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A relief valve or pressure relief valve (PRV) is a type of safety valve used to control or limit the pressure in a system; excessive pressure might otherwise build up and create a process upset, instrument or equipment failure, explosion, or fire. == Pressure relief == Excess pressure is relieved by allowing the pressurized fluid to flow from an auxiliary passage out of the system. The relief valve is designed or set to open at a predetermined set pressure to protect pressure vessels and other equipment from being subjected to pressures that exceed their design limits. When the set pressure is exceeded, the relief valve becomes the "path of least resistance" as the valve is forced open and a portion of the fluid is diverted through the auxiliary route. In systems containing flammable fluids, the diverted fluid (liquid, gas or liquid-gas mixture) is either recaptured by a low pressure, high-flow vapor recovery system or is routed through a piping system known as a flare header or relief header to a central, elevated gas flare where it is burned, releasing naked combustion gases into the atmosphere. In non-hazardous systems, the fluid is often discharged to the atmosphere by a suitable discharge pipework designed to prevent rainwater ingress which can affect the set lift pressure, and positioned not to cause a hazard to personnel. As the fluid is diverted, the pressure inside the vessel will stop rising. Once it reaches the valve's reseating pressure, the valve will close. The blowdown is usually stated as a percentage of set pressure and refers to how much the pressure needs to drop before the valve reseats. The blowdown can vary roughly 2–20%, and some valves have adjustable blowdowns. In high-pressure gas systems, it is recommended that the outlet of the relief valve be in the
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open air. In systems where the outlet is connected to piping, the opening of a relief valve will give a pressure build-up in the piping system downstream of the relief valve. This often means that the relief valve will not re-seat once the set pressure is reached. For these systems often so-called "differential" relief valves are used. This means that the pressure is only working on an area that is much smaller than the area of the opening of the valve. If the valve is opened, the pressure has to decrease enormously before the valve closes and also the outlet pressure of the valve can easily keep the valve open. Another consideration is that if other relief valves are connected to the outlet pipe system, they may open as the pressure in the exhaust pipe system increases. This may cause undesired operation. In some cases, a so-called bypass valve acts as a relief valve by being used to return all or part of the fluid discharged by a pump or gas compressor back to either a storage reservoir or the inlet of the pump or gas compressor. This is done to protect the pump or gas compressor and any associated equipment from excessive pressure. The bypass valve and bypass path can be internal (an integral part of the pump or compressor) or external (installed as a component in the fluid path). Many fire engines have such relief valves to prevent the overpressurization of fire hoses. In other cases, equipment must be protected against being subjected to an internal vacuum (i.e., low pressure) that is lower than the equipment can withstand. In such cases, vacuum relief valves are used to open at a predetermined low-pressure limit and to admit air or an inert gas into the equipment to control the amount
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of vacuum. == Technical terms == In the petroleum refining, petrochemical and chemical manufacturing, natural gas processing and power generation industries, the term relief valve is associated with the terms pressure relief valve (PRV), pressure safety valve (PSV) and safety valve: Pressure relief valve (PRV) or Pressure Release valve (PRV) or pressure safety valve (PSV): The difference is that PSVs have a manual lever to activate the valve in case of emergency. Most PRVs are spring operated. At lower pressures some use a diaphragm in place of a spring. The oldest PRV designs use a weight to seal the valve. Set pressure: When the system pressure increases to this value, the PRV opens. The accuracy of the set pressure may follow guidelines set by the American Society of Mechanical Engineers (ASME). Relief valve (RV): A valve is used on a liquid service, which opens proportionally as the increasing pressure overcomes the spring pressure. Safety valve (SV): Used in gas service. Most SVs are full lift or snap-acting, in that they pop completely open. Safety relief valve (SRV): A relief valve that can be used for gas or liquid service. However, the set pressure will usually only be accurate for one type of fluid at a time. Pilot-operated relief valve (POSRV, PORV, POPRV): A device that relieves by remote command from a pilot valve which is connected to the upstream system pressure. Low-pressure safety valve (LPSV): An automatic system that relieves by the static pressure of a gas. The relieving pressure is small and near the atmospheric pressure. Vacuum pressure safety valve (VPSV): An automatic system that relieves by the static pressure of a gas. The relieving pressure is small, negative, and near the atmospheric pressure. Low and vacuum pressure safety valve (LVPSV): An automatic system that relieves by the static
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pressure of a gas. The relieving pressure is small, negative, or positive, and near the atmospheric pressure. Pressure vacuum release valve (PVRV): A combination of vacuum pressure and a relief valve in one housing. Used on storage tanks for liquids to prevent implosion or overpressure. Snap acting: The opposite of modulating, refers to a valve that "pops" open. It snaps into a full lift in milliseconds. Usually accomplished with a skirt on the disc so that the fluid passing the seat suddenly affects a larger area and creates more lifting force. Modulating: Opens in proportion to the overpressure. == Legal and code requirements in industry == In most countries, industries are legally required to protect pressure vessels and other equipment by using relief valves. Also in most countries, equipment design codes such as those provided by the American Society of Mechanical Engineers (ASME), American Petroleum Institute (API) and other organizations like ISO (ISO 4126) must be complied with and those codes include design standards for relief valves. The main standards, laws, or directives are: AD Merkblatt (German) American Petroleum Institute (API); Standards 520, 521, 526, and 2000 American Society of Mechanical Engineers (ASME); Boiler & Pressure Vessel Code, Section VIII Division 1 and Section I American Water Works Association (AWWA), storage tanks EN 764-7; European Standard based on pressure Equipment Directive 97/23/EC Eurocode EN 1993-4-2, storage tanks. International Organization for Standardization; ISO 4126 Pressure Systems Safety Regulations 2000 (PSSR); UK == Design Institute for Emergency Relief Systems (DIERS) == Formed in 1977, the Design Institute for Emergency Relief Systems was a consortium of 29 companies under the auspices of the American Institute of Chemical Engineers (AIChE) that developed methods for the design of emergency relief systems to handle runaway reactions. Its purpose was to develop the technology and methods needed
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for sizing pressure relief systems for chemical reactors, particularly those in which exothermic reactions are carried out. Such reactions include many classes of industrially important processes including polymerizations, nitrations, diazotizations, sulphonations, epoxidations, aminations, esterifications, neutralizations, and many others. Pressure relief systems can be difficult to design, not least because what is expelled can be gas/vapor, liquid, or a mixture of the two – just as with a can of carbonated drink when it is suddenly opened. For chemical reactions, it requires extensive knowledge of both chemical reaction hazards and fluid flow. DIERS has investigated the two-phase vapor-liquid onset/disengagement dynamics and the hydrodynamics of emergency relief systems with extensive experimental and analysis work. Of particular interest to DIERS were the prediction of two-phase flow venting and the applicability of various sizing methods for two-phase vapor-liquid flashing flow. DIERS became a user's group in 1985. European DIERS Users' Group (EDUG) is a group of mainly European industrialists, consultants and academics who use the DIERS technology. The EDUG started in the late 1980s and has an annual meeting. A summary of many of key aspects of the DIERS technology has been published in the UK by the HSE. == See also == == References == == External links == Media related to Relief valves at Wikimedia Commons PED 97/23/EC; Pressure Equipment Directive – European Union.
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The Hertzsprung gap is a feature of the Hertzsprung–Russell diagram for a star cluster. This diagram is a plot of effective temperature versus luminosity for a population of stars. The gap is named after Ejnar Hertzsprung, who first noticed the absence of stars in the region of the Hertzsprung–Russell diagram between A5 and G0 spectral type and between +1 and −3 absolute magnitudes. This gap lies between the top of the main sequence and the base of red giants for stars above roughly 1.5 solar mass. When a star during its evolution crosses the Hertzsprung gap, it means that it has finished core hydrogen burning. Stars do exist in the Hertzsprung gap region, but because they move through this section of the Hertzsprung–Russell diagram very quickly in comparison to the lifetime of the star (thousands of years, compared to millions or billions of years for the lifetime of the star), that portion of the diagram is less densely populated. Full Hertzsprung–Russell diagrams of the 11,000 Hipparcos mission targets show a handful of stars in that region. Well-known stars inside of or towards the end of the Hertzsprung gap include: Epsilon Pegasi Pi Puppis Epsilon Geminorum Beta Arae Gamma Cygni Capella B Canopus, Iota Carinae, and Upsilon Carinae are also starting to enter the gap. == See also == Subgiant == References ==
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In surface science, a double layer (DL, also called an electrical double layer, EDL) is a structure that appears on the surface of an object when it is exposed to a fluid. The object might be a solid particle, a gas bubble, a liquid droplet, or a porous body. The DL refers to two parallel layers of charge surrounding the object. The first layer, the surface charge (either positive or negative), consists of ions which are adsorbed onto the object due to chemical interactions. The second layer is composed of ions attracted to the surface charge via the Coulomb force, electrically screening the first layer. This second layer is loosely associated with the object. It is made of free ions that move in the fluid under the influence of electric attraction and thermal motion rather than being firmly anchored. It is thus called the "diffuse layer". Interfacial DLs are most apparent in systems with a large surface-area-to-volume ratio, such as a colloid or porous bodies with particles or pores (respectively) on the scale of micrometres to nanometres. However, DLs are important to other phenomena, such as the electrochemical behaviour of electrodes. DLs play a fundamental role in many everyday substances. For instance, homogenized milk exists only because fat droplets are covered with a DL that prevents their coagulation into butter. DLs exist in practically all heterogeneous fluid-based systems, such as blood, paint, ink and ceramic and cement slurry. The DL is closely related to electrokinetic phenomena and electroacoustic phenomena. == Development of the (interfacial) double layer == === Helmholtz === When an electronic conductor is brought in contact with a solid or liquid ionic conductor (electrolyte), a common boundary (interface) among the two phases appears. Hermann von Helmholtz was the first to realize that charged electrodes immersed in electrolyte solutions
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repel the co-ions of the charge while attracting counterions to their surfaces. Two layers of opposite polarity form at the interface between electrode and electrolyte. In 1853, he showed that an electrical double layer (DL) is essentially a molecular dielectric and stores charge electrostatically. Below the electrolyte's decomposition voltage, the stored charge is linearly dependent on the voltage applied. This early model predicted a constant differential capacitance independent from the charge density depending on the dielectric constant of the electrolyte solvent and the thickness of the double-layer. This model, while a good foundation for the description of the interface, does not consider important factors including diffusion/mixing of ions in solution, the possibility of adsorption onto the surface, and the interaction between solvent dipole moments and the electrode. === Gouy–Chapman === Louis Georges Gouy in 1910 and David Leonard Chapman in 1913 both observed that capacitance was not a constant and that it depended on the applied potential and the ionic concentration. The "Gouy–Chapman model" made significant improvements by introducing a diffuse model of the DL. In this model, the charge distribution of ions as a function of distance from the metal surface allows Maxwell–Boltzmann statistics to be applied. Thus the electric potential decreases exponentially away from the surface of the fluid bulk. Gouy-Chapman layers may bear special relevance in bioelectrochemistry. The observation of long-distance inter-protein electron transfer through the aqueous solution has been attributed to a diffuse region between redox partner proteins (cytochromes c and c1) that is depleted of cations in comparison to the solution bulk, thereby leading to reduced screening, electric fields extending several nanometers, and currents decreasing quasi exponentially with the distance at rate ~1 nm−1. This region is termed "Gouy-Chapman conduit" and is strongly regulated by phosphorylation, which adds one negative charge to the protein surface
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that disrupts cationic depletion and prevents long-distance charge transport. Similar effects are observed at the redox active site of photosynthetic complexes. === Stern === The Gouy-Chapman model fails for highly charged DLs. In 1924, Otto Stern suggested combining the Helmholtz model with the Gouy-Chapman model: in Stern's model, some ions adhere to the electrode as suggested by Helmholtz, giving an internal Stern layer, while some form a Gouy-Chapman diffuse layer. The Stern layer accounts for ions' finite size and consequently an ion's closest approach to the electrode is on the order of the ionic radius. The Stern model has its own limitations, namely that it effectively treats ions as point charges, assumes all significant interactions in the diffuse layer are Coulombic, assumes dielectric permittivity to be constant throughout the double layer, and that fluid viscosity is constant plane. === Grahame === D. C. Grahame modified the Stern model in 1947. He proposed that some ionic or uncharged species can penetrate the Stern layer, although the closest approach to the electrode is normally occupied by solvent molecules. This could occur if ions lose their solvation shell as they approach the electrode. He called ions in direct contact with the electrode "specifically adsorbed ions". This model proposed the existence of three regions. The inner Helmholtz plane (IHP) passes through the centres of the specifically adsorbed ions. The outer Helmholtz plane (OHP) passes through the centres of solvated ions at the distance of their closest approach to the electrode. Finally the diffuse layer is the region beyond the OHP. === Bockris/Devanathan/Müller (BDM) === In 1963, J. O'M. Bockris, M. A. V. Devanathan and Klaus Müller proposed the BDM model of the double-layer that included the action of the solvent in the interface. They suggested that the attached molecules of the solvent, such as
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water, would have a fixed alignment to the electrode surface. This first layer of solvent molecules displays a strong orientation to the electric field depending on the charge. This orientation has great influence on the permittivity of the solvent that varies with field strength. The IHP passes through the centers of these molecules. Specifically adsorbed, partially solvated ions appear in this layer. The solvated ions of the electrolyte are outside the IHP. Through the centers of these ions pass the OHP. The diffuse layer is the region beyond the OHP. === Trasatti/Buzzanca === Further research with double layers on ruthenium dioxide films in 1971 by Sergio Trasatti and Giovanni Buzzanca demonstrated that the electrochemical behavior of these electrodes at low voltages with specific adsorbed ions was like that of capacitors. The specific adsorption of the ions in this region of potential could also involve a partial charge transfer between the ion and the electrode. It was the first step towards understanding pseudocapacitance. === Conway === Between 1975 and 1980, Brian Evans Conway conducted extensive fundamental and development work on ruthenium oxide electrochemical capacitors. In 1991, he described the difference between 'Supercapacitor' and 'Battery' behavior in electrochemical energy storage. In 1999, he coined the term supercapacitor to explain the increased capacitance by surface redox reactions with faradaic charge transfer between electrodes and ions. His "supercapacitor" stored electrical charge partially in the Helmholtz double-layer and partially as the result of faradaic reactions with "pseudocapacitance" charge transfer of electrons and protons between electrode and electrolyte. The working mechanisms of pseudocapacitors are redox reactions, intercalation and electrosorption. === Marcus === The physical and mathematical basics of electron charge transfer absent chemical bonds leading to pseudocapacitance was developed by Rudolph A. Marcus. Marcus Theory explains the rates of electron transfer reactions—the rate at which an
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electron can move from one chemical species to another. It was originally formulated to address outer sphere electron transfer reactions, in which two chemical species change only in their charge, with an electron jumping. For redox reactions without making or breaking bonds, Marcus theory takes the place of Henry Eyring's transition state theory which was derived for reactions with structural changes. Marcus received the Nobel Prize in Chemistry in 1992 for this theory. == Mathematical description == There are detailed descriptions of the interfacial DL in many books on colloid and interface science and microscale fluid transport. There is also a recent IUPAC technical report on the subject of interfacial double layer and related electrokinetic phenomena. As stated by Lyklema, "...the reason for the formation of a "relaxed" ("equilibrium") double layer is the non-electric affinity of charge-determining ions for a surface..." This process leads to the buildup of an electric surface charge, expressed usually in C/m2. This surface charge creates an electrostatic field that then affects the ions in the bulk of the liquid. This electrostatic field, in combination with the thermal motion of the ions, creates a counter charge, and thus screens the electric surface charge. The net electric charge in this screening diffuse layer is equal in magnitude to the net surface charge, but has the opposite polarity. As a result, the complete structure is electrically neutral. The diffuse layer, or at least part of it, can move under the influence of tangential stress. There is a conventionally introduced slipping plane that separates mobile fluid from fluid that remains attached to the surface. Electric potential at this plane is called electrokinetic potential or zeta potential (also denoted as ζ-potential). The electric potential on the external boundary of the Stern layer versus the bulk electrolyte is referred to as
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Stern potential. Electric potential difference between the fluid bulk and the surface is called the electric surface potential. Usually zeta potential is used for estimating the degree of DL charge. A characteristic value of this electric potential in the DL is 25 mV with a maximum value around 100 mV (up to several volts on electrodes). The chemical composition of the sample at which the ζ-potential is 0 is called the point of zero charge or the iso-electric point. It is usually determined by the solution pH value, since protons and hydroxyl ions are the charge-determining ions for most surfaces. Zeta potential can be measured using electrophoresis, electroacoustic phenomena, streaming potential, and electroosmotic flow. The characteristic thickness of the DL is the Debye length, κ−1. It is reciprocally proportional to the square root of the ion concentration C. In aqueous solutions it is typically on the scale of a few nanometers and the thickness decreases with increasing concentration of the electrolyte. The electric field strength inside the DL can be anywhere from zero to over 109 V/m. These steep electric potential gradients are the reason for the importance of the DLs. The theory for a flat surface and a symmetrical electrolyte is usually referred to as the Gouy-Chapman theory. It yields a simple relationship between electric charge in the diffuse layer σd and the Stern potential Ψd: σ d = − 8 ε 0 ε m C R T sinh F Ψ d 2 R T {\displaystyle \sigma ^{d}=-{\sqrt {{8\varepsilon _{0}}{\varepsilon _{m}}CRT}}\sinh {\frac {F\Psi ^{d}}{2RT}}} There is no general analytical solution for mixed electrolytes, curved surfaces or even spherical particles. There is an asymptotic solution for spherical particles with low charged DLs. In the case when electric potential over DL is less than 25 mV, the so-called Debye-Huckel approximation
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holds. It yields the following expression for electric potential Ψ in the spherical DL as a function of the distance r from the particle center: Ψ ( r ) = Ψ d a r exp ( − κ ( r − a ) ) {\displaystyle {\Psi }(r)={\Psi ^{d}}{\frac {a}{r}}\exp({-\kappa }(r-a))} There are several asymptotic models which play important roles in theoretical developments associated with the interfacial DL. The first one is "thin DL". This model assumes that DL is much thinner than the colloidal particle or capillary radius. This restricts the value of the Debye length and particle radius as following: κ a ≫ 1 {\displaystyle \kappa a\gg 1} This model offers tremendous simplifications for many subsequent applications. Theory of electrophoresis is just one example. The theory of electroacoustic phenomena is another example. The thin DL model is valid for most aqueous systems because the Debye length is only a few nanometers in such cases. It breaks down only for nano-colloids in solution with ionic strengths close to water. The opposing "thick DL" model assumes that the Debye length is larger than particle radius: κ a < 1 {\displaystyle \kappa a<1} This model can be useful for some nano-colloids and non-polar fluids, where the Debye length is much larger. The last model introduces "overlapped DLs". This is important in concentrated dispersions and emulsions when distances between particles become comparable with the Debye length. == Electrical double layers == The electrical double layer (EDL) is the result of the variation of electric potential near a surface, and has a significant influence on the behaviour of colloids and other surfaces in contact with solutions or solid-state fast ion conductors. The primary difference between a double layer on an electrode and one on an interface is the mechanism of surface charge formation.
