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Similar to how plant peroxisomal enzymes bind propionyl-CoA and isobutyryl-CoA, Gen5, an acetyltransferase in humans, binds to propionyl-CoA and butyryl-CoA. These specifically bind to the catalytic domain of Gen5L2. This conserved acetyltransferase is responsible for the regulation of transcription by lysine acetylation of the histone N-terminal tails. This function of acetylation has a much higher reaction rate than propionylation or butyrylation. Because of the structure of propionyl-CoA, Gen5 distinguishes between different acyl-CoA molecules. In fact, it was found that the propyl group of butyrl-CoA cannot bind due to lack of stereospecificity to the active binding site of Gen5 due to the unsaturated acyl chains. On the other hand, the third carbon of propionyl-CoA can fit into the active site of Gen5 with the correct orientation. | 1 | Biochemistry |
Over the time, methods for supramolecular polymerization has expanded, and the range of its useable monomers has diversified. In addition to plethora of molecular motifs, biomolecules such as DNA, DNA nanostructures and proteins as well as inorganic objects as unconventional monomers has recently been investigated for supramolecular polymerization. In all of these cases, monomers are in much higher size, usually several nanometers, and the non-covalent interactions varies from hydrogen bonding, host-guest and metal coordination. A notable example is Mgassisted multivalent supramolecular polymerization of ATP-responsive biomolecular machines, chaperonine GroEL, resulting in a highly stable protein nanotube. Importantly, this nanotube shows an ATPase activity and dissociates into short-chain oligomers when treated with ATP because of the opening/closing motions of the constituent GroEL units. | 6 | Supramolecular Chemistry |
To determine the change in enthalpy in a neutralization reaction (ΔH), a known amount of basic solution may be placed in a calorimeter, and the temperature of this solution alone recorded. Then, a known amount of acidic solution may be added and the change in temperature measured using a thermometer. The difference in temperature (ΔT, in units K or °C) may be calculated by subtracting the initial temperature from the final temperature. The enthalpy of neutralization ΔH may then be calculated according to the following equation:
Regardless of the specific chemical process, with a known calorimeter constant and a known change in temperature the heat added to the system may be calculated by multiplying the calorimeter constant by that change in temperature. | 7 | Physical Chemistry |
Chvorinov's rule is a physical relationship that relates the solidification time for a simple casting to the volume and surface area of the casting. It was first expressed by Czech engineer Nicolas Chvorinov in 1940. | 8 | Metallurgy |
A fraction of the input DNA obtained after the sonication step above is labeled with cyanine-5 (Cy5; red) deoxy-cytosine-triphosphate while the methylated DNA, enriched after the immunoprecipitation step, is labeled with cyanine-3 (Cy3; green). The labeled DNA samples are cohybridized on a 2-channel, high-density genomic microarray to probe for presence and relative quantities. The purpose of this comparison is to identify sequences that show significant differences in hybridization levels, thereby confirming the sequence of interest is enriched.
Array-based identification of MeDIP sequences are limited to the array design. As a result, the resolution is restricted to the probes in the array design. There are additional standard steps required in signal processing to correct for hybridization issues such as noise, as is the case with most array technologies.
See for more details. | 1 | Biochemistry |
The Set-Point Theory, first introduced in 1953, postulated that each body has a preprogrammed fixed weight, with regulatory mechanisms to compensate. This theory was quickly adopted and used to explain failures in developing effective and sustained weight loss procedures. A 2019 systematic review of multiple weight change interventions on humans, including dieting, exercise and overeating, found systematic "energetic errors", the non-compensated loss or gain of calories, for all these procedures. This shows that the body cannot precisely compensate for errors in energy/calorie intake, contrary to what the Set-Point Theory hypothesizes, and potentially explaining both weight loss and weight gain such as obesity. This review was conducted on short-term studies, therefore such a mechanism cannot be excluded in the long term, as evidence is currently lacking on this timeframe. | 1 | Biochemistry |
The dominant luminous component in a cluster of galaxies is the 10 to 10 kelvin intracluster medium. The emission from the intracluster medium is characterized by thermal bremsstrahlung. This radiation is in the energy range of X-rays and can be easily observed with space-based telescopes such as Chandra X-ray Observatory, XMM-Newton, ROSAT, ASCA, EXOSAT, Suzaku, RHESSI and future missions like IXO [https://web.archive.org/web/20080303062108/http://constellation.gsfc.nasa.gov/] and Astro-H [https://web.archive.org/web/20071112015825/http://www.astro.isas.ac.jp/future/NeXT/].
Bremsstrahlung is also the dominant emission mechanism for H II regions at radio wavelengths. | 7 | Physical Chemistry |
Siddiqui was the first scientist to bring the anthelmintic, antifungal, antibacterial, and antiviral constituents of the Neem tree to the attention of natural products chemists. In 1942, he extracted three bitter compounds from neem oil, which he named as nimbin, nimbinin, and nimbidin respectively. The process involved extracting the water-insoluble components with ether, petrol ether, ethyl acetate and dilute alcohol. The provisional naming was nimbin (sulphur-free crystalline product with melting point at 205 °C, empirical composition CHO), nimbinin (with similar principle, melting at 192 °C), and nimbidin (cream-coloured containing amorphous sulphur, melting at 90–100 °C). Siddiqui identified nimbidin as the main active antibacterial ingredient, and the highest yielding bitter component in the neem oil. These compounds are stable and found in substantial quantities in the Neem. They also serve as natural insecticides.
In acknowledgement of these revolutionary discoveries, he was awarded the Order of the British Empire in 1946.
In his later career, Siddiqui continued to discover and isolate numerous unique anti-bacterial compounds from various parts (leaves, bark, etc.) of the Neem and other plants. He had more than 50 chemical compounds patented in his name in addition to those discovered as a result of his joint research with other colleagues and students. Most of these discoveries still remain vital natural ingredients of various medicines as well as biopesticides. | 0 | Organic Chemistry |
Some enzymes can function as electrocatalysts. Nitrogenase, an enzyme that contains a MoFe cluster, can be leveraged to fix atmospheric nitrogen, i.e. convert nitrogen gas into molecules such as ammonia. Immobilizing the protein onto an electrode surface and employing an electron mediator greatly improves the efficiency of this process. The effectiveness of bioelectrocatalysts generally depends on the ease of electron transport between the active site of the enzyme and the electrode surface. Other enzymes provide insight for the development of synthetic catalysts. For example, formate dehydrogenase, a nickel-containing enzyme, has inspired the development of synthetic complexes with similar molecular structures for use in CO reduction. Microbial fuel cells are another way that biological systems can be leveraged for electrocatalytic applications. Microbial-based systems leverage the metabolic pathways of an entire organism, rather than the activity of a specific enzyme, meaning that they can catalyze a broad range of chemical reactions. Microbial fuel cells can derive current from the oxidation of substrates such as glucose, and be leveraged for processes such as CO reduction. | 7 | Physical Chemistry |
The angles used for each facet play a crucial role in the outcome of a gem. While the general facet arrangement of a particular gemstone cut may appear the same in any given gem material, the angles of each facet must be carefully adjusted to maximize the optical performance. The angles used will vary based on the refractive index of the gem material. When light passes through a gemstone and strikes a polished facet, the minimum angle possible for the facet to reflect the light back into the gemstone is called the critical angle. If the ray of light strikes a surface lower than this angle, it will leave the gem material instead of reflecting through the gem as brilliance. These lost light rays are sometimes referred to as "light leakage", and the effect caused by it is called "windowing" as the area will appear transparent and without brilliance. This is especially common in poorly cut commercial gemstones. Gemstones with higher refractive indexes generally make more desirable gemstones, the critical angle decreases as refractive indices increase, allowing for greater internal reflections as the light is less likely to escape. | 3 | Analytical Chemistry |
A hormone (from the Greek participle , "setting in motion") is a class of signaling molecules in multicellular organisms that are sent to distant organs or tissues by complex biological processes to regulate physiology and behavior. Hormones are required for the correct development of animals, plants and fungi. Due to the broad definition of a hormone (as a signaling molecule that exerts its effects far from its site of production), numerous kinds of molecules can be classified as hormones. Among the substances that can be considered hormones, are eicosanoids (e.g. prostaglandins and thromboxanes), steroids (e.g. oestrogen and brassinosteroid), amino acid derivatives (e.g. epinephrine and auxin), protein or peptides (e.g. insulin and CLE peptides), and gases (e.g. ethylene and nitric oxide).
Hormones are used to communicate between organs and tissues. In vertebrates, hormones are responsible for regulating a wide range of processes including both physiological processes and behavioral activities such as digestion, metabolism, respiration, sensory perception, sleep, excretion, lactation, stress induction, growth and development, movement, reproduction, and mood manipulation. In plants, hormones modulate almost all aspects of development, from germination to senescence.
Hormones affect distant cells by binding to specific receptor proteins in the target cell, resulting in a change in cell function. When a hormone binds to the receptor, it results in the activation of a signal transduction pathway that typically activates gene transcription, resulting in increased expression of target proteins. Hormones can also act in non-genomic pathways that synergize with genomic effects. Water-soluble hormones (such as peptides and amines) generally act on the surface of target cells via second messengers. Lipid soluble hormones, (such as steroids) generally pass through the plasma membranes of target cells (both cytoplasmic and nuclear) to act within their nuclei. Brassinosteroids, a type of polyhydroxysteroids, are a sixth class of plant hormones and may be useful as an anticancer drug for endocrine-responsive tumors to cause apoptosis and limit plant growth. Despite being lipid soluble, they nevertheless attach to their receptor at the cell surface.
In vertebrates, endocrine glands are specialized organs that secrete hormones into the endocrine signaling system. Hormone secretion occurs in response to specific biochemical signals and is often subject to negative feedback regulation. For instance, high blood sugar (serum glucose concentration) promotes insulin synthesis. Insulin then acts to reduce glucose levels and maintain homeostasis, leading to reduced insulin levels. Upon secretion, water-soluble hormones are readily transported through the circulatory system. Lipid-soluble hormones must bond to carrier plasma glycoproteins (e.g., thyroxine-binding globulin (TBG)) to form ligand-protein complexes. Some hormones, such as insulin and growth hormones, can be released into the bloodstream already fully active. Other hormones, called prohormones, must be activated in certain cells through a series of steps that are usually tightly controlled. The endocrine system secretes hormones directly into the bloodstream, typically via fenestrated capillaries, whereas the exocrine system secretes its hormones indirectly using ducts. Hormones with paracrine function diffuse through the interstitial spaces to nearby target tissue.
Plants lack specialized organs for the secretion of hormones, although there is spatial distribution of hormone production. For example, the hormone auxin is produced mainly at the tips of young leaves and in the shoot apical meristem. The lack of specialised glands means that the main site of hormone production can change throughout the life of a plant, and the site of production is dependent on the plant's age and environment. | 1 | Biochemistry |
Polyfluorenes are also used in polymer solar cells because of their affinity for property tuning. Copolymerization of fluorene with other monomers allows researchers to optimize the absorption and electronic energy levels as a means to increase the photovoltaic performance. For instance, by lowering the band gap of polyfluorenes, the absorption spectrum of the polymer can be adjusted to coincide with the maximum photon flux region of the solar spectrum. This helps the solar cell absorb more of the sun's energy and to increase its energy conversion efficiency; donor-acceptor structured copolymers of fluorene have achieved efficiencies above 4% when their absorption edge was pushed to 700 nm.
The voltage of polymer solar cells has also been increased through the design of polyfluorenes. These devices are typically produced by blending electron accepting and electron donating molecules which help separate charge to produce power. In polymer blend solar cells, the voltage produced by the device is determined by the difference between the electron donating polymer’s highest occupied molecular orbital (HOMO) energy level and the electron accepting molecules lowest unoccupied molecular orbital (LUMO) energy level. By adding electron withdrawing pendant molecules to conjugated polymers, their HOMO energy level can be lowered. For instance by adding electronegative groups on the end of conjugated side chains, researchers lowered the HOMO of a polyfluorene copolymer to −5.30 eV and increased the voltage of a solar cell to 0.99 V.
