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During lagging strand synthesis, DNA ligase I connects the Okazaki fragments, following replacement of the RNA primers with DNA nucleotides by DNA polymerase δ. Okazaki fragments that are not ligated could cause double-strand-breaks, which cleaves the DNA. Since only a small number of double-strand breaks are tolerated, and only a small number can be repaired, enough ligation failures could be lethal to the cell.
Further research implicates the supplementary role of proliferating cell nuclear antigen (PCNA) to DNA ligase Is function of joining Okazaki fragments. When the PCNA binding site on DNA ligase I is inactive, DNA ligase Is ability to connect Okazaki fragments is severely impaired. Thus, a proposed mechanism follows: after a PCNA-DNA polymerase δ complex synthesizes Okazaki fragments, the DNA polymerase δ is released. Then, DNA ligase I binds to the PCNA, which is clamped to the nicks of the lagging strand, and catalyzes the formation of phosphodiester bonds. | 1 | Biochemistry |
The scientific branch that studies and diagnoses diseases on the cellular level is called cytopathology. Cytopathology is generally used on samples of free cells or tissue fragments, in contrast to the pathology branch of histopathology, which studies whole tissues. Cytopathology is commonly used to investigate diseases involving a wide range of body sites, often to aid in the diagnosis of cancer but also in the diagnosis of some infectious diseases and other inflammatory conditions. For example, a common application of cytopathology is the Pap smear, a screening test used to detect cervical cancer, and precancerous cervical lesions that may lead to cervical cancer. | 1 | Biochemistry |
Some biopolymers- such as PLA, naturally occurring zein, and poly-3-hydroxybutyrate can be used as plastics, replacing the need for polystyrene or polyethylene based plastics.
Some plastics are now referred to as being degradable, oxy-degradable or UV-degradable. This means that they break down when exposed to light or air, but these plastics are still primarily (as much as 98 per cent) oil-based and are not currently certified as biodegradable under the European Union directive on Packaging and Packaging Waste (94/62/EC). Biopolymers will break down, and some are suitable for domestic composting.
Biopolymers (also called renewable polymers) are produced from biomass for use in the packaging industry. Biomass comes from crops such as sugar beet, potatoes, or wheat: when used to produce biopolymers, these are classified as non food crops. These can be converted in the following pathways:
Sugar beet > Glyconic acid > Polyglyconic acid
Starch > (fermentation) > Lactic acid > Polylactic acid (PLA)
Biomass > (fermentation) > Bioethanol > Ethene > Polyethylene
Many types of packaging can be made from biopolymers: food trays, blown starch pellets for shipping fragile goods, thin films for wrapping. | 1 | Biochemistry |
Catalysis is a major focus of research. Two classes of catalysts are generally recognized for the construction of solar fuel cells for hydrogen production:
1) A homogeneous system is one such that catalysts are not compartmentalized, that is, components are present in the same compartment. This means that hydrogen and oxygen are produced in the same location. This can be a drawback, since they compose an explosive mixture, demanding gas product separation. Also, all components must be active in approximately the same conditions (e.g., pH).
2) A heterogeneous system has two separate electrodes, an anode and a cathode, making possible the separation of oxygen and hydrogen production. Furthermore, different components do not necessarily need to work in the same conditions. However, the increased complexity of these systems makes them harder to develop and more expensive. | 5 | Photochemistry |
The phase structure of quark matter remains mostly conjectural because it is difficult to perform calculations predicting the properties of quark matter. The reason is that QCD, the theory describing the dominant interaction between quarks, is strongly coupled at the densities and temperatures of greatest physical interest, and hence it is very hard to obtain any predictions from it. Here are brief descriptions of some of the standard approaches. | 7 | Physical Chemistry |
The leukocyte immunoglobulin-like receptors (LILR) are a family of receptors possessing extracellular immunoglobulin domains.
They are also known as CD85, ILTs and LIR, and can exert immunomodulatory effects on a wide range of immune cells. The human genes encoding these receptors are found in a gene cluster at chromosomal region 19q13.4.
They include
* LILRA1
* LILRA2
* LILRA3
* LILRA4
* LILRA5
* LILRA6
* LILRB1
* LILRB2
* LILRB3
* LILRB4
* LILRB5
* LILRB6 or LILRA6
* LILRB7 or LILRA5
A subset of LILR recognise MHC class I (also known as HLA class I in humans). The LILR family is a cluster of paired receptors with both activating and inhibitory functions. Of these, the inhibitory receptors LILRB1 and LILRB2 show a broad specificity for classical and non-classical MHC alleles with preferential binding to b2m-associated complexes. In contrast, the activating receptors LILRA1 and LILRA3 prefer b2m-independent free heavy chains of MHC class I, and in particular HLA-C alleles. | 1 | Biochemistry |
Lactonases are able to interfere with AHL-mediated quorum sensing. Some examples of these lactonases are AiiA produced by Bacillus species, AttM and AiiB produced by Agrobacterium tumefaciens, and QIcA produced by Hyphomicrobiales species.
Lactonases have been reported for Bacillus, Agrobacterium, Rhodococcus, Streptomyces, Arthrobacter, Pseudomonas, and Klebsiella. The Bacillus cereus group (consisting of B. cereus, B. thuringiensis, B. mycoides, and B. anthracis) was found to contain nine genes homologous to the AiiA gene that encode AHL-inactivating enzymes, with the catalytic zinc-binding motif conserved in all cases.
In the phytopathogen A. tumefaciens, AiiB lactonase acts as a fine modulator that essentially delays the release of lactone OC8-HSL and the resultant number of tumors produced by the pathogen. AttM lactonase mediates the degradation of the lactone OC8-HSL in wounded plant tissues.
The primary activity of the anti-atherosclerotic paraoxonase (PON) enzymes is as lactonase. Oxidized polyunsaturated fatty acids (notably in oxidized low-density lipoprotein) form lactone-like structures that are PON substrates. | 1 | Biochemistry |
The insertion of ethylene and propylene into titanium alkyls is the cornerstone of Ziegler-Natta catalysis, the commercial route of polyethylene and polypropylene. This technology mainly involves heterogeneous catalysts, but it is widely assumed that the principles and observations on homogeneous systems are applicable to the solid-state versions. Related technologies include the Shell Higher Olefin Process which produces detergent precursors. the olefin can be coordinated to the metal before insertion. Depending on the ligand density of the metal, ligand dissociation may be necessary to provide a coordination site for the olefin. | 0 | Organic Chemistry |
In studies of enzymes, the current results from the catalytic oxydation or reduction of the enzyme's substrate.
The electroactive coverage of large redox enzymes (such as laccase, hydrogenase etc.) is often too low to detect any signal in the absence of substrate, but the electrochemical signal is amplified by catalysis: indeed, the catalytic current is proportional to turnover rate times electroactive coverage. The effect of varying the electrode potential, the pH or the concentration of substrates and inhibitors etc. can be examined to learn about various steps in the catalytic mechanism. | 7 | Physical Chemistry |
Since the patient group receiving radioligand therapy is narrow, many health care providers are not equipped or eligible to administer radioligand therapy. PET imaging machines, a lead shielded area, and trained professionals must be available. | 1 | Biochemistry |
Data may also be created in the manufacturing of the media, as is the case with most optical disc formats for commercial data distribution. In this case, the user can not write to the disc it is a ROM format. Data may be written by a nonlinear optical method, but in this case the use of very high power lasers is acceptable so media sensitivity becomes less of an issue.
The fabrication of discs containing data molded or printed into their 3D structure has also been demonstrated. For example, a disc containing data in 3D may be constructed by sandwiching together a large number of wafer-thin discs, each of which is molded or printed with a single layer of information. The resulting ROM disc can then be read using a 3D reading method. | 5 | Photochemistry |
Aromatic hydrocarbons are cyclic, and are much less abundant than the other two main hydrocarbon compounds. They are represented by the formula CH, where n is a positive integer. | 9 | Geochemistry |
Demethylation is relevant to epigenetics. Demethylation of DNA is catalyzed by demethylases. These enzymes oxidize N-methyl groups, which occur in histones, in lysine derivatives, and in some forms of DNA.
:RN-CH + O → RN-H + CHO
One family of such oxidative enzymes is the cytochrome P450. Alpha-ketoglutarate-dependent hydroxylases are also active for demethylation of DNA, operating by a similar stoichiometry. These reactions, which proceed via hydroxylation, exploit the slightly weakened C-H bonds of methylamines and methyl ethers.
Demethylation of some sterols are steps in the biosynthesis of testosterone and cholesterol. Methyl groups are lost as formate. | 0 | Organic Chemistry |
Photosynthesis, plant water transport (xylem) and gas exchange are regulated by stomatal function which is important in the functioning of plants.
Stomata are responsive to light with blue light being almost 10 times as effective as red light in causing stomatal response. Research suggests this is because the light response of stomata to blue light is independent of other leaf components like chlorophyll. Guard cell protoplasts swell under blue light provided there is sufficient availability of potassium. Multiple studies have found support that increasing potassium concentrations may increase stomatal opening in the mornings, before the photosynthesis process starts, but that later in the day sucrose plays a larger role in regulating stomatal opening. Zeaxanthin in guard cells acts as a blue light photoreceptor which mediates the stomatal opening. The effect of blue light on guard cells is reversed by green light, which isomerizes zeaxanthin.