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With an electrode, it is possible to regulate the surface charge by applying an external electric potential. This application, however, is impossible in colloidal and porous double layers, because for colloidal particles, one does not have access to the interior of the particle to apply a potential difference. EDLs are analogous to the double layer in plasma. === Differential capacitance === EDLs have an additional parameter defining their characterization: differential capacitance. Differential capacitance, denoted as C, is described by the equation below: C = d σ d Ψ {\displaystyle C={\frac {d\sigma }{d\Psi }}} where σ is the surface charge and ψ is the electric surface potential. === Electron transfer in electrical double layer === The formation of electrical double layer (EDL) has been traditionally assumed to be entirely dominated by ion adsorption and redistribution. With considering the fact that the contact electrification between solid-solid is dominated by electron transfer, it is suggested by Wang that the EDL is formed by a two-step process. In the first step, when the molecules in the solution first approach a virgin surface that has no pre-existing surface charges, it may be possible that the atoms/molecules in the solution directly interact with the atoms on the solid surface to form strong overlap of electron clouds. Electron transfer occurs first to make the “neutral” atoms on solid surface become charged, i.e., the formation of ions. In the second step, if there are ions existing in the liquid, such as H+ and OH–, the loosely distributed negative ions in the solution would be attracted to migrate toward the surface bonded ions due to electrostatic interactions, forming an EDL. Both electron transfer and ion transfer co-exist at liquid-solid interface. == Dynamics of the electrical double layer == The dynamics of the electrical double layer (EDL) at the air–electrolyte
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interface have been investigated at high electrolyte concentrations using an all-optical technique. In these experiments, the surface propensity of protons (H3O+) at the air–aqueous interface was perturbed quasi-instantaneously, and the subsequent relaxation of the EDL was monitored using femtosecond time-resolved vibrational spectroscopy. The EDL reorganization occurred on picosecond timescales and exhibited a strong dependence on ion concentration. Non-equilibrium molecular dynamics (MD) simulations and mean-field analytical modeling, based on a modified form of the Poisson–Nernst–Planck equations combined with the Smoluchowski diffusion equation, revealed that ion conduction is the primary mechanism governing EDL dynamics. The combined experimental and theoretical results showed that the classical Debye–Falkenhagen theory can accurately describe EDL relaxation even at high ionic strengths, suggesting its applicability beyond the dilute-solution regime. == See also == Depletion region (structure of semiconductor junction) DLVO theory Electroosmotic pump Interface and colloid science Nanofluidics Poisson-Boltzmann equation Supercapacitor == References == == Further reading == Stillinger, Frank H.; Kirkwood, John G. (1960). "Theory of the Diffuse Double Layer". The Journal of Chemical Physics. 33 (5): 1282–1290. Bibcode:1960JChPh..33.1282S. doi:10.1063/1.1731401. ISSN 0021-9606. Paul C. Hiemenz (1986). Principles of Colloid and Surface Chemistry. M. Dekker. ISBN 978-0-8247-7476-9. Paul C. Hiemenz; Raj Rajagopalan (18 March 1997). Principles of Colloid and Surface Chemistry, Third Edition, Revised and Expanded. CRC Press. ISBN 978-0-8247-9397-5. == External links == The Electrical Double Layer
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The mating of yeast, also known as yeast sexual reproduction, is a biological process that promotes genetic diversity and adaptation in yeast species. Yeast species, such as Saccharomyces cerevisiae (baker's yeast), are single-celled eukaryotes that can exist as either haploid cells, which contain a single set of chromosomes, or diploid cells, which contain two sets of chromosomes. Haploid yeast cells come in two mating types, a and α, each producing specific pheromones to identify and interact with the opposite type, thus displaying simple sexual differentiation. A yeast cell's mating type is determined by a specific genetic locus known as MAT, which governs its mating behaviour. Haploid yeast can switch mating types through a form of genetic recombination, allowing them to change mating type as often as every cell cycle. When two haploid cells of opposite mating types encounter each other, they undergo a complex signaling process that leads to cell fusion and the formation of a diploid cell. Diploid cells can reproduce asexually, but under nutrient-limiting conditions, they undergo meiosis to produce new haploid spores. The differences between a and α cells, driven by specific gene expression patterns regulated by the MAT locus, are crucial for the mating process. Additionally, the decision to mate involves a highly sensitive and complex signaling pathway that includes pheromone detection and response mechanisms. In nature, yeast mating often occurs between closely related cells, although mating type switching and pheromone signaling allow for occasional outcrossing to enhance genetic variation. Certain yeast species have unique mating behaviors, demonstrating the diversity and adaptability of yeast reproductive strategies. == Mating types == Yeast cells can stably exist in either a diploid or a haploid form. Both haploid and diploid yeast cells reproduce by mitosis, in which daughter cells bud from mother cells. Haploid cells are capable of mating
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with other haploid cells of the opposite mating type (an a cell can only mate with an α cell and vice versa) to produce a stable diploid cell. Diploid cells, usually upon facing stressful conditions like nutrient depletion, can undergo meiosis to produce four haploid spores: two a spores and two α spores. === Differences between a and α cells === a cells produce a-factor, a mating pheromone which signals the presence of an a cell to neighbouring α cells. a cells respond to α-factor, the α cell mating pheromone, by growing a projection (known as a shmoo, due to its distinctive shape resembling the Al Capp cartoon character Shmoo) towards the source of α-factor. Similarly, α cells produce α-factor, and respond to a-factor by growing a projection towards the source of the pheromone. The selective response of haploid cells to the mating pheromones of the opposite mating type allows mating between a and α cells, but not between cells of the same mating type. These phenotypic differences between a and α cells are due to a different set of genes being actively transcribed and repressed in cells of the two mating types. a cells activate genes which produce a-factor and produce a cell surface receptor (Ste2) which binds to α-factor and triggers signaling within the cell. a cells also repress the genes associated with being an α cell. Conversely, α cells activate genes which produce α-factor and produce a cell surface receptor (Ste3) which binds and responds to a-factor, and α cells repress the genes associated with being an a cell. === MAT locus === The different sets of transcriptional repression and activation, which characterize a and α cells, are caused by the presence of one of two alleles for a mating-type locus called MAT: MATa or MATα located
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on chromosome III. The MAT locus is usually divided into five regions (W, X, Y, Z1, and Z2) based on the sequences shared among the two mating types. The difference lie in the Y region (Ya and Yα), which contains most of the genes and promoters. The MATa allele of MAT encodes a gene called a1, which directs the a-specific transcriptional program (such as expressing STE2 and repressing STE3) that defines an a haploid cell. The MATα allele of MAT encodes the α1 and α2 genes, which directs the α-specific transcriptional program (such as expressing STE3, repressing STE2, and producing prepro-α-factor) that defines an α haploid cell. S. cerevisiae has an a2 gene with no apparent function that shares much of its sequence with α2; however, other yeast species like Candida albicans do have a functional and distinct MATa2 gene. === Differences between haploid and diploid cells === Haploid cells are one of two mating types (a or α) and respond to the mating pheromone produced by haploid cells of the opposite mating type. Haploid cells cannot undergo meiosis. Diploid cells do not produce or respond to either mating pheromone and do not mate, but they can undergo meiosis to produce four haploid cells. Like the differences between haploid a and α cells, different patterns of gene repression and activation are responsible for the phenotypic differences between haploid and diploid cells. In addition to the transcriptional patterns of a and α cells, haploid cells of both mating types share a haploid transcriptional pattern which activates haploid-specific genes (such as HO) and represses diploid-specific genes (such as IME1). Conversely, diploid cells activate diploid-specific genes and repress haploid-specific genes. The different gene expression patterns of haploid and diploid cells are attributable to the MAT locus. Haploid cells only contain one copy of
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each of the 16 chromosomes and therefore only possess one MAT allele (either MATa or MATα), which determines their mating type. Diploid cells result from the mating of an a cell and an α cell, and they possess 32 chromosomes (in 16 pairs), including one chromosome bearing the MATa allele and another chromosome bearing the MATα allele. The combination of the information encoded by the MATa allele (the a1 gene) and the MATα allele (the α1 and α2 genes) triggers the diploid transcriptional program. Conversely, the presence of only one MAT allele, either MATa or MATα, triggers the haploid transcriptional program. Through genetic engineering, a MATa allele can be added to a MATα haploid cell, causing it to behave like a diploid cell. The cell will not produce or respond to mating pheromones, and when starved, the cell will unsuccessfully attempt to undergo meiosis with fatal results. Similarly, deletion of one copy of the MAT locus in a diploid cell, leaving either a MATa or MATα allele, will cause a diploid cell to behave like a haploid cell of the associated mating type. === a-like faker cells === α cells with inactivated α1 and α2 genes at the MAT locus will exhibit the mating behavior of a cells. When an a-like faker (alf) cell mates with an α cell, they form a diploid cell lacking an active copy of the a1 gene. As a result, these diploid cells cannot form the a1-α2 protein complex needed to repress haploid-specific genes. This diploid cell will act like a haploid α cell, producing α pheromones to mate with an a haploid cell, resulting in aneuploidy. Since α cells do not ordinarily mate with each other, the presence of a-like faker cells in a population of α cells can be detected in an a-like
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faker assay. This test exposes the MATα population, which lacks an active copy of the HIS3 gene, to a tester strain like YPH316 yeast, which lack a HIS1 gene, on YEPD agar. After transferring the pairs of yeast strains onto Sabouraud agar, only those that formed diploid cells by having a-like faker cells mate with the tester strain will be capable of synthesizing the amino acid histidine to survive. The extent of chromosome instability can be inferred from the proportion of surviving pairs since a-like faker cells naturally arise from damage to Chromosome III in yeast cells. == Decision to mate == Mating in yeast is stimulated by a cells' a-factor or α cells' α-factor pheromones binding the Ste3 receptor of α cells or Ste2 receptor of a cells, respectively, activating a heterotrimeric G protein. The dimeric portion of this G-protein recruits Ste5 and its MAPK cascade to the membrane, resulting in the phosphorylation of Fus3. The switching mechanism arises as a result of competition between the Fus3 protein (a MAPK protein) and the phosphatase Ptc1. These proteins both attempt to control the four phosphorylation sites of Ste5, a scaffold protein, with Fus3 attempting to phosphorylate the phosphosites and Ptc1 attempting to dephosphorylate them. Presence of α-factor induces recruitment of Ptc1 to Ste5 via a four-amino acid motif located within the Ste5 phosphosites. Ptc1 then dephosphorylates Ste5, resulting in the dissociation of the Fus3-Ste5 complex. Fus3 dissociates in a switch-like manner, dependent on the phosphorylation state of the four phosphosites. All four phosphosites must be dephosphorylated in order for Fus3 to dissociate. Fus3's ability to compete with Ptc1 decreases as Ptc1 is recruited, and thus the rate of dephosphorylation increases with the presence of pheromone. Kss1, a homologue of Fus3, does not affect shmooing, and does not contribute to the
|
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switch-like mating decision. In yeast, mating as well as the production of shmoos occur via an all-or-none, switch-like mechanism. This switch-like mechanism allows yeast cells to avoid making an unwise commitment to a highly demanding procedure. The decision to mate must balance being energy-conservative and fast enough to avoid losing the potential mate. Yeast maintain an ultra-sensitivity to mating through: Multi-site phosphorylation – Fus3 only dissociates from Ste5 and becomes fully active when all four of the phosphosites are dephosphorylated. Even one phosphorylated site will result in immunity to α-factor. Two-stage binding – Fus3 and Ptc1 bind to separate docking sites on Ste5. Only after docking can they act on the phosphosites. Steric hindrance – competition between Fus3 and Ptc1 to control the four phosphosites on Ste3 a and α yeast share the same mating response pathway, with the only difference being the type of receptor that each mating type possesses. Thus, the above description of an a-type yeast stimulated with α-factor resembles the mechanism of an α-type yeast stimulated with a-factor. == Mating type switching == Wild type haploid yeast are capable of switching mating type between a and α. Consequently, even if a single haploid cell of a given mating type founds a colony of yeast, mating type switching will cause cells of both a and α mating types to be present in the population. Combined with the strong drive for haploid cells to mate with cells of the opposite mating type and form diploids, mating type switching and consequent mating will cause the majority of cells in a colony to be diploid, regardless of whether a haploid or diploid cell founded the colony. The vast majority of yeast strains studied in laboratories have been altered such that they cannot perform mating type switching (by deletion of the
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{
"page_id": 3343370,
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HO gene; see below). This allows the stable propagation of haploid yeast, as haploid cells of the a mating type will remain a cells (and α cells will remain α cells), unable to form diploid cells unless artificially exposed to the other mating type. === HML and HMR: the silent mating cassettes === Haploid yeast switch mating type by replacing the information present at the MAT locus. For example, an a cell will switch to an α cell by replacing the MATa allele with the MATα allele. This replacement of one allele of MAT for the other is possible because yeast cells carry an additional silenced copy of both the MATa and MATα alleles: the HML (homothallic mating left) locus typically carries a silenced copy of the MATα allele, and the HMR (homothallic mating right) locus typically carries a silenced copy of the MATa allele. The silent HML and HMR loci are often referred to as the silent mating cassettes, as the information present there is 'read into' the active MAT locus. These additional copies of the mating type information do not interfere with the function of whatever allele is present at the MAT locus because they are not expressed, so a haploid cell with the MATa allele present at the active MAT locus is still an a cell, despite also having a silenced copy of the MATα allele present at HML. Only the allele present at the active MAT locus is transcribed, and thus only the allele present at MAT will influence cell behaviour. Hidden mating type loci are epigenetically silenced by SIR proteins, which form a heterochromatin scaffold that prevents transcription from the silent mating cassettes. === Mechanics of the mating type switch === The process of mating type switching is a gene conversion event initiated by the
|
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"page_id": 3343370,
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HO gene. The HO gene is a tightly regulated haploid-specific gene that is only activated in haploid cells during the G1 phase of the cell cycle. The protein encoded by the HO gene is a DNA endonuclease, which physically cleaves DNA, but only at the MAT locus (due to the DNA sequence specificity of the HO endonuclease). Once HO cuts the DNA at MAT, exonucleases are attracted to the cut DNA ends and begin to degrade the DNA on both sides of the cut site. This DNA degradation by exonucleases eliminates the DNA which encoded the MAT allele; however, the resulting gap in the DNA is repaired by copying in the genetic information present at either HML or HMR, filling in a new allele of either the MATa or MATα gene. Thus, the silenced alleles of MATa and MATα present at HML and HMR serve as a source of genetic information to repair the HO-induced DNA damage at the active MAT locus. === Directionality of the mating type switch === The repair of the MAT locus after cutting by the HO endonuclease almost always results in a mating type switch. When an a cell cuts the MATa allele present at the MAT locus, the cut at MAT will almost always be repaired by copying the information present at HML. This results in MAT being repaired to the MATα allele, switching the mating type of the cell from a to α. Similarly, an α cell which has its MATα allele cut by the HO endonuclease will almost always repair the damage using the information present at HMR, copying the MATa gene to the MAT locus and switching the mating type of α cell to a. This is the result of a recombination enhancer (RE) located on the left arm of chromosome
|
{
"page_id": 3343370,
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III. Normally, a cells have Mcm1 bind to the RE to promote recombination using the HML region. Deletion of the RE causes a cells to instead repair using HMR, maintaining their status as a cells rather than switching mating types. In α cells, the α2 factor binds at the RE to repress recombination using the HML region. Thus, yeast have a predetermined tendency toward DNA repair of the MAT locus using the HMR region. == Mating and inbreeding == In 2006, evolutionary geneticist Leonid Kruglyak found that S. cerevisiae matings only involve out-crossing between different strains roughly once every 50,000 cell divisions. The vast majority of yeast mating instead involves members of the same strain because mating type switching allows a single ascus to produce both mating types from a single haploid cell. This suggests that yeast primarily maintain their capability to mate through recombinational DNA repair during meiosis, rather than natural selection for fitness among a population with high genetic variability. == Special cases == === Fission yeast === Schizosaccharomyces pombe is a facultative sexual yeast that can undergo mating when nutrients are limited. Exposure of S. pombe to hydrogen peroxide, which causes oxidative stress to DNA, strongly induces mating, meiosis, and formation of meiotic spores. Thus, meiosis and meiotic recombination may be an adaptation for repairing DNA damage. The MAT locus' structure in S. pombe resembles S. cerevisiae. The mating-type switching system is similar but evolved independently. === Self-mating in Cryptococcus neoformans === Cryptococcus neoformans is a basidiomycetous fungus that grows as a budding yeast in culture and infected hosts. C. neoformans causes life-threatening meningoencephalitis in immunocompromised patients. It undergoes a filamentous transition during the sexual cycle to produce spores, the suspected infectious agent. The vast majority of environmental and clinical isolates of C. neoformans are of mating
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"page_id": 3343370,
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type α. Filaments ordinarily have haploid nuclei, but these can undergo a process of diploidization (perhaps by endoreduplication or stimulated nuclear fusion) to form diploid cells termed blastospores. The diploid nuclei of blastospores can then undergo meiosis, including recombination, to form haploid basidiospores that can then be dispersed. This process is referred to as monokaryotic fruiting. This process depends on the gene dmc1, a conserved homologue of the bacterial RecA and eukaryotic RAD51 genes. Dmc1 mediates homologous chromosome pairing during meiosis and repair of double-strand breaks in DNA. Meiosis in C. neoformans may be performed to promote DNA repair in DNA-damaging environments, such as host-mediated responses to infection. == Notes == == References == == Further reading == == External links == Andrew Murray's Seminar: Yeast Sex The Mating-Type Chromosome in the Filamentous Ascomycete Neurospora tetrasperma Represents a Model for Early Evolution of Sex Chromosomes