Typical polymer solar cells utilize fullerene molecules as electron acceptors because of their low LUMO energy level (high electron affinity). However the tunability of polyfluorenes allows their LUMO to be lowered to a level appropriate for use as an electron acceptor. Thus, polyfluorene copolymers have also been used in polymer:polymer blend solar cells, where their electron accepting, electron conducting and light absorbing properties permit device performance. | 7 | Physical Chemistry |
In dead Sphagnum, sphagnan a polysaccharide with D-lyxo-5-hexosulouronic acid is a major remaining substance. It makes the bog very acidic, so that bacteria cannot grow. Not only that, the plant ensures there is no available nitrogen. Holocellulose also absorbs any digestive enzymes around. Together this leads to major accumulation of peat under sphagnum bogs. | 9 | Geochemistry |
Association theory (also aggregate theory) is a theory first advanced by chemist Thomas Graham in 1861 to describe the molecular structure of colloidal substances such as cellulose and starch, now understood to be polymers. Association theory postulates that such materials are solely composed of a collection of smaller molecules bound together by an unknown force. Graham termed these materials colloids. Prior to the development of macromolecular theory by Hermann Staudinger in the 1920s, which stated that individual polymers are composed of chains of covalently bonded monomers, association theory remained the most prevalent model of polymer structure in the scientific community.
Importantly, although polymers consist of long chains of covalently linked molecules, the individual polymer chains can often still associate and undergo phase transitions and phase separation to form colloids, liquid crystals, solid crystals, or aggregates. For biopolymers, association leads to formation of biomolecular condensates, micelles and other examples of molecular self-assembly. | 7 | Physical Chemistry |
Polyfluorenes are an important class of polymers which have the potential to act as both electroactive and photoactive materials. This in part due to the shape of fluorene. Fluorene is generally planar; p-orbital overlap at the linkage between its two benzene rings results in conjugation across the molecule. This in turn allows for a reduced band gap as the excited state molecular orbitals are delocalized.
Since the degree of delocalization and the spatial location of the orbitals on the molecule is influenced by the electron donating (or withdrawing) character of its substituents, the band gap energy can be varied. This chemical control over the band gap directly influences the color of the molecule by limiting the energies of light which it absorbs.
Interest in polyfluorene derivatives has increased because of their high photoluminescence quantum efficiency, high thermal stability, and their facile color tunability, obtained by introducing low-band-gap co-monomers. Research in this field has increased significantly due to its potential application in tuning organic light-emitting diodes (OLEDs). In OLEDs, polyfluorenes are desirable because they are the only family of conjugated polymers that can emit colors spanning the entire visible range with high efficiency and low operating voltage. Furthermore, polyfluorenes are relatively soluble in most solvents, making them ideal for general applications.
Another important quality of polyfluorenes is their thermotropic liquid crystallinity which allows the polymers to align on rubbed polyimide layers. Thermotropic liquid crystallinity refers to the polymers' ability to exhibit a phase transition into the liquid crystal phase as the temperature is changed. This is very important to the development of liquid crystal displays (LCDs) because the synthesis of liquid crystal displays requires that the liquid-crystal molecules at the two glass surfaces of the cell be aligned parallel to the two polarizer foils.
This can only be done by coating the inner-surfaces of the cell with a thin, transparent film of polyamide which is then rubbed with a velvet cloth. Microscopic grooves are then generated in the polyamide layer and the liquid crystal in contact with the polyamide, the polyfluorene, can align in the rubbing direction. In addition to LCDs, polyfluorene can also be used to synthesize light-emitting diodes (LEDs). Polyfluorene has led to LEDs that can emit polarized light with polarization ratios of more than 20 and with brightness of 100 cd m. Even though this is very impressive, it is not sufficient for general applications. | 7 | Physical Chemistry |
*1999 - Outstanding Faculty Award, State Council of Higher Education of Virginia (SCHEV)
*2007 - Jabir Ibn Hyyan (Geber) Award, Saudi Chemical Society
*2008 - SAE International Award for Research on Automotive Lubricants, Society of Automotive Engineering
*2012–13 - Jefferson Science Fellow (JSF), U.S. Department of State and USAID
*2012 - Fellow, American Physical Society (APS) "For pioneering contributions to the fields of ion-induced nucleation, ion mobility, thermochemistry and structures of molecular cluster ions, gas phase cluster polymerization, nanostructured materials and nanocatalysis"
*2013 - Fellow, American Association for the Advancement of Science (AAAS) "For Distinguished contributions to the fields of clusters, nucleation, nanostructured materials and nanocatalysis, particularly for the novel synthesis of advanced nanomaterials"
*2018 - Virginia Outstanding Scientist, Awarded by the Virginia Governor
*2021 - Distinguished Service Award, Virginia Section of the American Chemical Society | 7 | Physical Chemistry |
Thermophysical properties of matter and the kinetics of interaction and energy exchange among the principal carriers are based on the atomic-level configuration and interaction. Transport properties such as thermal conductivity are calculated from these atomic-level properties using classical and quantum physics. Quantum states of principal carriers (e.g.. momentum, energy) are derived from the Schrödinger equation (called first principle or ab initio) and the interaction rates (for kinetics) are calculated using the quantum states and the quantum perturbation theory (formulated as the Fermi golden rule). Variety of ab initio (Latin for from the beginning) solvers (software) exist (e.g., ABINIT, CASTEP, Gaussian, Q-Chem, Quantum ESPRESSO, SIESTA, VASP, WIEN2k). Electrons in the inner shells (core) are not involved in heat transfer, and calculations are greatly reduced by proper approximations about the inner-shells electrons.
The quantum treatments, including equilibrium and nonequilibrium ab initio molecular dynamics (MD), involving larger lengths and times are limited by the computation resources, so various alternate treatments with simplifying assumptions have been used and kinetics. In classical (Newtonian) MD, the motion of atom or molecule (particles) is based on the empirical or effective interaction potentials, which in turn can be based on curve-fit of ab initio calculations or curve-fit to thermophysical properties. From the ensembles of simulated particles, static or dynamics thermal properties or scattering rates are derived.
At yet larger length scales (mesoscale, involving many mean free paths), the Boltzmann transport equation (BTE) which is based on the classical Hamiltonian-statistical mechanics is applied. BTE considers particle states in terms of position and momentum vectors (x, p) and this is represented as the state occupation probability. The occupation has equilibrium distributions (the known boson, fermion, and Maxwell–Boltzmann particles) and transport of energy (heat) is due to nonequilibrium (cause by a driving force or potential). Central to the transport is the role of scattering which turn the distribution toward equilibrium. The scattering is presented by the relations time or the mean free path. The relaxation time (or its inverse which is the interaction rate) is found from other calculations (ab initio or MD) or empirically. BTE can be numerically solved with Monte Carlo method, etc.
Depending on the length and time scale, the proper level of treatment (ab initio, MD, or BTE) is selected. Heat transfer physics analyses may involve multiple scales (e.g., BTE using interaction rate from ab initio or classical MD) with states and kinetic related to thermal energy storage, transport and transformation.
So, heat transfer physics covers the four principal energy carries and their kinetics from classical and quantum mechanical perspectives. This enables multiscale (ab initio, MD, BTE and macroscale) analyses, including low-dimensionality and size effects. | 7 | Physical Chemistry |
When Amagats law is valid and' the gas mixture is made of ideal gases,
where:
: is the pressure of the gas mixture,
: is the volume of the i-th component of the gas mixture,
: is the total volume of the gas mixture,
: is the amount of substance of i-th component of the gas mixture (in mol),
: is the total amount of substance of gas mixture (in mol),
: is the ideal, or universal, gas constant, equal to the product of the Boltzmann constant and the Avogadro constant,
: is the absolute temperature of the gas mixture (in K),
: is the mole fraction of the i-th component of the gas mixture.
It follows that the mole fraction and volume fraction are the same. This is true also for other equation of state. | 7 | Physical Chemistry |
In non-photosynthetic eukaryotes such as animals, fungi, and protozoa, as well as the class Alphaproteobacteria of bacteria, it is produced by the enzyme ALA synthase, from glycine and succinyl-CoA. This reaction is known as the Shemin pathway, which occurs in mitochondria.
In plants, algae, bacteria (except for the class Alphaproteobacteria) and archaea, it is produced from glutamic acid via glutamyl-tRNA and glutamate-1-semialdehyde. The enzymes involved in this pathway are glutamyl-tRNA synthetase, glutamyl-tRNA reductase, and glutamate-1-semialdehyde 2,1-aminomutase. This pathway is known as the C5 or Beale pathway. In most plastid-containing species, glutamyl-tRNA is encoded by a plastid gene, and the transcription, as well as the following steps of C5 pathway, take place in plastids. | 1 | Biochemistry |
Changes in these quantities are useful for assessing the degree to which a chemical reaction will proceed. The relevant quantity depends on the reaction conditions, as shown in the following table. denotes the change in the potential and at equilibrium the change will be zero.
Most commonly one considers reactions at constant and , so the Gibbs free energy is the most useful potential in studies of chemical reactions. | 7 | Physical Chemistry |
Phosphines accept electron density from metal p or d orbitals into combinations of P–C σ* antibonding orbitals that have π symmetry. When phosphines bond to electron-rich metal atoms, backbonding would be expected to lengthen P–C bonds as P–C σ* orbitals become populated by electrons. The expected lengthening of the P–C distance is often hidden by an opposing effect: as the phosphorus lone pair is donated to the metal, P(lone pair)–R(bonding pair) repulsions decrease, which acts to shorten the P–C bond. The two effects have been deconvoluted by comparing the structures of pairs of metal-phosphine complexes that differ only by one electron. Oxidation of RP–M complexes results in longer M–P bonds and shorter P–C bonds, consistent with π-backbonding. In early work, phosphine ligands were thought to utilize 3d orbitals to form M–P pi-bonding, but it is now accepted that d-orbitals on phosphorus are not involved in bonding as they are too high in energy. | 0 | Organic Chemistry |
Plants take up phosphorus through several pathways: the arbuscular mycorrhizal pathway and the direct uptake pathway. | 0 | Organic Chemistry |
A uniform polymer (often referred to as a monodisperse polymer) is composed of molecules of the same mass. Nearly all natural polymers are uniform. Synthetic near-uniform polymer chains can be made by processes such as anionic polymerization, a method using an anionic catalyst to produce chains that are similar in length. This technique is also known as living polymerization. It is used commercially for the production of block copolymers. Uniform collections can be easily created through the use of template-based synthesis, a common method of synthesis in nanotechnology.
A polymer material is denoted by the term disperse, or non-uniform, if its chain lengths vary over a wide range of molecular masses. This is characteristic of man-made polymers. Natural organic matter produced by the decomposition of plants and wood debris in soils (humic substances) also has a pronounced polydispersed character. It is the case of humic acids and fulvic acids, natural polyelectrolyte substances having respectively higher and lower molecular weights. Another interpretation of dispersity is explained in the article Dynamic light scattering (cumulant method subheading). In this sense, the dispersity values are in the range from 0 to 1.
The dispersity (Đ), also known as the polydispersity index (PDI) or heterogeneity index, is a measure of the distribution of molecular mass in a given polymer sample. Đ (PDI) of a polymer is calculated:
where is the weight average molecular weight and is the number average molecular weight. is more sensitive to molecules of low molecular mass, while is more sensitive to molecules of high molecular mass. The dispersity indicates the distribution of individual molecular masses in a batch of polymers. Đ has a value equal to or greater than 1, but as the polymer chains approach uniform chain length, Đ approaches unity (1). For some natural polymers Đ is almost taken as unity. | 7 | Physical Chemistry |
Electrochemiluminescence or electrogenerated chemiluminescence (ECL) is a kind of luminescence produced during electrochemical reactions in solutions. In electrogenerated chemiluminescence, electrochemically generated intermediates undergo a highly exergonic reaction to produce an electronically excited state that then emits light upon relaxation to a lower-level state. This wavelength of the emitted photon of light corresponds to the energy gap between these two states. ECL excitation can be caused by energetic electron transfer (redox) reactions of electrogenerated species. Such luminescence excitation is a form of chemiluminescence where one/all reactants are produced electrochemically on the electrodes.