Stomatal density and aperture (length of stomata) varies under a number of environmental factors such as atmospheric CO concentration, light intensity, air temperature and photoperiod (daytime duration).
Decreasing stomatal density is one way plants have responded to the increase in concentration of atmospheric CO ([CO]). Although changes in [CO] response is the least understood mechanistically, this stomatal response has begun to plateau where it is soon expected to impact transpiration and photosynthesis processes in plants.
Drought inhibits stomatal opening, but research on soybeans suggests moderate drought does not have a significant effect on stomatal closure of its leaves. There are different mechanisms of stomatal closure. Low humidity stresses guard cells causing turgor loss, termed hydropassive closure. Hydroactive closure is contrasted as the whole leaf affected by drought stress, believed to be most likely triggered by abscisic acid. | 5 | Photochemistry |
The water molecule is an asymmetric top, that is, it has three independent moments of inertia. Rotation about the 2-fold symmetry axis is illustrated at the left. Because of the low symmetry of the molecule, a large number of transitions can be observed in the far infrared region of the spectrum. Measurements of microwave spectra have provided a very precise value for the O−H bond length, 95.84 ± 0.05 pm and H−O−H bond angle, 104.5 ± 0.3°. | 7 | Physical Chemistry |
Non-Kekulé molecules with two formal radical centers (non-Kekulé diradicals) can be classified into non-disjoint and disjoint by the shape of their two non-bonding molecular orbitals (NBMOs).
Both NBMOs of molecules with non-disjoint characteristics such as trimethylenemethane have electron density at the same atom. According to Hunds rule, each orbital is filled with one electron with parallel spin, avoiding the Coulomb repulsion by filling one orbital with two electrons. Therefore, such molecules with non-disjoint' NBMOs are expected to prefer a triplet ground state.
In contrast, the NBMOs of the molecules with disjoint characteristics such as tetramethyleneethane can be described without having electron density at the same atom. With such MOs, the destabilization factor by the Coulomb repulsion becomes much smaller than with non-disjoint type molecules, and therefore the relative stability of the singlet ground state to the triplet ground state will be nearly equal, or even reversed because of exchange interaction. | 0 | Organic Chemistry |
In quantum mechanics, an absorption band is a range of wavelengths, frequencies or energies in the electromagnetic spectrum that are characteristic of a particular transition from initial to final state in a substance.
According to quantum mechanics, atoms and molecules can only hold certain defined quantities of energy, or exist in specific states. When such quanta of electromagnetic radiation are emitted or absorbed by an atom or molecule, energy of the radiation changes the state of the atom or molecule from an initial state to a final state. | 7 | Physical Chemistry |
Detailed predictions were made in the late 1970s for the production of jets at the CERN Super Proton–Antiproton Synchrotron. UA2 observed the first evidence for jet production in hadron collisions in 1981, which shortly after was confirmed by UA1.
The subject was later revived at RHIC. One of the most striking physical effects obtained at RHIC energies is the effect of quenching jets. At the first stage of interaction of colliding relativistic nuclei, partons of the colliding nuclei give rise to the secondary partons with a large transverse impulse ≥ 3–6 GeV/s. Passing through a highly heated compressed plasma, partons lose energy. The magnitude of the energy loss by the parton depends on the properties of the quark–gluon plasma (temperature, density). In addition, it is also necessary to take into account the fact that colored quarks and gluons are the elementary objects of the plasma, which differs from the energy loss by a parton in a medium consisting of colorless hadrons. Under the conditions of a quark–gluon plasma, the energy losses resulting from the RHIC energies by partons are estimated as . This conclusion is confirmed by comparing the relative yield of hadrons with a large transverse impulse in nucleon-nucleon and nucleus-nucleus collisions at the same collision energy. The energy loss by partons with a large transverse impulse in nucleon-nucleon collisions is much smaller than in nucleus-nucleus collisions, which leads to a decrease in the yield of high-energy hadrons in nucleus-nucleus collisions. This result suggests that nuclear collisions cannot be regarded as a simple superposition of nucleon-nucleon collisions. For a short time, ~1 μs, and in the final volume, quarks and gluons form some ideal liquid. The collective properties of this fluid are manifested during its movement as a whole. Therefore, when moving partons in this medium, it is necessary to take into account some collective properties of this quark–gluon liquid. Energy losses depend on the properties of the quark–gluon medium, on the parton density in the resulting fireball, and on the dynamics of its expansion. Losses of energy by light and heavy quarks during the passage of a fireball turn out to be approximately the same.
In November 2010 CERN announced the first direct observation of jet quenching, based on experiments with heavy-ion collisions. | 7 | Physical Chemistry |
3-Methylcrotonyl-CoA (β-Methylcrotonyl-CoA or MC-CoA) is an intermediate in the metabolism of leucine.
It is found in mitochondria, where it is formed from isovaleryl-coenzyme A by isovaleryl coenzyme A dehydrogenase. It then reacts with CO to yield 3-Methylcrotonyl-CoA carboxylase. | 1 | Biochemistry |
Base calling can be assessed by two metrics, read accuracy and consensus accuracy. Read accuracy refers to the called base's accuracy to a known reference. Consensus accuracy refers to how accurate a consensus sequence is compared to overlapping reads from the same genetic locus. | 1 | Biochemistry |
Mastic asphalt is a type of asphalt that differs from dense graded asphalt (asphalt concrete) in that it has a higher bitumen (binder) content, usually around 7–10% of the whole aggregate mix, as opposed to rolled asphalt concrete, which has only around 5% asphalt. This thermoplastic substance is widely used in the building industry for waterproofing flat roofs and tanking underground. Mastic asphalt is heated to a temperature of and is spread in layers to form an impervious barrier about thick. | 7 | Physical Chemistry |
Two functional groups contribute significantly to aminosteroidal neuromuscular blocking potency, it is presumed to enable them to bind the receptor at two points. A bis-quaternary two point arrangement on A and D-ring (binding inter-site) or a D-ring acetylcholine moiety (binding at two points intra-site) are most likely to succeed. A third group can have variable effects. The quaternary and acetyl groups on the A and D ring of pipecuronium prevent it from binding intra-site (binding to two points at the same site). Instead, it must bind as bis-quaternary (inter-site). These structures are very dissimilar from acetylcholine and free pipecuronium from nicotinic or muscarinic side-effects linked to acetylcholine moiety. Also, they protect the molecule from hydrolysis by cholinesterases, which explain its nature of kidney excretion. The four methyl-groups on the quaternary N atoms make it less lipophilic than most aminosteroids. This also affects pipecuroniums metabolism by resisting hepatic uptake, metabolism, and biliary excretion. The length of the molecule (2.1 nm, close to ideal) and its rigidness make pipecuronium the most potent and clean one-bulk bis-quaternary. Even though the N-N distance (1.6 nm) is far away from what is considered ideal, its onium heads are well-exposed, and the quaternary groups help to bring together the onium heads to the anionic centers of the receptors without chirality issues.
Adding more than two onium heads in general does not add to potency. Though the third onium head in gallamine seems to help position the two outside heads near the optimum molecular length, it can interfere unfavorably and gallamine turns out to be a weak muscle relaxant, like all multi-quaternary compounds.
Considering acetylcholine a quaternizing group larger than methyl and an acyl group larger than acetyl would reduce the molecule's potency. The charged N and the carbonyl O atoms are distanced from structures they bind to on receptive sites and, thus, decrease potency. The carbonyl O in vecuronium for example is thrust outward to appose the H-bond donor of the receptive site. This also helps explain why gallamine, rocuronium, and rapacuronium are of relatively low potency.
In general, methyl quaternization is optimal for potency but, opposing this rule, the trimethyl derivatives of gallamine are of lower potency than gallamine. The reason for this is that gallamine has a suboptimal N-N distance. Substituting the ethyl groups with methyl groups would make the molecular length also shorter than optimal. Methoxylation of tetrahydroisoquinolinium agents seems to improve their potency. How methoxylation improves potency is still unclear.
Histamine release is a common attribute of benzylisoquinolinium muscle relaxants. This problem generally decreases with increased potency and smaller doses. The need for larger doses increases the degree of this side-effect. Conformational or structural explanations for histamine release are not clear. | 1 | Biochemistry |
Although strong, the (aryl)C−SO bond can be broken by nucleophilic reagents. Of historic and continuing significance is the α-sulfonation of anthroquinone followed by displacement of the sulfonate group by other nucleophiles, which cannot be installed directly. An early method for producing phenol involved the base hydrolysis of sodium benzenesulfonate, which can be generated readily from benzene.