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"page_id": 3343370,
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Dalton's law (also called Dalton's law of partial pressures) states that in a mixture of non-reacting gases, the total pressure exerted is equal to the sum of the partial pressures of the individual gases. This empirical law was observed by John Dalton in 1801 and published in 1802. Dalton's law is related to the ideal gas laws. == Formula == Mathematically, the pressure of a mixture of non-reactive gases can be defined as the summation: p total = ∑ i = 1 n p i = p 1 + p 2 + p 3 + ⋯ + p n {\displaystyle p_{\text{total}}=\sum _{i=1}^{n}p_{i}=p_{1}+p_{2}+p_{3}+\cdots +p_{n}} where p1, p2, ..., pn represent the partial pressures of each component. p i = p total x i {\displaystyle p_{i}=p_{\text{total}}x_{i}} where xi is the mole fraction of the ith component in the total mixture of n components. == Volume-based concentration == The relationship below provides a way to determine the volume-based concentration of any individual gaseous component p i = p total c i {\displaystyle p_{i}=p_{\text{total}}c_{i}} where ci is the concentration of component i. Dalton's law is not strictly followed by real gases, with the deviation increasing with pressure. Under such conditions the volume occupied by the molecules becomes significant compared to the free space between them. In particular, the short average distances between molecules increases intermolecular forces between gas molecules enough to substantially change the pressure exerted by them, an effect not included in the ideal gas model. == See also == == References ==
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{
"page_id": 66570,
"source": null,
"title": "Dalton's law"
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Anatoly I. Frenkel (born 1964 in Leningrad, USSR) is an American physicist and professor. Frenkel is a researcher in the physicochemical properties of materials, focusing on the processes that link the nanoscale details of their structure to the mechanisms of work. His work has led to new techniques for materials characterization, including machine learning methods for X-ray absorption spectroscopy and multimodal, operando methods for catalytic studies using synchrotron radiation. == Education and work == Frenkel earned his B.S. and M.Sc. degree in physics from Leningrad State University in 1987, and Ph.D. degree in physics from Tel Aviv University in 1995. He completed his postdoctoral appointment at University of Washington with Edward A. Stern in 1996. He held a position as professor of physics in Yeshiva University until 2016. He is currently a professor at the Department of Materials Science and Chemical Engineering at Stony Brook University, and a senior chemist (joint appointment) at the Division of Chemistry at Brookhaven National Laboratory. == Research == His interests are in materials science, nanotechnology, catalysis, optoelectronic and electromechanical materials. He is a specialist in the field of X-ray absorption spectroscopy, operando characterization and method developments for their data analysis and applications. == Workshops and short courses on X-ray absorption spectroscopy == Since 2005, Frenkel has organized annual short courses and workshops on X-ray absorption spectroscopy at Brookhaven National Laboratory. He has run and instructed at multiple synchrotron summer schools and short courses in USA, China, Israel, Netherlands, Brazil, Germany, Switzerland, Spain and Canada. He is a co-director of Synchrotron Catalysis Consortium at Brookhaven National Laboratory. == Awards and achievements == 2023 - Fellow of the American Association for the Advancement of Science 2017 - Fellow of the American Physical Society 2015-2024 - Weston Visiting Professorship fellow, Weizmann Institute of Science 2003 - Outstanding
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{
"page_id": 77071370,
"source": null,
"title": "Anatoly Frenkel"
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|
Junior Faculty Award, Yeshiva University == References ==
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{
"page_id": 77071370,
"source": null,
"title": "Anatoly Frenkel"
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A nutrient is a substance used by an organism to survive, grow and reproduce. The requirement for dietary nutrient intake applies to animals, plants, fungi and protists. Nutrients can be incorporated into cells for metabolic purposes or excreted by cells to create non-cellular structures such as hair, scales, feathers, or exoskeletons. Some nutrients can be metabolically converted into smaller molecules in the process of releasing energy such as for carbohydrates, lipids, proteins and fermentation products (ethanol or vinegar) leading to end-products of water and carbon dioxide. All organisms require water. Essential nutrients for animals are the energy sources, some of the amino acids that are combined to create proteins, a subset of fatty acids, vitamins and certain minerals. Plants require more diverse minerals absorbed through roots, plus carbon dioxide and oxygen absorbed through leaves. Fungi live on dead or living organic matter and meet nutrient needs from their host. Different types of organisms have different essential nutrients. Ascorbic acid (vitamin C) is essential to humans and some animal species but most other animals and many plants are able to synthesize it. Nutrients may be organic or inorganic: organic compounds include most compounds containing carbon, while all other chemicals are inorganic. Inorganic nutrients include nutrients such as iron, selenium, and zinc, while organic nutrients include, protein, fats, sugars and vitamins. A classification used primarily to describe nutrient needs of animals divides nutrients into macronutrients and micronutrients. Consumed in relatively large amounts (grams or ounces), macronutrients (carbohydrates, fats, proteins, water) are primarily used to generate energy or to incorporate into tissues for growth and repair. Micronutrients are needed in smaller amounts (milligrams or micrograms); they have subtle biochemical and physiological roles in cellular processes, like vascular functions or nerve conduction. Inadequate amounts of essential nutrients or diseases that interfere with absorption, result
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"page_id": 66575,
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"title": "Nutrient"
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in a deficiency state that compromises growth, survival and reproduction. Consumer advisories for dietary nutrient intakes such as the United States Dietary Reference Intake, are based on the amount required to prevent deficiency and provide macronutrient and micronutrient guides for both lower and upper limits of intake. In many countries, regulations require that food product labels display information about the amount of any macronutrients and micronutrients present in the food in significant quantities. Nutrients in larger quantities than the body needs may have harmful effects. Edible plants also contain thousands of compounds generally called phytochemicals which have unknown effects on disease or health including a diverse class with non-nutrient status called polyphenols which remain poorly understood as of 2024. == Types == === Macronutrients === Macronutrients are defined in several ways. The chemical elements humans consume in the largest quantities are carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulphur, summarized as CHNOPS. The chemical compounds that humans consume in the largest quantities and provide bulk energy are classified as carbohydrates, proteins, and fats. Water must be also consumed in large quantities but does not provide caloric value. Calcium, sodium, potassium, magnesium, and chloride ions, along with phosphorus and sulfur, are listed with macronutrients because they are required in large quantities compared to micronutrients, i.e., vitamins and other minerals, the latter often described as trace or ultratrace minerals. Macronutrients provide energy: Carbohydrates are compounds made up of types of sugar. Carbohydrates are classified according to their number of sugar units: monosaccharides (such as glucose and fructose), disaccharides (such as sucrose and lactose), oligosaccharides, and polysaccharides (such as starch, glycogen, and cellulose). Proteins are organic compounds that consist of amino acids joined by peptide bonds. Since the body cannot manufacture some of the amino acids (termed essential amino acids), the diet must supply
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"page_id": 66575,
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them. Through digestion, proteins are broken down by proteases back into free amino acids. Fats consist of a glycerin molecule with three fatty acids attached. Fatty acid molecules contain a -COOH group attached to unbranched hydrocarbon chains connected by single bonds alone (saturated fatty acids) or by both double and single bonds (unsaturated fatty acids). Fats are needed for construction and maintenance of cell membranes, to maintain a stable body temperature, and to sustain the health of skin and hair. Because the body does not manufacture certain fatty acids (termed essential fatty acids), they must be obtained through one's diet. Ethanol is not an essential nutrient, but it does provide calories. The United States Department of Agriculture uses a figure of 6.93 kilocalories (29.0 kJ) per gram of alcohol (5.47 kcal or 22.9 kJ per ml) for calculating food energy. For distilled spirits, a standard serving in the U.S. is 44 ml (1.5 US fl oz), which at 40% ethanol (80 proof) would be 14 grams and 98 calories. === Micronutrients === Micronutrients are essential dietary elements required in varying quantities throughout life to serve metabolic and physiological functions. Dietary minerals, such as potassium, sodium, and iron, are elements native to Earth, and cannot be synthesized. They are required in the diet in microgram or milligram amounts. As plants obtain minerals from the soil, dietary minerals derive directly from plants consumed or indirectly from edible animal sources. Vitamins are organic compounds required in microgram or milligram amounts. The importance of each dietary vitamin was first established when it was determined that a disease would develop if that vitamin was absent from the diet. == Essentiality == === Essential nutrients === An essential nutrient is a nutrient required for normal physiological function that cannot be synthesized in the body – either
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at all or in sufficient quantities – and thus must be obtained from a dietary source. Apart from water, which is universally required for the maintenance of homeostasis in mammals, essential nutrients are indispensable for various cellular metabolic processes and for the maintenance and function of tissues and organs. The nutrients considered essential for humans comprise nine amino acids, two fatty acids, thirteen vitamins, fifteen minerals and choline. In addition, there are several molecules that are considered conditionally essential nutrients since they are indispensable in certain developmental and pathological states. ==== Amino acids ==== An essential amino acid is an amino acid that is required by an organism but cannot be synthesized de novo by it, and therefore must be supplied in its diet. Out of the twenty standard protein-producing amino acids, nine cannot be endogenously synthesized by humans: phenylalanine, valine, threonine, tryptophan, methionine, leucine, isoleucine, lysine, and histidine. ==== Fatty acids ==== Essential fatty acids (EFAs) are fatty acids that humans and other animals must ingest because the body requires them for good health but cannot synthesize them. Only two fatty acids are known to be essential for humans: alpha-linolenic acid (an omega-3 fatty acid) and linoleic acid (an omega-6 fatty acid). ==== Vitamins and vitamers ==== Vitamins occur in a variety of related forms known as vitamers. The vitamers of a given vitamin perform the functions of that vitamin and prevent symptoms of deficiency of that vitamin. Vitamins are those essential organic molecules that are not classified as amino acids or fatty acids. They commonly function as enzymatic cofactors, metabolic regulators or antioxidants. Humans require thirteen vitamins in their diet, most of which are actually groups of related molecules (e.g. vitamin E includes tocopherols and tocotrienols): vitamins A, C, D, E, K, thiamine (B1), riboflavin (B2), niacin (B3),
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pantothenic acid (B5), pyridoxine (B6), biotin (B7), folate (B9), and cobalamin (B12). The requirement for vitamin D is conditional, as people who get sufficient exposure to ultraviolet light, either from the sun or an artificial source, synthesize vitamin D in the skin. ==== Minerals ==== Minerals are the exogenous chemical elements indispensable for life. Although the four elements carbon, hydrogen, oxygen, and nitrogen (CHON) are essential for life, they are so plentiful in food and drink that these are not considered nutrients and there are no recommended intakes for these as minerals. The need for nitrogen is addressed by requirements set for protein, which is composed of nitrogen-containing amino acids. Sulfur is essential, but again does not have a recommended intake. Instead, recommended intakes are identified for the sulfur-containing amino acids methionine and cysteine. The essential nutrient trace elements for humans, listed in order of recommended dietary allowance (expressed as a mass), are potassium, chloride, sodium, calcium, phosphorus, magnesium, iron, zinc, manganese, copper, iodine, chromium, molybdenum, and selenium. Additionally, cobalt is a component of vitamin B12 which is essential. There are other minerals which are essential for some plants and animals, but may or may not be essential for humans, such as boron and silicon. ==== Choline ==== Choline is an essential nutrient. The cholines are a family of water-soluble quaternary ammonium compounds. Choline is the parent compound of the cholines class, consisting of ethanolamine having three methyl substituents attached to the amino function. Healthy humans fed artificially composed diets that are deficient in choline develop fatty liver, liver damage, and muscle damage. Choline was not initially classified as essential because the human body can produce choline in small amounts through phosphatidylcholine metabolism. === Conditionally essential === Conditionally essential nutrients are certain organic molecules that can normally be synthesized by
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"page_id": 66575,
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an organism, but under certain conditions in insufficient quantities. In humans, such conditions include premature birth, limited nutrient intake, rapid growth, and certain disease states. Inositol, taurine, arginine, glutamine and nucleotides are classified as conditionally essential and are particularly important in neonatal diet and metabolism. === Non-essential === Non-essential nutrients are substances within foods that can have a significant impact on health. Dietary fiber is not absorbed in the human digestive tract. Soluble fiber is metabolized to butyrate and other short-chain fatty acids by bacteria residing in the large intestine. Soluble fiber is marketed as serving a prebiotic function with claims for promoting "healthy" intestinal bacteria. === Non-nutrients === Ethanol (C2H5OH) is not an essential nutrient, but it does supply approximately 29 kilojoules (7 kilocalories) of food energy per gram. For spirits (vodka, gin, rum, etc.) a standard serving in the United States is 44 millilitres (1+1⁄2 US fluid ounces), which at 40% ethanol (80 proof) would be 14 grams and 410 kJ (98 kcal). At 50% alcohol, 17.5 g and 513 kJ (122.5 kcal). Wine and beer contain a similar amount of ethanol in servings of 150 and 350 mL (5 and 12 US fl oz), respectively, but these beverages also contribute to food energy intake from components other than ethanol. A 150 mL (5 US fl oz) serving of wine contains 420 to 540 kJ (100 to 130 kcal). A 350 mL (12 US fl oz) serving of beer contains 400 to 840 kJ (95 to 200 kcal). According to the U.S. Department of Agriculture, based on NHANES 2013–2014 surveys, women ages 20 and up consume on average 6.8 grams of alcohol per day and men consume on average 15.5 grams per day. Ignoring the non-alcohol contribution of those beverages, the average ethanol contributions to daily food energy
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"page_id": 66575,
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intake are 200 and 450 kJ (48 and 108 kcal), respectively. Alcoholic beverages are considered empty calorie foods because, while providing energy, they contribute no essential nutrients. By definition, phytochemicals include all nutritional and non-nutritional components of edible plants. Included as nutritional constituents are provitamin A carotenoids, whereas those without nutrient status are diverse polyphenols, flavonoids, resveratrol, and lignans that are present in numerous plant foods. Some phytochemical compounds are under preliminary research for their potential effects on human diseases and health. However, the qualification for nutrient status of compounds with poorly defined properties in vivo is that they must first be defined with a Dietary Reference Intake level to enable accurate food labeling, a condition not established for most phytochemicals that are claimed to provide antioxidant benefits. == Deficiencies and toxicity == See Vitamin, Mineral (nutrient), Protein (nutrient) An inadequate amount of a nutrient is a deficiency. Deficiencies can be due to several causes, including an inadequacy in nutrient intake, called a dietary deficiency, or any of several conditions that interfere with the utilization of a nutrient within an organism. Some of the conditions that can interfere with nutrient utilization include problems with nutrient absorption, substances that cause a greater-than-normal need for a nutrient, conditions that cause nutrient destruction, and conditions that cause greater nutrient excretion. Nutrient toxicity occurs when excess consumption of a nutrient does harm to an organism. In the United States and Canada, recommended dietary intake levels of essential nutrients are based on the minimum level that "will maintain a defined level of nutriture in an individual", a definition somewhat different from that used by the World Health Organization and Food and Agriculture Organization of a "basal requirement to indicate the level of intake needed to prevent pathologically relevant and clinically detectable signs of a dietary
|
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inadequacy". In setting human nutrient guidelines, government organizations do not necessarily agree on amounts needed to avoid deficiency or maximum amounts to avoid the risk of toxicity. For example, for vitamin C, recommended intakes range from 40 mg/day in India to 155 mg/day for the European Union. The table below shows U.S. Estimated Average Requirements (EARs) and Recommended Dietary Allowances (RDAs) for vitamins and minerals, PRIs for the European Union (same concept as RDAs), followed by what three government organizations deem to be the safe upper intake. RDAs are set higher than EARs to cover people with higher-than-average needs. Adequate Intakes (AIs) are set when there is insufficient information to establish EARs and RDAs. Countries establish tolerable upper intake levels, also referred to as upper limits (ULs), based on amounts that cause adverse effects. Governments are slow to revise information of this nature. For the U.S. values, except calcium and vitamin D, all data date from 1997 to 2004. * The daily recommended amounts of niacin and magnesium are higher than the tolerable upper limit because, for both nutrients, the ULs identify the amounts that will not increase the risk of adverse effects when the nutrients are consumed as a serving of a dietary supplement. Magnesium supplementation above the UL may cause diarrhea. Supplementation with niacin above the UL may cause flushing of the face and a sensation of body warmth. Each country or regional regulatory agency decides on a safety margin below when symptoms occur so that the ULs may differ based on the source. EAR U.S. Estimated Average Requirements. RDA U.S. Recommended Dietary Allowances; higher for adults than children and may be even higher for pregnant or lactating women. AI U.S. Adequate Intake; AIs are established when there is insufficient information to set EARs and RDAs. PRI Population
|
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Reference Intake is the European Union equivalent of RDA; it is higher for adults than for children and maybe even higher for pregnant or lactating women. For Thiamin and Niacin, the PRIs are expressed as amounts per megajoule (239 kilocalories) of food energy consumed. Upper Limit Tolerable upper intake levels. ND ULs have not been determined. NE EARs, PRIs, or AIs have not yet been established or will not be (EU does not consider chromium an essential nutrient). == Plant == Plants absorb carbon, hydrogen, and oxygen from air and soil as carbon dioxide and water. Other nutrients are absorbed from soil (exceptions include some parasitic or carnivorous plants). Counting these, there are 17 important nutrients for plants: these are macronutrients; nitrogen (N), phosphorus (P), potassium (K), calcium (Ca), sulfur (S), magnesium (Mg), carbon (C), oxygen(O) and hydrogen (H), and the micronutrients; iron (Fe), boron (B), chlorine (Cl), manganese (Mn), zinc (Zn), copper (Cu), molybdenum (Mo) and nickel (Ni). In addition to carbon, hydrogen, and oxygen, nitrogen, phosphorus, and sulfur are also needed in relatively large quantities. Together, these six are the elemental macronutrients for all organisms. They are sourced from inorganic matter (for example, carbon dioxide, water, nitrates, phosphates, sulfates, and diatomic molecules of nitrogen and, especially, oxygen) and organic compounds such as carbohydrates, lipids, proteins. == See also == == References == == External links == USDA. Dietary Reference Intakes