ECL is usually observed during application of potential (several volts) to electrodes of electrochemical cell that contains solution of luminescent species (polycyclic aromatic hydrocarbons, metal complexes, quantum dots or nanoparticles) in aprotic organic solvent (ECL composition).
In organic solvents both oxidized and reduced forms of luminescent species can be produced at different electrodes simultaneously or at a single one by sweeping its potential between oxidation and reduction. The excitation energy is obtained from recombination of oxidized and reduced species.
In aqueous medium, which is mostly used for analytical applications, simultaneous oxidation and reduction of luminescent species is difficult to achieve due to electrochemical splitting of water itself so the ECL reaction with the coreactants is used. In the latter case luminescent species are oxidized at the electrode together with the coreactant which gives a strong reducing agent after some chemical transformations (the oxidative reduction mechanism). | 5 | Photochemistry |
Other MALS applications include nanoparticle sizing, protein aggregation studies, protein-protein interactions, electrophoretic mobility or zeta potential. MALS techniques have been adopted for the study of pharmaceutical drug stability and use in nanomedicine. | 7 | Physical Chemistry |
Triphosgene's low vapor pressure makes it possible for it to reach concentrations that are considered toxicologically unsafe. While several properties of triphosgene are not yet readily available, it is known that it is very toxic if inhaled. A toxic gas is emitted if it comes in contact with water. There is a lack of information and variability regarding the proper handling of triphosgene. It is assumed to have the same risks as phosgene. | 0 | Organic Chemistry |
MicroPIXE is a useful technique for the non-destructive analysis of paintings and antiques. Although it provides only an elemental analysis, it can be used to distinguish and measure layers within the thickness of an artifact. The technique is comparable with destructive techniques such as the ICP family of analyses. | 7 | Physical Chemistry |
Since the 1990s, pRb was known to be inactivated via phosphorylation. Until, the prevailing model was that Cyclin D- Cdk 4/6 progressively phosphorylated it from its unphosphorylated to its hyperphosphorylated state (14+ phosphorylations). However, it was recently shown that pRb only exists in three states: un-phosphorylated, mono-phosphorylated, and hyper-phosphorylated. Each has a unique cellular function.
Before the development of 2D IEF, only hyper-phosphorylated pRb was distinguishable from all other forms, i.e. un-phosphorylated pRb resembled mono-phosphorylated pRb on immunoblots. As pRb was either in its active “hypo-phosphorylated” state or inactive “hyperphosphorylated” state. However, with 2D IEF, it is now known that pRb is un-phosphorylated in G0 cells and mono-phosphorylated in early G1 cells, prior to hyper-phosphorylation after the restriction point in late G1. | 1 | Biochemistry |
Reducing the species and its related precursors with sodium or potassium have given dimeric magnesium(I) compounds such as [{(Priso)Mg}] and other compounds with substituted versions of β-diketiminato. These compounds, with a general formula of [{(ArNacnac)Mg}]. However, as the size of the substituent on Nacnac decreased, the difficulty to isolate a magnesium(I) dimer increased. This can be shown by phenol, where only a Mg(II) dimer was gained, given by [(PhNacnac)Mg]. For a bulkier analogue such as [{(Nacnac)Mg}] a different synthesis route was carried out. Dibutyl magnesium and iodine were chosen since the free β -diketimine, tBuNacnacH has a different reactivity.This is due to tBuNacnacH not reacting with the Grignard reagent shown above. Instead, it can be heated with dibutylmagnesium and become deprotonated.
For the reactant, the was stabilized by utilizing a bulkier, or more sterically demanding, N-ligand. This reaction is carried out through potassium reduction of the α-diimine, DAB and Mg(II) chloride in tetrahydrofuran (THF). It can be noted that DAB can be shown by the chemical formula as [(DipNCMe)]). The shown Mg(I) complexes are all thermally stable. Some can even tolerate temperatures up to 300 °C. They also range in colors from colorless to orange. As these compounds are investigated further, the dimers have been found to be kinetically stabilized by multiple β-diketiminate derivatives, a guanidinate, a diiminophosphinate, an enediamide, and several diimine-enolates. | 7 | Physical Chemistry |
The perturbation proof by Kacser and Burns is given as follows.
Given the simple linear pathway catalyzed by two enzymes and :
where is the fixed boundary species. Let us increase the concentration of enzyme by an amount . This will cause the steady state flux and concentration of , and all downstream species
beyond to increase. The concentration of is now decreased such that the flux and steady-state concentration of is restored back to their original values. These changes allow one to write down the following local and systems equations for the changes that occurred:
There is no term in either equation because the concentration of is unchanged. Both right-hand sides of the equations are guaranteed to be zero by construction. The term can be eliminated by combining both equations. If we also assume that the reaction rate for an enzyme-catalyzed reaction is proportional to the enzyme concentration, then , therefore:
Since
this yields:
This proof can be generalized to the case where may act at multiple sites. | 1 | Biochemistry |
Anti-Smith (Anti-Sm) antibodies are a very specific marker for SLE. Approximately 99% of individuals without SLE lack anti-Sm antibodies, but only 20% of people with SLE have the antibodies. They are associated with central nervous system involvement, kidney disease, lung fibrosis and pericarditis in SLE, but they are not associated with disease activity. The antigens of the anti-Sm antibodies are the core units of the small nuclear ribonucleoproteins (snRNPs), termed A to G, and will bind to the U1, U2, U4, U5 and U6 snRNPs. Most commonly, the antibodies are specific for the B, B' and D units. Molecular and epidemiological studies suggest that anti-Sm antibodies may be induced by molecular mimicry because the protein shows some similarity to Epstein-Barr virus proteins. | 1 | Biochemistry |
The allows for visualization of two misoriented materials and their interface such as crystal twins or grain boundaries. The user interface provides three views: two smaller views, each depicting one unit cell of selected material and orientation, and a larger view depicting an appropriate interface of the two structures. The interface can be visualized in four modes:
* 3D model of both unit cells,
* wire-frame model of both unit cells,
* cross section of the interface,
* bulk representation (up to several hundred atoms).
All three views in the user interface are functionally interconnected. If the content of one view is rotated by the user, the other views follow. If a crystallographic plane or direction is selected in one view, it is shown in other views and corresponding crystallographic indices are stated. The tool also allows to highlight coincident site lattice or calculate the list of planes and directions which are parallel or nearly parallel in the two misoriented materials. | 3 | Analytical Chemistry |
Chronic pain and neuropathic pain are indications for which there is high unmet need in the clinic. PEA has been tested in a variety of animal models for chronic and neuropathic pain, because cannabinoids, such as THC, have been proven to be effective in neuropathic pain states. The analgesic and antihyperalgesic effects of PEA in two models of acute and persistent pain seemed to be explained at least partly via the de novo neurosteroid synthesis. In chronic granulomatous pain and inflammation model, PEA could prevent nerve formation and sprouting, mechanical allodynia, and PEA inhibited dorsal root ganglia activation, which is a hallmark for winding up in neuropathic pain. The mechanism of action of PEA as an analgesic and anti-inflammatory molecule is probably based on different aspects. PEA inhibits the release of both preformed and newly synthesised mast cell mediators, such as histamine and TNF-alpha. PEA, as well as its analogue adelmidrol (di-amide derivative of azelaic acid), can both down-regulate mast cells. PEA reduces the expression of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) and prevents IkB-alpha degradation and p65 NF-kappaB nuclear translocation, the latter related to PEA as an endogenous PPAR-alpha agonist.
In 2012 it became clear that PEA can also reduce reperfusion injury and the negative impact of shock on various outcome parameters, such as renal dysfunction, ischemic injury and inflammation, most probably via the PPAR-alpha pathway. Studies have shown that PEA activates PPAR-alpha and TRPV1 receptors that control inflammation and the sensation of pain. Among the reperfusion and inflammation markers measured PEA could reduce the increase in creatinine, γGT, AST, nuclear translocation of NF-κBp65; kidney MPO activity and MDA levels, nitrotyrosine, PAR and adhesion molecules expression, the infiltration and activation of mast cells and apoptosis.
The biological responses to PEA dosing in animal models and in humans are being investigated vis-à-vis its involvement in a repair mechanism relevant to patient conditions of chronic inflammation and chronic pain. In a model of visceral pain (inflammation of the urinary bladder) PEA was able to attenuate the viscero-visceral hyper-reflexia induced by inflammation of the urinary bladder, one of the reasons why PEA is currently explored in the painful bladder syndrome. In a different model for bladder pain, the turpentine-induced urinary bladder inflammation in the rat, PEA also attenuated a referred hyperalgesia in a dose-dependent way. Chronic pelvic pain in patients seem to respond favourably to a treatment with PEA. | 1 | Biochemistry |
Microbes produce two reduced variants of chlorin, bacteriochlorins and isobacteriochlorins. Bacteriochlorins are found in some bacteriochlorophylls; the ring structure is produced by Chlorophyllide a reductase (COR) reducing a chlorin ring at the C7-8 double boud. Isobacteriochlorins are found in nature mostly as sirohydrochlorin, a biosynthetic intermediate of vitamin B, produced without going through a chlorin. In living organisms, both are ultimately derived from uroporphyrinogen III, a near-universal intermediate in tetrapyrrole biosynthesis. | 1 | Biochemistry |
The fungal component of a lichen is called the mycobiont. The mycobiont may be an Ascomycete or Basidiomycete. The associated lichens are called either ascolichens or basidiolichens, respectively. Living as a symbiont in a lichen appears to be a successful way for a fungus to derive essential nutrients, since about 20% of all fungal species have acquired this mode of life.
Thalli produced by a given fungal symbiont with its differing partners may be similar, and the secondary metabolites identical, indicating that the fungus has the dominant role in determining the morphology of the lichen. But the same mycobiont with different photobionts may also produce very different growth forms. Lichens are known in which there is one fungus associated with two or even three algal species.
Although each lichen thallus generally appears homogeneous, some evidence seems to suggest that the fungal component may consist of more than one genetic individual of that species.
Two or more fungal species can interact to form the same lichen.
The following table lists the orders and families of fungi that include lichen-forming species. | 2 | Environmental Chemistry |
There are several methods that can be used as an alternative to FAIRE-seq. DNase-seq uses the ability of the DNase I enzyme to cleave free/open/accessible DNA to identify and sequence open chromatin. The subsequently developed ATAC-seq employs the Tn5 transposase, which inserts specified fragments or transposons into accessible regions of the genome to identify and sequence open chromatin. | 1 | Biochemistry |
The reaction requires metal catalysts. Most commercially important processes employ heterogeneous catalysts. The heterogeneous catalysts are often prepared by in-situ activation of a metal halide (MCl) using organoaluminium or organotin compounds, e.g. combining MCl–EtAlCl. A typical catalyst support is alumina. Commercial catalysts are often based on molybdenum and ruthenium. Well-defined organometallic compounds have mainly been investigated for small-scale reactions or in academic research. The homogeneous catalysts are often classified as Schrock catalysts and Grubbs catalysts. Schrock catalysts feature molybdenum(VI)- and tungsten(VI)-based centers supported by alkoxide and imido ligands.
Grubbs catalysts, on the other hand, are ruthenium(II) carbenoid complexes. Many variations of Grubbs catalysts are known. Some have been modified with a chelating isopropoxybenzylidene ligand to form the related Hoveyda–Grubbs catalyst. | 0 | Organic Chemistry |
The Gross-Pitaevskii equation is a partial differential equation in space and time variables. Usually it does not have analytic solution and
different numerical methods, such as split-step
Crank-Nicolson
and Fourier spectral methods, are used for its solution. There are different Fortran and C programs for its solution for contact interaction
and long-range dipolar interaction which can be freely used. | 7 | Physical Chemistry |
The Joint Global Ocean Flux Study (JGOFS) was an international research programme on the fluxes of carbon between the atmosphere and ocean, and within the ocean interior. Initiated by the Scientific Committee on Oceanic Research (SCOR), the programme ran from 1987 through to 2003, and became one of the early core projects of the International Geosphere-Biosphere Programme (IGBP).