:CHSONa + NaOH → CHOH + NaSO
The conditions for this reaction are harsh, however, requiring fused alkali or molten sodium hydroxide at 350 °C for benzenesulfonic acid itself. Unlike the mechanism for the fused alkali hydrolysis of chlorobenzene, which proceeds through elimination-addition (benzyne mechanism), benzenesulfonic acid undergoes the analogous conversion by an SAr mechanism, as revealed by a C labeling, despite the lack of stabilizing substituents. Sulfonic acids with electron-withdrawing groups (e.g., with NO or CN substituents) undergo this transformation much more readily. | 0 | Organic Chemistry |
The lac gene and its derivatives are amenable to use as a reporter gene in a number of bacterial-based selection techniques such as two hybrid analysis, in which the successful binding of a transcriptional activator to a specific promoter sequence must be determined. In LB plates containing X-gal, the colour change from white colonies to a shade of blue corresponds to about 20–100 β-galactosidase units, while tetrazolium lactose and MacConkey lactose media have a range of 100–1000 units, being most sensitive in the high and low parts of this range respectively. Since MacConkey lactose and tetrazolium lactose media both rely on the products of lactose breakdown, they require the presence of both lacZ and lacY genes. The many lac fusion techniques which include only the lacZ gene are thus suited to X-gal plates or ONPG liquid broths. | 1 | Biochemistry |
DNA recombinases are widely used in multicellular organisms to manipulate the structure of genomes, and to control gene expression. These enzymes, derived from bacteria (bacteriophages) and fungi, catalyze directionally sensitive DNA exchange reactions between short (30–40 nucleotides) target site sequences that are specific to each recombinase. These reactions enable four basic functional modules: excision/insertion, inversion, translocation and cassette exchange, which have been used individually or combined in a wide range of configurations to control gene expression.
Types include:
* Cre recombinase
* Hin recombinase
* Tre recombinase
* FLP recombinase | 1 | Biochemistry |
Neurturin (NRTN) is a protein that is encoded in humans by the NRTN gene. Neurturin belongs to the glial cell line-derived neurotrophic factor (GDNF) family of neurotrophic factors, which regulate the survival and function of neurons. Neurturin’s role as a growth factor places it in the transforming growth factor beta (TGF-beta) subfamily along with its homologs persephin, artemin, and GDNF. It shares a 42% similarity in amino acid sequence with mature GDNF. It is also considered a trophic factor and critical in the development and growth of neurons in the brain. Neurotrophic factors like neurturin have been tested in several clinical trial settings for the potential treatment of neurodegenerative diseases, specifically Parkinson's disease. | 1 | Biochemistry |
The Wnt protein family includes a large number of cysteine-rich glycoproteins. The Wnt proteins activate signal transduction cascades via three different pathways, the canonical Wnt pathway, the noncanonical planar cell polarity (PCP) pathway, and the noncanonical Wnt/Ca pathway. Wnt proteins appear to control a wide range of developmental processes and have been seen as necessary for control of spindle orientation, cell polarity, cadherin mediated adhesion, and early development of embryos in many different organisms. Current research has indicated that deregulation of Wnt signaling plays a role in tumor formation, because at a cellular level, Wnt proteins often regulated cell proliferation, cell morphology, cell motility, and cell fate. | 1 | Biochemistry |
*Abundance in weight: spectroscopic nucleic acid quantitation
*Absolute abundance in number: real-time polymerase chain reaction (quantitative PCR)
*High-throughput relative abundance: DNA microarray
*High-throughput absolute abundance: serial analysis of gene expression (SAGE)
*Size: gel electrophoresis | 1 | Biochemistry |
Recent attempts have been made to relabel antifreeze proteins as ice structuring proteins to more accurately represent their function and to dispose of any assumed negative relation between AFPs and automotive antifreeze, ethylene glycol. These two things are completely separate entities, and show loose similarity only in their function. | 1 | Biochemistry |
Physiological concentrations (ppb-range) of Fe, Cu, Zn, Ni, Mo, Pd, Co, Mn, Pt, Cr, Cd and other metal cofactor species can be identified and absolutely quantified in an aliquot of a fraction by inductively coupled plasma mass spectrometry (ICP-MS) or total reflection X-ray fluorescence (TXRF), for example. In case of ICP-MS the structural information of the associated metallobiomolecules is irreversibly lost due to ionization of the sample with plasma. Another established high sensitive detection method for the determination of trace elements in biological samples is graphite furnace atomic absorption spectrometry (GF-AAS) (cf. fig. Electropherogram). Because of high purity and optimized concentration of the separated metalloproteins, for example, therapeutic recombinant plant-made pharmaceuticals such as copper chaperone for superoxide dismutase (CCS) from medicinal plants, in a few specific PAGE fractions, the related structures of these bioactive analytes can be elucidated quantitatively by using solution NMR spectroscopy under non-denaturing conditions. | 3 | Analytical Chemistry |
Thermodynamics is principally based on a set of four laws which are universally valid when applied to systems that fall within the constraints implied by each. In the various theoretical descriptions of thermodynamics these laws may be expressed in seemingly differing forms, but the most prominent formulations are the following. | 7 | Physical Chemistry |
Maxwell-Wagner polarization processes should be taken into account during the investigation of inhomogeneous materials like suspensions or colloids, biological materials, phase separated polymers, blends, and crystalline or liquid crystalline polymers. | 7 | Physical Chemistry |
Alfaprostol is a bioactive analog of prostaglandin F. Alfaprostol is a luteolytic agent used injectably for scheduling of estrus in mares for purposes of planned breeding. It is also used for treating of postweaning anestrus in economically important farm animals. For these purposes, alfaprostol is more potent than naturally occurring prostaglandin F. | 0 | Organic Chemistry |
Plants absorb nitrogen from the soil in the form of nitrate (NO) and ammonium (NH). In aerobic soils where nitrification can occur, nitrate is usually the predominant form of available nitrogen that is absorbed. However this is not always the case as ammonia can predominate in grasslands and in flooded, anaerobic soils like rice paddies. Plant roots themselves can affect the abundance of various forms of nitrogen by changing the pH and secreting organic compounds or oxygen. This influences microbial activities like the inter-conversion of various nitrogen species, the release of ammonia from organic matter in the soil and the fixation of nitrogen by non-nodule-forming bacteria.
Ammonium ions are absorbed by the plant via ammonia transporters. Nitrate is taken up by several nitrate transporters that use a proton gradient to power the transport. Nitrogen is transported from the root to the shoot via the xylem in the form of nitrate, dissolved ammonia and amino acids. Usually (but not always) most of the nitrate reduction is carried out in the shoots while the roots reduce only a small fraction of the absorbed nitrate to ammonia. Ammonia (both absorbed and synthesized) is incorporated into amino acids via the glutamine synthetase-glutamate synthase (GS-GOGAT) pathway. While nearly all the ammonia in the root is usually incorporated into amino acids at the root itself, plants may transport significant amounts of ammonium ions in the xylem to be fixed in the shoots. This may help avoid the transport of organic compounds down to the roots just to carry the nitrogen back as amino acids.
Nitrate reduction is carried out in two steps. Nitrate is first reduced to nitrite (NO) in the cytosol by nitrate reductase using NADH or NADPH. Nitrite is then reduced to ammonia in the chloroplasts (plastids in roots) by a ferredoxin dependent nitrite reductase. In photosynthesizing tissues, it uses an isoform of ferredoxin (Fd1) that is reduced by PSI while in the root it uses a form of ferredoxin (Fd3) that has a less negative midpoint potential and can be reduced easily by NADPH. In non photosynthesizing tissues, NADPH is generated by glycolysis and the pentose phosphate pathway.
In the chloroplasts, glutamine synthetase incorporates this ammonia as the amide group of glutamine using glutamate as a substrate. Glutamate synthase (Fd-GOGAT and NADH-GOGAT) transfer the amide group onto a 2-oxoglutarate molecule producing two glutamates. Further transaminations are carried out make other amino acids (most commonly asparagine) from glutamine. While the enzyme glutamate dehydrogenase (GDH) does not play a direct role in the assimilation, it protects the mitochondrial functions during periods of high nitrogen metabolism and takes part in nitrogen remobilization. | 1 | Biochemistry |
There are different spectroelectrochemical techniques based on the combination of spectroscopic and electrochemical techniques. Regarding electrochemistry, the most common techniques used are:
*Chronoamperometry, which measures current intensity as a function of time by applying a constant difference of potential to the working electrode.
*Chronopotentiometry, which measures the difference of potential as a function of time by applying a constant current.
*Voltammetry, which measures the change of current as a function of the linear change of the working electrode potential.
*Pulse techniques, which measure the change of current as a function of difference of potential, applying pulse potential functions to the working electrode.
The general classification of the spectroelectrochemical techniques is based on the spectroscopic technique chosen. | 7 | Physical Chemistry |
In a unimolecular reaction, a single molecule rearranges atoms, forming different molecules. This is illustrated by the equation
where refers to chemical product(s). The reaction or reaction step is an isomerization if there is only one product molecule, or a dissociation if there is more than one product molecule.
In either case, the rate of the reaction or step is described by the first order rate law
where is the concentration of species A, is time, and is the reaction rate constant.