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"page_id": 66575,
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Tierra is a computer simulation developed by ecologist Thomas S. Ray in the early 1990s in which computer programs compete for time (central processing unit (CPU) time) and space (access to main memory). In this context, the computer programs in Tierra are considered to be evolvable and can mutate, self-replicate and recombine. Tierra's virtual machine is written in C. It operates on a custom instruction set designed to facilitate code changes and reordering, including features such as jump to template (as opposed to the relative or absolute jumps common to most instruction sets). == Simulations == The basic Tierra model has been used to experimentally explore in silico the basic processes of evolutionary and ecological dynamics. Processes such as the dynamics of punctuated equilibrium, host-parasite co-evolution and density-dependent natural selection are amenable to investigation within the Tierra framework. A notable difference between Tierra and more conventional models of evolutionary computation, such as genetic algorithms, is that there is no explicit, or exogenous fitness function built into the model. Often in such models there is the notion of a function being "optimized"; in the case of Tierra, the fitness function is endogenous: there is simply survival and death. According to Thomas S. Ray and others, this may allow for more "open-ended" evolution, in which the dynamics of the feedback between evolutionary and ecological processes can itself change over time (see evolvability), although this claim has not been realized – like other digital evolution systems, it eventually reaches a point where novelty ceases to be created, and the system at large begins either looping or ceases to 'evolve'. The issue of how true open-ended evolution can be implemented in an artificial system is still an open question in the field of artificial life. Mark Bedau and Norman Packard developed a statistical method
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{
"page_id": 328721,
"source": null,
"title": "Tierra (computer simulation)"
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|
of classifying evolutionary systems and in 1997, Bedau et al. applied these statistics to Evita, an Artificial life model similar to Tierra and Avida, but with limited organism interaction and no parasitism, and concluded that Tierra-like systems do not exhibit the open-ended evolutionary signatures of naturally evolving systems. Russell K. Standish has measured the informational complexity of Tierran 'organisms', and has similarly not observed complexity growth in Tierran evolution. Tierra is an abstract model, but any quantitative model is still subject to the same validation and verification techniques applied to more traditional mathematical models, and as such, has no special status. The creation of more detailed models in which more realistic dynamics of biological systems and organisms are incorporated is now an active research field (see systems biology). == See also == Avida Digital organism Digital organism simulator Evolutionary computation Fitness landscape == References == == Further reading == Bentley, Peter, J. 2001, "Digital Biology:How Nature is transforming Our Technology and Our Lives", Simon & Schuster, New York, NY. Previously published in Great Britain in 2001 by Headline Book Publishing. Ray, T. S. 1991, "Evolution and optimization of digital organisms", in Billingsley K.R. et al. (eds), Scientific Excellence in Supercomputing: The IBM 1990 Contest Prize Papers, Athens, GA, 30602: The Baldwin Press, The University of Georgia. Publication date: December 1991, pp. 489–531. Casti, John L. (1997). Would-Be-Worlds. John Wiley & Sons, Inc. New York ISBN 0-471-12308-0 == External links == Tierra home page
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{
"page_id": 328721,
"source": null,
"title": "Tierra (computer simulation)"
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Methallorphan may refer to: Dextrallorphan Levallorphan == See also == Methorphan
|
{
"page_id": 57738257,
"source": null,
"title": "Methallorphan"
}
|
A biotone is a biogeographical region characterized not by distinctive biota but rather by a distinctive transition from one set of biota to another. They often contain the limits of distribution of the biota of neighbouring regions. Biotones are especially useful in marine biogeography, where the movement of water may result in substantial overlap in the floral and faunal components of adjacent regions. In such case, the regions of overlap is considered a biotone. A simple example would be mid-latitude waters where tropical and temperate waters mix. This region is a biotone characterized by the transition between tropical and temperate waters. It would contain both tropical and temperate biota. Tropical biota that do not extend into temperate areas would be at the limit of their range in this biotone, and vice versa. The co-occurrence of biota that are normally distinct can result in unusual ecological relationships. == References ==
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{
"page_id": 15991827,
"source": null,
"title": "Biotone"
}
|
The Historical Museum of the Palatinate (German: Historisches Museum der Pfalz) is a museum in the city of Speyer in the Palatinate region of the German state of Rhineland-Palatinate. It is situated across the square from the Speyer Cathedral. The museum's focus is on the History of the Palatinate; it has a collection of about 1 million artifacts, the oldest being an approximately 190,000-year-old hand axe. The museum is among the most important in Germany, and is known for its special exhibitions. With over 200,000 visitors per year it is one of the major attractions of Speyer. The museum is a trust borne by the City of Speyer, the Evangelical Church of the Palatinate, the Roman Catholic Diocese of Speyer, the State of Rhineland-Palatinate, the Historical Society of the Palatinate, and the Bezirksverband Palz (County Association). == History == The museum was established in 1869 and the collections of the Historical Society of the Palatinate, the former Rhine District, and the City of Speyer were combined. The building at the present site was built in 1910 by architect Gabriel von Seidl; a modern annex was added in 1990. == Exhibitions == The Museum offers two kinds of exhibitions: permanent and special ones. While the permanent exhibitions focus on the history of the Palatinate, the special ones can have general historical topics. === Special exhibitions === "Germany and the World Football Championships since 1954" (2004), on occasion of the 50th anniversary of the World Football Championship 1954 "Looted and Sunk in the Rhine – The Barbarian’s Treasure of Neupotz" (2006) Over 1,000 pieces of silver, bronze, brass and iron (weapons, tools, coins, tableware, kitchenware etc.)., weighing more than 700 kg, sunk in the waters of the Rhine 1,700 years ago, the largest Roman-era trove of metals found in Europe, dug up
|
{
"page_id": 39584789,
"source": null,
"title": "Historical Museum of the Palatinate"
}
|
in a gravel quarry near Neupotz, 30 km south of Speyer. "Attila and the Huns" (2007) "The Samurai" (2008) "The Vikings" (2009) "Witches – Myth and Reality" (2010) "Amazons – mysterious Female Warriors" (2010/2011) "The Salian Dynasty – Changing Power" (2011) "Discovering Egypt’s Treasurs. Masterworks from the Egyptian Museum in Turin" (2012) === Permanent exhibitions === The five permanent exhibitions covering 8,000 m2 are: Prehistory, Roman Era, Cathedral Treasure, Modern Era and the Wine Museum. Cathedral Treasure – The cathedral treasure contains the most important testimonies of the Salian Dynasty. One of them is the imperial crown of Conrad II from 1039. The Emperor's last clothes – This exhibition shows the restoration and conservation of remnants of clothing found in the imperial and royal graves in the Speyer Cathedral. Prehistory – The exhibits show the cultural, social and economical development in the Palatinate beginning from the earliest findings to the eve of the Roman occupation. One of the most prominent exhibits is the Golden Hat of Schifferstadt found near Schifferstadt. Roman Era – The Roman Era collection shows findings from the Palatinate, which once was part of the Roman province of Germania Superior (Upper Germany). A special exhibit is the head of a centaur, dating around 10 B. C., found in Homburg-Schwarzenacker. Modern Era – Information and exhibits from the Renaissance till the end of the Second World War. Highlights are the Frankental China, baroque paintings and precious gowns as well as the German Flag (black-red-gold) flown at the Hambach Festival. There are also paintings by the Speyer painter Anselm Feuerbach. Wine Museum – The collection contains unique artifacts from the world of wine, among them the oldest wine ever found, the Speyer wine bottle, dating from the 4th century. Evangelical Church of the Palatinate – This exhibition shows the
|
{
"page_id": 39584789,
"source": null,
"title": "Historical Museum of the Palatinate"
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|
tight connection between the development of the Protestant Church and Palatinate history. == The Young Museum == The first museum of its kind, it playfully gets children in touch with history. It offers workshops during school holidays and programmes for school classes. == The Forum == The 650 m2-area of covered courtyard offers opportunities for communication, concerts, workshops, theatre, discussions etc. == References == == External links == Objektsammlung des Historischen Museums der Pfalz Historischer Verein der Pfalz Homepage of the museum (English version) Archived 11 January 2019 at the Wayback Machine
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{
"page_id": 39584789,
"source": null,
"title": "Historical Museum of the Palatinate"
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The Fission Product Pilot Plant, building 3515 at Oak Ridge National Laboratory (ORNL), was built in 1948 to extract radioactive isotopes from liquid radioactive waste. It was formerly known as the 'ruthenium-106 tank arrangement'. It is a relatively small facility; the task of extracting radioactive isotopes later took place at a number of specialised buildings nearby. References differ as to when the plant was built; 'radioactive waste management at ORNL' says that it was completed in 1957, the 1955 Annual Report has engineering drawings indicating that the building was fully designed in 1955, but other references suggest that there was a building on the site in 1948. == Contamination issues == The plant was extensively contaminated during operation, particularly by waste produced while flushing out the tanks inside for maintenance. Traces of human feces were found in the tanks. == End of life == Operations at FPPP ended in the early 1960s, and the plant was entombed in concrete up to 1.5 metres (4.9 ft) thick; there was a proposal made in 1993 for dismantling the plant by robot from the inside, but it's not clear whether this was carried out. == References == http://www.osti.gov/bridge/purl.cover.jsp?purl=/392043-Fisb6G/webviewable/ A proposal for disposing of FPPP Radioactive waste management at ORNL 1955 Annual Report on the radioisotope production programs at ORNL, pages 10 through 14 describe the 'F3P' lab. Purposes of various buildings on the ORNL site
|
{
"page_id": 16188434,
"source": null,
"title": "Fission Product Pilot Plant"
}
|
Stable and persistent phosphorus radicals are phosphorus-centred radicals that are isolable and can exist for at least short periods of time. Radicals consisting of main group elements are often very reactive and undergo uncontrollable reactions, notably dimerization and polymerization. The common strategies for stabilising these phosphorus radicals usually include the delocalisation of the unpaired electron over a pi system or nearby electronegative atoms, and kinetic stabilisation with bulky ligands. Stable and persistent phosphorus radicals can be classified into three categories: neutral, cationic, and anionic radicals. Each of these classes involve various sub-classes, with neutral phosphorus radicals being the most extensively studied. Phosphorus exists as one isotope 31P (I = 1/2) with large hyperfine couplings relative to other spin active nuclei, making phosphorus radicals particularly attractive for spin-labelling experiments. == Neutral phosphorus radicals == Neutral phosphorus radicals include a large range of conformations with varying spin densities at the phosphorus. Generally, they can categorised as mono- and bi/di-radicals (also referred to as bisradicals and biradicaloids) for species containing one or two radical phosphorus centres respectively. === Monoradicals === In 1966, Muller et. al published the first electron paramagnetic resonance (EPR/ESR) spectra displaying evidence for the existence of phosphorus-containing radicals. Since then a variety of phosphorus monoradicals have been synthesised and isolated. Common ones include phosphinyl (R2P•), phosphonyl (R2PO•), and phosphoranyl (R4P•) radicals. ==== Synthesis ==== Synthetic methods for obtaining neutral phosphorus mondoradicals include photolytic reduction of trivalent phosphorus chlorides, P-P homolytic cleavage, single electron oxidation of phosphines, and cleavage of P-S or P-Se bonds. The first persistent two-coordinate phosphorus-centred radicals [(Me3Si)2N]2P• and [(Me3Si)2CH]2P• were reported in 1976 by Lappert and co-workers. They are prepared by photolysis of the corresponding three-coordinate phosphorus chlorides in toluene in the presence of an electron-rich olifin. In 2000, the Power group found that this species can
|
{
"page_id": 72418328,
"source": null,
"title": "Stable phosphorus radicals"
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be synthesised from the dissolution, melting or evaporation of the dimer. In 2001, Grützmacher et al. reported the first stable diphosphanyl radical [Mes*MeP-PMes*]• (Mes = 1,3,5-trimethylbenzene) from the reduction of the phosphonium salt [Mes*MeP-PMes*]+(O3SCF3)− in an acetonitrile solution containing tetrakis(dimethylamino)ethylene (TDE) at room temperature, yielding yellow crystals. The monomer is stable below -30 ºC in the solid state for a few days. At room temperature the species decomposes in solution and in the solid state with a half life of 30 minutes at 3 x 10−2 M. The first structurally characterised phosphorus radical [Me3SiNP(μ3-NtBu)3{μ3-Li(thf)}3X]• (X = Br, I) was synthesised by Armstrong et al. in 2004 by the oxidation of the starting material with halogens bromide or iodine in a mixture of toluene and THF at 297 K. This produces blue crystals that can be characterised by X-ray crystallography. The steric bulk of the alkyl-imido groups was identified as playing a major role in the stabilising of these radicals. In 2006, Ito et al. prepared an air tolerant and thermally stable 1,3-diphosphayclobutenyl radical. Sterically bulky phospholkyne (Mes*C≡P) is treated with 0.5 equiv of t-BuLi in THF to form a 1,3 diphosphaalkyl anion. This is reduced with iodine solution to form a red product. The species is a planar four-membered diphosphacyclobutane (C2P2) ring with the Mes* having torsional angles with the C2P2 plane. ===== Metal stabilised radicals ===== In 2007, Cummins et al. synthsised a phosphorus radical using nitridovanadium trisanilide metallo-ligands with similar form to Lappert, Power and co-workers' "jack-in-the-box" diphosphines. This is made by the synthesis of the radical precursor ClP[NV{N(Np)Ar}]3]2 followed by its one electron reduction with Ti[N(tBu)Ar]3 or potassium graphite to yield dark brown crystals in 77% yield. EPR data showed delocalisation of electron spin across the two 51V and one 31P nuclei. This was consistent with computation,
|
{
"page_id": 72418328,
"source": null,
"title": "Stable phosphorus radicals"
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|
supporting the reported resonance structures. This delocalisation across the vanadium atoms was identified as the source of stabilisation for this species due to the ease for transition metals to undergo one-electron chemistry. Cummins and co-workers postulated that the p-character of the system could be tuned by changing the metal centres. Other metals stabilised radicals have been reported by Scheer et al, and Schneider et al using ligand containing tungsten and osmium respectively. ==== Structure and properties ==== As previously mentioned, kinetic stabilisation through bulky ligands has been an effective strategy for producing persisting phosphorus radicals. Delocalisation of the electron has also shown a stabilising effect on phosphorus radical species. This conversely results in more delocalised spin densities, and lower coupling constants relative to 31P localised electron spin. For this reason the spin localisation on the phosphorus atom varies widely for different phosphorus radical species. Cyclic radicals like that by Ito at al have delocalisation across the rings. In this case X-ray, EPR spectroscopy, and ab initio calculations found that 80-90% of the spin was delocalised on the carbons in the C2P2 ring and the rest on the phosphorus atoms. Despite this, the aP2 constant shows similar spectroscopic property to organic radicals that contain conjugated P=C doubles bond, justifying the resonance structure used for this species. The phosphinyl radicals synthesised by Lappert and co-workers were found to be stable at room temperature for periods of over 15 days with no effect from short-term heating at 360 K. This stability was assigned to the steric bulk of the substituents and the absence of beta-hydrogen atoms. A structural study of this species conducted using X-ray crystallography, gas-phase electron diffraction, and ab initio molecular orbital calculations found that the source of this stability was not the bulkiness of the CH(SiMe3)2 ligands but the release
|
{
"page_id": 72418328,
"source": null,
"title": "Stable phosphorus radicals"
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|
of strain energy during homolytic cleavage at the P-P bond of the dimer that favoured the existence of the radical. The dimer shows a syn,anti conformation, which allows for better packing but has excessive crowding at the trimethylsilyl groups, while the radical monomer displays syn,syn conformation. Theoretical calculations showed that the process of cleaving the P-P bond (endothermic), relaxation to release steric strain, and rotation about the P-C bond to yield syn,syn conformation on the monomer radical (exothermic by 67.5 kJ for each unit) is an overall exothermic process. The stability of this species can therefore be attributed to the energy release of strain energy by the reorganisation of the ligands as the dimer converts to the radical monomer. This effect have been observed in other systems containing the CH(SiMe3)2 ligand and was dubbed the "Jack-in-the-box" model. Other ligand with similar flexibility, and ability to undergo conformational changes were identified as PnR2 (Pn - P, As, Sb) and ERR'2 (E = Si, Ge, Sn; R' = bulky ligand). In 2022, Streubel and co-workers investigated the electron density distribution across centres in metal-coordinated phosphanoxyl complexes. This study showed that tungsten-containing radical complexes have small amounts of spin density on the metal nuclei while in the case of manganese and iron, the spins are purely metal-centred. === Biradicals === Biradicals are molecules bearing two unpaired electrons. These radicals can interact ferromagnetically (triplet), antiferromagnetically (open-shell singlet) or not interact at all (two-doublet). Biradicaloids/diradicaloids are a class of biradicals with significant radical centre interaction. ==== Synthesis ==== The first phosphorus biradical was reported in 2011 by T. Breweies and co-workers. The biradicaloid [P(μ-NR)]2 (R=Hyp, Ter) was synthesised by the reduction of cyclo-1,3-diphospha (III)-2,4-diazanes using [(Cp2TiCl}2] as the reducing agent. The bulky Ter (trimesitylphenyl) and Hyp (hypersilyl) substituents provide a large stabilising effect. This effect
|
{
"page_id": 72418328,
"source": null,
"title": "Stable phosphorus radicals"
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|
