few non-primate mammals commonly move bipedally with an alternating leg gait. Exceptions are the ground pangolin and in some circumstances the tree kangaroo. One black bear, Pedals, became famous locally and on the internet for having a frequent bipedal gait, although this is attributed to injuries on the bear's front paws. A two-legged fox was filmed in a Derbyshire garden in 2023, most likely having been born that way.
Primates
Most bipedal animals move with their backs close to horizontal, using a long tail to balance the weight of their bodies. The primate version of bipedalism is unusual because the back is close to upright (completely upright in humans), and the tail may be absent entirely. Many primates can stand upright on their hind legs without any support.
Chimpanzees, bonobos, gorillas, gibbons and baboons exhibit forms of bipedalism. On the ground sifakas move like all indrids with bipedal sideways hopping movements of the hind legs, holding their forelimbs up for balance. Geladas, although usually quadrupedal, will sometimes move between adjacent feeding patches with a squatting, shuffling bipedal form of locomotion. However, they can only do so for brief amounts, as their bodies are not adapted for constant bipedal locomotion.
Humans are the only primates who are normally biped, due to an extra curve in the spine which stabilizes the upright position, as well as shorter arms relative to the legs than is the case for the nonhuman great apes. The evolution of human bipedalism began in primates about four million years ago, or as early as seven million years ago with Sahelanthropus or about 12 million years ago with Danuvius guggenmosi. One hypothesis for human bipedalism is that it evolved as a result of differentially successful survival from carrying food to share with group members, although there are alternative hypotheses. | Bipedalism | Wikipedia | 498 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Injured individuals
Injured chimpanzees and bonobos have been capable of sustained bipedalism.
Three captive primates, one macaque Natasha and two chimps, Oliver and Poko (chimpanzee), were found to move bipedally. Natasha switched to exclusive bipedalism after an illness, while Poko was discovered in captivity in a tall, narrow cage. Oliver reverted to knuckle-walking after developing arthritis. Non-human primates often use bipedal locomotion when carrying food, or while moving through shallow water.
Limited bipedalism
Limited bipedalism in mammals
Other mammals engage in limited, non-locomotory, bipedalism. A number of other animals, such as rats, raccoons, and beavers will squat on their hindlegs to manipulate some objects but revert to four limbs when moving (the beaver will move bipedally if transporting wood for their dams, as will the raccoon when holding food). Bears will fight in a bipedal stance to use their forelegs as weapons. A number of mammals will adopt a bipedal stance in specific situations such as for feeding or fighting. Ground squirrels and meerkats will stand on hind legs to survey their surroundings, but will not walk bipedally. Dogs (e.g. Faith) can stand or move on two legs if trained, or if birth defect or injury precludes quadrupedalism. The gerenuk antelope stands on its hind legs while eating from trees, as did the extinct giant ground sloth and chalicotheres. The spotted skunk will walk on its front legs when threatened, rearing up on its front legs while facing the attacker so that its anal glands, capable of spraying an offensive oil, face its attacker. | Bipedalism | Wikipedia | 376 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Limited bipedalism in non-mammals (and non-birds)
Bipedalism is unknown among the amphibians. Among the non-archosaur reptiles bipedalism is rare, but it is found in the "reared-up" running of lizards such as agamids and monitor lizards. Many reptile species will also temporarily adopt bipedalism while fighting. One genus of basilisk lizard can run bipedally across the surface of water for some distance. Among arthropods, cockroaches are known to move bipedally at high speeds. Bipedalism is rarely found outside terrestrial animals, though at least two species of octopus walk bipedally on the sea floor using two of their arms, allowing the remaining arms to be used to camouflage the octopus as a mat of algae or a floating coconut.
Evolution of human bipedalism | Bipedalism | Wikipedia | 181 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
There are at least twelve distinct hypotheses as to how and why bipedalism evolved in humans, and also some debate as to when. Bipedalism evolved well before the large human brain or the development of stone tools. Bipedal specializations are found in Australopithecus fossils from 4.2 to 3.9 million years ago and recent studies have suggested that obligate bipedal hominid species were present as early as 7 million years ago. Nonetheless, the evolution of bipedalism was accompanied by significant evolutions in the spine including the forward movement in position of the foramen magnum, where the spinal cord leaves the cranium. Recent evidence regarding modern human sexual dimorphism (physical differences between male and female) in the lumbar spine has been seen in pre-modern primates such as Australopithecus africanus. This dimorphism has been seen as an evolutionary adaptation of females to bear lumbar load better during pregnancy, an adaptation that non-bipedal primates would not need to make. Adapting bipedalism would have required less shoulder stability, which allowed the shoulder and other limbs to become more independent of each other and adapt for specific suspensory behaviors. In addition to the change in shoulder stability, changing locomotion would have increased the demand for shoulder mobility, which would have propelled the evolution of bipedalism forward. The different hypotheses are not necessarily mutually exclusive and a number of selective forces may have acted together to lead to human bipedalism. It is important to distinguish between adaptations for bipedalism and adaptations for running, which came later still. | Bipedalism | Wikipedia | 348 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
The form and function of modern-day humans' upper bodies appear to have evolved from living in a more forested setting. Living in this kind of environment would have made it so that being able to travel arboreally would have been advantageous at the time. Although different to human walking, bipedal locomotion in trees was thought to be advantageous. It has also been proposed that, like some modern-day apes, early hominins had undergone a knuckle-walking stage prior to adapting the back limbs for bipedality while retaining forearms capable of grasping. Numerous causes for the evolution of human bipedalism involve freeing the hands for carrying and using tools, sexual dimorphism in provisioning, changes in climate and environment (from jungle to savanna) that favored a more elevated eye-position, and to reduce the amount of skin exposed to the tropical sun. It is possible that bipedalism provided a variety of benefits to the hominin species, and scientists have suggested multiple reasons for evolution of human bipedalism. There is also not only the question of why the earliest hominins were partially bipedal but also why hominins became more bipedal over time. For example, the postural feeding hypothesis describes how the earliest hominins became bipedal for the benefit of reaching food in trees while the savanna-based theory describes how the late hominins that started to settle on the ground became increasingly bipedal. | Bipedalism | Wikipedia | 301 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Multiple factors
Napier (1963) argued that it is unlikely that a single factor drove the evolution of bipedalism. He stated "It seems unlikely that any single factor was responsible for such a dramatic change in behaviour. In addition to the advantages of accruing from ability to carry objects – food or otherwise – the improvement of the visual range and the freeing of the hands for purposes of defence and offence may equally have played their part as catalysts." Sigmon (1971) demonstrated that chimpanzees exhibit bipedalism in different contexts, and one single factor should be used to explain bipedalism: preadaptation for human bipedalism. Day (1986) emphasized three major pressures that drove evolution of bipedalism: food acquisition, predator avoidance, and reproductive success. Ko (2015) stated that there are two main questions regarding bipedalism 1. Why were the earliest hominins partially bipedal? and 2. Why did hominins become more bipedal over time? He argued that these questions can be answered with combination of prominent theories such as Savanna-based, Postural feeding, and Provisioning.
Savannah-based theory | Bipedalism | Wikipedia | 243 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
According to the Savanna-based theory, hominines came down from the tree's branches and adapted to life on the savanna by walking erect on two feet. The theory suggests that early hominids were forced to adapt to bipedal locomotion on the open savanna after they left the trees. One of the proposed mechanisms was the knuckle-walking hypothesis, which states that human ancestors used quadrupedal locomotion on the savanna, as evidenced by morphological characteristics found in Australopithecus anamensis and Australopithecus afarensis forelimbs, and that it is less parsimonious to assume that knuckle walking developed twice in genera Pan and Gorilla instead of evolving it once as synapomorphy for Pan and Gorilla before losing it in Australopithecus. The evolution of an orthograde posture would have been very helpful on a savanna as it would allow the ability to look over tall grasses in order to watch out for predators, or terrestrially hunt and sneak up on prey. It was also suggested in P. E. Wheeler's "The evolution of bipedality and loss of functional body hair in hominids", that a possible advantage of bipedalism in the savanna was reducing the amount of surface area of the body exposed to the sun, helping regulate body temperature. In fact, Elizabeth Vrba's turnover pulse hypothesis supports the savanna-based theory by explaining the shrinking of forested areas due to global warming and cooling, which forced animals out into the open grasslands and caused the need for hominids to acquire bipedality. | Bipedalism | Wikipedia | 333 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Others state hominines had already achieved the bipedal adaptation that was used in the savanna. The fossil evidence reveals that early bipedal hominins were still adapted to climbing trees at the time they were also walking upright. It is possible that bipedalism evolved in the trees, and was later applied to the savanna as a vestigial trait. Humans and orangutans are both unique to a bipedal reactive adaptation when climbing on thin branches, in which they have increased hip and knee extension in relation to the diameter of the branch, which can increase an arboreal feeding range and can be attributed to a convergent evolution of bipedalism evolving in arboreal environments. Hominine fossils found in dry grassland environments led anthropologists to believe hominines lived, slept, walked upright, and died only in those environments because no hominine fossils were found in forested areas. However, fossilization is a rare occurrence—the conditions must be just right in order for an organism that dies to become fossilized for somebody to find later, which is also a rare occurrence. The fact that no hominine fossils were found in forests does not ultimately lead to the conclusion that no hominines ever died there. The convenience of the savanna-based theory caused this point to be overlooked for over a hundred years.