As can be deduced from the rate law equation, the number of A molecules that decay is proportional to the number of A molecules available. An example of a unimolecular reaction, is the isomerization of cyclopropane to propene:
Unimolecular reactions can be explained by the Lindemann-Hinshelwood mechanism. | 7 | Physical Chemistry |
Research is being done into RCB and NCP, two non-catalytic thioredoxin-like proteins that activate chloroplast transcription. Knowing the exact mechanism can be useful to allow increasing photosynthesis (i.e. through genetic modification). | 5 | Photochemistry |
A sulfonium ion is a positively charged ion featuring three organic substituents attached to sulfur, with the formula [RS]. Together with their negatively charged counterpart, the anion, the compounds are called sulfonium salts. An oxosulfonium ion is a positively charged ion featuring three organic substituents and an oxygen attached to sulfur, with the formula [RS=O]. Together with their negatively charged counterpart, the anion, the compounds are called oxosulfonium salts. Related species include alkoxysulfonium and chlorosulfonium ions, [RSOR] and [RSCl], respectively. | 9 | Geochemistry |
Arctic Apples are a suite of trademarked apples that contain a nonbrowning trait created by using gene silencing to reduce the expression of polyphenol oxidase (PPO). It is the first approved food product to use this technique. | 1 | Biochemistry |
In biochemistry, the metallome is the distribution of metal ions in a cellular compartment. The term was coined in analogy with proteome as metallomics is the study of metallome: the "comprehensive analysis of the entirety of metal and metalloid species within a cell or tissue type". Therefore, metallomics can be considered a branch of metabolomics, even though the metals are not typically considered as metabolites.
An alternative definition of "metallomes" as metalloproteins or any other metal-containing biomolecules, and "metallomics" as a study of such biomolecules. | 1 | Biochemistry |
ATSDR represents the Department of Health and Human Services on the National Response Team and works with other agencies to provide technical assistance during emergencies involving hazardous substances, such as chemical spills. In July 2007, for example, ATSDR responded to the Verdigris River flood in Coffeyville, Kansas, after an oil refinery spilled crude oil into the floodwaters, contaminating many homes in the city. ATSDR worked with EPA and state and local authorities to provide health information to local residents and advised those agencies during the clean-up process. ATSDR also assists with responding to terrorism incidents, which have included the September 11 attacks and the 2001 anthrax attacks. ATSDR responded to 132 chemical emergency events in 2008.
In addition to working with communities and other agencies in the aftermath of chemical emergencies, ATSDR has developed the Managing Hazardous Materials Incidents series, which includes several tools to assist emergency medical services personnel and hospital emergency departments during chemical emergencies. This includes important information on emergency planning, emergency response, and rescuer protection. Another tool is the Medical Management Guidelines, which summarize important information on exposure to common chemicals and provide suggestions for safely treating and decontaminating patients. | 1 | Biochemistry |
Salts containing fluoride are numerous and adopt myriad structures. Typically the fluoride anion is surrounded by four or six cations, as is typical for other halides. Sodium fluoride and sodium chloride adopt the same structure. For compounds containing more than one fluoride per cation, the structures often deviate from those of the chlorides, as illustrated by the main fluoride mineral fluorite (CaF) where the Ca ions are surrounded by eight F centers. In CaCl, each Ca ion is surrounded by six Cl centers. The difluorides of the transition metals often adopt the rutile structure whereas the dichlorides have cadmium chloride structures. | 1 | Biochemistry |
Histone post-translational modifications were first identified and listed as having a potential regulatory role on the synthesis of RNA in 1964. Since then, over several decades, chromatin theory has evolved. Chromatin subunit models as well as the notion of the nucleosome were established in 1973 and 1974, respectively. Richmond and his research group has been able to elucidate the crystal structure of the histone octamer with DNA wrapped up around it at a resolution of 7 Å in 1984. The structure of the octameric core complex was revisited seven years later and a resolution of 3.1 Å was elucidated for its crystal at a high salt concentration. Though sequence similarity is low between the core histones, each of the four have a repeated element consisting of a helix-loop-helix called the histone fold motif. Furthermore, the details of protein-protein and protein-DNA interactions were fine-tuned by X-ray crystallography studies at 2.8 and 1.9 Å, respectively, in the 2000s. | 1 | Biochemistry |
In statistical mechanics, the microcanonical ensemble is a particular statistical ensemble which is used to make predictions about the outcomes of experiments performed on isolated systems that are believed to be in equilibrium with an exactly known energy. The microcanonical ensemble is based upon the assumption that, when such an equilibrated system is probed, the probability for it to be found in any of the microscopic states with the same total energy have equal probability. With this assumption, the ensemble average of an observable quantity is found by averaging the value of that observable over all microstates with the correct total energy:
Importantly, this quantity is independent of everything about the initial state except for its energy.
The assumptions of ergodicity are well-motivated in classical mechanics as a result of dynamical chaos, since a chaotic system will in general spend equal time in equal areas of its phase space. If we prepare an isolated, chaotic, classical system in some region of its phase space, then as the system is allowed to evolve in time, it will sample its entire phase space, subject only to a small number of conservation laws (such as conservation of total energy). If one can justify the claim that a given physical system is ergodic, then this mechanism will provide an explanation for why statistical mechanics is successful in making accurate predictions. For example, the hard sphere gas has been rigorously proven to be ergodic.
This argument cannot be straightforwardly extended to quantum systems, even ones that are analogous to chaotic classical systems, because time evolution of a quantum system does not uniformly sample all vectors in Hilbert space with a given energy. Given the state at time zero in a basis of energy eigenstates
the expectation value of any observable is
Even if the are incommensurate, so that this expectation value is given for long times by
the expectation value permanently retains knowledge of the initial state in the form of the coefficients .
In principle it is thus an open question as to whether an isolated quantum mechanical system, prepared in an arbitrary initial state, will approach a state which resembles thermal equilibrium, in which a handful of observables are adequate to make successful predictions about the system. However, a variety of experiments in cold atomic gases have indeed observed thermal relaxation in systems which are, to a very good approximation, completely isolated from their environment, and for a wide class of initial states. The task of explaining this experimentally observed applicability of equilibrium statistical mechanics to isolated quantum systems is the primary goal of the eigenstate thermalization hypothesis. | 7 | Physical Chemistry |
Captopril, the first ACE inhibitor, is a functional and structural analog of a peptide derived from the venom of the jararaca, a Brazilian pit viper (Bothrops jararaca). Enalapril is a derivative, designed by scientists at Merck to overcome the rash and bad taste caused by captopril.
Enalapril is actually a prodrug; the active metabolite is enalaprilat.
The di-acid metabolite of enalapril, enalaprilat, and its lysine analogue lisinopril are potent inhibitors of angiotensin converting enzyme (ACE); they do not contain sulphydryl groups. Both drugs can be assayed by high pressure liquid chromatography and by radioimmunoassay and plasma ACE inhibition remains stable under normal storage conditions. It is therefore possible to study their pharmacokinetics as well as their pharmacodynamic effects in humans. Enalaprilat and lisinopril as well as ACE activity have been measured in blood taken during the course of two studies of the effects of these drugs on blood pressure and autonomic responsiveness.
Lisinopril is a synthetic peptide derivative of captopril. Scientists at Merck created lisinopril by systematically altering each structural unit of enalaprilat, substituting various amino acids. Adding lysine at one end of the drug turned out to have strong activity and had adequate bioavailability when given orally; analogs of that compound resulted in lisinopril, which takes its name from the discovery with lysine. Merck conducted clinical trials, and the drug was approved for hypertension in 1987 and congestive heart failure in 1993.
The discovery posed a problem, since sales of enalapril were strong for Merck, and the company did not want to diminish those sales. Merck ended up entering into an agreement with Zeneca under which Zeneca received the right to co-market lisinopril, and Merck received the exclusive rights to an earlier stage aldose reductase inhibitor drug candidate, a potential treatment for diabetes. Zenecas marketing and brand name, "Zestril", turned out to be stronger than Mercks effort. The drug became a blockbuster for AstraZeneca (formed in 1998), with annual sales in 1999 of $1.2B.
The US patents expired in 2002. Since then, lisinopril has been available under many brand names worldwide; it is also available in combination drugs with diuretic hydrochlorothiazide (as lisinopril/hydrochlorothiazide), and with calcium channel blocker amlodipine (as lisinopril/amlodipine). | 4 | Stereochemistry |
As with synthetic kinetic resolution procedures, enzymatic acylation kinetic resolutions have seen the broadest application in a synthetic context. Especially important has been the use of enzymatic kinetic resolution to efficiently and cheaply prepare amino acids. On a commercial scale, Degussa's methodology employing acylases is capable of resolving numerous natural and unnatural amino acids. The racemic mixtures can be prepared via Strecker synthesis, and the use of either porcine kidney acylase (for straight chain substrates) or an enzyme from the mold Aspergillus oryzae (for branched side chain substrates) can effectively yield enantioenriched amino acids in high (85-90%) yields. The unreacted starting material can be racemized in situ, thus making this a dynamic kinetic resolution.
In addition, lipases are used extensively for kinetic resolution in both academic and industrial settings.
Lipases have been used to resolve primary alcohols, secondary alcohols, a limited number of tertiary alcohols, carboxylic acids, diols, and even chiral allenes. Lipase from Pseudomonas cepacia (PSL) is the most widely used in the resolution of primary alcohols and has been used with vinyl acetate as an acylating agent to kinetically resolve the primary alcohols shown below.