The overarching goal of JGOFS was to advance the understanding of, as well as improve the measurement of, the biogeochemical processes underlying the exchange of carbon across the air—sea interface and within the ocean. The programme aimed to study these processes from regional to global spatial scales, and from seasonal to interannual temporal scales, and to establish their sensitivity to external drivers such as climate change.
Early in the programme in 1988, two long-term time-series projects were established in the Atlantic and Pacific basins. These — Bermuda Atlantic Time-series Study (BATS) and Hawaii Ocean Time-series (HOT) — continue to make observations of ocean hydrography, chemistry and biology to the present-day. In 1989, JGOFS undertook the multinational North Atlantic Bloom Experiment (NABE) to investigate and characterise the annual spring bloom of phytoplankton, a key feature in the carbon cycle of the open ocean.
An important aspect of JGOFS lay in its objective to develop an increased network of observations, made using routine procedures, and curated such that they were easily available to researchers. JGOFS also oversaw the development of models of the marine system based on understanding gained from its observational programme. | 9 | Geochemistry |
One of the limitations of the Arrhenius definition is its reliance on water solutions. Edward Curtis Franklin studied the acid–base reactions in liquid ammonia in 1905 and pointed out the similarities to the water-based Arrhenius theory. Albert F.O. Germann, working with liquid phosgene, , formulated the solvent-based theory in 1925, thereby generalizing the Arrhenius definition to cover aprotic solvents.
Germann pointed out that in many solutions, there are ions in equilibrium with the neutral solvent molecules:
* solvonium ions: a generic name for positive ions. These are also sometimes called solvo-acids; when protonated solvent, they are lyonium ions.
* solvate ions: a generic name for negative ions. These are also sometimes called solve-bases; when deprotonated solvent, they are lyate ions.
For example, water and ammonia undergo such dissociation into hydronium and hydroxide, and ammonium and amide, respectively:
Some aprotic systems also undergo such dissociation, such as dinitrogen tetroxide into nitrosonium and nitrate, antimony trichloride into dichloroantimonium and tetrachloroantimonate, and phosgene into chlorocarboxonium and chloride:
A solute that causes an increase in the concentration of the solvonium ions and a decrease in the concentration of solvate ions is defined as an acid. A solute that causes an increase in the concentration of the solvate ions and a decrease in the concentration of the solvonium ions is defined as a base.
Thus, in liquid ammonia, (supplying ) is a strong base, and (supplying ) is a strong acid. In liquid sulfur dioxide (), thionyl compounds (supplying ) behave as acids, and sulfites (supplying ) behave as bases.
The non-aqueous acid–base reactions in liquid ammonia are similar to the reactions in water:
Nitric acid can be a base in liquid sulfuric acid:
The unique strength of this definition shows in describing the reactions in aprotic solvents; for example, in liquid :
Because the solvent system definition depends on the solute as well as on the solvent itself, a particular solute can be either an acid or a base depending on the choice of the solvent: is a strong acid in water, a weak acid in acetic acid, and a weak base in fluorosulfonic acid; this characteristic of the theory has been seen as both a strength and a weakness, because some substances (such as and ) have been seen to be acidic or basic on their own right. On the other hand, solvent system theory has been criticized as being too general to be useful. Also, it has been thought that there is something intrinsically acidic about hydrogen compounds, a property not shared by non-hydrogenic solvonium salts. | 7 | Physical Chemistry |
Dr. Senapathy's original objective in developing a method for identifying splice sites was to find complete genes in raw uncharacterized genomic sequence that could be used in the human genome project. In the landmark paper with this objective, he described the basic method for identifying the splice sites within a given sequence based on the Position Weight Matrix (PWM) of the splicing sequences in different eukaryotic organism groups for the first time. He also created the first exon detection method by defining the basic characteristics of an exon as the sequence bounded by an acceptor and a donor splice sites that had S&S scores above a threshold, and by an ORF that was mandatory for an exon. An algorithm for finding complete genes based on the identified exons was also described by Dr. Senapathy for the first time.
Dr. Senapathy demonstrated that only deleterious mutations in the donor or acceptor splice sites that would drastically make the protein defective would reduce the splice site score (later known as the Shapiro–Senapathy score), and other non-deleterious variations would not reduce the score. The S&S method was adapted for researching the cryptic splice sites caused by mutations leading to diseases. This method for detecting deleterious splicing mutations in eukaryotic genes has been used extensively in disease research in the humans, animals and plants over the past three decades, as described above.
The basic method for splice site identification, and for defining exons and genes was subsequently used by researchers in finding splice sites, exons and eukaryotic genes in a variety of organisms. These methods also formed the basis of all subsequent tools development for discovering genes in uncharacterized genomic sequences. It also was used in a different computational approaches including machine learning and neural network, and in alternative splicing research. | 1 | Biochemistry |
Bowen lived for most of his working life in Park Town and is buried in Wolvercote Cemetery, north of Oxford. Bowen was married to Edith née Moule and they had a son (also a chemist) and a daughter. He died on 19 November 1980 after a short illness. | 5 | Photochemistry |
Although ELPs generally form reversible spherical aggregates due to their proline and glycine content, there is a possibility that, under certain conditions such as exceedingly high temperatures, ELPs will form amyloids, or irreversible aggregates of insoluble protein. It is also believed that changes in the ELP backbone leading to a reduction in the proline and glycine content may lead to ELPs with a greater propensity for the amyloid state. As amyloids are implicated in the progression of Alzheimer's disease as well as in prion-based diseases, such as Creutzfeldt-Jakob disease (CJD), modeling of ELP amyloid formation may be useful from a biomedical standpoint. | 7 | Physical Chemistry |
Vixotrigine (, ), formerly known as raxatrigine (, ), is an analgesic which is under development by Convergence Pharmaceuticals for the treatment of lumbosacral radiculopathy (sciatica) and trigeminal neuralgia (TGN). Vixotrigine was originally claimed to be a selective central Na1.3 blocker, but was subsequently redefined as a selective peripheral Na1.7 blocker. Following this, vixotrigine was redefined once again, as a non-selective voltage-gated sodium channel blocker. As of January 2018, it is in phase III clinical trials for trigeminal neuralgia and is in phase II clinical studies for erythromelalgia and neuropathic pain. It was previously under investigation for the treatment of bipolar disorder, but development for this indication was discontinued. | 4 | Stereochemistry |
Although sedimentation might occur in tanks of other shapes, removal of accumulated solids is easiest with conveyor belts in rectangular tanks or with scrapers rotating around the central axis of circular tanks. Settling basins and clarifiers should be designed based on the settling velocity (v) of the smallest particle to be theoretically 100% removed. The overflow rate is defined as:
:Overflow rate (v ) = Flow of water (Q (m/s)) /(Surface area of settling basin (A(m))
In many countries this value is named as surface loading in m/h per m. Overflow rate is often used for flow over an edge (for example a weir) in the unit m/h per m.
The unit of overflow rate is usually meters (or feet) per second, a velocity. Any particle with settling velocity (v) greater than the overflow rate will settle out, while other particles will settle in the ratio v/v.
There are recommendations on the overflow rates for each design that ideally take into account the change in particle size as the solids move through the operation:
* Quiescent zones: per second
* Full-flow basins: per second
* Off-line basins: per second
However, factors such as flow surges, wind shear, scour, and turbulence reduce the effectiveness of settling. To compensate for these less than ideal conditions, it is recommended doubling the area calculated by the previous equation.
It is also important to equalize flow distribution at each point across the cross-section of the basin. Poor inlet and outlet designs can produce extremely poor flow characteristics for sedimentation.
Settling basins and clarifiers can be designed as long rectangles (Figure 1.a), that are hydraulically more stable and easier to control for large volumes. Circular clarifiers (Fig. 1.b) work as a common thickener (without the usage of rakes), or as upflow tanks (Fig. 1.c).
Sedimentation efficiency does not depend on the tank depth. If the forward velocity is low enough so that the settled material does not re-suspend from the tank floor, the area is still the main parameter when designing a settling basin or clarifier, taking care that the depth is not too low. | 3 | Analytical Chemistry |
Type V restriction enzymes (e.g., the cas9-gRNA complex from CRISPRs) utilize guide RNAs to target specific non-palindromic sequences found on invading organisms. They can cut DNA of variable length, provided that a suitable guide RNA is provided. The flexibility and ease of use of these enzymes make them promising for future genetic engineering applications. | 1 | Biochemistry |
An induction furnace is an electrical furnace in which the heat is applied by induction heating of metal.
Induction furnace capacities range from less than one kilogram to one hundred tons, and are used to melt iron and steel, copper, aluminum, and precious metals.
The advantage of the induction furnace is a clean, energy-efficient and well-controlled melting process, compared to most other means of metal melting.
Most modern foundries use this type of furnace, and many iron foundries are replacing cupola furnaces with induction furnaces to melt cast iron, as the former emit much dust and other pollutants.
Induction furnaces do not require an arc, as in an electric arc furnace, or combustion, as in a blast furnace. As a result, the temperature of the charge (the material entered into the furnace for heating, not to be confused with electric charge) is no higher than required to melt it; this can prevent the loss of valuable alloying elements.
The one major drawback to induction furnace usage in a foundry is the lack of refining capacity: charge materials must be free of oxides and be of a known composition, and some alloying elements may be lost due to oxidation, so they must be re-added to the melt. | 8 | Metallurgy |
Singlet oxygen refers to one of two singlet electronic excited states. The two singlet states are denoted Σ and Δ (the preceding superscript "1" indicates a singlet state). The singlet states of oxygen are 158 and 95 kilojoules per mole higher in energy than the triplet ground state of oxygen. Under most common laboratory conditions, the higher energy Σ singlet state rapidly converts to the more stable, lower energy Δ singlet state. This more stable of the two excited states has its two valence electrons spin-paired in one π* orbital while the second π* orbital is empty. This state is referred to by the title term, singlet oxygen, commonly abbreviated O, to distinguish it from the triplet ground state molecule, O.
Molecular orbital theory predicts the electronic ground state denoted by the molecular term symbol Σ, and two low-lying excited singlet states with term symbols Δ and Σ. These three electronic states differ only in the spin and the occupancy of oxygens two antibonding π-orbitals, which are degenerate (equal in energy). These two orbitals are classified as antibonding and are of higher energy. Following Hunds first rule, in the ground state, these electrons are unpaired and have like (same) spin. This open-shell triplet ground state of molecular oxygen differs from most stable diatomic molecules, which have singlet (Σ) ground states.
Two less stable, higher energy excited states are readily accessible from this ground state, again in accordance with Hund's first rule; the first moves one of the high energy unpaired ground state electrons from one degenerate orbital to the other, where it "flips" and pairs the other, and creates a new state, a singlet state referred to as the Δ state (a term symbol, where the preceding superscripted "1" indicates it as a singlet state). Alternatively, both electrons can remain in their degenerate ground state orbitals, but the spin of one can "flip" so that it is now opposite to the second (i.e., it is still in a separate degenerate orbital, but no longer of like spin); this also creates a new state, a singlet state referred to as the Σ state. The ground and first two singlet excited states of oxygen can be described by the simple scheme in the figure below.
The Δ singlet state is 7882.4 cm above the triplet Σ ground state., which in other units corresponds to 94.29 kJ/mol or 0.9773 eV. The Σ singlet is 13 120.9 cm (157.0 kJ/mol or 1.6268 eV) above the ground state.
Radiative transitions between the three low-lying electronic states of oxygen are formally forbidden as electric dipole processes. The two singlet-triplet transitions are forbidden both because of the spin selection rule ΔS = 0 and because of the parity rule that g-g transitions are forbidden. The singlet-singlet transition between the two excited states is spin-allowed but parity-forbidden.