is more pronounced with Ter where the biradical is stable in inert atmospheres in the solid state for long periods of time at temperatures up to 224 C. Computational studies determined that the [P(μ-NTer)]2 radical shows an openshell singlet ground state biradical character. Villinger et al later synthesised a stable cyclopentane-1,3-diyl biradical by the insertion of CO into a P–N bond of diphosphadiazanediyl. In 2017 D. Rottschäfer et al reported a N-heterocyclic vinylindene-stabilised singlet biradicaloid phosphorus compound (iPr)CP]2 (iPr = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene). Significant π-e− density is transferred to C2P2 ring. The species was found to be diamagnetic with temperature-independent NMR resonances, so can be considered a non-Kekulé molecule. ==== Structure and properties ==== The species by Villinger can undergo reaction with phosphaalkyne forming a five-membered P2N2C heterocycle with a P-C bridge. It can also undergo halogenation and reaction with elemental sulfur. === Characterisation === Phosphorus radicals are commonly characterized by EPR/ESR to elucidate the spin localisation of the radical across the radical species. Higher coupling constants are indicative of higher localisation on phosphorus nuclei. Quantum chemical calculations on these systems are also used to support this experimental data. Before the characterization by X-ray crystallography by Armstrong et al, the structure of the phosphorus centred radical [(Me3Si)2CH]2P• had been determined by electron diffraction. The diphosphanyl radical [Mes*MeP-PMes*]• had been stabilised through doping into crystals of Mes*MePPMeMes*. The radical synthesised by Armstrong et al was found to exist as a distorted PN3Li3X cube in the solid state. They found that upon dissolution in THF, this cubic structure is disrupted, leaving the species to form a solvent-separated ion pair. == Phosphorus radical cations == === Synthesis === Phosphorus radical cations are often obtained from the one-electron oxidation of diphosphinidenes and phosphalkenes. In 2010, the Bertrand group found that carbene-stabilised diphosphinidenes can undergo one-electron oxidation
|
{
"page_id": 72418328,
"source": null,
"title": "Stable phosphorus radicals"
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|
in toluene with Ph3C+B(C6F5)4− at room temperature in inert atmosphere to produce radical cations (Dipp=2,6-Diisopropylphenyl). The Bertrand group reported the synthesis of [(cAAC)P2]•+ , [(NHC)P2]•+ and [(NHC)P2]++ . The EPR signal for [(cAAC)P2]•+ is a triplet of quintents, resulting form coupling to with 2 P nuclei and a small coupling with 2 N nuclei. NBO analysis showed spin delocalisation across two phosphorus atoms (0.27e each) and nitrogen atoms(0.14e each). Contrastingly, the [(NHC)P2]•+complex showed delocalisation mostly on phosphorus (0.33e and 0.44e) with little contribution of other elements. Other diradicals synthesised by the Bertrand group involved species single phosphorus atoms. These included [(TMP)P(cAAC)]•+ where spin is localised on phosphorus (67%) and [bis(carbene)-PN]•+ with spin density distributed over phosphorus (0.40e), central nitrogen atom (0.18e), and N atom of cAAC (0.19e). Treatment with this later cation with KC8 returns it to its neutral analogue.In 2003, Geoffroy et al. synthesised Mes*P•-(C(NMe2)2)+ through a one electron oxidation of a phosphaalkenes with [Cp2Fe]PF6. A solution of Mes*P•-(C(NMe2)2)+ is stable in inert atmosphere in the solid state for a few weeks and a few days in solution. Hyperfine couplings on EPR show strong localisation of the spin to the phosphorus nuclei (0.75e in p orbital). In 2015, the Wang group was able to isolate the crystal structure of this species with use of the oxidant of a weakly coordinating anion Ag[Al(ORF)4]−. The electron spin density, found by EPR, resides principally on phosphorus 3p and 3s orbitals (68.2% and 2.46% respectively). This was supported by DFT calculations where 80.9% of spin density was found to be localised on phosphorus atom. Weakly coordinating anions were also used to stabilise cyclic biradical cations synthesised by Schulz and colleagues where the spin density was found to reside exclusively on the phosphorus atoms (0.46e each) in the case of [P(μ-NTer)2P]•+. In the case
|
{
"page_id": 72418328,
"source": null,
"title": "Stable phosphorus radicals"
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of [P(μ-NTer)2As]•+ the spin was found to mostly reside on the As nuclei (70.6% on As compared to 29.4% on P atom). Many other cyclic radical cations have been reported. It is difficult to form radical cations with diphosphenes due to low lying HOMO at the phosphorus centre. Ghadwal and co-workers were able to synthesise a diphosphene radical cation [{(NHC)C(Ph)}P]2•+ using an NHC-derived divinyldiphosphene with a high lying HOMO and a small HOMO-LUMO gap. The stability of the species was identified as the delocalisation of the spin density across the CP2C-unit. The spin density was found to be 11-14% on each P nuclei and 17-21% on each C nuclei. === Structure and properties === A unique source of stability for phosphorus radical cations is the electrostatic repulsion between radical cations that prevents dimerisation. Weakly coordinating anions have been used to stabilise biradical cations. == Phosphorus radical anions == === Synthesis === The most common method for accessing radical anions is through the use of reducing agents. In 2014 the Wang group reported the synthesis of a phosphorus-centred radical anion through the reduction of a phosphaalkene using either Li in DME or K in THF yielding purple crystals. EPR data showed localisation of the spin on 3p (51.09%) and 3s (1.62%) orbitals of phosphorus. They later synthesised a diphosphorus-centred radial anion and the first di-radical di-anion from the reduction of the diphosphaalkene with KC8 in THF in the presence of 18-crown-6. In both cases the spin density resides principally on the phosphorus nuclei. Tan and co-workers used a charge transfer approach to synthesis the phosphorus radical anion coordinated CoII and FeII complexes. Here diazafluorenylidene-substituted phosphaalkene is reacted with low valent transition metal complexes to form phosphorus radical anions coordinated with metal complexes. This species displays a quartet ground state showing weak
|
{
"page_id": 72418328,
"source": null,
"title": "Stable phosphorus radicals"
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|
antiferromagnetic interaction of the phosphorus radical with the high-spim TMII ion. The spin density is mostly localised on TM and phosphorus nuclei. The group further synthesised radical anion lanthanide complexes which also showed antiferromagnetic interaction. The π-acid properties of boryl substituents were employed by Yamashita and co-workers to stabilise phosphorus radical anions. Here the diazafluorenylidene-substituted phosphaalkene is reacted with [Cp*2Ln][BPh4] (Ln = Dy, Tb, and Gd) followed by reduction with KC8 in the absence or presence of 2,2,2-cryptand yielding complexes with radical anion phosphaalkene fragments. EPR and DFT calculations indicate spin density mostly localised on the P nuclei (67.4%). == Further reading == === Reviews === Marque, Sylvain; Tordo, Paul (2005). "Reactivity of Phosphorus Centered Radicals". New Aspects in Phosphorus Chemistry V. Topics in Current Chemistry. Vol. 250. pp. 43–76. doi:10.1007/b100981. ISBN 978-3-540-22498-3. Armstrong, A.; Chivers, T.; Boeré, R. T. (2005). "The Diversity of Stable and Persistent Phosphorus-Containing Radicals". Modern Aspects of Main Group Chemistry. ACS Symposium Series. Vol. 917. pp. 66–80. doi:10.1021/bk-2005-0917.ch005. ISBN 9780841239265. Das, Bindusagar; Makol, Abhishek; Kundu, Subrata (2022). "Phosphorus radicals and radical ions". Dalton Transactions. 51 (33): 12404–12426. doi:10.1039/D2DT01499H. PMID 35920252. S2CID 250659955. === Reactivity === Leca, Dominique; Fensterbank, Louis; Lacôte, Emmanuel; Malacria, Max (2005). "Recent advances in the use of phosphorus-centered radicals in organic chemistry". Chemical Society Reviews. 34 (10): 858–865. doi:10.1039/b500511f. PMID 16172675. Marque, Sylvain; Tordo, Paul (2005). "Reactivity of Phosphorus Centered Radicals". New Aspects in Phosphorus Chemistry V. Topics in Current Chemistry. Vol. 250. pp. 43–76. doi:10.1007/b100981. ISBN 978-3-540-22498-3. Ren, Wei; Yang, Qiang; Yang, Shang-Dong (2019). "Applications of transition metal catalyzed P-radical for synthesis of organophosphorus compounds". Pure and Applied Chemistry. 91: 87–94. doi:10.1515/pac-2018-0919. S2CID 104379013. === Potential applications === Cataldo, Laurent; Dutan, Cosmina; Misra, Sushil K.; Loss, Sandra; Grützmacher, Hansjörg; Geoffroy, Michel (2005). "Using the Diphosphanyl Radical as a Potential Spin Label:
|
{
"page_id": 72418328,
"source": null,
"title": "Stable phosphorus radicals"
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Effect of Motion on the EPR Spectrum of an R1(R2)PPR1 Radical". Chemistry - A European Journal. 11 (11): 3463–3468. doi:10.1002/chem.200401276. PMID 15818567. S2CID 1128664. == References ==
|
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"page_id": 72418328,
"source": null,
"title": "Stable phosphorus radicals"
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In statistical mechanics of continuous systems, a potential for a many-body system is called H-stable (or simply stable) if the potential energy per particle is bounded below by a constant that is independent of the total number of particles. In many circumstances, if a potential is not H-stable, it is not possible to define a grand canonical partition function in finite volume, because of catastrophic configurations with infinite particles located in a finite space. == Classical statistical mechanics == === Definition === Consider a system of particles in positions x 1 , x 2 , … ∈ R ν {\displaystyle x_{1},x_{2},\ldots \in R^{\nu }} ; the interaction or potential between a particle in position x i {\displaystyle x_{i}} and a particle in position x j {\displaystyle x_{j}} is ϕ ( x i − x j ) {\displaystyle \phi (x_{i}-x_{j})\,} where ϕ ( x ) {\displaystyle \phi (x)} is a real, even (possibly unbounded) function. Then ϕ ( x ) {\displaystyle \phi (x)} is H-stable if there exists B > 0 {\displaystyle B>0} such that, for any n ≥ 1 {\displaystyle n\geq 1} and any x 1 , x 2 , … , x n ∈ R ν {\displaystyle x_{1},x_{2},\ldots ,x_{n}\in R^{\nu }} , V n ( x 1 , x 2 , … x n ) := ∑ i < j = 1 n ϕ ( x i − x j ) ≥ − B n {\displaystyle V_{n}(x_{1},x_{2},\ldots x_{n}):=\sum _{i<j=1}^{n}\phi (x_{i}-x_{j})\geq -Bn\,} === Applications === If ϕ ( 0 ) < ∞ {\displaystyle \phi (0)<\infty } and, for every n ≥ 1 {\displaystyle n\geq 1} and every x 1 , x 2 , … x n ∈ R ν {\displaystyle x_{1},x_{2},\ldots x_{n}\in R^{\nu }} , it holds ∑ i , j = 1 n ϕ ( x i − x
|
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"page_id": 26412061,
"source": null,
"title": "H-stable potential"
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j ) ≥ 0 {\displaystyle \sum _{i,j=1}^{n}\phi (x_{i}-x_{j})\geq 0} then the potential ϕ ( x ) {\displaystyle \phi (x)} is stable (with the constant B {\displaystyle B} given by ϕ ( 0 ) 2 {\displaystyle {\frac {\phi (0)}{2}}} ). This condition applies for example to potentials that are: a) positive functions; b) positive-definite functions. If the potential ϕ ( x ) {\displaystyle \phi (x)} is stable, then, for any bounded domain Λ {\displaystyle \Lambda } , any β > 0 {\displaystyle \beta >0} and z > 0 {\displaystyle z>0} , the series ∑ n ≥ 1 z n n ! ∫ Λ n d x 1 ⋯ d x n exp [ − β V n ( x 1 , x 2 , … x n ) ] {\displaystyle \sum _{n\geq 1}{\frac {z^{n}}{n!}}\int _{\Lambda ^{n}}\!dx_{1}\cdots dx_{n}\;\exp[-\beta V_{n}(x_{1},x_{2},\ldots x_{n})]} is convergent. In fact, for bounded, upper-semi-continuous potentials the hypothesis is not only sufficient, but also necessary! The grand canonical partition function, in finite volume, is Ξ ( β , z , Λ ) := 1 + ∑ n ≥ 1 z n n ! ∫ Λ n d x 1 ⋯ d x n exp [ − β V n ( x 1 , x 2 , … x n ) ] {\displaystyle \Xi (\beta ,z,\Lambda ):=1+\sum _{n\geq 1}{\frac {z^{n}}{n!}}\int _{\Lambda ^{n}}\!dx_{1}\cdots dx_{n}\;\exp[-\beta V_{n}(x_{1},x_{2},\ldots x_{n})]} hence the H-stability is a sufficient condition for the partition function to exists in finite volume. H-stability doesn't necessary imply the existence of the infinite volume pressure. For example, in a Coulomb system (in dimension three) the potential is ϕ ( x ) = 1 4 π | x | {\displaystyle \phi (x)={\frac {1}{4\pi |x|}}} and, if the charges of all the particles are equal, then the potential energy is V n ( x
|
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"page_id": 26412061,
"source": null,
"title": "H-stable potential"
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1 , … , x n ) = ∑ i < j ϕ ( x i − x j ) {\displaystyle V_{n}(x_{1},\ldots ,x_{n})=\sum _{i<j}\phi (x_{i}-x_{j})} and the system is H-stable with B = 0 {\displaystyle B=0} ; but the thermodynamic limit doesn't exist, because the potential is not tempered. If the potential is not bounded, H-stability is not a necessary condition for the existence of the grand canonical partition function in finite volume. For example, in the case of Yukawa interaction in two dimensions, ϕ ( x ) ∼ − 1 2 π ln m | x | f o r x ∼ 0 {\displaystyle \phi (x)\sim -{\frac {1}{2\pi }}\ln {m|x|}\qquad {\rm {for}}\quad x\sim 0} if the particles can have charges with different signs, the potential energy is H n ( q _ , x _ ) = ∑ i < j q i q j ϕ ( x i − x j ) {\displaystyle H_{n}({\underline {q}},{\underline {x}})=\sum _{i<j}q_{i}q_{j}\phi (x_{i}-x_{j})} where q j {\displaystyle q_{j}} is the charge of the particle j {\displaystyle j} . H n ( q _ , x _ ) {\displaystyle H_{n}({\underline {q}},{\underline {x}})} in not bounded from below: for example, when n = 2 {\displaystyle n=2} and q 1 q 2 = 1 {\displaystyle q_{1}q_{2}=1} , the two body potential has infimum inf x 1 , x 2 ϕ ( x 1 − x 2 ) = − ∞ {\displaystyle \inf _{x_{1},x_{2}}\phi (x_{1}-x_{2})=-\infty } Yet, Frohlich proved the existence of the thermodynamics limit for β < 4 π {\displaystyle \beta <4\pi } . == Quantum statistical mechanics == The notion of H-stability in quantum mechanics is more subtle. While in the classical case the kinetic part of the Hamiltonian is not important as it can be zero independently of the position of the particles,
|
{
"page_id": 26412061,
"source": null,
"title": "H-stable potential"
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in the quantum case the kinetic term plays an important role in the lower bound for the total energy because of the uncertainty principle. (In fact, stability of matter was the historical reason for introducing such a principle in mechanics.) The definition of stability is : ∃ B : E 0 N > − B , {\displaystyle \exists B:{\frac {E_{0}}{N}}>-B,\,} where E0 is the ground state energy. Classical H-stability implies quantum H-stability, but the converse is false. The criterion is especially useful in statistical mechanics, where H-stability is necessary to the existence of thermodynamics, i.e. if a system is not H-stable, the thermodynamic limit does not exist. == References == J.L. Lebowitz and Elliott H. Lieb [1] (Physical Review Letters, 1969)
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{
"page_id": 26412061,
"source": null,
"title": "H-stable potential"
}
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In population ecology, density-dependent processes occur when population growth rates are regulated by the density of a population. This article will focus on density dependence in the context of macroparasite life cycles. == Positive density-dependence == Positive density-dependence, density-dependent facilitation, or the Allee effect describes a situation in which population growth is facilitated by increased population density. === Examples === In dioecious (separate sex) obligatory parasites, mated female worms are required to complete a transmission cycle. At low parasite densities, the probability of a female worm encountering a male worm and forming a mating pair can become so low that reproduction is restricted due to single sex infections. At higher parasite densities, the probability of mating pairs forming and successful reproduction increases. This has been observed in the population dynamics of Schistosomes. Positive density-dependence processes occur in macroparasite life cycles that rely on vectors with a cibarial armature, such as Anopheles or Culex mosquitoes. For Wuchereria bancrofti, a filarial nematode, well-developed cibarial armatures in vectors can damage ingested microfilariae and impede the development of infective L3 larvae. At low microfilariae densities, most microfilariae can be ruptured by teeth, preventing successful development of infective L3 larvae. As more larvae are ingested, the ones that become entangled in the teeth may protect the remaining larvae, which are then left undamaged during ingestion. Positive density-dependence processes may also occur in macroparasite infections that lead to immunosuppression. Onchocerca volvulus infection promotes immunosuppressive processes within the human host that suppress immunity against incoming infective L3 larvae. This suppression of anti-parasite immunity causes parasite establishment rates to increase with higher parasite burden. == Negative density-dependence == Negative density-dependence, or density-dependent restriction, describes a situation in which population growth is curtailed by crowding, predators and competition. In cell biology, it describes the reduction in cell division. When
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"page_id": 11797534,
"source": null,
"title": "Density dependence"
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|
a cell population reaches a certain density, the amount of required growth factors and nutrients available to each cell becomes insufficient to allow continued cell growth. This is also true for other organisms because an increased density means an increase in intraspecific competition. Greater competition means an individual has a decreased contribution to the next generation i.e. offspring. Density-dependent mortality can be overcompensating, undercompensating or exactly compensating. There also exists density-independent inhibition, where other factors such as weather or environmental conditions and disturbances may affect a population's carrying capacity. An example of a density-dependent variable is crowding and competition. === Examples === Density-dependent fecundity exists, where the birth rate falls as competition increases. In the context of gastrointestinal nematodes, the weight of female Ascaris lumbricoides and its rates of egg production decrease as host infection intensity increases. Thus, the per-capita contribution of each worm to transmission decreases as a function of infection intensity. Parasite-induced vector mortality is a form of negative density-dependence. The Onchocerciasis life cycle involves transmission via a black fly vector. In this life-cycle, the life expectancy of the black fly vector decreases as the worm load ingested by the vector increases. Because O. volvulus microfilariae require at least seven days to mature into infective L3 larvae in the black fly, the worm load is restricted to levels that allow the black fly to survive for long enough to pass infective L3 larvae onto humans. == In macroparasite life cycles == In macroparasite life cycles, density-dependent processes can influence parasite fecundity, survival, and establishment. Density-dependent processes can act across multiple points of the macroparasite life cycle. For filarial worms, density-dependent processes can act at the host/vector interface or within the host/vector life-cycle stages. At the host/vector interface, density-dependence may influence the input of L3 larvae into the host's
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{
"page_id": 11797534,
"source": null,
"title": "Density dependence"
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|
skin and the ingestion of microfilariae by the vector. Within the life-cycle stages taking place in the vector, density-dependence may influence the development of L3 larvae in vectors and vector life expectancy. Within the life-cycle stages taking place in the host, density-dependence may influence the development of microfilariae and host life expectancy. In reality, combinations of negative (restriction) and positive (facilitation) density-dependent processes occur in the life cycles of parasites. However, the extent to which one process predominates over the other vary widely according to the parasite, vector, and host involved. This is illustrated by the W. bancrofti life cycle. In Culex mosquitoes, which lack a well-developed cibarial armature, restriction processes predominate. Thus, the number of L3 larvae per mosquito declines as the number of ingested microfilariae increases. Conversely, in Aedes and Anopheles mosquitoes, which have well-developed cibarial armatures, facilitation processes predominate. Consequently, the number of L3 larvae per mosquito increases as the number of ingested microfilariae increases. == Implications for parasite persistence and control == Negative density-dependent (restriction) processes contribute to the resilience of macroparasite populations. At high parasite populations, restriction processes tend to restrict population growth rates and contribute to the stability of these populations. Interventions that lead to a reduction in parasite populations will cause a relaxation of density-dependent restrictions, increasing per-capita rates of reproduction or survival, thereby contributing to population persistence and resilience. Contrariwise, positive density-dependent or facilitation processes make elimination of a parasite population more likely. Facilitation processes cause the reproductive success of the parasite to decrease with lower worm burden. Thus, control measures that reduce parasite burden will automatically reduce per-capita reproductive success and increase the likelihood of elimination when facilitation processes predominate. === Extinction threshold === The extinction threshold refers to minimum parasite density level for the parasite to persist in a population.