For the resolution of secondary alcohols, pseudomonas cepecia lipase (PSL-C) has been employed effectively to generate excellent ees of the (R')-enantiomer of the alcohol. The use of isopropenyl acetate as the acylating agent results in acetone as the byproduct, which is effectively removed from the reaction using molecular sieves. | 4 | Stereochemistry |
Methylene blue is widely used as a redox indicator in analytical chemistry. Solutions of this substance are blue when in an oxidizing environment, but will turn colorless if exposed to a reducing agent. The redox properties can be seen in a classical demonstration of chemical kinetics in general chemistry, the "blue bottle" experiment. Typically, a solution is made of glucose (dextrose), methylene blue, and sodium hydroxide. Upon shaking the bottle, oxygen oxidizes methylene blue, and the solution turns blue. The dextrose will gradually reduce the methylene blue to its colorless, reduced form. Hence, when the dissolved dextrose is entirely consumed, the solution will turn blue again. The redox midpoint potential E' is +0.01 V. | 3 | Analytical Chemistry |
Corrosion under insulation (CUI) is a severe form of localized external corrosion that occurs in carbon and low alloy steel equipment that has been insulated. This form of corrosion occurs when water is absorbed by or collected in the insulation. The equipment begins to corrode as it is exposed to water and oxygen. CUI is common in refineries and process plants that typically operate equipment at high temperatures.
Corrosion occurs where there is thermal cycling. In this instance the moist condenses back on to the core material until it is flashed off when the plant is brought back into operation.
It also occurs in carbon and low alloy steels at temperatures between 10°F and 350°F (-12°C and 175°C), and in austenitic stainless steels and duplex stainless steels at temperatures between 140°F and 400°F (60°C and 205°C) | 8 | Metallurgy |
The Montreal Protocol targeted 1,1,1-trichloroethane as one of those compounds responsible for ozone depletion and banned its use beginning in 1996. Since then, its manufacture and use have been phased out throughout most of the world. Its atmospheric presence has declined rapidly due to its relatively short atmospheric lifetime of about 5 years. | 2 | Environmental Chemistry |
The silicon cycle has gained increasingly in scientific attention the past decade for several reasons:
Firstly, the modern marine silica cycle is widely believed to be dominated by diatoms for the fixation and export of particulate matter (including organic carbon), from the euphotic zone to the deep ocean, via a process known as the biological pump. As a result, diatoms, and other silica-secreting organisms, play a crucial role in the global carbon cycle, and have the ability to affect atmospheric CO concentrations on a variety of time scales, by sequestering CO in the ocean. This connection between biogenic silica and organic carbon, together with the significantly higher preservation potential of biogenic siliceous compounds, compared to organic carbon, makes opal accumulation records very interesting for paleoceanography and paleoclimatology.
Secondly, biogenic silica accumulation on the sea floor contains lot of information about where in the ocean export production has occurred on time scales ranging from hundreds to millions of years. For this reason, opal deposition records provide valuable information regarding large-scale oceanographic reorganizations in the geological past, as well as paleoproductivity.
Thirdly, the mean oceanic residence time for silicate is approximately 10,000–15,000 yr. This relative short residence time, makes oceanic silicate concentrations and fluxes sensitive to glacial/interglacial perturbations, and thus an excellent proxy for evaluating climate changes.
Increasingly, isotope ratios of oxygen (O:O) and silicon (Si:Si) are analysed from biogenic silica preserved in lake and marine sediments to derive records of past climate change and nutrient cycling (De La Rocha, 2006; Leng and Barker, 2006). This is a particularly valuable approach considering the role of diatoms in global carbon cycling. In addition, isotope analyses from BSi are useful for tracing past climate changes in regions such as in the Southern Ocean, where few biogenic carbonates are preserved. | 1 | Biochemistry |
Brine rejection is a process that occurs when salty water freezes. The salts do not fit in the crystal structure of water ice, so the salt is expelled.
Since the oceans are salty, this process is important in nature. Salt rejected by the forming sea ice drains into the surrounding seawater, creating saltier, denser brine. The denser brine sinks, influencing ocean circulation. | 9 | Geochemistry |
In the first system, a wild-type Moloney Murine Leukemia Virus (M-MLV) reverse transcriptase was fused to the Cas9 H840A nickase C-terminus. Detectable editing efficiencies were observed. | 1 | Biochemistry |
Examples of alkaliphiles include Halorhodospira halochloris, Natronomonas pharaonis, and Thiohalospira alkaliphila. | 1 | Biochemistry |
Polymerization is the process of combining many small molecules known as monomers into a covalently bonded chain or network. During the polymerization process, some chemical groups may be lost from each monomer. This happens in the polymerization of PET polyester. The monomers are terephthalic acid (HOOCCHCOOH) and ethylene glycol (HOCHCHOH) but the repeating unit is OCCHCOOCHCHO, which corresponds to the combination of the two monomers with the loss of two water molecules. The distinct piece of each monomer that is incorporated into the polymer is known as a repeat unit or monomer residue.
Synthetic methods are generally divided into two categories, step-growth polymerization and chain polymerization. The essential difference between the two is that in chain polymerization, monomers are added to the chain one at a time only, such as in polystyrene, whereas in step-growth polymerization chains of monomers may combine with one another directly, such as in polyester. Step-growth polymerization can be divided into polycondensation, in which low-molar-mass by-product is formed in every reaction step, and polyaddition.
Newer methods, such as plasma polymerization do not fit neatly into either category. Synthetic polymerization reactions may be carried out with or without a catalyst. Laboratory synthesis of biopolymers, especially of proteins, is an area of intensive research. | 7 | Physical Chemistry |
The eyespot apparatus (or stigma) is a photoreceptive organelle found in the flagellate or (motile) cells of green algae and other unicellular photosynthetic organisms such as euglenids. It allows the cells to sense light direction and intensity and respond to it, prompting the organism to either swim towards the light (positive phototaxis), or away from it (negative phototaxis). A related response ("photoshock" or photophobic response) occurs when cells are briefly exposed to high light intensity, causing the cell to stop, briefly swim backwards, then change swimming direction. Eyespot-mediated light perception helps the cells in finding an environment with optimal light conditions for photosynthesis. Eyespots are the simplest and most common "eyes" found in nature, composed of photoreceptors and areas of bright orange-red red pigment granules. Signals relayed from the eyespot photoreceptors result in alteration of the beating pattern of the flagella, generating a phototactic response. | 1 | Biochemistry |
Chuen Yan Cheng () is a Senior Scientist for the Population Council's Center for Biomedical Research. He is most well known as the inventor of the non-steroid male contraceptive drug——Adjudin, which is the first male contraceptive drug on the market now finished clinical trials showing no side effects. | 1 | Biochemistry |
A Paul trap is a type of quadrupole ion trap that uses static direct current (DC) and radio frequency (RF) oscillating electric fields to trap ions. Paul traps are commonly used as components of a mass spectrometer. The invention of the 3D quadrupole ion trap itself is attributed to Wolfgang Paul who shared the Nobel Prize in Physics in 1989 for this work. The trap consists of two hyperbolic metal electrodes with their foci facing each other and a hyperbolic ring electrode halfway between the other two electrodes. Ions are trapped in the space between these three electrodes by the oscillating and static electric fields. | 7 | Physical Chemistry |
Acid anhydrides () have two acyl groups linked by an oxygen atom. If both acyl groups are the same, then the name of the carboxylic acid with the word acid is replaced with the word anhydride and the IUPAC name consists of two words. If the acyl groups are different, then they are named in alphabetical order in the same way, with anhydride replacing acid and IUPAC name consists of three words. For example, is called ethanoic anhydride and is called ethanoic propanoic anhydride. | 0 | Organic Chemistry |
Flexibility and plasticity allow proteins to bind to ligands, form oligomers, aggregate, and perform mechanical work. Large conformational changes in proteins play an important role in cellular signaling. Adenylate Kinase is a signal transducing protein; thus, the balance between conformations regulates protein activity. ADK has a locally unfolded state that becomes depopulated upon binding.
A 2007 study by Whitford et al. shows the conformations of ADK when binding with ATP or AMP. The study shows that there are three relevant conformations or structures of ADK—CORE, Open, and Closed. In ADK, there are two small domains called the LID and NMP. ATP binds in the pocket formed by the LID and CORE domains. AMP binds in the pocket formed by the NMP and CORE domains. The Whitford study also reported findings that show that localized regions of a protein unfold during conformational transitions. This mechanism reduces the strain and enhances catalytic efficiency. Local unfolding is the result of competing strain energies in the protein.