The lower, O(Δ) state is commonly referred to as singlet oxygen. The energy difference of 94.3 kJ/mol between ground state and singlet oxygen corresponds to a forbidden singlet-triplet transition in the near-infrared at ~1270 nm. As a consequence, singlet oxygen in the gas phase is relatively long lived (54-86 milliseconds), although interaction with solvents reduces the lifetime to microseconds or even nanoseconds. In 2021, the lifetime of airborne singlet oxygen at air/solid interfaces was measured to be 550 microseconds.
The higher Σ state is very short lived. In the gas phase, it relaxes primarily to the ground state triplet with a mean lifetime of 11.8 s. However in solvents such as CS and CCl, it relaxes to the lower singlet Δ in milliseconds due to nonradiative decay channels. | 7 | Physical Chemistry |
Arylsulfatase (EC 3.1.6.1, sulfatase, nitrocatechol sulfatase, phenolsulfatase, phenylsulfatase, p-nitrophenyl sulfatase, arylsulfohydrolase, 4-methylumbelliferyl sulfatase, estrogen sulfatase) is a type of sulfatase enzyme with systematic name aryl-sulfate sulfohydrolase. This enzyme catalyses the following chemical reaction
: an aryl sulfate + HO a phenol + sulfate
It catalyses an analogous reaction for sulfonated hexoses. Types include:
*Arylsulfatase A (also known as "cerebroside-sulfatase")
*Arylsulfatase B (also known as "N-acetylgalactosamine-4-sulfatase")
*Steroid sulfatase (formerly known as "arylsulfatase C")
*ARSC2
*ARSD
*ARSF
*ARSG
*ARSH
*ARSI
*ARSJ
*ARSK
*ARSL (formerly known as "arylsulfatase E", "ARSE") | 1 | Biochemistry |
Altszyler et al. (2017) have shown that these ultrasensitivity measures can be linked by the following equation:
where denoted the mean value of the variable x over the range [a,b]. | 1 | Biochemistry |
Proteorhodopsin functions throughout the Earth's oceans as a light-driven H+ pump, by a mechanism similar to that of bacteriorhodopsin. As in bacteriorhodopsin, the retinal chromophore of proteorhodopsin is covalently bound to the apoprotein via a protonated Schiff base at Lys231. The configuration of the retinal chromophore in unphotolyzed proteorhodopsin is predominantly all-trans
, and isomerizes to 13-cis upon illumination with light. Several models of the complete proteorhodopsin photocycle have been proposed, based on FTIR and UV–visible spectroscopy; they resemble established photocycle models for bacteriorhodopsin. Complete proteorhodopsin based photosystems have been discovered and expressed in E. coli, giving them additional light mediated energy gradient capability for ATP generation without external need for retinal or precursors; with the PR, gene five other proteins code for the photopigment biosynthetic pathway. | 5 | Photochemistry |
A monolithic HPLC column, or monolithic column, is a column used in high-performance liquid chromatography (HPLC). The internal structure of the monolithic column is created in such a way that many channels form inside the column. The material inside the column which separates the channels can be porous and functionalized. In contrast, most HPLC configurations use particulate packed columns; in these configurations, tiny beads of an inert substance, typically a modified silica, are used inside the column. Monolithic columns can be broken down into two categories, silica-based and polymer-based monoliths. Silica-based monoliths are known for their efficiency in separating smaller molecules while, polymer-based are known for separating large protein molecules. | 3 | Analytical Chemistry |
APDS monitors air and water for the three types of biological threat agents: bacteria, viruses, and toxins. The autonomous detection system is capable of (1) rapidly processing and accurately analyzing aerosol or water samples with a high level of confidence; (2) automating and integrating the major system functions into the detector, including sample collection, preparation, analysis, and analytical results reporting; (3) operating in its intended indoor and outdoor environments; and (4) disseminating and archiving analysis results and system operational data via the C3 network, known as the BioWatch Gen-3 Operations Support Service.
APDS operates continuously; the system can detect low concentrations of bioagents that might go undetected by a system that is triggered only when the overall number of particles in the air is high. APDS collects samples, prepares them for analysis, and tests for multiple biological agents. This automation reduces the cost and staffing that would be required to manually analyze samples.
As APDS collects air or water samples, it first runs them through an immunoassay detector. If that detector returns a positive result, APDS performs a second assay based on nucleic-acid amplification and detection. Having two different assay systems increases system reliability and minimizes the possibility of false positives.
The immunoassay detector incorporates liquid arrays, a multiplexed assay that uses small-diameter polystyrene beads (microbeads) coated with thousands of antibodies. Each microbead is colored with a unique combination of red- and orange-emitting dyes. The number of agents that can be detected in a sample is limited only by the number of colored bead sets. When the sample is exposed to the beads, a bioagent, if present, binds to the bead with the appropriate antibody. A second fluorescently labeled antibody is then added to the sample, resulting in a highly fluorescent target for flow analysis. Preparing the sample and performing this first analysis takes less than 30 minutes.
Nucleic acid assays require amplification of one or more target sequences of nucleic acid. Short strands of single-stranded DNA are synthesized in known sequences and attached to spots in the array in a predetermined way Detection of these spots that contain hybridized target DNA allows one to the sequence of DNA in the unknown target. RNA readily hybridizes to form double-stranded structures to its complementary sequence (A-T, C-G, G-C, U-A). Thus, arrays of single-stranded DNA can be used to detect RNA via hybridization.
TABLE 1.1 Centers for Disease Control and Prevention (CDC) Prioritized List of Biological Threat Agents
Research Internationals sells standalone and portable systems for use in mailrooms, called ASAP II. ASAP II gives real time detection of bio-warfare agents, chemical agents and toxic industrial chemicals, explosives in particulate and vapor form and nuclear materials. The system can be customised according to the need of the mailroom.
ASAP II is an automated chemical, biological and nuclear detection and identification system. The system can detect and identify from four (RAPTOR module) to eight (BioHawk module) bio-agents in real time. Periodically or on demand, a concentrated sample is sent to the modules and within fifteen minutes these systems will identify the presence of any bioagents and notify the operator if a hazardous agent is detected.
The systems need to be in a negative pressure room on a downward draft table. An air sampling module within the systems draws air into the downward draft table for analysis. Sampling is continuous until the batch of mail is complete, which may take a few minutes, hours or days. The systems are able to handle thousands of pieces of mail per hour. | 3 | Analytical Chemistry |
Assays for studying interactions of proteins with DNA include:
*DNase footprinting assay
*Filter binding assay
*Gel shift assay | 1 | Biochemistry |
Acyl-CoA is a group of coenzymes that metabolize fatty acids. Acyl-CoA's are susceptible to beta oxidation, forming, ultimately, acetyl-CoA. The acetyl-CoA enters the citric acid cycle, eventually forming several equivalents of ATP. In this way, fats are converted to ATP, the universal biochemical energy carrier. | 1 | Biochemistry |
The n-octanol-water partition coefficient, K is a partition coefficient for the two-phase system consisting of n-octanol and water. K is also frequently referred to by the symbol P, especially in the English literature. It is also called n-octanol-water partition ratio.
K serves as a measure of the relationship between lipophilicity (fat solubility) and hydrophilicity (water solubility) of a substance. The value is greater than one if a substance is more soluble in fat-like solvents such as n-octanol, and less than one if it is more soluble in water.
If a substance is present as several chemical species in the octanol-water system due to association or dissociation, each species is assigned its own K value. A related value, D, does not distinguish between different species, only indicating the concentration ratio of the substance between the two phases. | 7 | Physical Chemistry |
MPI-Marburg is scheduled to expand with a new [http://www.uni-marburg.de/synmikro/synmikro?set_language=en Department for Synthetic Microbiology (SYNMIKRO)], in collaboration with the Max Planck Society and the University of Marburg. The new department will serve as a research centre for SYNMIKRO with about 100 scientific positions expected to be made available. A grant of about 21 million Euro has been allocated for the period of 2010-12 alone. | 9 | Geochemistry |
The cys-loop receptors are named after a characteristic loop formed by a disulfide bond between two cysteine residues in the N terminal extracellular domain.
They are part of a larger family of pentameric ligand-gated ion channels that usually lack this disulfide bond, hence the tentative name "Pro-loop receptors".
A binding site in the extracellular N-terminal ligand-binding domain gives them receptor specificity for (1) acetylcholine (AcCh), (2) serotonin, (3) glycine, (4) glutamate and (5) γ-aminobutyric acid (GABA) in vertebrates. The receptors are subdivided with respect to the type of ion that they conduct (anionic or cationic) and further into families defined by the endogenous ligand. They are usually pentameric with each subunit containing 4 transmembrane helices constituting the transmembrane domain, and a beta sheet sandwich type, extracellular, N terminal, ligand binding domain. Some also contain an intracellular domain like shown in the image.
The prototypic ligand-gated ion channel is the nicotinic acetylcholine receptor. It consists of a pentamer of protein subunits (typically ααβγδ), with two binding sites for acetylcholine (one at the interface of each alpha subunit). When the acetylcholine binds it alters the receptor's configuration (twists the T2 helices which moves the leucine residues, which block the pore, out of the channel pathway) and causes the constriction in the pore of approximately 3 angstroms to widen to approximately 8 angstroms so that ions can pass through. This pore allows Na ions to flow down their electrochemical gradient into the cell. With a sufficient number of channels opening at once, the inward flow of positive charges carried by Na ions depolarizes the postsynaptic membrane sufficiently to initiate an action potential.
A bacterial homologue to an LIC has been identified, hypothesized to act nonetheless as a chemoreceptor. This prokaryotic nAChR variant is known as the GLIC receptor, after the species in which it was identified; loeobacter igand-gated on hannel. | 1 | Biochemistry |
Relaxase nomenclature is varied. In conjugative bacterial plasmids, Mob-class relaxases go by names such as TraI (in plasmid RP4), VirD2 (pTi), TrwC (R388), TraI (F-plasmid), MobB (CloDF13), or TrsK (pGO1). | 1 | Biochemistry |
The phenomenon of predissociation occurs when an electronic transition results in dissociation of the molecule at an excitation energy less than the normal dissociation limit of the upper state. This can occur when the potential energy curve of the upper state crosses the curve for a repulsive state, so that the two states have equal energy at some internuclear distance. This allows the possibility of a radiationless transition to the repulsive state whose energy levels form a continuum, so that there is blurring of the particular vibrational band in the vibrational progression. | 7 | Physical Chemistry |
The common name for an aldehyde is derived from the common name of the corresponding carboxylic acid by dropping the word acid and changing the suffix from -ic or -oic to -aldehyde.
*Formaldehyde
*Acetaldehyde | 0 | Organic Chemistry |
Charles Darwin was the first to observe the transport of dust particles but Louis Pasteur was the first to research microbes and their activity within the air. Prior to Pasteur’s work, laboratory cultures were used to grow and isolate different bioaerosols.
Since not all microbes can be cultured, many were undetected before the development of DNA-based tools. Pasteur also developed experimental procedures for sampling bioaerosols and showed that more microbial activity occurred at lower altitudes and decreased at higher altitudes. | 7 | Physical Chemistry |
Lovastatin is usually well tolerated, with the most common side effects being, in approximately descending order of frequency: creatine phosphokinase elevation, flatulence, abdominal pain, constipation, diarrhoea, muscle aches or pains, nausea, indigestion, weakness, blurred vision, rash, dizziness and muscle cramps. As with all statin drugs, it can rarely cause myopathy, hepatotoxicity (liver damage), dermatomyositis or rhabdomyolysis. This can be life-threatening if not recognised and treated in time, so any unexplained muscle pain or weakness whilst on lovastatin should be promptly mentioned to the prescribing doctor. Other uncommon side effects that should be promptly mentioned to either the prescribing doctor or an emergency medical service include:
These less serious side effects should still be reported if they persist or increase in severity: | 0 | Organic Chemistry |
A metallodendrimer is a type of dendrimer with incorporated metal atoms. The development of this type of material is actively pursued in academia. | 6 | Supramolecular Chemistry |
In contrast to the general similarity in structure and function of the electron transport chains in eukaryotes, bacteria and archaea possess a large variety of electron-transfer enzymes. These use an equally wide set of chemicals as substrates. In common with eukaryotes, prokaryotic electron transport uses the energy released from the oxidation of a substrate to pump ions across a membrane and generate an electrochemical gradient. In the bacteria, oxidative phosphorylation in Escherichia coli is understood in most detail, while archaeal systems are at present poorly understood.
