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Reacting a silyl enol ether with PhSCl, a good and soft electrophile, provides a carbonyl compound sulfenylated at an alpha carbon. In this reaction, the trimethylsilyl group of the silyl enol ether is removed by the chloride ion released from the PhSCl upon attack of its electrophilic sulfur atom. | 0 | Organic Chemistry |
Alexander George Ogston FAA FRS (30 January 1911 – 29 June 1996) was a British biochemist who specialised in the thermodynamics of biological systems. He was a grandson of Sir Alexander Ogston, a Scottish surgeon who discovered Staphylococcus. | 4 | Stereochemistry |
Vagusstoff (literally translated from German as "Vagus Substance") refers to the substance released by stimulation of the vagus nerve which causes a reduction in the heart rate. Discovered in 1921 by physiologist Otto Loewi, vagusstoff was the first confirmation of chemical synaptic transmission and the first neurotransmitter ever discovered. It was later confirmed to be acetylcholine, which was first identified by Sir Henry Hallett Dale in 1914. Because of his pioneering experiments, in 1936 Loewi was awarded the Nobel Prize in Physiology or Medicine, which he shared with Dale. | 1 | Biochemistry |
Esketamine is eliminated from the human body more quickly than arketamine (R(–)-ketamine) or racemic ketamine, although arketamine slows the elimination of esketamine. | 4 | Stereochemistry |
The photons of a light beam have a characteristic energy, called photon energy, which is proportional to the frequency of the light. In the photoemission process, when an electron within some material absorbs the energy of a photon and acquires more energy than its binding energy, it is likely to be ejected. If the photon energy is too low, the electron is unable to escape the material. Since an increase in the intensity of low-frequency light will only increase the number of low-energy photons, this change in intensity will not create any single photon with enough energy to dislodge an electron. Moreover, the energy of the emitted electrons will not depend on the intensity of the incoming light of a given frequency, but only on the energy of the individual photons.
While free electrons can absorb any energy when irradiated as long as this is followed by an immediate re-emission, like in the Compton effect, in quantum systems all of the energy from one photon is absorbed—if the process is allowed by quantum mechanics—or none at all. Part of the acquired energy is used to liberate the electron from its atomic binding, and the rest contributes to the electron's kinetic energy as a free particle. Because electrons in a material occupy many different quantum states with different binding energies, and because they can sustain energy losses on their way out of the material, the emitted electrons will have a range of kinetic energies. The electrons from the highest occupied states will have the highest kinetic energy. In metals, those electrons will be emitted from the Fermi level.
When the photoelectron is emitted into a solid rather than into a vacuum, the term internal photoemission is often used, and emission into a vacuum is distinguished as external photoemission. | 7 | Physical Chemistry |
Degradation begins inside macrophages of the spleen, which remove old and damaged erythrocytes from the circulation.
In the first step, heme is converted to biliverdin by the enzyme heme oxygenase (HO). NADPH is used as the reducing agent, molecular oxygen enters the reaction, carbon monoxide (CO) is produced and the iron is released from the molecule as the ferrous ion (Fe). CO acts as a cellular messenger and functions in vasodilation.
In addition, heme degradation appears to be an evolutionarily-conserved response to oxidative stress. Briefly, when cells are exposed to free radicals, there is a rapid induction of the expression of the stress-responsive heme oxygenase-1 (HMOX1) isoenzyme that catabolizes heme (see below). The reason why cells must increase exponentially their capability to degrade heme in response to oxidative stress remains unclear but this appears to be part of a cytoprotective response that avoids the deleterious effects of free heme. When large amounts of free heme accumulates, the heme detoxification/degradation systems get overwhelmed, enabling heme to exert its damaging effects.
In the second reaction, biliverdin is converted to bilirubin by biliverdin reductase (BVR):
Bilirubin is transported into the liver by facilitated diffusion bound to a protein (serum albumin), where it is conjugated with glucuronic acid to become more water-soluble. The reaction is catalyzed by the enzyme UDP-glucuronosyltransferase.