The local (thermodynamic) stability of the substrate-binding domains ATP and AMP has been shown to be significantly lower when compared with the CORE domain in ADK. Furthermore, it has been shown that the two subdomains (ATP and AMP) can fold and unfold in a "non-cooperative manner." Binding of the substrates causes preference for closed conformations amongst those that are sampled by ADK. These closed conformations are hypothesized to help with removal of water from the active site to avoid wasteful hydrolysis of ATP in addition to helping optimize alignment of substrates for phosphoryl-transfer. Furthermore, it has been shown that the apoenzyme will still sample the closed conformations of the ATP and AMP domains in the absence of substrates. When comparing the rate of opening of the enzyme (which allows for product release) and the rate of closing that accompanies substrate binding, closing was found to be the slower process. | 1 | Biochemistry |
The gene for the LHCGR is found on chromosome 2 p21 in humans, close to the FSH receptor gene. It consists of 70 kbp (versus 54 kpb for the FSHR). The gene is similar to the gene for the FSH receptor and the TSH receptor. | 1 | Biochemistry |
Pyridine is a basic heterocyclic organic compound with the chemical formula . It is structurally related to benzene, with one methine group replaced by a nitrogen atom . It is a highly flammable, weakly alkaline, water-miscible liquid with a distinctive, unpleasant fish-like smell. Pyridine is colorless, but older or impure samples can appear yellow. due to the formation of extended, unsaturated polymeric chains, which show significant electrical conductivity. The pyridine ring occurs in many important compounds, including agrochemicals, pharmaceuticals, and vitamins. Historically, pyridine was produced from coal tar. As of 2016, it is synthesized on the scale of about 20,000 tons per year worldwide. | 0 | Organic Chemistry |
A bimolecular elimination reaction will occur in a molecule where the breaking carbon-hydrogen bond and the leaving group are anti-periplanar (Figure 8). This geometry is preferred because it aligns σ and σ* orbitals. Figure 9 shows the σ orbital and the σ* orbital parallel to each other, allowing the σ orbital to donate into the σ* anti-bonding orbital through hyperconjugation. This serves to weaken C-H and C-X bond, both of which are broken in an E reaction. It also sets up the molecule to more easily move its σ electrons into a π orbital (Figure 10). | 0 | Organic Chemistry |
The four JAK family members are:
* Janus kinase 1 (JAK1)
* Janus kinase 2 (JAK2)
* Janus kinase 3 (JAK3)
* Tyrosine kinase 2 (TYK2)
Transgenic mice that do not express JAK1 have defective responses to some cytokines, such as interferon-gamma. JAK1 and JAK2 are involved in type II interferon (interferon-gamma) signalling, whereas JAK1 and TYK2 are involved in type I interferon signalling. Mice that do not express TYK2 have defective natural killer cell function. | 1 | Biochemistry |
It is important to consider the downstream applications of the plasmid DNA when choosing a purification method. For example, if the plasmid is to be used for transfection or electroporation, a purification method that results in high purity and low endotoxin levels is desirable. Similarly, if the plasmid is to be used for sequencing or PCR, a purification method that results in high yield and minimal contaminants is desirable. However, multiple methods of nucleic acid purification exist. All work on the principle of generating conditions where either only the nucleic acid precipitates, or only other biomolecules precipitate, allowing the nucleic acid to be separated. | 1 | Biochemistry |
* 2014 – 2017 Corbion, Corbion Thermophiles. Prime investigator €530k
* 2010-2013 Purac, Competence in industrial Bacillus strains. Prime investigator €420k
* 2004 – 2007 DSM Bakery Ingredients B.V. Sense: Screening for protein secretion using secretion stress indicators. Prime investigator €640k
* 2001 – 2005 Frico + DSM Directing Starters Together 2 (several partners). Prime investigator €554k
* 2000 – 2006 Intervet International B.V. Expression of heterologous proteins in Bacillus. Prime investigator €433k | 0 | Organic Chemistry |
In the English speaking world, the term "clarke" was not even used in Wells(1937) which introduced Fersmans proposal, nor in later USGS articles such as Fleischer(1953). They used the term "relative abundance of the elements". Brian Mason also mentioned the term "clarke" in Mason(1952)(mistakenly attributing it to Vladimir Vernadsky, later corrected to Fersman in Mason(1958)), but the definition slightly differed from Fersmans, limiting it only to the average percentage in Earth's crust, but allowed to exclude hydrosphere and atmosphere. Besides for explaining the term, Mason himself did not use the term "clarke".
A variant term "clarke value" is occasionally used (examples:). However, "clarke value" can have a different meaning, the clarke of concentration (example:).
Terms "clarke number" and "Clarke number" are found in articles written by Japanese authors (example:). | 9 | Geochemistry |
Cresol red can also be used as an electrophoretic color marker to monitor the process of agarose gel electrophoresis and polyacrylamide gel electrophoresis. In a 1% agarose gel, it runs approximately at the size of a 125 base pair (bp) DNA molecule (it depends on the concentration of buffer and other component). Bromophenol blue and xylene cyanol can also be used for this purpose. | 3 | Analytical Chemistry |
Precession electron diffraction (PED), invented by Roger Vincent and Paul Midgley in 1994, is a method to collect electron diffraction patterns in a transmission electron microscope (TEM). The technique involves rotating (precessing) a tilted incident electron beam around the central axis of the microscope, compensating for the tilt after the sample so a spot diffraction pattern is formed, similar to a SAED pattern. However, a PED pattern is an integration over a collection of diffraction conditions, see Figure 19. This integration produces a quasi-kinematical diffraction pattern that is more suitable as input into direct methods algorithms using electrons to determine the crystal structure of the sample. Because it avoids many dynamical effects it can also be used to better identify crystallographic phases. | 7 | Physical Chemistry |
* Several inconsistencies exist between gene, enzyme, reaction databases, and published literature sources regarding the metabolic information of an organism. A reconstruction is a systematic verification and compilation of data from various sources that takes into account all of the discrepancies.
* The combination of relevant metabolic and genomic information of an organism.
* Metabolic comparisons can be performed between various organisms of the same species as well as between different organisms.
* Analysis of synthetic lethality
* Predict adaptive evolution outcomes
* Use in metabolic engineering for high value outputs
Reconstructions and their corresponding models allow the formulation of hypotheses about the presence of certain enzymatic activities and the production of metabolites that can be experimentally tested, complementing the primarily discovery-based approach of traditional microbial biochemistry with hypothesis-driven research. The results these experiments can uncover novel pathways and metabolic activities and decipher between discrepancies in previous experimental data. Information about the chemical reactions of metabolism and the genetic background of various metabolic properties (sequence to structure to function) can be utilized by genetic engineers to modify organisms to produce high value outputs whether those products be medically relevant like pharmaceuticals; high value chemical intermediates such as terpenoids and isoprenoids; or biotechnological outputs like biofuels, or polyhydroxybutyrates also known as bioplastics.
Metabolic network reconstructions and models are used to understand how an organism or parasite functions inside of the host cell. For example, if the parasite serves to compromise the immune system by lysing macrophages, then the goal of metabolic reconstruction/simulation would be to determine the metabolites that are essential to the organisms proliferation inside of macrophages. If the proliferation cycle is inhibited, then the parasite would not continue to evade the hosts immune system. A reconstruction model serves as a first step to deciphering the complicated mechanisms surrounding disease. These models can also look at the minimal genes necessary for a cell to maintain virulence. The next step would be to use the predictions and postulates generated from a reconstruction model and apply it to discover novel biological functions such as drug-engineering and drug delivery techniques. | 1 | Biochemistry |
The term sublimation refers specifically to a physical change of state and is not used to describe the transformation of a solid to a gas in a chemical reaction. For example, the dissociation on heating of solid ammonium chloride into hydrogen chloride and ammonia is not sublimation but a chemical reaction. Similarly the combustion of candles, containing paraffin wax, to carbon dioxide and water vapor is not sublimation but a chemical reaction with oxygen. | 3 | Analytical Chemistry |
In clinical terms, a potentiator is a reagent that enhances sensitization of an antigen. Potentiators are used in the clinical laboratory for performing blood banking procedures that require enhancement of agglutination to detect the presence of antibodies or antigens in a patient's blood sample. Examples of potentiators include albumin, LISS (low ionic-strength saline) and PEG (polyethylene glycol). Potentiators are also known as enhancement reagents.
Albumin acts as a potentiator by reducing the zeta potential around the suspended red blood cells, thus dispersing the repulsive negative charges and enhancing agglutination. Low ionic strength saline (LISS) is a potentiator that acts by not only reducing the zeta potential, but also by increasing the amount of antibody taken up by the red blood cell during sensitization. LISS is a solution of glycine and albumin. Polyethylene glycol (PEG) in a LISS solution removes water from the system and thus concentrates the antibodies present. PEG can cause non-specific aggregation of cells, thus eliminating the necessity for centrifugation after incubation. PEG is not appropriate for use in samples from patients with increased plasma protein, such as patients with multiple myeloma. False-positive results may occur more frequently with the use of polyethylene glycol due to its strong agglutination capabilities. | 0 | Organic Chemistry |
Cupellation was also being used in parts of Europe to extract gold, silver, zinc, and tin by the late ninth to tenth century AD. Here, one of the earliest examples of an integrated unit process for extracting more than one precious metal was first introduced by Theophilus around the twelfth century. First, the gold-silver ore is melted down in the crucible, but with an excess amount of lead. The intense heat then oxidizes the lead which reacts quickly and binds with the impurities in the gold-silver ore. Since both gold and silver have low reactivity with the impurities, they remain behind once the slag is removed. The last stage involves parting, in which the silver is separated from the gold. First the gold-silver alloy is hammered into thin sheets and placed into a vessel. The sheets were then covered in urine, which contains sodium chloride (NaCl). The vessel is then capped and heated for several hours until the chlorides bind with the silver, creating silver chloride (AgCl). Finally, the silver chloride powder is then removed and smelted to recover the silver, while the pure gold remains intact. | 8 | Metallurgy |
Katsonis joined the Centre National de la Recherche Scientifique (CNRS) in 2007 and started to work on light-responsive chiral liquid crystals. She was made a Group Leader at the University of Groningen and held a visiting position at KU Leuven. In 2012 she was awarded a Royal Society International Exchange grant to work with Steve Fletcher on light responsive polymers. Katsonis proposed the materials could be used for microfluidics or soft robotics. Her research is inspired by nature, where helical structures are often created for movement.