Some of the fossils found actually showed that there was still an adaptation to arboreal life. For example, Lucy, the famous Australopithecus afarensis, found in Hadar in Ethiopia, which may have been forested at the time of Lucy's death, had curved fingers that would still give her the ability to grasp tree branches, but she walked bipedally. "Little Foot", a nearly-complete specimen of Australopithecus africanus, has a divergent big toe as well as the ankle strength to walk upright. "Little Foot" could grasp things using his feet like an ape, perhaps tree branches, and he was bipedal. Ancient pollen found in the soil in the locations in which these fossils were found suggest that the area used to be much more wet and covered in thick vegetation and has only recently become the arid desert it is now. | Bipedalism | Wikipedia | 451 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Traveling efficiency hypothesis
An alternative explanation is that the mixture of savanna and scattered forests increased terrestrial travel by proto-humans between clusters of trees, and bipedalism offered greater efficiency for long-distance travel between these clusters than quadrupedalism. In an experiment monitoring chimpanzee metabolic rate via oxygen consumption, it was found that the quadrupedal and bipedal energy costs were very similar, implying that this transition in early ape-like ancestors would not have been very difficult or energetically costing. This increased travel efficiency is likely to have been selected for as it assisted foraging across widely dispersed resources.
Postural feeding hypothesis
The postural feeding hypothesis has been recently supported by Dr. Kevin Hunt, a professor at Indiana University. This hypothesis asserts that chimpanzees were only bipedal when they eat. While on the ground, they would reach up for fruit hanging from small trees and while in trees, bipedalism was used to reach up to grab for an overhead branch. These bipedal movements may have evolved into regular habits because they were so convenient in obtaining food. Also, Hunt's hypotheses states that these movements coevolved with chimpanzee arm-hanging, as this movement was very effective and efficient in harvesting food. When analyzing fossil anatomy, Australopithecus afarensis has very similar features of the hand and shoulder to the chimpanzee, which indicates hanging arms. Also, the Australopithecus hip and hind limb very clearly indicate bipedalism, but these fossils also indicate very inefficient locomotive movement when compared to humans. For this reason, Hunt argues that bipedalism evolved more as a terrestrial feeding posture than as a walking posture. | Bipedalism | Wikipedia | 356 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
A related study conducted by University of Birmingham, Professor Susannah Thorpe examined the most arboreal great ape, the orangutan, holding onto supporting branches in order to navigate branches that were too flexible or unstable otherwise. In more than 75 percent of observations, the orangutans used their forelimbs to stabilize themselves while navigating thinner branches. Increased fragmentation of forests where A. afarensis as well as other ancestors of modern humans and other apes resided could have contributed to this increase of bipedalism in order to navigate the diminishing forests. Findings also could shed light on discrepancies observed in the anatomy of A. afarensis, such as the ankle joint, which allowed it to "wobble" and long, highly flexible forelimbs. If bipedalism started from upright navigation in trees, it could explain both increased flexibility in the ankle as well as long forelimbs which grab hold of branches.
Provisioning model
One theory on the origin of bipedalism is the behavioral model presented by C. Owen Lovejoy, known as "male provisioning". Lovejoy theorizes that the evolution of bipedalism was linked to monogamy. In the face of long inter-birth intervals and low reproductive rates typical of the apes, early hominids engaged in pair-bonding that enabled greater parental effort directed towards rearing offspring. Lovejoy proposes that male provisioning of food would improve the offspring survivorship and increase the pair's reproductive rate. Thus the male would leave his mate and offspring to search for food and return carrying the food in his arms walking on his legs. This model is supported by the reduction ("feminization") of the male canine teeth in early hominids such as Sahelanthropus tchadensis and Ardipithecus ramidus, which along with low body size dimorphism in Ardipithecus and Australopithecus, suggests a reduction in inter-male antagonistic behavior in early hominids. In addition, this model is supported by a number of modern human traits associated with concealed ovulation (permanently enlarged breasts, lack of sexual swelling) and low sperm competition (moderate sized testes, low sperm mid-piece volume) that argues against recent adaptation to a polygynous reproductive system. | Bipedalism | Wikipedia | 475 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
However, this model has been debated, as others have argued that early bipedal hominids were instead polygynous. Among most monogamous primates, males and females are about the same size. That is sexual dimorphism is minimal, and other studies have suggested that Australopithecus afarensis males were nearly twice the weight of females. However, Lovejoy's model posits that the larger range a provisioning male would have to cover (to avoid competing with the female for resources she could attain herself) would select for increased male body size to limit predation risk. Furthermore, as the species became more bipedal, specialized feet would prevent the infant from conveniently clinging to the mother - hampering the mother's freedom and thus make her and her offspring more dependent on resources collected by others. Modern monogamous primates such as gibbons tend to be also territorial, but fossil evidence indicates that Australopithecus afarensis lived in large groups. However, while both gibbons and hominids have reduced canine sexual dimorphism, female gibbons enlarge ('masculinize') their canines so they can actively share in the defense of their home territory. Instead, the reduction of the male hominid canine is consistent with reduced inter-male aggression in a pair-bonded though group living primate. | Bipedalism | Wikipedia | 282 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Early bipedalism in homininae model
Recent studies of 4.4 million years old Ardipithecus ramidus suggest bipedalism. It is thus possible that bipedalism evolved very early in homininae and was reduced in chimpanzee and gorilla when they became more specialized. Other recent studies of the foot structure of Ardipithecus ramidus suggest that the species was closely related to African-ape ancestors. This possibly provides a species close to the true connection between fully bipedal hominins and quadruped apes. According to Richard Dawkins in his book "The Ancestor's Tale", chimps and bonobos are descended from Australopithecus gracile type species while gorillas are descended from Paranthropus. These apes may have once been bipedal, but then lost this ability when they were forced back into an arboreal habitat, presumably by those australopithecines from whom eventually evolved hominins. Early hominines such as Ardipithecus ramidus may have possessed an arboreal type of bipedalism that later independently evolved towards knuckle-walking in chimpanzees and gorillas and towards efficient walking and running in modern humans (see figure). It is also proposed that one cause of Neanderthal extinction was a less efficient running.
Warning display (aposematic) model
Joseph Jordania from the University of Melbourne recently (2011) suggested that bipedalism was one of the central elements of the general defense strategy of early hominids, based on aposematism, or warning display and intimidation of potential predators and competitors with exaggerated visual and audio signals. According to this model, hominids were trying to stay as visible and as loud as possible all the time. Several morphological and behavioral developments were employed to achieve this goal: upright bipedal posture, longer legs, long tightly coiled hair on the top of the head, body painting, threatening synchronous body movements, loud voice and extremely loud rhythmic singing/stomping/drumming on external subjects. Slow locomotion and strong body odor (both characteristic for hominids and humans) are other features often employed by aposematic species to advertise their non-profitability for potential predators. | Bipedalism | Wikipedia | 476 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Other behavioural models
There are a variety of ideas which promote a specific change in behaviour as the key driver for the evolution of hominid bipedalism. For example, Wescott (1967) and later Jablonski & Chaplin (1993) suggest that bipedal threat displays could have been the transitional behaviour which led to some groups of apes beginning to adopt bipedal postures more often. Others (e.g. Dart 1925) have offered the idea that the need for more vigilance against predators could have provided the initial motivation. Dawkins (e.g. 2004) has argued that it could have begun as a kind of fashion that just caught on and then escalated through sexual selection. And it has even been suggested (e.g. Tanner 1981:165) that male phallic display could have been the initial incentive, as well as increased sexual signaling in upright female posture.
Thermoregulatory model
The thermoregulatory model explaining the origin of bipedalism is one of the simplest theories so far advanced, but it is a viable explanation. Dr. Peter Wheeler, a professor of evolutionary biology, proposes that bipedalism raises the amount of body surface area higher above the ground which results in a reduction in heat gain and helps heat dissipation. When a hominid is higher above the ground, the organism accesses more favorable wind speeds and temperatures. During heat seasons, greater wind flow results in a higher heat loss, which makes the organism more comfortable. Also, Wheeler explains that a vertical posture minimizes the direct exposure to the sun whereas quadrupedalism exposes more of the body to direct exposure. Analysis and interpretations of Ardipithecus reveal that this hypothesis needs modification to consider that the forest and woodland environmental preadaptation of early-stage hominid bipedalism preceded further refinement of bipedalism by the pressure of natural selection. This then allowed for the more efficient exploitation of the hotter conditions ecological niche, rather than the hotter conditions being hypothetically bipedalism's initial stimulus. A feedback mechanism from the advantages of bipedality in hot and open habitats would then in turn make a forest preadaptation solidify as a permanent state. | Bipedalism | Wikipedia | 462 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Carrying models
Charles Darwin wrote that "Man could not have attained his present dominant position in the world without the use of his hands, which are so admirably adapted to the act of obedience of his will". Darwin (1871:52) and many models on bipedal origins are based on this line of thought. Gordon Hewes (1961) suggested that the carrying of meat "over considerable distances" (Hewes 1961:689) was the key factor. Isaac (1978) and Sinclair et al. (1986) offered modifications of this idea, as indeed did Lovejoy (1981) with his "provisioning model" described above. Others, such as Nancy Tanner (1981), have suggested that infant carrying was key, while others again have suggested stone tools and weapons drove the change. This stone-tools theory is very unlikely, as though ancient humans were known to hunt, the discovery of tools was not discovered for thousands of years after the origin of bipedalism, chronologically precluding it from being a driving force of evolution. (Wooden tools and spears fossilize poorly and therefore it is difficult to make a judgment about their potential usage.) | Bipedalism | Wikipedia | 237 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Wading models
The observation that large primates, including especially the great apes, that predominantly move quadrupedally on dry land, tend to switch to bipedal locomotion in waist deep water, has led to the idea that the origin of human bipedalism may have been influenced by waterside environments. This idea, labelled "the wading hypothesis", was originally suggested by the Oxford marine biologist Alister Hardy who said: "It seems to me likely that Man learnt to stand erect first in water and then, as his balance improved, he found he became better equipped for standing up on the shore when he came out, and indeed also for running." It was then promoted by Elaine Morgan, as part of the aquatic ape hypothesis, who cited bipedalism among a cluster of other human traits unique among primates, including voluntary control of breathing, hairlessness and subcutaneous fat. The "aquatic ape hypothesis", as originally formulated, has not been accepted or considered a serious theory within the anthropological scholarly community. Others, however, have sought to promote wading as a factor in the origin of human bipedalism without referring to further ("aquatic ape" related) factors. Since 2000 Carsten Niemitz has published a series of papers and a book on a variant of the wading hypothesis, which he calls the "amphibian generalist theory" ().