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{
"page_id": 11797534,
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"title": "Density dependence"
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Interventions that reduce parasite density to a level below this threshold will ultimately lead to the extinction of that parasite in that population. Facilitation processes increase the extinction threshold, making it easier to achieve using parasite control interventions. Conversely, restriction processes complicates control measures by decreasing the extinction threshold. == Implications for parasite distribution == Anderson and Gordon (1982) propose that the distribution of macroparasites in a host population is regulated by a combination of positive and negative density-dependent processes. In overdispersed distributions, a small proportion of hosts harbour most of the parasite population. Positive density-dependent processes contribute to overdispersion of parasite populations, whereas negative density-dependent processes contribute to underdispersion of parasite populations. As mean parasite burden increases, negative density-dependent processes become more prominent and the distribution of the parasite population tends to become less overdispersed. Consequently, interventions that lead to a reduction in parasite burden will tend to cause the parasite distribution to become overdispersed. For instance, time-series data for Onchocerciasis infection demonstrates that 10 years of vector control lead to reduced parasite burden with a more overdispersed distribution. == See also == Frequency-dependent selection Plant density == References == == External links == Density dependence Eradicability of filarial diseases
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{
"page_id": 11797534,
"source": null,
"title": "Density dependence"
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In molecular biology, mir-281 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms. mir-281 is found in an intron of the Drosophila ornithine decarboxylase antizyme (ODA) gene. Using the RACE technique the pri-miRNA was shown to be 2,149 nucleotides in length. The expression level of the microRNA was found to be independent of the level of ODA. == See also == MicroRNA == References == == External links == Page for mir-281 microRNA precursor family at Rfam
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{
"page_id": 36373535,
"source": null,
"title": "Mir-281 microRNA precursor family"
}
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Elmer Drew Merrill (October 15, 1876 – February 25, 1956) was an American botanist and taxonomist. He spent more than twenty years in the Philippines where he became a recognized authority on the flora of the Asia-Pacific region. Through the course of his career he authored nearly 500 publications, described approximately 3,000 new plant species, and amassed over one million herbarium specimens. In addition to his scientific work he was an accomplished administrator, college dean, university professor and editor of scientific journals. == Early life == Merrill and his twin brother, Dana, were born and raised in East Auburn, Maine, the youngest of six children born to Daniel C. and Mary (Noyes) Merrill. Merrill showed an early interest in natural history, collecting and identifying plants, birds' eggs, rocks, and minerals. In 1894 he entered the University of Maine with the intention of studying engineering but soon switched to a general science curriculum where he focused on the biology and classification of flowering plants. He was the valedictorian of his graduation class in 1898 and then stayed on for an additional year working as an assistant in the Department of Natural Science. During his time in college Merrill built a sizable herbarium of almost 2,000 specimens which he eventually donated to the New England Botanical Club. In 1899 Merrill accepted a position with the United States Department of Agriculture in Washington D.C. as an assistant to Frank Lamson-Scribner, an authority on the classification of grasses and a pioneer plant pathologist. At the USDA he learned the principles of plant taxonomy and became proficient in the development and management of a herbarium. His training was supplemented by fieldwork in Idaho, Montana, and Wyoming. == Philippines == At the end of the Spanish–American War, the United States Taft Commission established the Insular Bureau
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"title": "Elmer Drew Merrill"
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of Agriculture in Manila. Merrill was appointed to the post of botanist in the new organization and arrived in 1902 in Manila where he was to work for the next twenty-two years. Merrill was dismayed to discover that the herbarium he was expecting to find had been destroyed during the war, along with the botanical library and scientific equipment. Nevertheless, starting with just an empty building, he set out to rebuild the herbarium and library. Within a few months his role was expanded to include a joint appointment with the Bureau of Forestry. Over the years Merrill's responsibilities continued to grow until he became both the Director of the Bureau of Sciences and a Professor of Botany at the University of the Philippines. He collected and studied plants not only from the Philippines but also from the greater Asia-Pacific region including Indonesia, Malaysia, Indochina, China, and Guam. Eventually the herbarium grew to over 250,000 specimens and the botanical library was recognized as one of the best in Asia. At that time he edited three exsiccata series, the largest with 1200 numbered units under the title Plantae Insularum Philippinensium. Another large series was devoted to plants described by Manuel Blanco Ramos and Antonio Llanos Aller. Merrill published more than 100 taxonomic papers on Philippine flora and several additional papers on the flora of the region. Many of his papers were published in The Philippine Journal of Science, a journal he helped establish and edited from 1907 to 1918. In 1912, he published a 500-page Flora of Manila covering some 1,000 species. In 1921, he completed a Bibliographic Enumeration of Bornean Plants, a volume of 637 pages. His most ambitious work was the Enumeration of Philippine Flowering Plants published in sections between 1923 and 1926. As documented by his Enumeration the list
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"title": "Elmer Drew Merrill"
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of known Philippine species had been extended from 2,500 plants of all types in 1900 to 8,120 species of flowering plants, 1,000 species of ferns, and 3,000 species of cryptogams. == University of California, Berkeley == In 1924 Merrill returned to the United States to join the University of California, Berkeley. There he was appointed Dean of the College of Agriculture and Director of the Agricultural Experiment Station. At Berkeley he led a reorganization of the faculty, revised the curriculum, emphasized academic training of staff, added buildings and equipment, and stressed fundamental research. In 1925, Merrill established the journal Hilgardia, named for Eugene W. Hilgard who organized the Agriculture Department and was the founding director of the Agricultural Experiment Station. During his spare time, Merrill continued to work on systematic botany of the Asia-Pacific flora and added more than 100,000 specimens from that region to the university herbarium. In 1926, a proposal was developed to establish the California Botanic Garden in Los Angeles. Merrill took part-time leave from the college to become director of the Garden Foundation. The plan involved the purchase of 4,500 acres (1,800 ha) at Mandeville Canyon in the Santa Monica Mountains. About 800 acres in the center of the tract were to be developed as a botanical garden financed by the sale of surrounding property for residential homes. During his short tenure as director Merrill built administrative offices and greenhouses, started a library, established an herbarium of 180,000 specimens and planted 1,200 species in the gardens. Unfortunately, not long after Merrill left, the plans collapsed when property prices plummeted as a result of the Great Depression. The herbarium was transferred to the University of California, Los Angeles and the gardens were subdivided and sold for housing. == New York Botanic Garden == In 1929, Merrill accepted
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"title": "Elmer Drew Merrill"
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dual appointments as Director of the New York Botanic Garden and Professor of Botany at Columbia University. He started his new job at the onset of the Great Depression and the Garden was facing severe financial constraints. Despite these difficulties, he was able to continue many of the programs by taking advantage of personnel provided by the Works Progress Administration. Up to 300 personnel were employed building walks, roads, fences and other infrastructure in the gardens; or they worked in the herbarium as mounters, artists, secretaries, librarians, clerks and technicians. The herbarium collection was completely rearranged, operations were improved, and specimens inventoried for the first time. Once the substantial backlog of unmounted material was complete, specimens were mounted for other institutions including the Arnold Arboretum and the Gray Herbarium. In 1931 Merrill established a new journal focused on systematic botany and plant geography, named Brittonia after Nathaniel Lord Britton, a co-founder of the Garden. == Harvard University == In 1935, Merrill left the Botanic Garden and took a job as Administrator of Botanical Collections at Harvard University, a new position created to consolidate the supervision of eight separate Harvard botanical units. A year after his arrival Merrill also became the Arnold Professor of Botany, and in 1937 the Director of the Arnold Arboretum. In his new roles Merrill devoted significant time to expanding the herbarium of the Arnold Arboretum and to research on Asiatic plants. Over the next ten years 220,000 plant specimens were acquired from all parts of Asia and the Asia-Pacific. Meanwhile, Merrill continued to publish numerous papers on Asia flora as well as articles dealing with the cultivation and dispersion of domesticated plants. During the Second World War he consulted with the United States War Department and wrote a handbook, Emergency Food Plants and Poisonous Plants of
|
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"page_id": 5637152,
"source": null,
"title": "Elmer Drew Merrill"
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the Islands of the Pacific. In 1946, at the age of seventy Merrill retired from his administrative duties and became Professor Emeritus in 1948. He continued with his research at Harvard and traveled as much as his age and health would allow. One of his last major contributions was The Botany of Cook's Voyages and its Unexpected Significance in Relation to Anthropology, Biogeography and History, published in 1952. Merrill died on February 25, 1956, in Forest Hills, Massachusetts, aged 79. His library of 2,600 titles was donated to the New York Botanical Garden and a fund was established to award an annual medal to "that individual within the entire field of botany irrespective of race, creed or nationality who was considered worthy of such an award". == Recognition and honors == Merrill was widely recognized for his many accomplishments. He received honorary doctorate degrees from the University of Maine in 1926, Harvard University in 1936, the University of California in 1936, and Yale University in 1951. He was a Guggenheim Fellow for the academic year 1951–1952. At various times he served as President of the Botanical Society of America, Acting President of the American Association for the Advancement of Science, and President of the New England Botanical Club, the American Society of Plant Taxonomists, and the International Union of Biological Sciences. He was a member of the American Academy of Arts and Sciences, the United States National Academy of Sciences, and the American Philosophical Society. Several plant genera; Merrillia (a synonym of Murraya J.Koenig ex L.), Merrillanthus (a synonym of Vincetoxicum Wolf), Merrilliobryum (a genus of moss), Merrilliodendron (the family Icacinaceae), Merrilliopanax (the family Araliaceae), Sinomerrillia (a synonym of Neuropeltis Wall.), and Elmerrillia (a synonym of Magnolia Plum. ex L.). Also over 200 species were named in his honour. ==
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"page_id": 5637152,
"source": null,
"title": "Elmer Drew Merrill"
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Bibliography == A handful of his most notable publications are listed below. A more comprehensive bibliography is contained in Robbins' Biographical Memoir. A Flora of Manila. 1912 An Interpretation of Rumphius's Herbarium Amboinense. 1917 A Bibliographic Enumeration of Bornean Plants. 1921 An Enumeration of Philippine Flowering Plants. 1923-26 An Enumeration of Hainan Plants. 1927 Polynesian Botanical Bibliography (1773-1935). 1937 Emergency Food Plants and Poisonous Plants of the Islands of the Pacific. 1943 A Botanical Bibliography of the Islands of the Pacific. 1946 Botany of Cook's Voyages and Its Unexpected Significance in Relation to Anthropology, Biogeography and History. 1954 == See also == Category:Taxa named by Elmer Drew Merrill == Notes == == References ==
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"page_id": 5637152,
"source": null,
"title": "Elmer Drew Merrill"
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Umbrella sampling is a technique in computational physics and chemistry, used to improve sampling of a system (or different systems) where ergodicity is hindered by the form of the system's energy landscape. It was first suggested by Torrie and Valleau in 1977. It is a particular physical application of the more general importance sampling in statistics. Systems in which an energy barrier separates two regions of configuration space may suffer from poor sampling. In Metropolis Monte Carlo runs, the low probability of overcoming the potential barrier can leave inaccessible configurations poorly sampled—or even entirely unsampled—by the simulation. An easily visualised example occurs with a solid at its melting point: considering the state of the system with an order parameter Q, both liquid (low Q) and solid (high Q) phases are low in energy, but are separated by a free-energy barrier at intermediate values of Q. This prevents the simulation from adequately sampling both phases. Umbrella sampling is a means of "bridging the gap" in this situation. The standard Boltzmann weighting for Monte Carlo sampling is replaced by a potential chosen to cancel the influence of the energy barrier present. The Markov chain generated has a distribution given by π ( r N ) = w ( r N ) exp ( − U ( r N ) k B T ) ∫ w ( r ′ N ) exp ( − U ( r ′ N ) k B T ) d r ′ N , {\displaystyle \pi (\mathbf {r} ^{N})={\frac {w({\textbf {r}}^{N})\exp {\left(-{\frac {U(\mathbf {r} ^{N})}{k_{B}T}}\right)}}{\int {w(\mathbf {r} '^{N})\exp {\left(-{\frac {U(\mathbf {r} '^{N})}{k_{B}T}}\right)}\,d\mathbf {r} '^{N}}}},} with U the potential energy, w(rN) a function chosen to promote configurations that would otherwise be inaccessible to a Boltzmann-weighted Monte Carlo run. In the example above, w may be chosen such
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{
"page_id": 12059679,
"source": null,
"title": "Umbrella sampling"
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that w = w(Q), taking high values at intermediate Q and low values at low/high Q, facilitating barrier crossing. Values for a thermodynamic property A deduced from a sampling run performed in this manner can be transformed into canonical-ensemble values by applying the formula ⟨ A ⟩ = ⟨ A / w ⟩ π ⟨ 1 / w ⟩ π , {\displaystyle \langle A\rangle ={\frac {\langle A/w\rangle _{\pi }}{\langle 1/w\rangle _{\pi }}},} with the π {\displaystyle \pi } subscript indicating values from the umbrella-sampled simulation. The effect of introducing the weighting function w(rN) is equivalent to adding a biasing potential V ( r N ) = − k B T ln w ( r N ) {\displaystyle V(\mathbf {r} ^{N})=-k_{B}T\ln w(\mathbf {r} ^{N})} to the potential energy of the system. If the biasing potential is strictly a function of a reaction coordinate or order parameter Q {\displaystyle Q} , then the (unbiased) free-energy profile on the reaction coordinate can be calculated by subtracting the biasing potential from the biased free-energy profile: F 0 ( Q ) = F π ( Q ) − V ( Q ) , {\displaystyle F_{0}(Q)=F_{\pi }(Q)-V(Q),} where F 0 ( Q ) {\displaystyle F_{0}(Q)} is the free-energy profile of the unbiased system, and F π ( Q ) {\displaystyle F_{\pi }(Q)} is the free-energy profile calculated for the biased, umbrella-sampled system. Series of umbrella sampling simulations can be analyzed using the weighted histogram analysis method (WHAM) or its generalization. WHAM can be derived using the maximum likelihood method. Subtleties exist in deciding the most computationally efficient way to apply the umbrella sampling method, as described in Frenkel and Smit's book Understanding Molecular Simulation. Alternatives to umbrella sampling for computing potentials of mean force or reaction rates are free-energy perturbation and transition interface sampling. A
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"page_id": 12059679,
"source": null,
"title": "Umbrella sampling"
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further alternative, which functions in full non-equilibrium, is S-PRES. == References == == Further reading == Daan Frenkel and Berend Smit: "Understanding Molecular Simulation: From Algorithms to Applications". Academic Press 2001, ISBN 978-0-12-267351-1 Johannes Kästner: “Umbrella Sampling”, WIREs Computational Molecular Science 1, 932 (2011) doi:10.1002/wcms.66
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{
"page_id": 12059679,
"source": null,
"title": "Umbrella sampling"
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Chiral inversion is the process of conversion of one enantiomer of a chiral molecule to its mirror-image version with no other change in the molecule. Chiral inversion happens depending on various factors (viz. biological-, solvent-, light-, temperature- induced, etc.) and the energy barrier energy barrier associated with the stereogenic element present in the chiral molecule. 2-Arylpropionic acid nonsteroidal anti-inflammatory drugs (NSAIDs) provide one of the best pharmaceutical examples of chiral inversion. Chirality is attributed to a molecule due to the presence of a stereogenic element (viz. center, planar, helical, or axis). Many pharmaceutical drugs are chiral and have a labile (configurationally unstable) stereogenic element. Chiral compounds with stereogenic center are found to have high energy barriers for inversion and generally undergo biologically mediated chiral inversion. While compounds with helical or planar chirality have low energy barriers and chiral inversions are often caused by solvent, light, temperature. When this happens, the configuration of the chiral molecule may rapidly change reversibly or irreversibly depending on the conditions. The chiral inversion has been intensively studied in the context of the pharmacological and toxicological consequences. Other than NSAIDs, chiral drugs with different chemical structures can also show this effect. Chiral drugs have different effects on the body depending on whether one enantiomer or both enantiomers act on different biological targets. As a result, chiral inversion can change how a pharmaceutical drug works in the body. From a pharmacological and toxicological point of view, it is very important to learn more about chiral inversion, the things that make it happen, and the tools used to figure out chiral inversion. == Types == Essentially there are two types of chiral inversion, unidirectional and bidirectional. Inversion process is dependent on species and substrate. Unidirectional chiral inversion (enzyme mediated) was described only with 2-arylpropionate nonsteroidal anti-inflammatory drugs (NSAIDs),
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namely ibuprofen, ketoprofen, fenoprofen, benoxaprophen, etc. For this group, only S-enantiomer (eutomer) is active i.e. has analgesic and anti-inflammatory effect. In the body, only inactive R-enantiomer can undergo chiral inversion by hepatic enzymes into the active S-enantiomer and not vice versa. The “inactive” R-isomer (distomer) may be responsible for the gastrointestinal irritation and related side-effects associated with NSAIDs. In certain situations, carbenicillin, ethiazide, etoposide, zopiclone, pantoprazole, clopidogrel, ketorolac, albendazole-sulfoxide, lifibrol, and 5-aryl-thiazolidinedione also go through unidirectional chiral inversion. Chiral inversions were found to happen in a group of important compounds called α-amino acids. Amino acids exist in two mirror-image versions (D- and L- configurations). Several D-amino acids, like D-methionine, D-proline, D-serine, D-alanine, D-aspartate, D-leucine, and D-phenylalanine, have been shown to go through unidirectional chiral inversion in mammals. Bidirectional chiral inversion or racemization type of inversion is shown by pharmaceutical drugs including 3-hydroxy-benzodiazapine class of drugs (oxazepam, lorazepam, temazepam), thalidomide, and tiaprofenic acid. A brief list of select pharmaceutical drugs that go through chiral inversion are presented in Table below.. == Mechanism == It is well documented that (R)-enantiomers of profens in the presence of coenzyme A (CoA), adenosine triphosphate (ATP) and Mg+2 are converted to active (S)-forms. The pathways of chiral inversion is illustrated taking ibuprofen as the prototype, in the scheme below. The pathway consists mainly of three steps: Stereoselective activation: Stereoselective activation of (R)-profen by the formation of the thioester, in the presence of CoA, ATP and Mg+2. (S)-profen does not form the thioester. Epimerization (Racemization): The enzyme epimerase 2-arylpropionic-CoA changes the (R)-thioester to the (S)-thioester. This process is called "racemization" or "epimerization." Hydrolysis: With the help of hydrolase/thioesterase, thioesters are broken down into their (R)- and (S)-forms Because the acyl-CoA thioester (profenyl-CoA) changes the structure of triglycerides and phospholipids, metabolic chiral inversion may cause toxic effects. ==