The main difference between eukaryotic and prokaryotic oxidative phosphorylation is that bacteria and archaea use many different substances to donate or accept electrons. This allows prokaryotes to grow under a wide variety of environmental conditions. In E. coli, for example, oxidative phosphorylation can be driven by a large number of pairs of reducing agents and oxidizing agents, which are listed below. The midpoint potential of a chemical measures how much energy is released when it is oxidized or reduced, with reducing agents having negative potentials and oxidizing agents positive potentials.
As shown above, E. coli can grow with reducing agents such as formate, hydrogen, or lactate as electron donors, and nitrate, DMSO, or oxygen as acceptors. The larger the difference in midpoint potential between an oxidizing and reducing agent, the more energy is released when they react. Out of these compounds, the succinate/fumarate pair is unusual, as its midpoint potential is close to zero. Succinate can therefore be oxidized to fumarate if a strong oxidizing agent such as oxygen is available, or fumarate can be reduced to succinate using a strong reducing agent such as formate. These alternative reactions are catalyzed by succinate dehydrogenase and fumarate reductase, respectively.
Some prokaryotes use redox pairs that have only a small difference in midpoint potential. For example, nitrifying bacteria such as Nitrobacter oxidize nitrite to nitrate, donating the electrons to oxygen. The small amount of energy released in this reaction is enough to pump protons and generate ATP, but not enough to produce NADH or NADPH directly for use in anabolism. This problem is solved by using a nitrite oxidoreductase to produce enough proton-motive force to run part of the electron transport chain in reverse, causing complex I to generate NADH.
Prokaryotes control their use of these electron donors and acceptors by varying which enzymes are produced, in response to environmental conditions. This flexibility is possible because different oxidases and reductases use the same ubiquinone pool. This allows many combinations of enzymes to function together, linked by the common ubiquinol intermediate. These respiratory chains therefore have a modular design, with easily interchangeable sets of enzyme systems.
In addition to this metabolic diversity, prokaryotes also possess a range of isozymes – different enzymes that catalyze the same reaction. For example, in E. coli, there are two different types of ubiquinol oxidase using oxygen as an electron acceptor. Under highly aerobic conditions, the cell uses an oxidase with a low affinity for oxygen that can transport two protons per electron. However, if levels of oxygen fall, they switch to an oxidase that transfers only one proton per electron, but has a high affinity for oxygen. | 1 | Biochemistry |
Ahmad Salahuddin (7 July 1937 – 26 November 1996) was an Indian biochemist who served as a professor of biochemistry and department chairman (1984–1996) at Aligarh Muslim University (AMU) Aligarh, India. He was a Founder Director of Interdisciplinary Biotechnology Unit at AMU in 1984. | 1 | Biochemistry |
The Knudsen number of the particle define three different dynamical regimes that govern the behaviour of an aerosol:
where is the mean free path of the suspending gas and is the diameter of the particle. For particles in the free molecular regime, K >> 1; particles small compared to the mean free path of the suspending gas. In this regime, particles interact with the suspending gas through a series of "ballistic" collisions with gas molecules. As such, they behave similarly to gas molecules, tending to follow streamlines and diffusing rapidly through Brownian motion. The mass flux equation in the free molecular regime is:
where a is the particle radius, P and P are the pressures far from the droplet and at the surface of the droplet respectively, k is the Boltzmann constant, T is the temperature, C is mean thermal velocity and α is mass accommodation coefficient. The derivation of this equation assumes constant pressure and constant diffusion coefficient.
Particles are in the continuum regime when K << 1. In this regime, the particles are big compared to the mean free path of the suspending gas, meaning that the suspending gas acts as a continuous fluid flowing round the particle. The molecular flux in this regime is:
where a is the radius of the particle A, M is the molecular mass of the particle A, D is the diffusion coefficient between particles A and B, R is the ideal gas constant, T is the temperature (in absolute units like kelvin), and P and P are the pressures at infinite and at the surface respectively.
The transition regime contains all the particles in between the free molecular and continuum regimes or K ≈ 1. The forces experienced by a particle are a complex combination of interactions with individual gas molecules and macroscopic interactions. The semi-empirical equation describing mass flux is:
where I is the mass flux in the continuum regime. This formula is called the Fuchs-Sutugin interpolation formula. These equations do not take into account the heat release effect. | 7 | Physical Chemistry |
Mill scale can be used as a raw material in granular refractory. When this refractory is cast and preheated, these scales provide escape routes for the evaporating water vapor, thus preventing cracks and resulting in a strong, monolithic structure. | 8 | Metallurgy |
thumb|right|450px|Fig. 2. Ser-Recombinases: The (essentially irreversible) subunit-rotation pathway.<br /><br />Contrary to Tyr-recombinases, the four participating DNA strands are cut in synchrony at points staggered by only 2 bp (leaving little room for proofreading). Subunit-rotation (180°) permits the exchange of strands while covalently linked to the protein partner. The intermediate exposure of double-strand breaks bears risks of triggering illegitimate recombination and thereby secondary reactions.<br /><br />Here, the synaptic complex arises from the association of pre-formed recombinase dimers with the respective target sites (CTD/NTD, C-/N-terminal domain). Like for Tyr-recombinases, each site contains two arms, each accommodating one protomer. As both arms are structured slightly differently, the subunits become conformationally tuned and thereby prepared for their respective role in the recombination cycle. Contrary to members of the Tyr-class the recombination pathway converts two different substrate sites (attP and attB) to site-hybrids [[site-specific recombinase technology|(attL and attR). This explains the irreversible nature of this particular recombination pathway, which can only be overcome by auxiliary "recombination directionality factors" (RDFs).]]
Based on amino acid sequence homologies and mechanistic relatedness, most site-specific recombinases are grouped into one of two families: the tyrosine (Tyr) recombinase family or serine (Ser) recombinase family. The names stem from the conserved nucleophilic amino acid residue present in each class of recombinase which is used to attack the DNA and which becomes covalently linked to it during strand exchange. The earliest identified members of the serine recombinase family were known as resolvases or DNA invertases, while the founding member of the tyrosine recombinases, lambda phage integrase (using attP/B recognition sites), differs from the now well-known enzymes such as Cre (from the P1 phage) and FLP (from the yeast Saccharomyces cerevisiae). Famous serine recombinases include enzymes such as gamma-delta resolvase (from the Tn1000 transposon), Tn3 resolvase (from the Tn3 transposon), and φC31 integrase (from the φC31 phage).
Although the individual members of the two recombinase families can perform reactions with the same practical outcomes, the families are unrelated to each other, having different protein structures and reaction mechanisms. Unlike tyrosine recombinases, serine recombinases are highly modular, as was first hinted by biochemical studies and later shown by crystallographic structures. Knowledge of these protein structures could prove useful when attempting to re-engineer recombinase proteins as tools for genetic manipulation. | 1 | Biochemistry |
The configuration index is a single digit which is the priority number of the ligand trans to the ligand of lowest priority in the plane perpendicular to the 4 fold axis. (If there is more than one choice then the highest numerical value second digit is taken.) NB this procedure gives the same result as SP-4, however in this case the polyhedral symbol specifies that the complex is non-planar. | 4 | Stereochemistry |
Trimmed sequences from the previous step are aligned to the reference genome using a Burrows–Wheeler aligner (BWA) and the unmapped reads are removed. The aligned reads that have the same 24-base pair tag sequence and genomic region are detected and grouped (family αβ and βα in Figure 2). Each group represents a “tag family.” Tag families with fewer than three members are not analyzed. To remove errors that arise during PCR amplification or sequencing, mutations that are supported by less than 70% of the members (reads) are filtered out from the analysis. A consensus sequence is then generated for each family using the identical sequences in each position of the remaining reads. The consensus sequence is called the SSCS. It increases the NGS accuracy to about 20 fold higher; however, this method relies on the sequencing information from single strands of DNA and therefore is sensitive to the errors induced at the first round or before PCR amplification. | 1 | Biochemistry |
There are two types of twinning that can occur during growth, accidental and ones where the twinned structure has lower energy.
In accidental growth twinning an atom joins a crystal face in a less than ideal position, forming a seed for growth of a twin. The original crystal and its twin then grow together and closely resemble each other. This is characteristic enough of certain minerals to suggest that it is thermodynamically or kinetically favored under conditions of rapid growth.
Different from these are twins found in nanoparticles such as the image here, these fivefold or decahedral nanoparticles being one of the most common. These cyclic twins occur as they are lower in energy at small sizes. For the five-fold case shown, there is a disclination along the common axis which leads to an additional strain energy. Balancing this there is a reduction in the surface free energy, in large part due to more (111) surface facets. In small nanoparticles the decahedral and a more complicated icosahedral structure (with twenty units) are lower energy, but at larger energies single crystals become lower energy. However, they do not have to transform into single crystals and can grow very large, and are known as fivelings, documented as early as 1831 by Gustav Rose; further drawings are available in the Atlas der Kristallformen, and see also the article on fiveling<nowiki/>s. | 3 | Analytical Chemistry |
In the same paper in which the structure of prFMN was deduced in the active site of AnFdc1 there was a proposal for the mechanism by which Fdc1 decarboxylates α,β-unsaturated carboxylic acids. Not all UbiD enzymes decarboxylate acrylic acid substrates and other mechanisms may be at play for alternative substrates. In the case of AnFdc1 it was noted that prFMN displays an azomethine ylide characteristic C4a-N5+=C1’(Figure 1). This is a well-known 1,3-dipole in organic chemistry, positioned in the enzyme active site near to the α,β-unsaturated carboxylic acid substrate which contains a 1,3-dipolarophile. Thus, it was proposed that a 1,3-dipolar cycloaddition mechanism was responsible for the enzymatic decarboxylation. This was confirmed in a later paper.
The mechanism proposed in for 1,3-dipolar cycloaddition by Fdc1 is as follows (intermediates represented in Figure 1):
# 1,3-dipolar cycloaddition between prFMN and the α,β-unsaturated substrate leads to a pyrrolidine cycloadduct (Int1)
# This pyrrolidine cycloadduct supports simultaneous decarboxylation and ring opening, resulting in the formation of a distinct prFMN-alkene adduct (Int2)
# A conserved glutamic acid residue (E282) donates a proton to the alkene moiety, resulting a second pyrrolidine cycloadduct (Int3)
# The reaction concludes with cycloelimination of Int3 and the release of the alkene product and CO
A study went on to present evidence for the 1,3-dipolar cycloaddition, due to suspected turnover of cinnamic acid a crystal structure of AnFdc1 in complex with α-fluorocinnamic acid revealed the substrate Cα and Cβ carbons are located directly above the prFMN C1’ and C4a respectively (shown as Sub in Figure 1 - with cinnamic acid as opposed to α-fluorocinnamic acid). Cinnamic acid was confirmed to bind in a similar manner using inactive AnFdc1 crystals containing FMN. The AnFdc1 E282Q mutant crystallised with cinnamic acid revealed a structure corresponding to the Int2 species, this was taken to mean that progression through the 1,3-dipolarcycloadition cycle was halted as E282 is unable to donate a proton to the alkene moiety.