Other theories have been proposed that suggest wading and the exploitation of aquatic food sources (providing essential nutrients for human brain evolution or critical fallback foods) may have exerted evolutionary pressures on human ancestors promoting adaptations which later assisted full-time bipedalism. It has also been thought that consistent water-based food sources had developed early hominid dependency and facilitated dispersal along seas and rivers.
Consequences
Prehistoric fossil records show that early hominins first developed bipedalism before being followed by an increase in brain size. The consequences of these two changes in particular resulted in painful and difficult labor due to the increased favor of a narrow pelvis for bipedalism being countered by larger heads passing through the constricted birth canal. This phenomenon is commonly known as the obstetrical dilemma. | Bipedalism | Wikipedia | 447 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Non-human primates habitually deliver their young on their own, but the same cannot be said for modern-day humans. Isolated birth appears to be rare and actively avoided cross-culturally, even if birthing methods may differ between said cultures. This is due to the fact that the narrowing of the hips and the change in the pelvic angle caused a discrepancy in the ratio of the size of the head to the birth canal. The result of this is that there is greater difficulty in birthing for hominins in general, let alone to be doing it by oneself.
Physiology
Bipedal movement occurs in a number of ways and requires many mechanical and neurological adaptations. Some of these are described below.
Biomechanics
Standing
Energy-efficient means of standing bipedally involve constant adjustment of balance, and of course these must avoid overcorrection. The difficulties associated with simple standing in upright humans are highlighted by the greatly increased risk of falling present in the elderly, even with minimal reductions in control system effectiveness.
Shoulder stability
Shoulder stability would decrease with the evolution of bipedalism. Shoulder mobility would increase because the need for a stable shoulder is only present in arboreal habitats. Shoulder mobility would support suspensory locomotion behaviors which are present in human bipedalism. The forelimbs are freed from weight-bearing requirements, which makes the shoulder a place of evidence for the evolution of bipedalism.
Walking
Unlike non-human apes that are able to practice bipedality such as Pan and Gorilla, hominins have the ability to move bipedally without the utilization of a bent-hip-bent-knee (BHBK) gait, which requires the engagement of both the hip and the knee joints. This human ability to walk is made possible by the spinal curvature humans have that non-human apes do not. Rather, walking is characterized by an "inverted pendulum" movement in which the center of gravity vaults over a stiff leg with each step. Force plates can be used to quantify the whole-body kinetic & potential energy, with walking displaying an out-of-phase relationship indicating exchange between the two. This model applies to all walking organisms regardless of the number of legs, and thus bipedal locomotion does not differ in terms of whole-body kinetics. | Bipedalism | Wikipedia | 475 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
In humans, walking is composed of several separate processes:
Vaulting over a stiff stance leg
Passive ballistic movement of the swing leg
A short 'push' from the ankle prior to toe-off, propelling the swing leg
Rotation of the hips about the axis of the spine, to increase stride length
Rotation of the hips about the horizontal axis to improve balance during stance
Running
Early hominins underwent post-cranial changes in order to better adapt to bipedality, especially running. One of these changes is having longer hindlimbs proportional to the forelimbs and their effects. As previously mentioned, longer hindlimbs assist in thermoregulation by reducing the total surface area exposed to direct sunlight while simultaneously allowing for more space for cooling winds. Additionally, having longer limbs is more energy-efficient, since longer limbs mean that overall muscle strain is lessened. Better energy efficiency, in turn, means higher endurance, particularly when running long distances.
Running is characterized by a spring-mass movement. Kinetic and potential energy are in phase, and the energy is stored & released from a spring-like limb during foot contact, achieved by the plantar arch and the Achilles tendon in the foot and leg, respectively. Again, the whole-body kinetics are similar to animals with more limbs.
Musculature
Bipedalism requires strong leg muscles, particularly in the thighs. Contrast in domesticated poultry the well muscled legs, against the small and bony wings. Likewise in humans, the quadriceps and hamstring muscles of the thigh are both so crucial to bipedal activities that each alone is much larger than the well-developed biceps of the arms. In addition to the leg muscles, the increased size of the gluteus maximus in humans is an important adaptation as it provides support and stability to the trunk and lessens the amount of stress on the joints when running.
Respiration | Bipedalism | Wikipedia | 384 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Quadrupeds, have more restrictive breathing respire while moving than do bipedal humans. "Quadrupedal species normally synchronize the locomotor and respiratory cycles at a constant ratio of 1:1 (strides per breath) in both the trot and gallop. Human runners differ from quadrupeds in that while running they employ several phase-locked patterns (4:1, 3:1, 2:1, 1:1, 5:2, and 3:2), although a 2:1 coupling ratio appears to be favored. Even though the evolution of bipedal gait has reduced the mechanical constraints on respiration in man, thereby permitting greater flexibility in breathing pattern, it has seemingly not eliminated the need for the synchronization of respiration and body motion during sustained running."
Respiration through bipedality means that there is better breath control in bipeds, which can be associated with brain growth. The modern brain utilizes approximately 20% of energy input gained through breathing and eating, as opposed to species like chimpanzees who use up twice as much energy as humans for the same amount of movement. This excess energy, leading to brain growth, also leads to the development of verbal communication. This is because breath control means that the muscles associated with breathing can be manipulated into creating sounds. This means that the onset of bipedality, leading to more efficient breathing, may be related to the origin of verbal language.
Bipedal robots
For nearly the whole of the 20th century, bipedal robots were very difficult to construct and robot locomotion involved only wheels, treads, or multiple legs. Recent cheap and compact computing power has made two-legged robots more feasible. Some notable biped robots are ASIMO, HUBO, MABEL and QRIO. Recently, spurred by the success of creating a fully passive, un-powered bipedal walking robot, those working on such machines have begun using principles gleaned from the study of human and animal locomotion, which often relies on passive mechanisms to minimize power consumption. | Bipedalism | Wikipedia | 427 | 4210 | https://en.wikipedia.org/wiki/Bipedalism | Biology and health sciences | Ethology | null |
Bioinformatics () is an interdisciplinary field of science that develops methods and software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term computational biology refers to building and using models of biological systems.
Computational, statistical, and computer programming techniques have been used for computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphisms (SNPs). These pipelines are used to better understand the genetic basis of disease, unique adaptations, desirable properties (especially in agricultural species), or differences between populations. Bioinformatics also includes proteomics, which tries to understand the organizational principles within nucleic acid and protein sequences.
Image and signal processing allow extraction of useful results from large amounts of raw data. In the field of genetics, it aids in sequencing and annotating genomes and their observed mutations. Bioinformatics includes text mining of biological literature and the development of biological and gene ontologies to organize and query biological data. It also plays a role in the analysis of gene and protein expression and regulation. Bioinformatics tools aid in comparing, analyzing and interpreting genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. At a more integrative level, it helps analyze and catalogue the biological pathways and networks that are an important part of systems biology. In structural biology, it aids in the simulation and modeling of DNA, RNA, proteins as well as biomolecular interactions.
History
The first definition of the term bioinformatics was coined by Paulien Hogeweg and Ben Hesper in 1970, to refer to the study of information processes in biotic systems. This definition placed bioinformatics as a field parallel to biochemistry (the study of chemical processes in biological systems).
Bioinformatics and computational biology involved the analysis of biological data, particularly DNA, RNA, and protein sequences. The field of bioinformatics experienced explosive growth starting in the mid-1990s, driven largely by the Human Genome Project and by rapid advances in DNA sequencing technology. | Bioinformatics | Wikipedia | 506 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Analyzing biological data to produce meaningful information involves writing and running software programs that use algorithms from graph theory, artificial intelligence, soft computing, data mining, image processing, and computer simulation. The algorithms in turn depend on theoretical foundations such as discrete mathematics, control theory, system theory, information theory, and statistics.
Sequences
There has been a tremendous advance in speed and cost reduction since the completion of the Human Genome Project, with some labs able to sequence over 100,000 billion bases each year, and a full genome can be sequenced for $1,000 or less.
Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s. Comparing multiple sequences manually turned out to be impractical. Margaret Oakley Dayhoff, a pioneer in the field, compiled one of the first protein sequence databases, initially published as books as well as methods of sequence alignment and molecular evolution. Another early contributor to bioinformatics was Elvin A. Kabat, who pioneered biological sequence analysis in 1970 with his comprehensive volumes of antibody sequences released online with Tai Te Wu between 1980 and 1991.
In the 1970s, new techniques for sequencing DNA were applied to bacteriophage MS2 and øX174, and the extended nucleotide sequences were then parsed with informational and statistical algorithms. These studies illustrated that well known features, such as the coding segments and the triplet code, are revealed in straightforward statistical analyses and were the proof of the concept that bioinformatics would be insightful.
Goals
In order to study how normal cellular activities are altered in different disease states, raw biological data must be combined to form a comprehensive picture of these activities. Therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. This also includes nucleotide and amino acid sequences, protein domains, and protein structures.
Important sub-disciplines within bioinformatics and computational biology include:
Development and implementation of computer programs to efficiently access, manage, and use various types of information.
Development of new mathematical algorithms and statistical measures to assess relationships among members of large data sets. For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, and to cluster protein sequences into families of related sequences. | Bioinformatics | Wikipedia | 474 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
The primary goal of bioinformatics is to increase the understanding of biological processes. What sets it apart from other approaches is its focus on developing and applying computationally intensive techniques to achieve this goal. Examples include: pattern recognition, data mining, machine learning algorithms, and visualization. Major research efforts in the field include sequence alignment, gene finding, genome assembly, drug design, drug discovery, protein structure alignment, protein structure prediction, prediction of gene expression and protein–protein interactions, genome-wide association studies, the modeling of evolution and cell division/mitosis.
Bioinformatics entails the creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management and analysis of biological data.