This form of bilirubin is excreted from the liver in bile. Excretion of bilirubin from liver to biliary canaliculi is an active, energy-dependent and rate-limiting process. The intestinal bacteria deconjugate bilirubin diglucuronide releasing free bilirubin, which can either be reabsorbed or reduced to urobilinogen by the bacterial enzyme bilirubin reductase.
Some urobilinogen is absorbed by intestinal cells and transported into the kidneys and excreted with urine (urobilin, which is the product of oxidation of urobilinogen, and is responsible for the yellow colour of urine). The remainder travels down the digestive tract and is converted to stercobilinogen. This is oxidized to stercobilin, which is excreted and is responsible for the brown color of feces. | 1 | Biochemistry |
The insertion of carbon monoxide and alkenes into metal-carbon bonds is a widely exploited reaction with major industrial applications.
Such reactions are subject to the usual parameters that affect other reactions in coordination chemistry, but steric effects are especially important in determining the stereochemistry and regiochemistry of the reactions. The reverse reaction, the de-insertion of CO and alkenes, are of fundamental significance in many catalytic cycles as well.
Widely employed applications of migratory insertion of carbonyl groups are hydroformylation and the carbonylative production of acetic acid. The former converts alkenes, hydrogen, and carbon monoxide into aldehydes. The production of acetic acid by carbonylation proceeds via two similar industrial processes. More traditional is the rhodium-based Monsanto acetic acid process, but this process has been superseded by the iridium-based Cativa process. By 2002, worldwide annual production of acetic acid stood at 6 million tons, of which approximately 60% is produced by the Cativa process.
The Cativa process catalytic cycle, shown above, includes both insertion and de-insertion steps. The oxidative addition reaction of methyl iodide with (1) involves the formal insertion of the iridium(I) centre into the carbon-iodine bond, whereas step (3) to (4) is an example of migratory insertion of carbon monoxide into the iridium-carbon bond. The active catalyst species is regenerated by the reductive elimination of acetyl iodide from (4), a de-insertion reaction. | 0 | Organic Chemistry |
On March 27, 1791, Galvani published a book about his work on animal electricity. It contained comprehensive details of his 11 years of research and experimentation on the topic.
The 1797 edition of Gren’s Grundriss der Naturlehre provides the first explicit definition of galvanism as clearly reflecting Volta’s opinion in the following terms: | 7 | Physical Chemistry |
ECL proved to be very useful in analytical applications as a highly sensitive and selective method. It combines analytical advantages of chemiluminescent analysis (absence of background optical signal) with ease of reaction control by applying electrode potential. As an analytical technique it presents outstanding advantages over other common analytical methods due to its versatility, simplified optical setup compared with photoluminescence (PL), and good temporal and spatial control compared with chemiluminescence (CL). Enhanced selectivity of ECL analysis is reached by variation of electrode potential thus controlling species that are oxidized/reduced at the electrode and take part in ECL reaction (see electrochemical analysis).
It generally uses Ruthenium complexes, especially [[tris(bipyridine)ruthenium(II) chloride|[Ru(bpy)]]] (bpy = 2,2'-bipyridine) which releases a photon at ~620 nm regenerating with TPrA (Tripropylamine) in liquid phase or liquid–solid interface. It can be used as monolayer immobilized on an electrode surface (made e.g. of nafion, or special thin films made by Langmuir–Blogett technique or self-assembly technique) or as a coreactant or more commonly as a tag and used in HPLC, Ru tagged antibody based immunoassays, Ru Tagged DNA probes for PCR etc., NADH or HO generation based biosensors, oxalate and organic amine detection and many other applications and can be detected from picomolar sensitivity to dynamic range of more than six orders of magnitude. Photon detection is done with photomultiplier tubes (PMT) or silicon photodiode or gold coated fiber-optic sensors. The importance of ECL techniques detection for bio-related applications has been well established. ECL is heavily used commercially for many clinical lab applications. | 5 | Photochemistry |
The most common way to measure surface energy is through contact angle experiments. In this method, the contact angle of the surface is measured with several liquids, usually water and diiodomethane. Based on the contact angle results and knowing the surface tension of the liquids, the surface energy can be calculated. In practice, this analysis is done automatically by a contact angle meter.