In order to observe the Int1 and Int3 structures alkyne analogues were used. Like alkenes these compounds can also act as dipolarophiles but cycloaddition would yield a cycloadduct containing a double bond. An inactive AnFdc1 enzyme (with prFMN bound) co-crystallised with the phenylpropiolic acid revealed binding in a similar manner to the α-fluorocinnamic acid AnFdc1 and cinnamic acid AnFdc1 with FMN bound (Inhib). An active AnFdc1 enzyme co-crystallised with phenylpropiolic acid revealed clear density for a 3-pyrroline cycloadduct (Int3’) between the alkyne and prFMN. Int3’ represents a structure post decarboxylation, so it was assumed that over the time it took for crystallisation (~24h) the decarboxylation had occurred. Using a rapid soaking procedure, a different cycloadduct was observed that retained the carboxyl moiety (Int1’). | 1 | Biochemistry |
ILs are potential heat transfer and storage media in solar thermal energy systems. Concentrating solar thermal facilities such as parabolic troughs and solar power towers focus the sun's energy onto a receiver, which can generate temperatures of around . This heat can then generate electricity in a steam or other cycle. For buffering during cloudy periods or to enable generation overnight, energy can be stored by heating an intermediate fluid. Although nitrate salts have been the medium of choice since the early 1980s, they freeze at and thus require heating to prevent solidification. Ionic liquids such as [Cmim][] have more favorable liquid-phase temperature ranges (-75 to 459 °C) and could therefore be excellent liquid thermal storage media and heat transfer fluids. | 7 | Physical Chemistry |
While prokaryotes are considered strictly unicellular, most can form stable aggregate communities. When such communities are encased in a stabilizing polymer matrix ("slime"), they may be called "biofilms". Cells in biofilms often show distinct patterns of gene expression (phenotypic differentiation) in time and space. Also, as with multicellular eukaryotes, these changes in expression often appear to result from cell-to-cell signaling, a phenomenon known as quorum sensing.
Biofilms may be highly heterogeneous and structurally complex and may attach to solid surfaces, or exist at liquid-air interfaces, or potentially even liquid-liquid interfaces. Bacterial biofilms are often made up of microcolonies (approximately dome-shaped masses of bacteria and matrix) separated by "voids" through which the medium (e.g., water) may flow easily. The microcolonies may join together above the substratum to form a continuous layer, closing the network of channels separating microcolonies. This structural complexity—combined with observations that oxygen limitation (a ubiquitous challenge for anything growing in size beyond the scale of diffusion) is at least partially eased by movement of medium throughout the biofilm—has led some to speculate that this may constitute a circulatory system and many researchers have started calling prokaryotic communities multicellular (for example ). Differential cell expression, collective behavior, signaling, programmed cell death, and (in some cases) discrete biological dispersal events all seem to point in this direction. However, these colonies are seldom if ever founded by a single founder (in the way that animals and plants are founded by single cells), which presents a number of theoretical issues. Most explanations of co-operation and the evolution of multicellularity have focused on high relatedness between members of a group (or colony, or whole organism). If a copy of a gene is present in all members of a group, behaviors that promote cooperation between members may permit those members to have (on average) greater fitness than a similar group of selfish individuals (see inclusive fitness and Hamilton's rule).
Should these instances of prokaryotic sociality prove to be the rule rather than the exception, it would have serious implications for the way we view prokaryotes in general, and the way we deal with them in medicine. Bacterial biofilms may be 100 times more resistant to antibiotics than free-living unicells and may be nearly impossible to remove from surfaces once they have colonized them. Other aspects of bacterial cooperation—such as bacterial conjugation and quorum-sensing-mediated pathogenicity, present additional challenges to researchers and medical professionals seeking to treat the associated diseases. | 1 | Biochemistry |
The cardiac action potential differs from the neuronal action potential by having an extended plateau, in which the membrane is held at a high voltage for a few hundred milliseconds prior to being repolarized by the potassium current as usual. This plateau is due to the action of slower calcium channels opening and holding the membrane voltage near their equilibrium potential even after the sodium channels have inactivated.
The cardiac action potential plays an important role in coordinating the contraction of the heart. The cardiac cells of the sinoatrial node provide the pacemaker potential that synchronizes the heart. The action potentials of those cells propagate to and through the atrioventricular node (AV node), which is normally the only conduction pathway between the atria and the ventricles. Action potentials from the AV node travel through the bundle of His and thence to the Purkinje fibers. Conversely, anomalies in the cardiac action potential—whether due to a congenital mutation or injury—can lead to human pathologies, especially arrhythmias. Several anti-arrhythmia drugs act on the cardiac action potential, such as quinidine, lidocaine, beta blockers, and verapamil. | 7 | Physical Chemistry |
For the measurement of the diversity of fragmentomic features, the PFE metric, derived from Shannons Index of entropy, is developed. The default number of 201 bins of lengths 100 to 300 are used for density estimation by the maximum likelihood method. The probability of having a fragment with size , () is computed by the division of the number of fragments with size by the total number of fragments. Shannons entropy is calculated with fthe formula: . | 1 | Biochemistry |
Hydrazones are usually very stable towards solvolysis, and conversion to the ketone can require vigorous conditions. Also, aldehydic hydrazones often instead disproportionate to a nitrile and amine.
Two principal workup environments are common: oxidation and solvolysis. Reductive conversions are possible with low-valent transition metals, but remained relatively unstudied .
Oxidative cleavage has high yields and is most frequently used. Ozone or singlet oxygen can ozonolyze the diazene bond (and any olefinic moieties present), leaving a carbonyl, a nitrosamine, and dioxygen. Lemieuxs gentler oxidation tolerates acetals and benzyl ethers. Peroxide reagents (e.g. NaBO, (tBuNSO), or m'-ClBzOH) cleave the hydrazone with varying speeds, selectivities, and mechanisms, but the Baeyer-Villiger oxidation is a common side-reaction. High-valent transition metal oxyhalides (e.g. WF, CoF, MoOCl) appear to primarily cleave via radicals. All except ozone and singlet oxygen generate nitriles from aldehydic hydrazones, either as the major or a substantial minor product.
Certain electrophiles also elicit nitriles: chloroformates, strongly-activated alkynes, or methyl iodide and a hindered base. Methyl iodide is also useful for hydrolysis: the alkylated hydrazonium iodide easily hydrolyzes to a carbonyl and hydrazoform, and air cleaves the hydrazoform to the hydrazine and carbon dioxide.
Indeed, a wide variety of acids promote hydrolysis. Bismuth trichloride cleaves arbitrary hydrazones in a microwave. Oxalic acid abstracts hydrazine from ketonic hydrazones; the oxalate adduct then decomposes to the original auxiliary in aqueous base. Silica gel hydrolyzes exquisitely acid-sensitive substrates, but is too weak to affect ketonic hydrazones adjacent to a primary carbon. Ketonic hydrazones adjacent to a secondary or tertiary carbon hydrolyze in the presence of catalytic cupric salts; that procedure also preserves substrates disturbed by oxidants or strong acids.
Boron trifluoride etherate catalyzes thioketalization, and Baker's yeast will hydrolyze non-bioactive substrates.
Hydrazone carbamates are cleaved much more readily than their parent hydrazones: para-toluenesulfonic acid affords the corresponding ketones in near-quantitative yields. | 0 | Organic Chemistry |
The heterokontophytes, also known as the stramenopiles, are a very large and diverse group of eukaryotes. The photoautotrophic lineage, Ochrophyta, including the diatoms and the brown algae, golden algae, and yellow-green algae, also contains red algal derived chloroplasts.
Heterokont chloroplasts are very similar to haptophyte chloroplasts, containing a pyrenoid, triplet thylakoids, and with some exceptions, having four layer plastidic envelope, the outermost epiplastid membrane connected to the endoplasmic reticulum. Like haptophytes, heterokontophytes store sugar in chrysolaminarin granules in the cytoplasm. Heterokontophyte chloroplasts contain chlorophyll a and with a few exceptions chlorophyll c, but also have carotenoids which give them their many colors. | 5 | Photochemistry |
At low voltages, the rate of migration of the DNA is proportional to the voltage applied, i.e. the higher the voltage, the faster the DNA moves. However, in increasing electric field strength, the mobility of high-molecular-weight DNA fragments increases differentially, and the effective range of separation decreases and resolution therefore is lower at high voltage. For optimal resolution of DNA greater than 2kb in size in standard gel electrophoresis, 5 to 8 V/cm is recommended. Voltage is also limited by the fact that it heats the gel and may cause the gel to melt if a gel is run at high voltage for a prolonged period, particularly for low-melting point agarose gel.
The mobility of DNA however may change in an unsteady field. In a field that is periodically reversed, the mobility of DNA of a particular size may drop significantly at a particular cycling frequency. This phenomenon can result in band inversion whereby larger DNA fragments move faster than smaller ones in PFGE. | 1 | Biochemistry |
Many chloro and bromoalkanes are formed naturally. The principal pathways involve the enzymes chloroperoxidase and bromoperoxidase. | 0 | Organic Chemistry |
The Baeyer–Emmerling indole synthesis is a method for synthesizing indole from a (substituted) ortho-nitrocinnamic acid and iron powder in strongly basic solution. This reaction was discovered by Adolf von Baeyer and Adolph Emmerling in 1869. | 0 | Organic Chemistry |
The output of SAGE is a list of short sequence tags and the number of times it is observed. Using sequence databases a researcher can usually determine, with some confidence, from which original mRNA (and therefore which gene) the tag was extracted.
Statistical methods can be applied to tag and count lists from different samples in order to determine which genes are more highly expressed. For example, a normal tissue sample can be compared against a corresponding tumor to determine which genes tend to be more (or less) active. | 1 | Biochemistry |
Cornforth was named the Australian of the Year in 1975, jointly with Maj. Gen. Alan Stretton. In 1977, Cornforth was recognised by his alma mater, the University of Sydney, with the award of an honorary Doctor of Science. Cornforth's other awards and recognitions follow:
* Davy Medal (1968)
* Elected a Fellow of the Royal Society (FRS) in 1953
* Commander of the Order of the British Empire (CBE; 1972)
* Nobel Prize in Chemistry (1975)
* Royal Medal (1976)
* Knight Bachelor (1977)
* Corresponding Fellow of the Australian Academy of Science (1977)
* Foreign member of the Royal Netherlands Academy of Arts and Sciences (since 1978)
* Copley Medal (1982)
* Companion of the Order of Australia (AC; 1991)
* Centenary Medal (2001)
Cornforth's certificate of election for the Royal Society reads: | 0 | Organic Chemistry |
Though the ropB protein has 7 histidines (H12, H81, H93, H144, H265, H266, and H277) structurally present, the ropB histidine switch primarily operates with a single functionally involved histidine (H144) conveniently placed to associate with ropB sidechains (Y176 and E185) that near each other upon the addition of a hydrogen ion to H144 in acidic conditions. Only one histidine (H12) is located on the N-domain while the rest lie in the C-terminal domain. | 1 | Biochemistry |
The Portlethen Moss is an acidic bog nature reserve located to the west of the town of Portlethen, Aberdeenshire in Scotland. Like other mosses, this wetland area supports a variety of plant and animal species, even though it has been subject to certain development and agricultural degradation pressures. For example, the Great Crested Newt was found here prior to the expansion of the town of Portlethen. Many acid loving vegetative species occur in Portlethen Moss, and the habitat is monitored by the Scottish Wildlife Trust.
Portlethen Moss is the location of considerable prehistoric, Middle Ages and seventeenth century history, largely due to a ridge near the bog which was the route of early travellers. By at least the Middle Ages this trackway was more formally constructed with raised stonework and called the Causey Mounth. Without this drovers' road, travel through the Portlethen Moss and several nearby bogs would have been impossible between Aberdeen and coastal points to the south. | 2 | Environmental Chemistry |
In pharmaceutics, hairstyling, personal hygiene, and cosmetics, emulsions are frequently used. These are usually oil and water emulsions but dispersed, and which is continuous depends in many cases on the pharmaceutical formulation. These emulsions may be called creams, ointments, liniments (balms), pastes, films, or liquids, depending mostly on their oil-to-water ratios, other additives, and their intended route of administration. The first 5 are topical dosage forms, and may be used on the surface of the skin, transdermally, ophthalmically, rectally, or vaginally. A highly liquid emulsion may also be used orally, or may be injected in some cases.