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"page_id": 67830819,
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"title": "Chiral inversion"
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Factors influencing inversion == Chiral drugs with stereo-labile configuration are likely to undergo interconversion of the enantiomers that may be enzymatic (biological) or non-enzymatic. Enzyme-mediated conversion is the process of chiral inversion that happens in a living organism. Non-enzymatic inversion of drugs is important and relevant in the pharmaceutical manufacturing process. This may have impact on the shelf-life of a drug and the economic feasibility of the resolution. Inversion can also happen without enzymes when precolumn derivatization is used in enantioselective chromatographic separation techniques. Racemization can also happen in the acidic environment of the stomach and other bodily fluids. === Enzyme-mediated (biological) === Enzyme-mediated (biological) chiral inversion of organic compounds is caused by highly chiral endogenous molecules found in receptors, enzymes, and other structures. While enzyme inhibitors suppress enzyme activity, enzyme inducers boost enzyme concentration and activity. The primary determinants of inter-individual variability in drug metabolism in humans are thought to include genetic polymorphism and a variety of other variables, including age, gender, biological conditions, pregnancy, illnesses, stress, nutrition, and drugs. For instance, Reichel et al. reported that a 2-arylpropionyl-coenzyme-A epimerase was molecularly cloned and expressed as a crucial enzyme in the inversion metabolism of ibuprofen. Ibuprofen's chiral inversion by enzymes has been documented in humans. ==== Species differences ==== ==== Tissue variations ==== The liver, gastrointestinal tract (GIT), lungs, kidney, and brain are among the tissues that participate in the chiral inversion of medicines. The liver has been shown to be the most crucial organ in the development of this mechanism. Although some studies contend that rat liver homogenates lack the enzymatic mechanisms necessary to invert the R-enantiomers of flurbiprofen, naproxen, suprofen, and ibuprofen, the liver may also be involved in the inversion of R-ibuprofen in rats. On the other hand, it was noted that certain medicines underwent chiral
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"page_id": 67830819,
"source": null,
"title": "Chiral inversion"
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inversion without the involvement of the liver (hepatocytes). Although liver did not play a substantial role in the inversion of benoxaprofen, studies using benoxaprofen and ketoprofen show that one of the primary sites of inversion in rats is the GI tract. ==== Route of administration ==== ==== Inter-individual variability ==== === Non-enzymatic === ==== Sample handling and manufacturing process ==== ==== Temperature and pH ==== == Analytical methods == Chiral inversion is a very important part of designing and making drugs. Because this process can change how chiral drugs work in the body and can cause side effects that can be serious or even fatal. Traditionally, chiral inversions have been studied with NMR spectroscopy at different temperatures and chiroptical methods like polarimetry. But strong, complementary methods based on dynamic chromatography (GC, HPLC, SFC, CEC, and MEKC) and electrophoresis have been made and used to figure out how the enantiomeric composition of stereo-labile chiral compounds changes over time. Most of the time, liquid chromatographic methods are used to do enantioselective analysis of chiral drugs. When an analyte with one stereogenic center or axis is separated well, the chromatogram will show two peaks. But if the analyte is stereo-labile, the peaks tend to merge. How much coalescence there is will depend on how fast chiral inversion and enantioresolution happen. Over time, the peaks will merge into a flat area. Dynamic chromatography shows how the elution profile changes over time. This makes it useful for figuring out how pH, temperature, and solvents affect chiral inversion, which can happen on the stationary phase, in the injector, or in the detector. Multidimensional approaches have been used to improve separation and detection. Table below shows a list of common methods and experiments used to figure out chiral inversion. Any of these methods can then be used
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{
"page_id": 67830819,
"source": null,
"title": "Chiral inversion"
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|
to determine chiral inversion. Which instrument is used to analyze a chiral compound depends on its physical and chemical properties (i.e., the solubility, vapor pressure, thermal and solvent stability, and detection). For example, capillary electrophoresis or liquid chromatography could be used if the analyte can be ionized and has a high vapor pressure, but it is also soluble in polar solvents. On the other hand, gas chromatography is the best way to test a substance that is stable at high temperatures but has a low vapor pressure. When compared to gas or liquid chromatography, supercritical fluid chromatography is a better way to measure chiral inversion because it uses mass spectrometers and a green method. == Significance in drug development == Enantiomers of a chiral drug often interact in an enantioselective way in a chiral environment. This may be offered by different biotic substances (viz. proteins, nucleic acids, phospholipids and oligosaccharides). They are made up of chiral building blocks that are put together in space in handed conformations. These biological targets function as receptors for the drug enantiomers. So, at the binding sites of these receptors, enantiomers will be seen as different chemical species. The three point attachment model (Easson & Stedman model) can be used to see how chiral discrimination works. Figure depicts how the enantiomers of a drug interact with receptors in a way that depends on the drug's shape. This model was made for chiral drugs with a single stereogenic center. It says that there are three binding sites in the receptor (B', C' and D') that match the drug's pharmacophoric groups (B, C, D). A three-point fit (good fit) is possible for the eutomer at BB', CC' and DD'(Fig. A). Even though the distomer is the wrong enantiomer, it can fit either a one-point interaction (bad fit),
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{
"page_id": 67830819,
"source": null,
"title": "Chiral inversion"
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|
or a two-point attachment (CC' and DD') with the same receptor site as shown in (Fig. B). Eutomer is the version that works the way you want it to, and distomer is the version that doesn't work or works in a way you don't want it to. Most of the time, the mirror-image versions have different binding affinities. In the eutomer, the ligands or moiety around a stereogenic element have more binding energy than in the distomer. When the eutomer goes through chiral inversion, it loses its ability to bind to a biological receptor. Because of these enantiospecific interactions, therapeutic and toxicological properties are enantioselective So, the stereo-stability of chiral drugs may have big effects on the process of making new drugs, especially when it comes to how pharmaceutical, pharmacokinetic, and pharmacodynamic information is read and understood. At every stage of designing, making, and testing a drug for safety, chiral inversion must be taken into account. == See also == Ibuprofen Dexibuprofen Ketoprofen Thalidomide Fenoprofen Chiral drugs Chiral switch == References == == External links == Media related to Chiral inversion at Wikimedia Commons
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{
"page_id": 67830819,
"source": null,
"title": "Chiral inversion"
}
|
Lovelock's theorem of general relativity says that from a local gravitational action which contains only second derivatives of the four-dimensional spacetime metric, then the only possible equations of motion are the Einstein field equations. The theorem was described by British physicist David Lovelock in 1971. == Statement == In four dimensional spacetime, any tensor A μ ν {\displaystyle A^{\mu \nu }} whose components are functions of the metric tensor g μ ν {\displaystyle g^{\mu \nu }} and its first and second derivatives (but linear in the second derivatives of g μ ν {\displaystyle g^{\mu \nu }} ), and also symmetric and divergence-free, is necessarily of the form A μ ν = a G μ ν + b g μ ν {\displaystyle A^{\mu \nu }=aG^{\mu \nu }+bg^{\mu \nu }} where a {\displaystyle a} and b {\displaystyle b} are constant numbers and G μ ν {\displaystyle G^{\mu \nu }} is the Einstein tensor. The only possible second-order Euler–Lagrange expression obtainable in a four-dimensional space from a scalar density of the form L = L ( g μ ν ) {\displaystyle {\mathcal {L}}={\mathcal {L}}(g_{\mu \nu })} is E μ ν = α − g [ R μ ν − 1 2 g μ ν R ] + λ − g g μ ν {\displaystyle E^{\mu \nu }=\alpha {\sqrt {-g}}\left[R^{\mu \nu }-{\frac {1}{2}}g^{\mu \nu }R\right]+\lambda {\sqrt {-g}}g^{\mu \nu }} == Consequences == Lovelock's theorem means that if we want to modify the Einstein field equations, then we have five options. Add other fields rather than the metric tensor; Use more or fewer than four spacetime dimensions; Add more than second order derivatives of the metric; Non-locality, e.g. for example the inverse d'Alembertian; Emergence – the idea that the field equations don't come from the action. == See also == Lovelock theory of gravity Vermeil's
|
{
"page_id": 52823070,
"source": null,
"title": "Lovelock's theorem"
}
|
theorem == References ==
|
{
"page_id": 52823070,
"source": null,
"title": "Lovelock's theorem"
}
|
In molecular biology, mir-282 microRNA is a short RNA molecule. MicroRNAs function to regulate the expression levels of other genes by several mechanisms. == See also == MicroRNA == References == == Further reading == == External links == Page for mir-282 microRNA precursor family at Rfam
|
{
"page_id": 36373543,
"source": null,
"title": "Mir-282 microRNA precursor family"
}
|
The UCL Prize Lecture in Life and Medical Sciences (previously UCL Prize Lecture in Clinical Science) is a prize awarded annually by University College London since 1997. The prize lecture has become the pre-eminent series on contemporary science in Europe and the annual lecture provides an opportunity to debate and celebrate important scientific advancements. == Recipients == 1997 Klaus Rajewsky 1998 Joseph L. Goldstein (Nobel Prize in Medicine 1985) 1999 Stanley B. Prusiner (Nobel Prize in Medicine 1997) 2000 James Watson (Nobel Prize in Medicine 1962) 2001 Judah Folkman 2002 J. Craig Venter 2003 Sydney Brenner (Nobel Prize in Medicine 2002) 2004 Robert Weinberg (Woolf Prize 2004) 2005 Richard Axel (Nobel Prize in Medicine 2004) 2006 Harold Varmus (Nobel Prize in Medicine 1989) 2007 Tadataka Yamada 2008 Susumu Tonegawa (Nobel Prize in Physiology or Medicine 1987) 2009 Martin Evans (Nobel Prize Physiology or Medicine 2007) 2010 Barry Marshall (Nobel Prize in Medicine 2005) 2011 Roger Tsien (Nobel Prize in Chemistry 2008) 2012 Jeffrey Friedman (Albert Lasker Award 2010) 2013 Gary Ruvkun (Louisa Gross Horwitz Prize 2009) 2014 Anthony W. Segal 2015 Sir John Gurdon (Nobel Prize in Physiology or Medicine 2012) 2016 Françoise Barré-Sinoussi (Nobel Prize in Physiology or Medicine 2008) 2017 Patrick Vallance 2018 James P. Allison (Nobel Prize in Physiology or Medicine 2018) 2019 Jennifer Doudna (Nobel Prize in Chemistry 2020) 2020 Ann Graybiel 2023 Demis Hassabis (Nobel Prize in Chemistry 2024) == See also == List of medicine awards List of prizes named after people == References ==
|
{
"page_id": 40043560,
"source": null,
"title": "UCL Prize Lecture in Life and Medical Sciences"
}
|
The molecular formula C7H6O2S may refer to: 4-Mercaptobenzoic acid Thiosalicylic acid
|
{
"page_id": 78906407,
"source": null,
"title": "C7H6O2S"
}
|
Protein–ligand docking is a molecular modelling technique. The goal of protein–ligand docking is to predict the position and orientation of a ligand (a small molecule) when it is bound to a protein receptor or enzyme. Pharmaceutical research employs docking techniques for a variety of purposes, most notably in the virtual screening of large databases of available chemicals in order to select likely drug candidates. There has been rapid development in computational ability to determine protein structure with programs such as AlphaFold, and the demand for the corresponding protein-ligand docking predictions is driving implementation of software that can find accurate models. Once the protein folding can be predicted accurately along with how the ligands of various structures will bind to the protein, the ability for drug development to progress at a much faster rate becomes possible. == History == Computer-aided drug design (CADD) was introduced in the 1980s in order to screen for novel drugs. The underlying premise is that by parsing an extremely large data set for chemical compounds which may be viable to make a certain pharmaceutical, researchers were able to minimize the amount of novel without testing them all experimentally. The ability to accurately predict target binding sites is a new phenomena, however, which expands on the ability to simply parse a data set of chemical compounds; now due to increasing computational capability, it is possible to inspect the actual geometries of the protein-ligand binding site in vitro. Hardware advancements in computation have made these structure-oriented methods of drug discovery the next frontier in the 21st century biopharma. In order to finely train the new algorithms to capture the accurate geometry of the protein-ligand binding capability, an experimentally gathered dataset can be used by applying techniques such as X-ray crystallography or NMR spectroscopy. == Available software == Several
|
{
"page_id": 5702698,
"source": null,
"title": "Protein–ligand docking"
}
|
protein–ligand docking software applications that calculate the site, geometry and energy of small molecules or peptides interacting with proteins are available, such as AutoDock and AutoDock Vina, rDock, FlexAID, Molecular Operating Environment, and Glide. Peptides are a highly flexible type of ligand that has proven to be a difficult type of structure to predict in protein bonding programs. DockThor implements up to 40 rotatable bonds to help model these complex physicochemical bindings at the target site. Root Mean Square Deviation is the standard method of evaluating various software performance within the binding mode of the protein-ligand structure. Specifically, it is the root-mean-squared deviation between the software-predicted docking pose of the ligand and the experimental binding mode. The RMSD measurement is computed for all of the computer-generated poses of the possible bindings between the protein and ligand. The program does not always perfectly predict the actual physical pose when evaluating the RMSD between candidates. In order to then evaluate the strength of a computer algorithm to predict protein docking, the ranking of RMSD among computer-generated candidates must be examined to determine whether the experimental pose actually was generated but not selected. == Protein flexibility == Computational capacity has increased dramatically over the last two decades making possible the use of more sophisticated and computationally intensive methods in computer-assisted drug design. However, dealing with receptor flexibility in docking methodologies is still a thorny issue. The main reason behind this difficulty is the large number of degrees of freedom that have to be considered in this kind of calculations. However, in most of the cases, neglecting it leads to poor docking results in terms of binding pose prediction in real-world settings. Using coarse grained protein models to overcome this problem seems to be a promising approach. Coarse-grained models are often implemented in the
|
{
"page_id": 5702698,
"source": null,
"title": "Protein–ligand docking"
}
|
case of protein-peptide docking, as they frequently involve large-scale conformation transitions of the protein receptor. AutoDock is one of the computational tools frequently used to model the interactions between proteins and ligands during the drug discovery process. Although the classically used algorithms to search for effective poses often assume the receptor proteins to be rigid while the ligand is moderately flexible, newer approaches are implementing models with limited receptor flexibility as well. AutoDockFR is a newer model that is able to simulate this partial flexibility within the receptor protein by letting side-chains of the protein to take various poses among their conformational space. This allows the algorithm to explore a vastly larger space of energetically relevant poses for each ligand tested. In order to simplify the complexity of the search space for prediction algorithms, various hypotheses have been tested. One such hypothesis is that side-chain conformational changes that contain more atoms and rotations of greater magnitude are actually less likely to occur than the smaller rotations due to the energy barriers that arise. Steric hindrance and rotational energy cost that are introduced with these larger changes made it less likely that they were included in the actual protein-ligand pose. Findings such as these can make it easier for scientists to develop heuristics that can lower the complexity of the search space and improve the algorithms. == Implementations == The original method of testing the molecular models of various binding sites was introduced in the 1980s where the receptor was estimated in a rough manner by spheres which occupied the surface clefts. The ligand was approximated by more spheres which would occupy the relevant volume. Then a search was executed for maximizing the steric overlap between the spheres of both the binding and receptor spheres. However, the new scoring functions to
|
{
"page_id": 5702698,
"source": null,
"title": "Protein–ligand docking"
}
|
evaluate molecular dynamics and protein-ligand docking potential are implementing supervised molecular dynamic approach. Essentially, the simulations are sequences of small time windows by which the distance between the center of mass of the ligand and protein is computed. The distance values are updated at regular frequencies and then regressively fitted linearly. When the slope is negative, the ligand is getting nearer to the binding site, and vice versa. When the ligand is departing from the binding site, the tree of possibilities is pruned right at that moment so as to avoid unnecessary computation. The advantage of this method is speed without the introduction of any energetic bias which could foul the model from accurate mappings to the experimental truths. == See also == Docking (molecular) Protein–protein docking Virtual screening List of protein-ligand docking software == References == == External links == BioLiP, a comprehensive ligand-protein interaction database DockThor
|
{
"page_id": 5702698,
"source": null,
"title": "Protein–ligand docking"
}
|
The Reed reaction is a chemical reaction that utilizes light to oxidize hydrocarbons to alkylsulfonyl chlorides. This reaction is employed in modifying polyethylene to give chlorosulfonated polyethylene (CSPE), which is noted for its toughness. == Commercial implementations == Polyethylene is treated with a mixture of chlorine and sulfur dioxide under UV-radiation. Vinylsulfonic acid can also be prepared beginning with the sulfochlorination of chloroethane. Dehydrohalogenation of the product gives vinylsulfonyl chloride, which subsequently is hydrolyzed to give vinylsulfonic acid: ClCH2CH3 + SO2 + Cl2 → ClCH2CH2SO2Cl + HCl ClCH2CH2SO2Cl → H2C=CHSO2Cl + HCl CH2=CHSO2Cl + H2O → H2C=CHSO3H + HCl == Mechanism == The reaction occurs via a free radical mechanism. UV-light initiates homolysis of chlorine, producing a pair of chlorine atoms: Chain initiation: Cl 2 → h ν 2 Cl ⋅ {\displaystyle {\ce {Cl2 ->[h\nu] 2Cl.}}} Thereafter a chlorine atom attacks the hydrocarbon chain, freeing hydrogen to form hydrogen chloride and an alkyl free radical. The resulting radical then captures SO2. The resulting sulfonyl radical attacks another chlorine molecule to produce the desired sulfonyl chloride and a new chlorine atom, which continues the reaction chain. Chain propagation steps: R − H + ⋅ Cl ⟶ R ⋅ + HCl {\displaystyle {\ce {{R-H}+ .Cl -> {R.}+ HCl}}} R ⋅ + : SO 2 ⟶ R − S ˙ O 2 {\displaystyle {\ce {{R.}+{:}SO2->R-{\dot {S}}O2}}} R − S ˙ O 2 + Cl 2 ⟶ R − SO 2 − Cl + Cl ⋅ {\displaystyle {\ce {{R-{\dot {S}}O2}+Cl2->{R-SO2-Cl}+Cl.}}} == See also == Chain reaction == Historical readings == Reed, C. F. U.S. patent 2,046,090; U.S. patent 2,174,110; U.S. patent 2,174,492. Asinger, Friedrich; Schmidt, Walter; Ebeneder, Franz (1942). "Zur Kenntnis der Produkte der gemeinsamen Einwirkung von Schwefeldioxyd und Chlor auf aliphatische Kohlenwasserstoffe im ultravioletten Licht, I. Mitteil.: Die Produkte der gemeinsamen Einwirkung von