Over the past few decades, rapid developments in genomic and other molecular research technologies and developments in information technologies have combined to produce a tremendous amount of information related to molecular biology. Bioinformatics is the name given to these mathematical and computing approaches used to glean understanding of biological processes.
Common activities in bioinformatics include mapping and analyzing DNA and protein sequences, aligning DNA and protein sequences to compare them, and creating and viewing 3-D models of protein structures.
Sequence analysis
Since the bacteriophage Phage Φ-X174 was sequenced in 1977, the DNA sequences of thousands of organisms have been decoded and stored in databases. This sequence information is analyzed to determine genes that encode proteins, RNA genes, regulatory sequences, structural motifs, and repetitive sequences. A comparison of genes within a species or between different species can show similarities between protein functions, or relations between species (the use of molecular systematics to construct phylogenetic trees). With the growing amount of data, it long ago became impractical to analyze DNA sequences manually. Computer programs such as BLAST are used routinely to search sequences—as of 2008, from more than 260,000 organisms, containing over 190 billion nucleotides.
DNA sequencing
Before sequences can be analyzed, they are obtained from a data storage bank, such as GenBank. DNA sequencing is still a non-trivial problem as the raw data may be noisy or affected by weak signals. Algorithms have been developed for base calling for the various experimental approaches to DNA sequencing.
Sequence assembly | Bioinformatics | Wikipedia | 462 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Most DNA sequencing techniques produce short fragments of sequence that need to be assembled to obtain complete gene or genome sequences. The shotgun sequencing technique (used by The Institute for Genomic Research (TIGR) to sequence the first bacterial genome, Haemophilus influenzae) generates the sequences of many thousands of small DNA fragments (ranging from 35 to 900 nucleotides long, depending on the sequencing technology). The ends of these fragments overlap and, when aligned properly by a genome assembly program, can be used to reconstruct the complete genome. Shotgun sequencing yields sequence data quickly, but the task of assembling the fragments can be quite complicated for larger genomes. For a genome as large as the human genome, it may take many days of CPU time on large-memory, multiprocessor computers to assemble the fragments, and the resulting assembly usually contains numerous gaps that must be filled in later. Shotgun sequencing is the method of choice for virtually all genomes sequenced (rather than chain-termination or chemical degradation methods), and genome assembly algorithms are a critical area of bioinformatics research.
Genome annotation
In genomics, annotation refers to the process of marking the stop and start regions of genes and other biological features in a sequenced DNA sequence. Many genomes are too large to be annotated by hand. As the rate of sequencing exceeds the rate of genome annotation, genome annotation has become the new bottleneck in bioinformatics.
Genome annotation can be classified into three levels: the nucleotide, protein, and process levels.
Gene finding is a chief aspect of nucleotide-level annotation. For complex genomes, a combination of ab initio gene prediction and sequence comparison with expressed sequence databases and other organisms can be successful. Nucleotide-level annotation also allows the integration of genome sequence with other genetic and physical maps of the genome.
The principal aim of protein-level annotation is to assign function to the protein products of the genome. Databases of protein sequences and functional domains and motifs are used for this type of annotation. About half of the predicted proteins in a new genome sequence tend to have no obvious function. | Bioinformatics | Wikipedia | 454 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Understanding the function of genes and their products in the context of cellular and organismal physiology is the goal of process-level annotation. An obstacle of process-level annotation has been the inconsistency of terms used by different model systems. The Gene Ontology Consortium is helping to solve this problem.
The first description of a comprehensive annotation system was published in 1995 by The Institute for Genomic Research, which performed the first complete sequencing and analysis of the genome of a free-living (non-symbiotic) organism, the bacterium Haemophilus influenzae. The system identifies the genes encoding all proteins, transfer RNAs, ribosomal RNAs, in order to make initial functional assignments. The GeneMark program trained to find protein-coding genes in Haemophilus influenzae is constantly changing and improving.
Following the goals that the Human Genome Project left to achieve after its closure in 2003, the ENCODE project was developed by the National Human Genome Research Institute. This project is a collaborative data collection of the functional elements of the human genome that uses next-generation DNA-sequencing technologies and genomic tiling arrays, technologies able to automatically generate large amounts of data at a dramatically reduced per-base cost but with the same accuracy (base call error) and fidelity (assembly error).
Gene function prediction
While genome annotation is primarily based on sequence similarity (and thus homology), other properties of sequences can be used to predict the function of genes. In fact, most gene function prediction methods focus on protein sequences as they are more informative and more feature-rich. For instance, the distribution of hydrophobic amino acids predicts transmembrane segments in proteins. However, protein function prediction can also use external information such as gene (or protein) expression data, protein structure, or protein-protein interactions.
Computational evolutionary biology | Bioinformatics | Wikipedia | 380 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Evolutionary biology is the study of the origin and descent of species, as well as their change over time. Informatics has assisted evolutionary biologists by enabling researchers to:
trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone,
compare entire genomes, which permits the study of more complex evolutionary events, such as gene duplication, horizontal gene transfer, and the prediction of factors important in bacterial speciation,
build complex computational population genetics models to predict the outcome of the system over time
track and share information on an increasingly large number of species and organisms
Future work endeavours to reconstruct the now more complex tree of life.
Comparative genomics
The core of comparative genome analysis is the establishment of the correspondence between genes (orthology analysis) or other genomic features in different organisms. Intergenomic maps are made to trace the evolutionary processes responsible for the divergence of two genomes. A multitude of evolutionary events acting at various organizational levels shape genome evolution. At the lowest level, point mutations affect individual nucleotides. At a higher level, large chromosomal segments undergo duplication, lateral transfer, inversion, transposition, deletion and insertion. Entire genomes are involved in processes of hybridization, polyploidization and endosymbiosis that lead to rapid speciation. The complexity of genome evolution poses many exciting challenges to developers of mathematical models and algorithms, who have recourse to a spectrum of algorithmic, statistical and mathematical techniques, ranging from exact, heuristics, fixed parameter and approximation algorithms for problems based on parsimony models to Markov chain Monte Carlo algorithms for Bayesian analysis of problems based on probabilistic models.
Many of these studies are based on the detection of sequence homology to assign sequences to protein families.
Pan genomics | Bioinformatics | Wikipedia | 376 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Pan genomics is a concept introduced in 2005 by Tettelin and Medini. Pan genome is the complete gene repertoire of a particular monophyletic taxonomic group. Although initially applied to closely related strains of a species, it can be applied to a larger context like genus, phylum, etc. It is divided in two parts: the Core genome, a set of genes common to all the genomes under study (often housekeeping genes vital for survival), and the Dispensable/Flexible genome: a set of genes not present in all but one or some genomes under study. A bioinformatics tool BPGA can be used to characterize the Pan Genome of bacterial species.
Genetics of disease
As of 2013, the existence of efficient high-throughput next-generation sequencing technology allows for the identification of cause many different human disorders. Simple Mendelian inheritance has been observed for over 3,000 disorders that have been identified at the Online Mendelian Inheritance in Man database, but complex diseases are more difficult. Association studies have found many individual genetic regions that individually are weakly associated with complex diseases (such as infertility, breast cancer and Alzheimer's disease), rather than a single cause. There are currently many challenges to using genes for diagnosis and treatment, such as how we don't know which genes are important, or how stable the choices an algorithm provides.
Genome-wide association studies have successfully identified thousands of common genetic variants for complex diseases and traits; however, these common variants only explain a small fraction of heritability. Rare variants may account for some of the missing heritability. Large-scale whole genome sequencing studies have rapidly sequenced millions of whole genomes, and such studies have identified hundreds of millions of rare variants. Functional annotations predict the effect or function of a genetic variant and help to prioritize rare functional variants, and incorporating these annotations can effectively boost the power of genetic association of rare variants analysis of whole genome sequencing studies. Some tools have been developed to provide all-in-one rare variant association analysis for whole-genome sequencing data, including integration of genotype data and their functional annotations, association analysis, result summary and visualization. Meta-analysis of whole genome sequencing studies provides an attractive solution to the problem of collecting large sample sizes for discovering rare variants associated with complex phenotypes.
Analysis of mutations in cancer | Bioinformatics | Wikipedia | 488 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
In cancer, the genomes of affected cells are rearranged in complex or unpredictable ways. In addition to single-nucleotide polymorphism arrays identifying point mutations that cause cancer, oligonucleotide microarrays can be used to identify chromosomal gains and losses (called comparative genomic hybridization). These detection methods generate terabytes of data per experiment. The data is often found to contain considerable variability, or noise, and thus Hidden Markov model and change-point analysis methods are being developed to infer real copy number changes.
Two important principles can be used to identify cancer by mutations in the exome. First, cancer is a disease of accumulated somatic mutations in genes. Second, cancer contains driver mutations which need to be distinguished from passengers.
Further improvements in bioinformatics could allow for classifying types of cancer by analysis of cancer driven mutations in the genome. Furthermore, tracking of patients while the disease progresses may be possible in the future with the sequence of cancer samples. Another type of data that requires novel informatics development is the analysis of lesions found to be recurrent among many tumors.
Gene and protein expression
Analysis of gene expression
The expression of many genes can be determined by measuring mRNA levels with multiple techniques including microarrays, expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression (SAGE) tag sequencing, massively parallel signature sequencing (MPSS), RNA-Seq, also known as "Whole Transcriptome Shotgun Sequencing" (WTSS), or various applications of multiplexed in-situ hybridization. All of these techniques are extremely noise-prone and/or subject to bias in the biological measurement, and a major research area in computational biology involves developing statistical tools to separate signal from noise in high-throughput gene expression studies. Such studies are often used to determine the genes implicated in a disorder: one might compare microarray data from cancerous epithelial cells to data from non-cancerous cells to determine the transcripts that are up-regulated and down-regulated in a particular population of cancer cells. | Bioinformatics | Wikipedia | 426 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Analysis of protein expression
Protein microarrays and high throughput (HT) mass spectrometry (MS) can provide a snapshot of the proteins present in a biological sample. The former approach faces similar problems as with microarrays targeted at mRNA, the latter involves the problem of matching large amounts of mass data against predicted masses from protein sequence databases, and the complicated statistical analysis of samples when multiple incomplete peptides from each protein are detected. Cellular protein localization in a tissue context can be achieved through affinity proteomics displayed as spatial data based on immunohistochemistry and tissue microarrays.