Microemulsions are used to deliver vaccines and kill microbes. Typical emulsions used in these techniques are nanoemulsions of soybean oil, with particles that are 400–600 nm in diameter. The process is not chemical, as with other types of antimicrobial treatments, but mechanical. The smaller the droplet the greater the surface tension and thus the greater the force required to merge with other lipids. The oil is emulsified with detergents using a high-shear mixer to stabilize the emulsion so, when they encounter the lipids in the cell membrane or envelope of bacteria or viruses, they force the lipids to merge with themselves. On a mass scale, in effect this disintegrates the membrane and kills the pathogen. The soybean oil emulsion does not harm normal human cells, or the cells of most other higher organisms, with the exceptions of sperm cells and blood cells, which are vulnerable to nanoemulsions due to the peculiarities of their membrane structures. For this reason, these nanoemulsions are not currently used intravenously (IV). The most effective application of this type of nanoemulsion is for the disinfection of surfaces. Some types of nanoemulsions have been shown to effectively destroy HIV-1 and tuberculosis pathogens on non-porous surfaces. | 7 | Physical Chemistry |
Sodium dodecyl sulfate, appearing as its synonym sodium lauryl sulfate (SLS), is considered a generally recognized as safe (GRAS) ingredient for food use according to the USFDA (21 CFR 172.822). It is used as an emulsifying agent and whipping aid. As an emulsifier in or with egg whites the United States Code of Federal Regulations require that it must not exceed 1,000 parts per million (0.1%) in egg white solids or 125 parts per million (0.0125%) in frozen or liquid egg whites and as a whipping agent for the preparation of marshmallows it must not exceed 0.5% of the weight of gelatine. SLS is reported to temporarily diminish perception of sweetness. | 1 | Biochemistry |
Melanie Jane Leng is a Professor of Isotope Geosciences at the University of Nottingham working on isotopes, palaeoclimate and geochemistry. She also serves as the Chief Scientist for Environmental Change Adaptation and Resilience at the British Geological Survey and Director of the Centre for Environmental Geochemistry, a collaboration between the University of Nottingham and the British Geological Survey. For many years (till 2019) she has been the UK convenor and representative of the UK geoscience community on the International Continental Scientific Drilling Program. | 9 | Geochemistry |
Lee received her BA summa cum laude in Chemistry at Cornell University in 1990. She obtained her PhD in organic chemistry at Harvard University in 1994.
From 1995 to 1997, Lee was a NIH Postdoctoral Research Fellow at UCLA in the lab of Kendall N. Houk.
Lee also teaches classes in organic chemistry for undergraduate students and advanced organic chemistry for graduate students. | 0 | Organic Chemistry |
Nayak decided to take on full-time anti-superstition activism in 2004 when he heard that a girl had been sacrificed in Gulbarga in Karnataka. He was an assistant professor of biochemistry when he took voluntary retirement on 25 November 2006, after working there for 28 years.
Before the general election in 2009, Nayak laid an open challenge to any soothsayer to answer 25 questions correctly about the forthcoming elections. The prize was set at (about ). About 450 responses were mailed to him, but none were found to be correct. The Federation of Indian Rationalist Associations has been conducting such challenges since 1991. During May 2013 Karnataka state assembly election, disappointed at the challenge being one-sided, Nayak had decided against the idea of challenging astrologers this time. But when a Bengaluru-based astrologer Shankar Hegde made claims to predict the election results accurately, he received the challenge. Nayak offered to hand over a cheque of Rs.10 lakh (after deducting taxes as applicable under income Tax Act), if 19 out of the 20 results were proven right. However, later on astrologer Hegde did not turn up.
Through the organisation named Aid Without Religion which was registered in July 2011, he has been helping people and institutions where there are no religious rituals, superstitious practices, unscientific systems of medicine and such supernatural beliefs. The registration was done at Rahu Kalam, a time of the day which is the most inauspicious – so it was a double rather a triple whammy, a Saturday, new moon day that too in the month of Ati which is considered to be the most unlucky time and at Rahu Kalam!
He has been featured on National Geographics television show Is it real?'. He has also appeared on the Discovery Channel. He has been a regular columnist at the newspaper Mangalore Today since its inception. He also serves on the editorial board of the Folks Magazine.
He has admitted to have been attacked for his activism a few times. He also has stated that his scooter's brake wires were once found severed, after an astrologer predicted his death or injury. He was a close associate to Gauri Lankesh, M. M. Kalburgi, and Narendra Dabholkar; all three like-minded and were assassinated in a more-or-less similar fashion.
He was also involved in fighting against Midbrain activation, an alleged modern technique that enables students to see objects despite being blindfolded.
In March 2017, there was an attempt on Narendra Nayaks life. During the early morning hours, while on his way to the Mangala swimming pool in his car, he was approached by two unidentified men in a bike wearing helmets and hinted that his tyres were punctured. An unfazed Nayak suspected foul play and with a great presence of mind drove all the way to a nearby gas station and saw that everything was in order. He immediately filed a Police Complain. Nayak suspected that this attempt on his life could possibly be the repercussions to his fight for the justice of the slain RTI activist Vinayak Baliga, who was murdered exactly a year previous to this episode. Nayaks personal gunman was on holidays. Nayak continues to have personal gunman handed over by Mangalore Police till date.
Narendra presented at the first Global Congress on Scientific Thinking and Action which was held on March 17–20, 2021. During Session III on Alternative Medicine, he talked about the wide use of alternative medicines in India, including homeopathy, and said that various alternative treatments are often claimed to be Indian in origin. In addition, he states that the relatively low death rate from COVID in India has been falsely attributed to the use of homeopathic medicines as preventative. When asked what should be done about the use of alternative medicines in India, he said, flatly, “They should be banned.” | 1 | Biochemistry |
Alterations in the pathways leading to the addition of the removal of the mA mark result in impaired gene expression and cellular function, which can lead to disease.
Normal mA levels are altered in a number of cancers. Reduced mA levels due to down regulation of METTL3 and/or METTL14 lead to the activation of a number of oncogenes, such as the gene encoding ADAM metallopeptidase domain 19 (ADAM19). Moreover, loss of mA also results in the down regulation of tumor suppressors like cyclin-dependent kinase inhibitor 2A (CDKN2A) and breast cancer 2 (BRCA2). On the other hand, increased mA levels inhibit tumor progression in certain types of cancer. In addition, single nucleotide polymorphisms (SNPs) on the gene encoding FTO have been associated with increased risk of breast and pancreatic cancer. Altered mA levels also contribute to hypoxia-induced enrichment of breast cancer stem cells phenotype. All things considered, "writers" and "erasers" of the mA mark may be good potential drug targets in cancer therapy.
Metabolic disorders are also affected by the mA mark due to the role of FTO. Overexpression of FTO results in increased body and fat mass, whereas loss of FTO leads to a reduction in lean body mass. However, the mechanisms by which changes in FTO expression affect body and fat mass are not understood.
Current research of the m6a epitranscriptome is continuing to uncover the implications of m6a and its post-physiological effects on ischemic stroke incidents. Microglial-mediated responses and contributing demethylases, including FTO and ALKBH5, appear to be a contributing factor for alterations of the cerebral m6a epitranscriptome. Mood disorders, such as major depressive disorder, have also been identified as disease processes associated with m6a epitranscriptome changes. | 1 | Biochemistry |
Advantages:
* Can be machined, brazed, formed, cut with available processes.
* Develops a protective oxide layer that is self-healing.
* This oxide layer is stable and has a high emission coefficient.
* Allows the design of thin-walled structures (sandwich).
* Resistant to harsh weather conditions in the troposphere.
* Low maintenance cost.
* Low material cost.
Disadvantages:
* It has a higher expansion coefficient than other materials, causing higher thermal stresses.
* Higher density.
* Lower maximum allowable temperature. | 8 | Metallurgy |
The flux control summation theorem was discovered independently by the Kacser/Burns group and the Heinrich/Rapoport group in the early 1970s and late 1960s. The flux control summation theorem implies that metabolic fluxes are systemic properties and that their control is shared by all reactions in the system. When a single reaction changes its control of the flux this is compensated by changes in the control of the same flux by all other reactions. | 1 | Biochemistry |
Methyl yellow, or C.I. 11020, is an organic compound with the formula CHNCHN(CH). It is an azo dye derived from dimethylaniline. It is a yellow solid. According to X-ray crystallography, the CN core of the molecule is planar.
It is used as a dye for plastics and may be used as a pH indicator. In aqueous solution at low pH, methyl yellow appears red. Between pH 2.9 and 4.0, methyl yellow undergoes a transition, to become yellow above pH 4.0. | 3 | Analytical Chemistry |
Combinations of the above techniques produce "hybrid" or "hyphenated" techniques. Several examples are in popular use today and new hybrid techniques are under development.
Hyphenated separation techniques refer to a combination of two or more techniques to separate chemicals from solutions and detect them. Most often, the other technique is some form of chromatography. Hyphenated techniques are widely used in chemistry and biochemistry. A slash is sometimes used instead of hyphen, especially if the name of one of the methods contains a hyphen itself.
Examples of hyphenated techniques:
*Gas chromatography-mass spectrometry (GC-MS)
*Liquid chromatography–mass spectrometry (LC-MS)
*Liquid chromatography-infrared spectroscopy (LC-IR)
*High-performance liquid chromatography/electrospray ionization-mass spectrometry (HPLC/ESI-MS)
*Chromatography-diode-array detection (LC-DAD)
*Capillary electrophoresis-mass spectrometry (CE-MS)
*Capillary electrophoresis-ultraviolet-visible spectroscopy (CE-UV)
*Ion-mobility spectrometry–mass spectrometry
*Prolate trochoidal mass spectrometer | 3 | Analytical Chemistry |
An annulation is defined as a transformation of one or more acyclic precursors resulting in the fusion of a new ring via two newly generated bonds. These strategies can be used to create aromatic systems from acyclic precursors in a single step, with many substituents already in place. A common synthetic annulation reaction is the Robinson annulation. It is a useful reactions for forming six-membered rings and generating polycyclic compounds. It is the combination of the Michael Addition and the Aldol Condensation reaction. | 0 | Organic Chemistry |
The above formula can be used to determine the 99% confidence level that all sequences in a genome are represented by using a vector with an insert size of twenty thousand basepairs (such as the phage lambda vector). The genome size of the organism is three billion basepairs in this example.
clones
Thus, approximately 688,060 clones are required to ensure a 99% probability that a given DNA sequence from this three billion basepair genome will be present in a library using a vector with an insert size of twenty thousand basepairs. | 1 | Biochemistry |
Dihydrobiopterin (BH) is a pteridine compound produced in the synthesis of L-DOPA, dopamine, serotonin, norepinephrine and epinephrine. It is restored to the required cofactor tetrahydrobiopterin by dihydrobiopterin reductase. | 1 | Biochemistry |
In dairy cattle, ketosis commonly occurs during the first weeks after giving birth to a calf and is sometimes referred to as acetonemia. This is the result of an energy deficit when intake is inadequate to compensate for the increased metabolic demand of lactating. The elevated β-hydroxybutyrate concentrations can depress gluconeogenesis, feed intake and the immune system, as well as have an impact on milk composition. Point of care diagnostic tests can be useful to screen for ketosis in cattle.
In sheep, ketosis, evidenced by hyperketonemia with beta-hydroxybutyrate in blood over 0.7 mmol/L, is referred to as pregnancy toxemia. This may develop in late pregnancy in ewes bearing multiple fetuses and is associated with the considerable metabolic demands of the pregnancy. In ruminants, because most glucose in the digestive tract is metabolized by rumen organisms, glucose must be supplied by gluconeogenesis. Pregnancy toxemia is most likely to occur in late pregnancy due to metabolic demand from rapid fetal growth and may be triggered by insufficient feed energy intake due to weather conditions, stress or other causes. Prompt recovery may occur with natural parturition, Caesarean section or induced abortion. Prevention through appropriate feeding and other management is more effective than treatment of advanced stages of pregnancy toxemia. | 1 | Biochemistry |
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