|
{
"page_id": 3146792,
"source": null,
"title": "Reed reaction"
}
|
Schwefeldioxyd und Chlor auf Propan in Tetrachlorkohlen". Berichte der Deutschen Chemischen Gesellschaft (A and B Series). 75: 34–41. doi:10.1002/cber.19420750105. Asinger, Friedrich; Ebeneder, Franz; Böck, Erich (1942). "Zur Kenntnis der Produkte der gemeinsamen Einwirkung von Schwefeldioxyd und Chlor auf aliphatische Kohlenwasserstoffe im ultravioletten Licht, II. Mitteil.: Die Produkte der gemeinsamen Einwirkung von Schwefeldioxyd und Chlor auf n-Butan in Tetrachlorkohl". Berichte der Deutschen Chemischen Gesellschaft (A and B Series). 75: 42–48. doi:10.1002/cber.19420750106. Asinger, Friedrich; Ebeneder, Franz (1942). "Zur Kenntnis der Produkte der gemeinsamen Einwirkung von Schwefeldioxyd und Chlor auf aliphatische Kohlenwasserstoffe im ultravioletten Licht, III. Mitteilung† : Über die Sulfochlorierung von Isobutan und die Isomerenbildung bei der Sulfochlorierung und Chlorierung gasförmiger Kohlenwasserstoffe". Berichte der Deutschen Chemischen Gesellschaft (A and B Series). 75 (4): 344–349. doi:10.1002/cber.19420750408. ISSN 1099-0682. Retrieved 2023-02-22. Helberger, J. H.; Manecka, G.; Fischer, H. M. (1949). "Zur Kenntnis organischer Sulfonsäuren. II. Mitt.: Die Sulfochlorierung des 1-Chlorbutans und anderer Halogenalkyle; Synthese von Sultonen und eines Sultams". Justus Liebigs Annalen der Chemie. 562: 23–35. doi:10.1002/jlac.19495620104. == References ==
|
{
"page_id": 3146792,
"source": null,
"title": "Reed reaction"
}
|
A phageome is a community of bacteriophages and their metagenomes localized in a particular environment, similar to a microbiome. Phageome is a subcategory of virome, which is all of the viruses that are associated with a host or environment. The term was first used in an article by Modi et al. in 2013 and has continued to be used in scientific articles that relate to bacteriophages and their metagenomes. A bacteriophage, or phage for short, is a virus that can infect bacteria and archaea, and can replicate inside of them. Phages make up the majority of most viromes and are currently understood as being the most abundant organism. Oftentimes scientists will look only at a phageome instead of a virome while conducting research. Variations due to many factors have also been explored such as diet, age, and geography. The phageome has been studied in humans in connection with a wide range of disorders of the human body, including IBD, IBS, and colorectal cancer. == In humans == Although bacteriophages cannot infect human cells, they are found in abundance in the human virome. Phageome research in humans has largely focused on the gut, however it is also being investigated in other areas like the skin, blood, and mouth. The composition of phages that make up a healthy human gut phageome is currently debated, since different methods of research can lead to different results. At birth, the human phageome, and the overall virome in general, is almost non-existent. The human phageome is thought to be brought about in newborns through prophage induction of bacteria passed on from the mother vaginally during birth. However, phages can be introduced through breastfeeding, made evident through studies finding near-exact matches of crAssphage sequences between mother and child. Variations in the human gut phageome continue across the
|
{
"page_id": 71697452,
"source": null,
"title": "Phageome"
}
|
lifespan. Siphoviridae and Myoviridae are the most abundant in infants and their numbers wane into childhood, whereas Crassvirales dominate in adults. The phageome can also experience changes as a result of diet, which can introduce new phages present in our foods. For example, in those with gluten-free diets, crAssphage were noted in higher abundance along with decreases in the families of Podoviridae. Global geographical differences in phageome composition have been noted, with further variation found within individuals living in rural and urban locations. For instance, residents in Hong Kong, China were found to have less phages associated with targeting pathogenic bacteria in comparison to those in Yunnan province. Furthermore, residing for longer periods of time in urban regions correlated with increases of Lactobacillus and Lactococcus phages. === In disease === Changes in the phageome have been seen in various disorders affecting the human body. In the gut, unique changes in the phageome have been described in both inflammatory bowel disease and irritable bowel syndrome. Even further specific changes exist in subtypes of the two disorders. IBS subtypes of IBS-D and IBS-C saw increases in different species belonging to Microviridae and Myoviridae. In Ulcerative colitis and Crohn's disease, which are subtypes of IBD, differences in levels of Caudovirales richness and species have been found. Furthermore, phages that target Acinetobacter have been found in the blood of patients with Crohn's disease. This is thought to occur due to the compromised, inflamed gut barrier allowing for bacteriophage transfer. In the mouth, periodontitis has been associated with Myoviridae residing under the gums along with a currently unspecified bacteriophage in the Siphoviridae family. Phageome changes have also been described in metabolic disorders including type-1 diabetes, type-2 diabetes and metabolic syndrome. In type-1 diabetes, overall shifts have been seen in Myoviridae and Podoviridae. The genome of
|
{
"page_id": 71697452,
"source": null,
"title": "Phageome"
}
|
bacteriophages residing in the gut in Type-2 diabetes patients have been shown to contain numerous genes implicated in disease development. Total phage representation in the virome is higher in individuals with Cardiovascular disease than healthy controls, totaling 63% and 18% respectively. Lastly, researchers studying Colorectal cancer have observed increased richness in a variety of phage genera, with the most notable differences seen in Inovirus and Tunalikevirus. == See also == Virosphere == References ==
|
{
"page_id": 71697452,
"source": null,
"title": "Phageome"
}
|
In statistics, path analysis is used to describe the directed dependencies among a set of variables. This includes models equivalent to any form of multiple regression analysis, factor analysis, canonical correlation analysis, discriminant analysis, as well as more general families of models in the multivariate analysis of variance and covariance analyses (MANOVA, ANOVA, ANCOVA). In addition to being thought of as a form of multiple regression focusing on causality, path analysis can be viewed as a special case of structural equation modeling (SEM) – one in which only single indicators are employed for each of the variables in the causal model. That is, path analysis is SEM with a structural model, but no measurement model. Other terms used to refer to path analysis include causal modeling and analysis of covariance structures. Path analysis is considered by Judea Pearl to be a direct ancestor to the techniques of causal inference. == History == Path analysis was developed around 1918 by geneticist Sewall Wright, who wrote about it more extensively in the 1920s. It has since been applied to a vast array of complex modeling areas, including biology, psychology, sociology, and econometrics. == Path modeling == Typically, path models consist of independent and dependent variables depicted graphically by boxes or rectangles. Variables that are independent variables, and not dependent variables, are called 'exogenous'. Graphically, these exogenous variable boxes lie at outside edges of the model and have only single-headed arrows exiting from them. No single-headed arrows point at exogenous variables. Variables that are solely dependent variables, or are both independent and dependent variables, are termed 'endogenous'. Graphically, endogenous variables have at least one single-headed arrow pointing at them. In the model below, the two exogenous variables (Ex1 and Ex2) are modeled as being correlated as depicted by the double-headed arrow. Both of
|
{
"page_id": 590893,
"source": null,
"title": "Path analysis (statistics)"
}
|
these variables have direct and indirect (through En1) effects on En2 (the two dependent or 'endogenous' variables/factors). In most real-world models, the endogenous variables may also be affected by variables and factors stemming from outside the model (external effects including measurement error). These effects are depicted by the "e" or error terms in the model. Using the same variables, alternative models are conceivable. For example, it may be hypothesized that Ex1 has only an indirect effect on En2, deleting the arrow from Ex1 to En2; and the likelihood or 'fit' of these two models can be compared statistically. == Path tracing rules == In order to validly calculate the relationship between any two boxes in the diagram, Wright (1934) proposed a simple set of path tracing rules, for calculating the correlation between two variables. The correlation is equal to the sum of the contribution of all the pathways through which the two variables are connected. The strength of each of these contributing pathways is calculated as the product of the path-coefficients along that pathway. The rules for path tracing are: You can trace backward up an arrow and then forward along the next, or forwards from one variable to the other, but never forward and then back. Another way to think of this rule is that you can never pass out of one arrow head and into another arrowhead: tails-tails, heads-tails, or tails-heads, but not heads-heads. You can pass through each variable only once in a given chain of paths. No more than one bi-directional arrow can be included in each path-chain. Again, the expected correlation due to each chain traced between two variables is the product of the standardized path coefficients, and the total expected correlation between two variables is the sum of these contributing path-chains. NB: Wright's rules
|
{
"page_id": 590893,
"source": null,
"title": "Path analysis (statistics)"
}
|
assume a model without feedback loops: the directed graph of the model must contain no cycles, i.e. it is a directed acyclic graph, which has been extensively studied in the causal analysis framework of Judea Pearl. === Path tracing in unstandardized models === If the modeled variables have not been standardized, an additional rule allows the expected covariances to be calculated as long as no paths exist connecting dependent variables to other dependent variables. The simplest case obtains where all residual variances are modeled explicitly. In this case, in addition to the three rules above, calculate expected covariances by: Compute the product of coefficients in each route between the variables of interest, tracing backwards, changing direction at a two-headed arrow, then tracing forwards. Sum over all distinct routes, where pathways are considered distinct if they contain different coefficients, or encounter those coefficients in a different order. Where residual variances are not explicitly included, or as a more general solution, at any change of direction encountered in a route (except for at two-way arrows), include the variance of the variable at the point of change. That is, in tracing a path from a dependent variable to an independent variable, include the variance of the independent-variable except where so doing would violate rule 1 above (passing through adjacent arrowheads: i.e., when the independent variable also connects to a double-headed arrow connecting it to another independent variable). In deriving variances (which is necessary in the case where they are not modeled explicitly), the path from a dependent variable into an independent variable and back is counted once only. == See also == Bayesian network Causality Causal loop diagram Hidden Markov model Latent variable model Path coefficient Structural equation model (SEM) == References == == External links == Ωnyx, a free software environment for
|
{
"page_id": 590893,
"source": null,
"title": "Path analysis (statistics)"
}
|
Structural Equation Modeling OpenMx - Advanced Structural Equation Modeling LISREL: model, methods and software for Structural Equation Modeling
|
{
"page_id": 590893,
"source": null,
"title": "Path analysis (statistics)"
}
|
Marine pharmacognosy is the investigation and identification of medically important plants and animals in the marine environment. It is a sub branch of terrestrial pharmacognosy. Generally the drugs are obtained from the marine species of bacteria, virus, algae, fungi and sponges. It is a relatively new field of study in western medicine, although many marine organisms were used in traditional Chinese medicine. It was not until 2004 that the first FDA approval of a drug came directly from the sea: ziconotide, which was isolated from a marine cone snail. With 79% of the Earth's surface covered by water, research into the chemistry of marine organisms is relatively unexplored and represents a vast resource for new medicines to combat major diseases such as cancer, AIDS or malaria. Research typically focuses on sessile organisms or slow moving animals because of their inherent need for chemical defenses. Standard research involves an extraction of the organism in a suitable solvent followed by either an assay of this crude extract for a particular disease target or a rationally guided isolation of new chemical compounds using standard chromatography techniques. == Marine organisms as sources of natural products == Over 70% of the Earth's surface is covered by oceans which contain 95% of the Earth's biosphere. It was over 3500 million years ago that organisms first appeared in the sea. Over time, they have evolved many different mechanisms to survive the various harsh environments which include extreme temperatures, salinity, pressure, different levels of aeration and radiation, overcoming effects of mutation, and combating infection, fouling and overgrowth by other organisms. Adaptations to survive the different environments could be by physical or chemical adaptation. Organisms with no apparent physical defense, like sessile organisms, are believed to have evolved chemical defenses to protect themselves. It is also believed that the
|
{
"page_id": 12715053,
"source": null,
"title": "Marine pharmacognosy"
}
|
compounds would have to be extremely potent due to the dilution effect of seawater. This has been described to be analogues to pheromones but with the purpose of repelling instead of attracting. As well, predators have evolved chemical weapons in order to paralyze or kill prey. Conus magus is an example of a cone snail that has a poisoned harpoon-like projectile which it uses to paralyze prey like small fish. Some organisms, like the Viperfish, are believed to attract small fish or prey by using its photophore. Many different marine organisms have been explored for bioactive compounds. Some vertebrate animals include fish, sharks and snakes. Some examples of invertebrates are sponges, coelenterates, tunicates, echinoderms, corals, algae, molluscs and bryozoans. Some microorganisms include bacteria, fungi and cyanobacteria. == True producer == There is an ongoing debate on what organisms are the actual true producers of some compounds. About 40% of the biomass of sponges can be from microorganisms. It's not surprising that some compounds may actually be produced by symbiotic microorganisms rather than the host. == Biological diversity in marine environments == Marine environments are considered more biologically diverse than terrestrial environments. Thirty-two different animal phyla are represented in the oceans of the 33 recognized phyla. Fifteen different phyla are represented only in marine environments, while only 1 is exclusively terrestrial. Marine phyla also contain functionally unique organisms such as filter feeders and sessile organisms which have no terrestrial counterpart. Also, marine autotrophs are more diverse than their terrestrial counterparts this is extremely important. Marine autotrophs are believed to stem from at least 8 ancient clades while terrestrial organisms mainly stem from one clade, Embyrophyta. Marine environments may contain over 80% of the world's plant and animal species. The diversity of coral reefs can be extraordinary with species diversity reaching 1000
|
{
"page_id": 12715053,
"source": null,
"title": "Marine pharmacognosy"
}
|
species per meter squared. The greatest marine tropical biodiversity is reported to be in the Indo-Pacific Ocean. == Sample collection technological requirements == Collecting marine samples can range from very simple and inexpensive to very complicated expensive. Samples from near or on shores are readily accessible via beach combing, wading or snorkeling. Sample collection from deep water can be completed via dredging however, this is a very invasive technique which destroys the local habitat, does not allow for repeated sampling from the same location and compromises sample integrity. Corers can be used for sediment sample collection from deep locations quickly, easily and inexpensively. SCUBA diving was introduced in the 1940s however, it was not widely used until it became popular in the 1970s. SCUBA diving is limited in the duration that divers can spend underwater when conducted from the surface. If prolonged dives were necessary, an underwater laboratory could be used. Aquarius is the only underwater laboratory dedicated to marine science. For sample collection from depths that cannot be achieved by SCUBA diving, submersibles may be used. Sample collection by submersibles can be extremely expensive with costs for a submersible, support ship, technicians and support staff ranging between $10,000 to $45,000 per day. == Chemical compound isolation == For the isolation of biologically active compounds from organisms, several different steps need to be completed. The different steps required to obtain a biologically active compound are: Extraction, chromatographic purification, dereplication, structure elucidation and bioassay testing. The steps do not have to follow that particular order and many steps may be completed simultaneously. In the first step, the sample may be triturated and extracted with a suitable solvent or macerated. Some solvents used are methanol:chloroform, ethanol, acetonitrile, or others. The purpose is to remove organic compounds that have a medium polarity which
|
{
"page_id": 12715053,
"source": null,
"title": "Marine pharmacognosy"
}
|
are considered more "drug-like". Ideally, polar compounds like salts, peptides, sugars as well as very non-polar compounds like lipids are left behind to simplify chromatography since they are not generally considered "drug-like". Drying of the sample could be completed before extraction by lyophilisation to remove any excess water and therefore limit the amount of highly polar compounds extracted. The next step depends on the methodology of individual laboratories. Bioassay-guided fractionation is a common method to find biologically active compounds. This involves testing the crude extract or preliminary fractions from chromatography in an assay or multiple assays, determining what fractions or crude extracts show activity in the specific assays, and further fractionating the active fractions or extracts. This step is than repeated where the new fractions are tested and the active fractions are further fractionated. This continues until the fraction only contains one compound. Dereplication is ideally performed as early as possible to determine if the active compound has been previously reported in order to prevent "rediscovering" a compound. This can be performed using Liquid Chromatography- Mass Spectrometry (LC-MS) data or Nuclear Magnetic Resonance (NMR) data obtained in the biological assay-guided process and then comparing the information to that found in databases of previously reported compounds. Structure elucidation is performed by using NMR data obtained of the compound and High Resolution Mass Spectrometry (HR-MS) Data. Tandem Mass Spectrometry can also be useful, especially for large molecules like glycolipids, proteins, polysaccharides or peptides. Completed characterization for publication purposes may require Infrared (IR), Ultraviolet-visible (UV-vis), specific rotation and melting point data. Obtaining a crystal structure via X-ray crystallography can greatly accelerate and simplify structure elucidation however, obtaining crystals can be quite difficult. There are many different bioassays available for testing. There are anticancer, antimicrobial, antiviral, anti-inflammatory, antiparasitic, anticholesterolemic, and many other differ assays.
|
{
"page_id": 12715053,
"source": null,
"title": "Marine pharmacognosy"
}
|
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