Analysis of regulation
Gene regulation is a complex process where a signal, such as an extracellular signal such as a hormone, eventually leads to an increase or decrease in the activity of one or more proteins. Bioinformatics techniques have been applied to explore various steps in this process.
For example, gene expression can be regulated by nearby elements in the genome. Promoter analysis involves the identification and study of sequence motifs in the DNA surrounding the protein-coding region of a gene. These motifs influence the extent to which that region is transcribed into mRNA. Enhancer elements far away from the promoter can also regulate gene expression, through three-dimensional looping interactions. These interactions can be determined by bioinformatic analysis of chromosome conformation capture experiments.
Expression data can be used to infer gene regulation: one might compare microarray data from a wide variety of states of an organism to form hypotheses about the genes involved in each state. In a single-cell organism, one might compare stages of the cell cycle, along with various stress conditions (heat shock, starvation, etc.). Clustering algorithms can be then applied to expression data to determine which genes are co-expressed. For example, the upstream regions (promoters) of co-expressed genes can be searched for over-represented regulatory elements. Examples of clustering algorithms applied in gene clustering are k-means clustering, self-organizing maps (SOMs), hierarchical clustering, and consensus clustering methods.
Analysis of cellular organization
Several approaches have been developed to analyze the location of organelles, genes, proteins, and other components within cells. A gene ontology category, cellular component, has been devised to capture subcellular localization in many biological databases.
Microscopy and image analysis
Microscopic pictures allow for the location of organelles as well as molecules, which may be the source of abnormalities in diseases. | Bioinformatics | Wikipedia | 505 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Protein localization
Finding the location of proteins allows us to predict what they do. This is called protein function prediction. For instance, if a protein is found in the nucleus it may be involved in gene regulation or splicing. By contrast, if a protein is found in mitochondria, it may be involved in respiration or other metabolic processes. There are well developed protein subcellular localization prediction resources available, including protein subcellular location databases, and prediction tools.
Nuclear organization of chromatin
Data from high-throughput chromosome conformation capture experiments, such as Hi-C (experiment) and ChIA-PET, can provide information on the three-dimensional structure and nuclear organization of chromatin. Bioinformatic challenges in this field include partitioning the genome into domains, such as Topologically Associating Domains (TADs), that are organised together in three-dimensional space.
Structural bioinformatics
Finding the structure of proteins is an important application of bioinformatics. The Critical Assessment of Protein Structure Prediction (CASP) is an open competition where worldwide research groups submit protein models for evaluating unknown protein models.
Amino acid sequence
The linear amino acid sequence of a protein is called the primary structure. The primary structure can be easily determined from the sequence of codons on the DNA gene that codes for it. In most proteins, the primary structure uniquely determines the 3-dimensional structure of a protein in its native environment. An exception is the misfolded protein involved in bovine spongiform encephalopathy. This structure is linked to the function of the protein. Additional structural information includes the secondary, tertiary and quaternary structure. A viable general solution to the prediction of the function of a protein remains an open problem. Most efforts have so far been directed towards heuristics that work most of the time.
Homology
In the genomic branch of bioinformatics, homology is used to predict the function of a gene: if the sequence of gene A, whose function is known, is homologous to the sequence of gene B, whose function is unknown, one could infer that B may share A's function. In structural bioinformatics, homology is used to determine which parts of a protein are important in structure formation and interaction with other proteins. Homology modeling is used to predict the structure of an unknown protein from existing homologous proteins. | Bioinformatics | Wikipedia | 491 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
One example of this is hemoglobin in humans and the hemoglobin in legumes (leghemoglobin), which are distant relatives from the same protein superfamily. Both serve the same purpose of transporting oxygen in the organism. Although both of these proteins have completely different amino acid sequences, their protein structures are virtually identical, which reflects their near identical purposes and shared ancestor.
Other techniques for predicting protein structure include protein threading and de novo (from scratch) physics-based modeling.
Another aspect of structural bioinformatics include the use of protein structures for Virtual Screening models such as Quantitative Structure-Activity Relationship models and proteochemometric models (PCM). Furthermore, a protein's crystal structure can be used in simulation of for example ligand-binding studies and in silico mutagenesis studies.
A 2021 deep-learning algorithms-based software called AlphaFold, developed by Google's DeepMind, greatly outperforms all other prediction software methods, and has released predicted structures for hundreds of millions of proteins in the AlphaFold protein structure database.
Network and systems biology
Network analysis seeks to understand the relationships within biological networks such as metabolic or protein–protein interaction networks. Although biological networks can be constructed from a single type of molecule or entity (such as genes), network biology often attempts to integrate many different data types, such as proteins, small molecules, gene expression data, and others, which are all connected physically, functionally, or both.
Systems biology involves the use of computer simulations of cellular subsystems (such as the networks of metabolites and enzymes that comprise metabolism, signal transduction pathways and gene regulatory networks) to both analyze and visualize the complex connections of these cellular processes. Artificial life or virtual evolution attempts to understand evolutionary processes via the computer simulation of simple (artificial) life forms.
Molecular interaction networks
Tens of thousands of three-dimensional protein structures have been determined by X-ray crystallography and protein nuclear magnetic resonance spectroscopy (protein NMR) and a central question in structural bioinformatics is whether it is practical to predict possible protein–protein interactions only based on these 3D shapes, without performing protein–protein interaction experiments. A variety of methods have been developed to tackle the protein–protein docking problem, though it seems that there is still much work to be done in this field. | Bioinformatics | Wikipedia | 476 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Other interactions encountered in the field include Protein–ligand (including drug) and protein–peptide. Molecular dynamic simulation of movement of atoms about rotatable bonds is the fundamental principle behind computational algorithms, termed docking algorithms, for studying molecular interactions.
Biodiversity informatics
Biodiversity informatics deals with the collection and analysis of biodiversity data, such as taxonomic databases, or microbiome data. Examples of such analyses include phylogenetics, niche modelling, species richness mapping, DNA barcoding, or species identification tools. A growing area is also macro-ecology, i.e. the study of how biodiversity is connected to ecology and human impact, such as climate change.
Others
Literature analysis
The enormous number of published literature makes it virtually impossible for individuals to read every paper, resulting in disjointed sub-fields of research. Literature analysis aims to employ computational and statistical linguistics to mine this growing library of text resources. For example:
Abbreviation recognition – identify the long-form and abbreviation of biological terms
Named-entity recognition – recognizing biological terms such as gene names
Protein–protein interaction – identify which proteins interact with which proteins from text
The area of research draws from statistics and computational linguistics.
High-throughput image analysis
Computational technologies are used to automate the processing, quantification and analysis of large amounts of high-information-content biomedical imagery. Modern image analysis systems can improve an observer's accuracy, objectivity, or speed. Image analysis is important for both diagnostics and research. Some examples are:
high-throughput and high-fidelity quantification and sub-cellular localization (high-content screening, cytohistopathology, Bioimage informatics)
morphometrics
clinical image analysis and visualization
determining the real-time air-flow patterns in breathing lungs of living animals
quantifying occlusion size in real-time imagery from the development of and recovery during arterial injury
making behavioral observations from extended video recordings of laboratory animals
infrared measurements for metabolic activity determination
inferring clone overlaps in DNA mapping, e.g. the Sulston score
High-throughput single cell data analysis
Computational techniques are used to analyse high-throughput, low-measurement single cell data, such as that obtained from flow cytometry. These methods typically involve finding populations of cells that are relevant to a particular disease state or experimental condition. | Bioinformatics | Wikipedia | 475 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Ontologies and data integration
Biological ontologies are directed acyclic graphs of controlled vocabularies. They create categories for biological concepts and descriptions so they can be easily analyzed with computers. When categorised in this way, it is possible to gain added value from holistic and integrated analysis.
The OBO Foundry was an effort to standardise certain ontologies. One of the most widespread is the Gene ontology which describes gene function. There are also ontologies which describe phenotypes.
Databases
Databases are essential for bioinformatics research and applications. Databases exist for many different information types, including DNA and protein sequences, molecular structures, phenotypes and biodiversity. Databases can contain both empirical data (obtained directly from experiments) and predicted data (obtained from analysis of existing data). They may be specific to a particular organism, pathway or molecule of interest. Alternatively, they can incorporate data compiled from multiple other databases. Databases can have different formats, access mechanisms, and be public or private.
Some of the most commonly used databases are listed below:
Used in biological sequence analysis: Genbank, UniProt
Used in structure analysis: Protein Data Bank (PDB)
Used in finding Protein Families and Motif Finding: InterPro, Pfam
Used for Next Generation Sequencing: Sequence Read Archive
Used in Network Analysis: Metabolic Pathway Databases (KEGG, BioCyc), Interaction Analysis Databases, Functional Networks
Used in design of synthetic genetic circuits: GenoCAD
Software and tools
Software tools for bioinformatics include simple command-line tools, more complex graphical programs, and standalone web-services. They are made by bioinformatics companies or by public institutions.
Open-source bioinformatics software
Many free and open-source software tools have existed and continued to grow since the 1980s. The combination of a continued need for new algorithms for the analysis of emerging types of biological readouts, the potential for innovative in silico experiments, and freely available open code bases have created opportunities for research groups to contribute to both bioinformatics regardless of funding. The open source tools often act as incubators of ideas, or community-supported plug-ins in commercial applications. They may also provide de facto standards and shared object models for assisting with the challenge of bioinformation integration. | Bioinformatics | Wikipedia | 468 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
Open-source bioinformatics software includes Bioconductor, BioPerl, Biopython, BioJava, BioJS, BioRuby, Bioclipse, EMBOSS, .NET Bio, Orange with its bioinformatics add-on, Apache Taverna, UGENE and GenoCAD.