She moved to the University of Twente in 2013, and was promoted to Professor in 2016. She returned to the University of Groningen as Professor of Active Molecular Systems in 2020. Katsonis has worked on squishy light responsive materials, which can convert light energy into mechanical work. She demonstrated that it is possible to switch between left and right-handed helixes in cholesteric liquid crystals using light. She has also showed that it is possible to use twisted liquid crystals as organising templates to design self-assemblies of superparamagnetic nanoparticles. In 2017 she was awarded a European Research Council Consolidator Grant in nanotechnology. Her recent work has been concerned with unravelling the molecular origin of purposeful motion, both in space and time at the nanoscale. | 0 | Organic Chemistry |
Associative substitution describes a pathway by which compounds interchange ligands. The terminology is typically applied to organometallic and coordination complexes, but resembles the Sn2 mechanism in organic chemistry. The opposite pathway is dissociative substitution, being analogous to the Sn1 pathway. Intermediate pathways exist between the pure associative and pure dissociative pathways, these are called interchange mechanisms.
Associative pathways are characterized by binding of the attacking nucleophile to give a discrete, detectable intermediate followed by loss of another ligand. Complexes that undergo associative substitution are either coordinatively unsaturated or contain a ligand that can change its bonding to the metal, e.g. change in hapticity or bending of a nitrogen oxide ligand (NO). In homogeneous catalysis, the associative pathway is desirable because the binding event, and hence the selectivity of the reaction, depends not only on the nature of the metal catalyst but also on the substrate.
Examples of associative mechanisms are commonly found in the chemistry of 16e square planar metal complexes, e.g. Vaska's complex and tetrachloroplatinate. These compounds (MX) bind the incoming (substituting) ligand Y to form pentacoordinate intermediates MXY that in a subsequent step dissociates one of their ligands. Dissociation of Y results in no detectable net reaction, but dissociation of X results in net substitution, giving the 16e complex MXY. The first step is typically rate determining. Thus, the entropy of activation is negative, which indicates an increase in order in the system. These reactions follow second order kinetics: the rate of the appearance of product depends on the concentration of MX and Y. The rate law is governed by the Eigen–Wilkins Mechanism. | 0 | Organic Chemistry |
Measurement of neopterin concentrations in body fluids like blood serum, cerebrospinal fluid or urine provides information about activation of cellular immune activation in humans under the control of T helper cells type 1. High neopterin production is associated with increased production of reactive oxygen species, neopterin concentrations also allow to estimate the extent of oxidative stress elicited by the immune system.
Increased neopterin production is found in, but not limited to, the following diseases:
*Viral infections including human immunodeficiency virus (HIV), hepatitis B and hepatitis C, SARS-CoV-1, SARS-CoV-2.
*Bacterial infections by intracellular living bacteria such as Borrelia (Lyme disease), Mycobacterium tuberculosis, and Helicobacter pylori.
*parasites such as Plasmodium (malaria)
*Autoimmune diseases such as rheumatoid arthritis (RA) and systemic lupus erythematosus (SLE)
*Malignant tumor diseases
*Allograft rejection episodes.
*A leukodystrophy called Aicardi-Goutieres syndrome
*Depression and somatization.
Neopterin concentrations usually correlate with the extent and activity of the disease, and are also useful to monitor during therapy in these patients. Elevated neopterin concentrations are among the best predictors of adverse outcome in patients with HIV infection, in cardiovascular disease and in various types of cancer.
In the laboratory it is measured by radioimmunoassay (RIA), ELISA, or high-performance liquid chromatography (HPLC). It has a native fluorescence of wavelength excitation at 353 nm and emission at 438 nm, rendering it readily detected. | 1 | Biochemistry |
The name is a dual reference to eastern blot and the geographical concept of the Far East (which includes Japan). | 1 | Biochemistry |
Glycolysis is performed by all living organisms and consists of 10 steps. The net reaction for the overall process of glycolysis is:
:Glucose + 2 NAD+ + 2 P + 2 ADP → 2 pyruvate + 2 ATP + 2 NADH + 2 HO
Steps 1 and 3 require the input of energy derived from the hydrolysis of ATP to ADP and P (inorganic phosphate), whereas steps 7 and 10 require the input of ADP, each yielding ATP. The enzymes necessary to break down glucose are found in the cytoplasm, the viscous fluid that fills living cells, where the glycolytic reactions take place. | 1 | Biochemistry |
Cycloalkenes with a small ring have about 20° more bond angle strain than a cycloalkane of the same size. This is because the bond angle for an alkene, C-C=C, is 122°, while the bond angle for an alkane, C-C-C, is 112°. When these carbons form a small ring, the alkene which has a larger bond angle will have to compress more than the alkane causing more bond angle strain.
Cycloalkenes have a lower melting point than cycloalkanes of the same size. The lowered melting point is due to the double bond preventing the compound from compact packing.
Cycloalkenes generally reflect physical properties of their cycloalkane. In physical states, only the smaller cycloalkenes are gases while the others are mostly liquid. These molecules are also more reactive than cycloalkanes due to increased electron density shifts of the double bond. | 0 | Organic Chemistry |
A frigorific mixture may be used to obtain a liquid medium that has a reproducible temperature below ambient temperature. Such mixtures were used to calibrate thermometers. In chemistry a cooling bath may be used to control the temperature of a strongly exothermic reaction.
A frigorific mixture may be used as an alternative to mechanical refrigeration. For example to fit two machined metal parts together, one part is placed in a frigorific mixture, causing it to contract so that may be easily inserted into the uncooled second part; on warming the two parts are held together tightly. | 7 | Physical Chemistry |
A reaction center comprises several (about 25-30) protein subunits, which provide a scaffold for a series of cofactors. The cofactors can be pigments (like chlorophyll, pheophytin, carotenoids), quinones, or iron-sulfur clusters.
Each photosystem has two main subunits: an antenna complex (a light harvesting complex or LHC) and a reaction center. The antenna complex is where light is captured, while the reaction center is where this light energy is transformed into chemical energy. At the reaction center, there are many polypeptides that are surrounded by pigment proteins. At the center of the reaction center is a special pair of chlorophyll molecules.
Each PSII has about 8 LHCII. These contain about 14 chlorophyll a and chlorophyll b molecules, as well as about four carotenoids. In the reaction center of PSII of plants and cyanobacteria, the light energy is used to split water into oxygen, protons, and electrons. The protons will be used in proton pumping to fuel the ATP synthase at the end of an electron transport chain. A majority of the reactions occur at the D1 and D2 subunits of PSII. | 5 | Photochemistry |
In metallurgy, alpha case is the oxygen-enriched surface phase that occurs when titanium and its alloys are exposed to heated air or oxygen. Alpha case is hard and brittle, and tends to create a series of microcracks that will reduce the metal's performance and its fatigue properties. Alpha case can be minimized or avoided by processing titanium at very deep vacuum levels. However once present on the surface, the currently applied method to remove the alpha case is by the subtractive methods of machining and/or chemical milling.
An emerging technique is to subject the metal to an electrochemical treatment in molten salts, such as calcium chloride or lithium chloride at elevated temperatures. This method removes the dissolved oxygen from the alpha case, hence restoring the oxygen-free metal. However, an unwanted consequence of the high temperature treatment is the growth of the grains in the metal. Grain growth may be limited by lowering the molten salt temperature. Alternatively, the metal may be rolling-pressed again to break the large grains into smaller ones. | 8 | Metallurgy |
* C: Frank Wigglesworth Clarke of USGS and Henry Stephens Washington
</references>
* U: United States Geological Survey (USGS)
</references>
* B:
</references>
* F: Alexander Fersman
</references>
* G: Victor Goldschmidt
</references>
* M: Brian Mason
</references>
* K:
</references>
* H: Research on the history of chemistry
</references> | 9 | Geochemistry |
Carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur are the six most important chemical elements whose covalent combinations make up most biological molecules on Earth. All of these elements are nonmetals.
In a human body, the four elements—C, H, O, and N—compose about 96% of the weight, and major minerals (macrominerals) and minor minerals (also called trace elements) compose the remainder.
Sulfur is contained in the amino acids cysteine and methionine.
Phosphorus is contained in phospholipids, a class of lipids that are a major component of all cell membranes, as they can form lipid bilayers, which keep ions, proteins, and other molecules where they are needed for cell function, and prevent them from diffusing into areas where they should not be. Phosphate groups are also an essential component of the backbone of nucleic acids (general name for DNA & RNA) and are required to form ATP – the main molecule used as energy powering the cell in all living creatures.
Carbonaceous asteroids are rich in CHON elements.
These asteroids are the most common type, and frequently collide with Earth as meteorites. Such collisions were especially common early in Earths history, and these impactors may have been crucial in the formation of the planets oceans.