The non-profit Open Bioinformatics Foundation and the annual Bioinformatics Open Source Conference promote open-source bioinformatics software.
Web services in bioinformatics
SOAP- and REST-based interfaces have been developed to allow client computers to use algorithms, data and computing resources from servers in other parts of the world. The main advantage are that end users do not have to deal with software and database maintenance overheads.
Basic bioinformatics services are classified by the EBI into three categories: SSS (Sequence Search Services), MSA (Multiple Sequence Alignment), and BSA (Biological Sequence Analysis). The availability of these service-oriented bioinformatics resources demonstrate the applicability of web-based bioinformatics solutions, and range from a collection of standalone tools with a common data format under a single web-based interface, to integrative, distributed and extensible bioinformatics workflow management systems.
Bioinformatics workflow management systems
A bioinformatics workflow management system is a specialized form of a workflow management system designed specifically to compose and execute a series of computational or data manipulation steps, or a workflow, in a Bioinformatics application. Such systems are designed to
provide an easy-to-use environment for individual application scientists themselves to create their own workflows,
provide interactive tools for the scientists enabling them to execute their workflows and view their results in real-time,
simplify the process of sharing and reusing workflows between the scientists, and
enable scientists to track the provenance of the workflow execution results and the workflow creation steps.
Some of the platforms giving this service: Galaxy, Kepler, Taverna, UGENE, Anduril, HIVE. | Bioinformatics | Wikipedia | 432 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
BioCompute and BioCompute Objects
In 2014, the US Food and Drug Administration sponsored a conference held at the National Institutes of Health Bethesda Campus to discuss reproducibility in bioinformatics. Over the next three years, a consortium of stakeholders met regularly to discuss what would become BioCompute paradigm. These stakeholders included representatives from government, industry, and academic entities. Session leaders represented numerous branches of the FDA and NIH Institutes and Centers, non-profit entities including the Human Variome Project and the European Federation for Medical Informatics, and research institutions including Stanford, the New York Genome Center, and the George Washington University.
It was decided that the BioCompute paradigm would be in the form of digital 'lab notebooks' which allow for the reproducibility, replication, review, and reuse, of bioinformatics protocols. This was proposed to enable greater continuity within a research group over the course of normal personnel flux while furthering the exchange of ideas between groups. The US FDA funded this work so that information on pipelines would be more transparent and accessible to their regulatory staff.
In 2016, the group reconvened at the NIH in Bethesda and discussed the potential for a BioCompute Object, an instance of the BioCompute paradigm. This work was copied as both a "standard trial use" document and a preprint paper uploaded to bioRxiv. The BioCompute object allows for the JSON-ized record to be shared among employees, collaborators, and regulators.
Education platforms
Bioinformatics is not only taught as in-person master's degree at many universities. The computational nature of bioinformatics lends it to computer-aided and online learning. Software platforms designed to teach bioinformatics concepts and methods include Rosalind and online courses offered through the Swiss Institute of Bioinformatics Training Portal. The Canadian Bioinformatics Workshops provides videos and slides from training workshops on their website under a Creative Commons license. The 4273π project or 4273pi project also offers open source educational materials for free. The course runs on low cost Raspberry Pi computers and has been used to teach adults and school pupils. 4273 is actively developed by a consortium of academics and research staff who have run research level bioinformatics using Raspberry Pi computers and the 4273π operating system. | Bioinformatics | Wikipedia | 498 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
MOOC platforms also provide online certifications in bioinformatics and related disciplines, including Coursera's Bioinformatics Specialization at the University of California, San Diego, Genomic Data Science Specialization at Johns Hopkins University, and EdX's Data Analysis for Life Sciences XSeries at Harvard University.
Conferences
There are several large conferences that are concerned with bioinformatics. Some of the most notable examples are Intelligent Systems for Molecular Biology (ISMB), European Conference on Computational Biology (ECCB), and Research in Computational Molecular Biology (RECOMB). | Bioinformatics | Wikipedia | 117 | 4214 | https://en.wikipedia.org/wiki/Bioinformatics | Biology and health sciences | Biology basics | Biology |
The cell is the basic structural and functional unit of all forms of life. Every cell consists of cytoplasm enclosed within a membrane; many cells contain organelles, each with a specific function. The term comes from the Latin word meaning 'small room'. Most cells are only visible under a microscope. Cells emerged on Earth about 4 billion years ago. All cells are capable of replication, protein synthesis, and motility.
Cells are broadly categorized into two types: eukaryotic cells, which possess a nucleus, and prokaryotic cells, which lack a nucleus but have a nucleoid region. Prokaryotes are single-celled organisms such as bacteria, whereas eukaryotes can be either single-celled, such as amoebae, or multicellular, such as some algae, plants, animals, and fungi. Eukaryotic cells contain organelles including mitochondria, which provide energy for cell functions; chloroplasts, which create sugars by photosynthesis, in plants; and ribosomes, which synthesise proteins.
Cells were discovered by Robert Hooke in 1665, who named them after their resemblance to cells inhabited by Christian monks in a monastery. Cell theory, developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states that all organisms are composed of one or more cells, that cells are the fundamental unit of structure and function in all living organisms, and that all cells come from pre-existing cells.
Cell types
Cells are broadly categorized into two types: eukaryotic cells, which possess a nucleus, and prokaryotic cells, which lack a nucleus but have a nucleoid region. Prokaryotes are single-celled organisms, whereas eukaryotes can be either single-celled or multicellular.
Prokaryotic cells | Cell (biology) | Wikipedia | 378 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
Prokaryotes include bacteria and archaea, two of the three domains of life. Prokaryotic cells were the first form of life on Earth, characterized by having vital biological processes including cell signaling. They are simpler and smaller than eukaryotic cells, and lack a nucleus, and other membrane-bound organelles. The DNA of a prokaryotic cell consists of a single circular chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid. Most prokaryotes are the smallest of all organisms, ranging from 0.5 to 2.0 μm in diameter.
A prokaryotic cell has three regions:
Enclosing the cell is the cell envelope, generally consisting of a plasma membrane covered by a cell wall which, for some bacteria, may be further covered by a third layer called a capsule. Though most prokaryotes have both a cell membrane and a cell wall, there are exceptions such as Mycoplasma (bacteria) and Thermoplasma (archaea) which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, serving as a protective filter. The cell wall consists of peptidoglycan in bacteria and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting (cytolysis) from osmotic pressure due to a hypotonic environment. Some eukaryotic cells (plant cells and fungal cells) also have a cell wall.
Inside the cell is the cytoplasmic region that contains the genome (DNA), ribosomes and various sorts of inclusions. The genetic material is freely found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular. Linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a nucleoid. Plasmids encode additional genes, such as antibiotic resistance genes.
On the outside, some prokaryotes have flagella and pili that project from the cell's surface. These are structures made of proteins that facilitate movement and communication between cells.
Eukaryotic cells | Cell (biology) | Wikipedia | 507 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
Plants, animals, fungi, slime moulds, protozoa, and algae are all eukaryotic. These cells are about fifteen times wider than a typical prokaryote and can be as much as a thousand times greater in volume. The main distinguishing feature of eukaryotes as compared to prokaryotes is compartmentalization: the presence of membrane-bound organelles (compartments) in which specific activities take place. Most important among these is a cell nucleus, an organelle that houses the cell's DNA. This nucleus gives the eukaryote its name, which means "true kernel (nucleus)". Some of the other differences are:
The plasma membrane resembles that of prokaryotes in function, with minor differences in the setup. Cell walls may or may not be present.
The eukaryotic DNA is organized in one or more linear molecules, called chromosomes, which are associated with histone proteins. All chromosomal DNA is stored in the cell nucleus, separated from the cytoplasm by a membrane. Some eukaryotic organelles such as mitochondria also contain some DNA.
Many eukaryotic cells are ciliated with primary cilia. Primary cilia play important roles in chemosensation, mechanosensation, and thermosensation. Each cilium may thus be "viewed as a sensory cellular antennae that coordinates a large number of cellular signaling pathways, sometimes coupling the signaling to ciliary motility or alternatively to cell division and differentiation."
Motile eukaryotes can move using motile cilia or flagella. Motile cells are absent in conifers and flowering plants. Eukaryotic flagella are more complex than those of prokaryotes.
Many groups of eukaryotes are single-celled. Among the many-celled groups are animals and plants. The number of cells in these groups vary with species; it has been estimated that the human body contains around 37 trillion (3.72×1013) cells, and more recent studies put this number at around 30 trillion (~36 trillion cells in the male, ~28 trillion in the female).
Subcellular components | Cell (biology) | Wikipedia | 453 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
All cells, whether prokaryotic or eukaryotic, have a membrane that envelops the cell, regulates what moves in and out (selectively permeable), and maintains the electric potential of the cell. Inside the membrane, the cytoplasm takes up most of the cell's volume. Except red blood cells, which lack a cell nucleus and most organelles to accommodate maximum space for hemoglobin, all cells possess DNA, the hereditary material of genes, and RNA, containing the information necessary to build various proteins such as enzymes, the cell's primary machinery. There are also other kinds of biomolecules in cells. This article lists these primary cellular components, then briefly describes their function.
Cell membrane
The cell membrane, or plasma membrane, is a selectively permeable biological membrane that surrounds the cytoplasm of a cell. In animals, the plasma membrane is the outer boundary of the cell, while in plants and prokaryotes it is usually covered by a cell wall. This membrane serves to separate and protect a cell from its surrounding environment and is made mostly from a double layer of phospholipids, which are amphiphilic (partly hydrophobic and partly hydrophilic). Hence, the layer is called a phospholipid bilayer, or sometimes a fluid mosaic membrane. Embedded within this membrane is a macromolecular structure called the porosome the universal secretory portal in cells and a variety of protein molecules that act as channels and pumps that move different molecules into and out of the cell. The membrane is semi-permeable, and selectively permeable, in that it can either let a substance (molecule or ion) pass through freely, to a limited extent or not at all. Cell surface membranes also contain receptor proteins that allow cells to detect external signaling molecules such as hormones.
Cytoskeleton | Cell (biology) | Wikipedia | 392 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
The cytoskeleton acts to organize and maintain the cell's shape; anchors organelles in place; helps during endocytosis, the uptake of external materials by a cell, and cytokinesis, the separation of daughter cells after cell division; and moves parts of the cell in processes of growth and mobility. The eukaryotic cytoskeleton is composed of microtubules, intermediate filaments and microfilaments. In the cytoskeleton of a neuron the intermediate filaments are known as neurofilaments. There are a great number of proteins associated with them, each controlling a cell's structure by directing, bundling, and aligning filaments. The prokaryotic cytoskeleton is less well-studied but is involved in the maintenance of cell shape, polarity and cytokinesis. The subunit protein of microfilaments is a small, monomeric protein called actin. The subunit of microtubules is a dimeric molecule called tubulin. Intermediate filaments are heteropolymers whose subunits vary among the cell types in different tissues. Some of the subunit proteins of intermediate filaments include vimentin, desmin, lamin (lamins A, B and C), keratin (multiple acidic and basic keratins), and neurofilament proteins (NF–L, NF–M).
Genetic material
Two different kinds of genetic material exist: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Cells use DNA for their long-term information storage. The biological information contained in an organism is encoded in its DNA sequence. RNA is used for information transport (e.g., mRNA) and enzymatic functions (e.g., ribosomal RNA). Transfer RNA (tRNA) molecules are used to add amino acids during protein translation.
Prokaryotic genetic material is organized in a simple circular bacterial chromosome in the nucleoid region of the cytoplasm. Eukaryotic genetic material is divided into different, linear molecules called chromosomes inside a discrete nucleus, usually with additional genetic material in some organelles like mitochondria and chloroplasts (see endosymbiotic theory). | Cell (biology) | Wikipedia | 483 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
A human cell has genetic material contained in the cell nucleus (the nuclear genome) and in the mitochondria (the mitochondrial genome). In humans, the nuclear genome is divided into 46 linear DNA molecules called chromosomes, including 22 homologous chromosome pairs and a pair of sex chromosomes. The mitochondrial genome is a circular DNA molecule distinct from nuclear DNA. Although the mitochondrial DNA is very small compared to nuclear chromosomes, it codes for 13 proteins involved in mitochondrial energy production and specific tRNAs.
Foreign genetic material (most commonly DNA) can also be artificially introduced into the cell by a process called transfection. This can be transient, if the DNA is not inserted into the cell's genome, or stable, if it is. Certain viruses also insert their genetic material into the genome.
Organelles
Organelles are parts of the cell that are adapted and/or specialized for carrying out one or more vital functions, analogous to the organs of the human body (such as the heart, lung, and kidney, with each organ performing a different function). Both eukaryotic and prokaryotic cells have organelles, but prokaryotic organelles are generally simpler and are not membrane-bound.
There are several types of organelles in a cell. Some (such as the nucleus and Golgi apparatus) are typically solitary, while others (such as mitochondria, chloroplasts, peroxisomes and lysosomes) can be numerous (hundreds to thousands). The cytosol is the gelatinous fluid that fills the cell and surrounds the organelles.
Eukaryotic | Cell (biology) | Wikipedia | 331 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
Cell nucleus: A cell's information center, the cell nucleus is the most conspicuous organelle found in a eukaryotic cell. It houses the cell's chromosomes, and is the place where almost all DNA replication and RNA synthesis (transcription) occur. The nucleus is spherical and separated from the cytoplasm by a double membrane called the nuclear envelope, space between these two membrane is called perinuclear space. The nuclear envelope isolates and protects a cell's DNA from various molecules that could accidentally damage its structure or interfere with its processing. During processing, DNA is transcribed, or copied into a special RNA, called messenger RNA (mRNA). This mRNA is then transported out of the nucleus, where it is translated into a specific protein molecule. The nucleolus is a specialized region within the nucleus where ribosome subunits are assembled. In prokaryotes, DNA processing takes place in the cytoplasm.
Mitochondria and chloroplasts: generate energy for the cell. Mitochondria are self-replicating double membrane-bound organelles that occur in various numbers, shapes, and sizes in the cytoplasm of all eukaryotic cells. Respiration occurs in the cell mitochondria, which generate the cell's energy by oxidative phosphorylation, using oxygen to release energy stored in cellular nutrients (typically pertaining to glucose) to generate ATP (aerobic respiration). Mitochondria multiply by binary fission, like prokaryotes. Chloroplasts can only be found in plants and algae, and they capture the sun's energy to make carbohydrates through photosynthesis. | Cell (biology) | Wikipedia | 353 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
Endoplasmic reticulum: The endoplasmic reticulum (ER) is a transport network for molecules targeted for certain modifications and specific destinations, as compared to molecules that float freely in the cytoplasm. The ER has two forms: the rough ER, which has ribosomes on its surface that secrete proteins into the ER, and the smooth ER, which lacks ribosomes. The smooth ER plays a role in calcium sequestration and release and also helps in synthesis of lipid.
Golgi apparatus: The primary function of the Golgi apparatus is to process and package the macromolecules such as proteins and lipids that are synthesized by the cell.
Lysosomes and peroxisomes: Lysosomes contain digestive enzymes (acid hydrolases). They digest excess or worn-out organelles, food particles, and engulfed viruses or bacteria. Peroxisomes have enzymes that rid the cell of toxic peroxides, Lysosomes are optimally active in an acidic environment. The cell could not house these destructive enzymes if they were not contained in a membrane-bound system.
Centrosome: the cytoskeleton organizer: The centrosome produces the microtubules of a cell—a key component of the cytoskeleton. It directs the transport through the ER and the Golgi apparatus. Centrosomes are composed of two centrioles which lie perpendicular to each other in which each has an organization like a cartwheel, which separate during cell division and help in the formation of the mitotic spindle. A single centrosome is present in the animal cells. They are also found in some fungi and algae cells.
Vacuoles: Vacuoles sequester waste products and in plant cells store water. They are often described as liquid filled spaces and are surrounded by a membrane. Some cells, most notably Amoeba, have contractile vacuoles, which can pump water out of the cell if there is too much water. The vacuoles of plant cells and fungal cells are usually larger than those of animal cells. Vacuoles of plant cells are surrounded by a membrane which transports ions against concentration gradients.
Eukaryotic and prokaryotic | Cell (biology) | Wikipedia | 463 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
Ribosomes: The ribosome is a large complex of RNA and protein molecules. They each consist of two subunits, and act as an assembly line where RNA from the nucleus is used to synthesise proteins from amino acids. Ribosomes can be found either floating freely or bound to a membrane (the rough endoplasmatic reticulum in eukaryotes, or the cell membrane in prokaryotes).
Plastids: Plastid are membrane-bound organelle generally found in plant cells and euglenoids and contain specific pigments, thus affecting the colour of the plant and organism. And these pigments also helps in food storage and tapping of light energy. There are three types of plastids based upon the specific pigments. Chloroplasts contain chlorophyll and some carotenoid pigments which helps in the tapping of light energy during photosynthesis. Chromoplasts contain fat-soluble carotenoid pigments like orange carotene and yellow xanthophylls which helps in synthesis and storage. Leucoplasts are non-pigmented plastids and helps in storage of nutrients.
Structures outside the cell membrane
Many cells also have structures which exist wholly or partially outside the cell membrane. These structures are notable because they are not protected from the external environment by the cell membrane. In order to assemble these structures, their components must be carried across the cell membrane by export processes.
Cell wall
Many types of prokaryotic and eukaryotic cells have a cell wall. The cell wall acts to protect the cell mechanically and chemically from its environment, and is an additional layer of protection to the cell membrane. Different types of cell have cell walls made up of different materials; plant cell walls are primarily made up of cellulose, fungi cell walls are made up of chitin and bacteria cell walls are made up of peptidoglycan.
Prokaryotic
Capsule
A gelatinous capsule is present in some bacteria outside the cell membrane and cell wall. The capsule may be polysaccharide as in pneumococci, meningococci or polypeptide as Bacillus anthracis or hyaluronic acid as in streptococci.
Capsules are not marked by normal staining protocols and can be detected by India ink or methyl blue, which allows for higher contrast between the cells for observation.
Flagella | Cell (biology) | Wikipedia | 501 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
Flagella are organelles for cellular mobility. The bacterial flagellum stretches from cytoplasm through the cell membrane(s) and extrudes through the cell wall. They are long and thick thread-like appendages, protein in nature. A different type of flagellum is found in archaea and a different type is found in eukaryotes.
Fimbriae
A fimbria (plural fimbriae also known as a pilus, plural pili) is a short, thin, hair-like filament found on the surface of bacteria. Fimbriae are formed of a protein called pilin (antigenic) and are responsible for the attachment of bacteria to specific receptors on human cells (cell adhesion). There are special types of pili involved in bacterial conjugation.
Cellular processes
Replication
Cell division involves a single cell (called a mother cell) dividing into two daughter cells. This leads to growth in multicellular organisms (the growth of tissue) and to procreation (vegetative reproduction) in unicellular organisms. Prokaryotic cells divide by binary fission, while eukaryotic cells usually undergo a process of nuclear division, called mitosis, followed by division of the cell, called cytokinesis. A diploid cell may also undergo meiosis to produce haploid cells, usually four. Haploid cells serve as gametes in multicellular organisms, fusing to form new diploid cells.
DNA replication, or the process of duplicating a cell's genome, always happens when a cell divides through mitosis or binary fission. This occurs during the S phase of the cell cycle.