The simplest compounds to contain all of the CHON elements are isomers fulminic acid (HCNO), isofulminic acid (HONC), cyanic acid (HOCN) and isocyanic acid (HNCO), having one of each atom. | 1 | Biochemistry |
In early "straight-through" urea plants, reactant recovery (the first step in "recycling") was done by letting down the system pressure to atmospheric to let the carbamate decompose back to ammonia and carbon dioxide. Originally, because it was not economic to recompress the ammonia and carbon dioxide for recycle, the ammonia at least would be used for the manufacture of other products such as ammonium nitrate or ammonium sulfate, and the carbon dioxide was usually wasted. Later process schemes made recycling unused ammonia and carbon dioxide practical. This was accomplished by the "total recycle process", developed in the 1940s to 1960s and now called the "conventional recycle process". It proceeds by depressurizing the reaction solution in stages (first to 18–25 bar and then to 2–5 bar) and passing it at each stage through a steam-heated carbamate decomposer, then recombining the resulting carbon dioxide and ammonia in a falling-film carbamate condenser and pumping the carbamate solution back into the urea reaction vessel. | 7 | Physical Chemistry |
Recently, preliminary results reported SNPs as important components of the epigenetic program in organisms. Moreover, cosmopolitan studies in European and South Asiatic populations have revealed the influence of SNPs in the methylation of specific CpG sites. In addition, meQTL enrichment analysis using GWAS database, demonstrated that those associations are important toward the prediction of biological traits. | 1 | Biochemistry |
The level of reducing sugars in wine, juice, and sugarcane are indicative of the quality of these food products, and monitoring the levels of reducing sugars during food production has improved market quality. The conventional method for doing so is the Lane-Eynon method, which involves titrating the reducing sugar with copper(II) in Fehling's solution in the presence of methylene blue, a common redox indicator. However, it is inaccurate, expensive, and sensitive to impurities. | 0 | Organic Chemistry |
During the 1980s, AT&T Bell Laboratories explored the use of nitrobenzyl-based PPGs as photoresists. Over the course of the decade, they developed a deep UV positive-tone photoresist where the protected substrate was added to a copolymer of poly(methyl methacrylate) and poly(methacrylic acid). Initially, the blend was insoluble. However, upon exposure to 260 ± 20 nm light, the PPG would be removed yielding 2-nitrosobenzaldehyde and a carboxylic acid that was soluble in aqueous base. | 5 | Photochemistry |
Borate buffered saline (abbreviated BBS) is a buffer used in some biochemical techniques to maintain the pH within a relatively narrow range. Borate buffers have an alkaline buffering capacity in the 8–10 range.
Boric acid has a pK of 9.14 at 25 °C. | 1 | Biochemistry |
Certain phosphoramidites are also used as monodentate chiral ligands in asymmetric synthesis. A large group of such ligands is derived from the chiral diol BINOL and can be synthesised by reaction of BINOL with phosphorus trichloride to the chlorophosphite and then reaction with simple secondary amines. This type of ligand was first used in 1996 in an asymmetric copper-catalysed addition of dialkylzincs to enones. | 0 | Organic Chemistry |
In physical chemistry, supersaturation occurs with a solution when the concentration of a solute exceeds the concentration specified by the value of solubility at equilibrium. Most commonly the term is applied to a solution of a solid in a liquid, but it can also be applied to liquids and gases dissolved in a liquid. A supersaturated solution is in a metastable state; it may return to equilibrium by separation of the excess of solute from the solution, by dilution of the solution by adding solvent, or by increasing the solubility of the solute in the solvent. | 7 | Physical Chemistry |
The Grove cell was the favored power source of the early American telegraph system in the period 1840 – 1860 because it offered a high current output and higher voltage than the earlier Daniell cell (at 1.9 volts and 1.1 volts, respectively). | 3 | Analytical Chemistry |
Pyrometallurgy is a branch of extractive metallurgy. It consists of the thermal treatment of minerals and metallurgical ores and concentrates to bring about physical and chemical transformations in the materials to enable recovery of valuable metals. Pyrometallurgical treatment may produce products able to be sold such as pure metals, or intermediate compounds or alloys, suitable as feed for further processing. Examples of elements extracted by pyrometallurgical processes include the oxides of less reactive elements like iron, copper, zinc, chromium, tin, and manganese.
Pyrometallurgical processes are generally grouped into one or more of the following categories:
* calcining,
* roasting,
* smelting,
* refining.
Most pyrometallurgical processes require energy input to sustain the temperature at which the process takes place. The energy is usually provided in the form of combustion or from electrical heat. When sufficient material is present in the feed to sustain the process temperature solely by exothermic reaction (i.e. without the addition of fuel or electrical heat), the process is said to be "autogenous". Processing of some sulfide ores exploit the exothermicity of their combustion | 8 | Metallurgy |
Its name is derived from the word “pigment” (P) and the presence of a major bleaching band centered around 680-685 nm in the flash-induced absorbance difference spectra of P680/ P680+•. | 5 | Photochemistry |
Expression vector in an expression host is now the usual method used in laboratories to produce proteins for research. Most proteins are produced in E. coli, but for glycosylated proteins and those with disulphide bonds, yeast, baculovirus and mammalian systems may be used. | 1 | Biochemistry |
A peptide chain of 10 residues in length is used in native chemical ligation with a larger recombinantly expressed protein.
* Residue 1: alanine
* Residue 2: one of glutamine, glycine, arginine, glutamic acid, serine, or methionine
* Residue 3: any one of the 20 amino acids
* Residue 4: acetyllysine
* Residue 5: alanine
* Residue 6: isoleucine
* Residue 7: aspartic acid
* Residue 8: phenylalanine
* Residue 9: acetyllysine
* Residue 10: arginine with the carboxy terminal thioester
With 7 possibilities at Residue 2 and 20 possibilities at Residue 3, the total would be or 140 different polypeptides in the library.
This peptide library would be useful for analyzing the effect of the post-translational modification acetylation on lysine which neutralizes the positive charge. Having the library of different peptides at residue 2 and 3 would let the investigator see if some change in chemical properties in the N-terminal tail of the ligated protein makes the protein more useful or useful in a different way. | 1 | Biochemistry |
RNA splicing errors have been estimated to occur in a third of genetic diseases. To understand pathogenesis and identify potential targets of therapeutic intervention in these diseases, explicating the splicing elements involved is essential. Determining the complete set of components involved in splicing presents many challenges due to the abundance of alternative splicing, which occurs in most human genes, and the specificity in which splicing is carried out in vivo. Splicing is distinctly conducted from cell type to cell type and across different stages of cellular development. Therefore, it is critical that any in vitro or bioinformatic assumptions about splicing regulation are confirmed in vivo. Minigenes are used to elucidate cis-regulatory elements, trans-regulatory elements and other regulators of pre-mature RNA splicing in vivo. Minigenes have been applied to the study of a diverse array of genetic diseases due to the aforementioned abundance of alternatively spliced genes and the specificity and variation observed in splicing regulation. The following are examples of minigene use in various diseases. While it is not an exhaustive list, it does provide a better understanding of how minigenes are utilized. | 1 | Biochemistry |
Botrytis–induced kinase 1 (BIK1) is a membrane-anchored enzyme in plants. It is a kinase that provides resistance to necrotrophic and biotrophic pathogens. As its name suggests, BIK1 is only active after being induced by Botrytis infection. When Botrytis cinerea is present, the BIK1 gene is transcribed so that the kinase is present to defend the cell. BIK1 functions to regulate the amount of salicylic acid (SA) present in the cell. When Botrytis cinerea or Alternaria brassicicola or any other necrotrophic pathogen is present, BIK1 is transcribed to regulate the pathogen response mechanisms. When BIK1 is present, SA levels decrease, allowing the nectrotrophic response to take place. When nectrotrophic pathogens are not present, BIK1 is not transcribed and SA levels increase, limiting the necrotrophic resistance pathway. Only the pathogenic defense response that is initiated by BIK1 is dependent on SA levels. Non-pathogenic cellular functions occur independently. In terms of non-pathogenic cellular functions, BIK1 is described as a critical component of ET signaling and PAMP-triggered immunity to pathogens. | 1 | Biochemistry |
Electroreflectance is often used to determine band gaps and electric properties of thin films of weaker semiconducting materials. Two different examples are listed below. | 7 | Physical Chemistry |
The bacteriophage P1 was first isolated by Dr. Giuseppe Bertani. In his study, he noticed that the lysogen produced abnormal non-continuous phages, and later found phage P1 was produced from the Lisbonne lysogen strain, in addition to bacteriophages P2 and P3. P1 has the ability to copy a bacteria's host genome and integrate that DNA information into other bacteria hosts, also known as generalized transduction. Later on, P1 was developed as a cloning vector by Nat Sternberg and colleagues in the 1990s. It is capable of Cre-Lox recombination. The P1 vector system was first developed to carry relatively large DNA fragments in plasmids (95-100kb). | 1 | Biochemistry |
Maxwells model was not the first plaster model of a thermodynamic surface: in 1871, even before Gibbs papers, James Thomson had constructed a plaster pressure-volume-temperature plot, based on data for carbon dioxide collected by Thomas Andrews.
Around 1900, the Dutch scientist Heike Kamerlingh Onnes, together with his student Johannes Petrus Kuenen and his assistant Zaalberg van Zelst, continued Maxwell's work by constructing their own plaster thermodynamic surface models. These models were based on accurate experimental data obtained in their laboratory, and were accompanied by specialised tools for drawing the lines of equal pressure. | 7 | Physical Chemistry |
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