In meiosis, the DNA is replicated only once, while the cell divides twice. DNA replication only occurs before meiosis I. DNA replication does not occur when the cells divide the second time, in meiosis II. Replication, like all cellular activities, requires specialized proteins for carrying out the job.
DNA repair | Cell (biology) | Wikipedia | 409 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
Cells of all organisms contain enzyme systems that scan their DNA for damage and carry out repair processes when it is detected. Diverse repair processes have evolved in organisms ranging from bacteria to humans. The widespread prevalence of these repair processes indicates the importance of maintaining cellular DNA in an undamaged state in order to avoid cell death or errors of replication due to damage that could lead to mutation. E. coli bacteria are a well-studied example of a cellular organism with diverse well-defined DNA repair processes. These include: nucleotide excision repair, DNA mismatch repair, non-homologous end joining of double-strand breaks, recombinational repair and light-dependent repair (photoreactivation).
Growth and metabolism
Between successive cell divisions, cells grow through the functioning of cellular metabolism. Cell metabolism is the process by which individual cells process nutrient molecules. Metabolism has two distinct divisions: catabolism, in which the cell breaks down complex molecules to produce energy and reducing power, and anabolism, in which the cell uses energy and reducing power to construct complex molecules and perform other biological functions.
Complex sugars can be broken down into simpler sugar molecules called monosaccharides such as glucose. Once inside the cell, glucose is broken down to make adenosine triphosphate (ATP), a molecule that possesses readily available energy, through two different pathways. In plant cells, chloroplasts create sugars by photosynthesis, using the energy of light to join molecules of water and carbon dioxide.
Protein synthesis
Cells are capable of synthesizing new proteins, which are essential for the modulation and maintenance of cellular activities. This process involves the formation of new protein molecules from amino acid building blocks based on information encoded in DNA/RNA. Protein synthesis generally consists of two major steps: transcription and translation. | Cell (biology) | Wikipedia | 371 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
Transcription is the process where genetic information in DNA is used to produce a complementary RNA strand. This RNA strand is then processed to give messenger RNA (mRNA), which is free to migrate through the cell. mRNA molecules bind to protein-RNA complexes called ribosomes located in the cytosol, where they are translated into polypeptide sequences. The ribosome mediates the formation of a polypeptide sequence based on the mRNA sequence. The mRNA sequence directly relates to the polypeptide sequence by binding to transfer RNA (tRNA) adapter molecules in binding pockets within the ribosome. The new polypeptide then folds into a functional three-dimensional protein molecule.
Motility
Unicellular organisms can move in order to find food or escape predators. Common mechanisms of motion include flagella and cilia.
In multicellular organisms, cells can move during processes such as wound healing, the immune response and cancer metastasis. For example, in wound healing in animals, white blood cells move to the wound site to kill the microorganisms that cause infection. Cell motility involves many receptors, crosslinking, bundling, binding, adhesion, motor and other proteins. The process is divided into three steps: protrusion of the leading edge of the cell, adhesion of the leading edge and de-adhesion at the cell body and rear, and cytoskeletal contraction to pull the cell forward. Each step is driven by physical forces generated by unique segments of the cytoskeleton.
Navigation, control and communication
In August 2020, scientists described one way cells—in particular cells of a slime mold and mouse pancreatic cancer-derived cells—are able to navigate efficiently through a body and identify the best routes through complex mazes: generating gradients after breaking down diffused chemoattractants which enable them to sense upcoming maze junctions before reaching them, including around corners.
Multicellularity
Cell specialization/differentiation
Multicellular organisms are organisms that consist of more than one cell, in contrast to single-celled organisms. | Cell (biology) | Wikipedia | 426 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
In complex multicellular organisms, cells specialize into different cell types that are adapted to particular functions. In mammals, major cell types include skin cells, muscle cells, neurons, blood cells, fibroblasts, stem cells, and others. Cell types differ both in appearance and function, yet are genetically identical. Cells are able to be of the same genotype but of different cell type due to the differential expression of the genes they contain.
Most distinct cell types arise from a single totipotent cell, called a zygote, that differentiates into hundreds of different cell types during the course of development. Differentiation of cells is driven by different environmental cues (such as cell–cell interaction) and intrinsic differences (such as those caused by the uneven distribution of molecules during division).
Origin of multicellularity
Multicellularity has evolved independently at least 25 times, including in some prokaryotes, like cyanobacteria, myxobacteria, actinomycetes, or Methanosarcina. However, complex multicellular organisms evolved only in six eukaryotic groups: animals, fungi, brown algae, red algae, green algae, and plants. It evolved repeatedly for plants (Chloroplastida), once or twice for animals, once for brown algae, and perhaps several times for fungi, slime molds, and red algae. Multicellularity may have evolved from colonies of interdependent organisms, from cellularization, or from organisms in symbiotic relationships.
The first evidence of multicellularity is from cyanobacteria-like organisms that lived between 3 and 3.5 billion years ago. Other early fossils of multicellular organisms include the contested Grypania spiralis and the fossils of the black shales of the Palaeoproterozoic Francevillian Group Fossil B Formation in Gabon.
The evolution of multicellularity from unicellular ancestors has been replicated in the laboratory, in evolution experiments using predation as the selective pressure.
Origins
The origin of cells has to do with the origin of life, which began the history of life on Earth.
Origin of life | Cell (biology) | Wikipedia | 440 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
Small molecules needed for life may have been carried to Earth on meteorites, created at deep-sea vents, or synthesized by lightning in a reducing atmosphere. There is little experimental data defining what the first self-replicating forms were. RNA may have been the earliest self-replicating molecule, as it can both store genetic information and catalyze chemical reactions.
Cells emerged around 4 billion years ago. The first cells were most likely heterotrophs. The early cell membranes were probably simpler and more permeable than modern ones, with only a single fatty acid chain per lipid. Lipids spontaneously form bilayered vesicles in water, and could have preceded RNA.
First eukaryotic cells
Eukaryotic cells were created some 2.2 billion years ago in a process called eukaryogenesis. This is widely agreed to have involved symbiogenesis, in which archaea and bacteria came together to create the first eukaryotic common ancestor. This cell had a new level of complexity and capability, with a nucleus and facultatively aerobic mitochondria. It evolved some 2 billion years ago into a population of single-celled organisms that included the last eukaryotic common ancestor, gaining capabilities along the way, though the sequence of the steps involved has been disputed, and may not have started with symbiogenesis. It featured at least one centriole and cilium, sex (meiosis and syngamy), peroxisomes, and a dormant cyst with a cell wall of chitin and/or cellulose. In turn, the last eukaryotic common ancestor gave rise to the eukaryotes' crown group, containing the ancestors of animals, fungi, plants, and a diverse range of single-celled organisms. The plants were created around 1.6 billion years ago with a second episode of symbiogenesis that added chloroplasts, derived from cyanobacteria.
History of research | Cell (biology) | Wikipedia | 408 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
In 1665, Robert Hooke examined a thin slice of cork under his microscope, and saw a structure of small enclosures. He wrote "I could exceeding plainly perceive it to be all perforated and porous, much like a Honey-comb, but that the pores of it were not regular". To further support his theory, Matthias Schleiden and Theodor Schwann both also studied cells of both animal and plants. What they discovered were significant differences between the two types of cells. This put forth the idea that cells were not only fundamental to plants, but animals as well.
1632–1723: Antonie van Leeuwenhoek taught himself to make lenses, constructed basic optical microscopes and drew protozoa, such as Vorticella from rain water, and bacteria from his own mouth.
1665: Robert Hooke discovered cells in cork, then in living plant tissue using an early compound microscope. He coined the term cell (from Latin cellula, meaning "small room") in his book Micrographia (1665).
1839: Theodor Schwann and Matthias Jakob Schleiden elucidated the principle that plants and animals are made of cells, concluding that cells are a common unit of structure and development, and thus founding the cell theory.
1855: Rudolf Virchow stated that new cells come from pre-existing cells by cell division (omnis cellula ex cellula).
1931: Ernst Ruska built the first transmission electron microscope (TEM) at the University of Berlin. By 1935, he had built an EM with twice the resolution of a light microscope, revealing previously unresolvable organelles.
1981: Lynn Margulis published Symbiosis in Cell Evolution detailing how eukaryotic cells were created by symbiogenesis. | Cell (biology) | Wikipedia | 367 | 4230 | https://en.wikipedia.org/wiki/Cell%20%28biology%29 | Biology and health sciences | Science and medicine | null |
In computer science, binary search, also known as half-interval search, logarithmic search, or binary chop, is a search algorithm that finds the position of a target value within a sorted array. Binary search compares the target value to the middle element of the array. If they are not equal, the half in which the target cannot lie is eliminated and the search continues on the remaining half, again taking the middle element to compare to the target value, and repeating this until the target value is found. If the search ends with the remaining half being empty, the target is not in the array.
Binary search runs in logarithmic time in the worst case, making comparisons, where is the number of elements in the array. Binary search is faster than linear search except for small arrays. However, the array must be sorted first to be able to apply binary search. There are specialized data structures designed for fast searching, such as hash tables, that can be searched more efficiently than binary search. However, binary search can be used to solve a wider range of problems, such as finding the next-smallest or next-largest element in the array relative to the target even if it is absent from the array.
There are numerous variations of binary search. In particular, fractional cascading speeds up binary searches for the same value in multiple arrays. Fractional cascading efficiently solves a number of search problems in computational geometry and in numerous other fields. Exponential search extends binary search to unbounded lists. The binary search tree and B-tree data structures are based on binary search.
Algorithm
Binary search works on sorted arrays. Binary search begins by comparing an element in the middle of the array with the target value. If the target value matches the element, its position in the array is returned. If the target value is less than the element, the search continues in the lower half of the array. If the target value is greater than the element, the search continues in the upper half of the array. By doing this, the algorithm eliminates the half in which the target value cannot lie in each iteration. | Binary search | Wikipedia | 427 | 4266 | https://en.wikipedia.org/wiki/Binary%20search | Mathematics | Algorithms | null |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.