There are several different models for calculating the surface energy based on the contact angle readings. The most commonly used method is OWRK, which requires the use of two probe liquids and gives out as a result the total surface energy as well as divides it into polar and dispersive components.
Contact angle method is the standard surface energy measurement method due to its simplicity, applicability to a wide range of surfaces and quickness. The measurement can be fully automated and is standardized.
In general, as surface energy increases, the contact angle decreases because more of the liquid is being "grabbed" by the surface. Conversely, as surface energy decreases, the contact angle increases, because the surface doesn't want to interact with the liquid. | 7 | Physical Chemistry |
2-C-Methyl--erythritol 4-phosphate (MEP) is an intermediate on the MEP pathway (non-mevalonate pathway) of isoprenoid precursor biosynthesis. It is the first committed metabolite on that pathway on the route to IPP and DMAPP. | 1 | Biochemistry |
Wide-scale production is credited to Edward Goodrich Acheson in 1891. Acheson was attempting to prepare artificial diamonds when he heated a mixture of clay (aluminium silicate) and powdered coke (carbon) in an iron bowl. He called the blue crystals that formed carborundum, believing it to be a new compound of carbon and aluminium, similar to corundum. Moissan also synthesized SiC by several routes, including dissolution of carbon in molten silicon, melting a mixture of calcium carbide and silica, and by reducing silica with carbon in an electric furnace.
Acheson patented the method for making silicon carbide powder on February 28, 1893. Acheson also developed the electric batch furnace by which SiC is still made today and formed the Carborundum Company to manufacture bulk SiC, initially for use as an abrasive. In 1900 the company settled with the Electric Smelting and Aluminum Company when a judge's decision gave "priority broadly" to its founders "for reducing ores and other substances by the incandescent method".
The first use of SiC was as an abrasive. This was followed by electronic applications. In the beginning of the 20th century, silicon carbide was used as a detector in the first radios. In 1907 Henry Joseph Round produced the first LED by applying a voltage to a SiC crystal and observing yellow, green and orange emission at the cathode. The effect was later rediscovered by O. V. Losev in the Soviet Union in 1923. | 8 | Metallurgy |
C plants capture carbon dioxide in their mesophyll cells (using an enzyme called phosphoenolpyruvate carboxylase which catalyzes the combination of carbon dioxide with a compound called phosphoenolpyruvate (PEP)), forming oxaloacetate. This oxaloacetate is then converted to malate and is transported into the bundle sheath cells (site of carbon dioxide fixation by RuBisCO) where oxygen concentration is low to avoid photorespiration. Here, carbon dioxide is removed from the malate and combined with RuBP by RuBisCO in the usual way, and the Calvin cycle proceeds as normal. The concentrations in the Bundle Sheath are approximately 10–20 fold higher than the concentration in the mesophyll cells.
This ability to avoid photorespiration makes these plants more hardy than other plants in dry and hot environments, wherein stomata are closed and internal carbon dioxide levels are low. Under these conditions, photorespiration does occur in C plants, but at a much lower level compared with C plants in the same conditions. C plants include sugar cane, corn (maize), and sorghum. | 5 | Photochemistry |
C-Nitroso compounds, such as nitrosobenzene, are typically prepared by oxidation of hydroxylamines:
:RNHOH + [O] → RNO + HO | 0 | Organic Chemistry |
Following Max Planck (1914), a radiative field is often described in terms of specific radiative intensity, which is a function of each geometrical point in a space region, at an instant of time. This is slightly different from Prevosts mode of definition, which was for regions of space. It is also slightly conceptually different from Prevosts definition: Prevost thought in terms of bound and free heat while today we think in terms of heat in kinetic and other dynamic energy of molecules, that is to say heat in matter, and the thermal photon gas. A detailed definition is given by R. M. Goody and Y. L. Yung (1989). They think of the interconversion between thermal radiation and heat in matter. From the specific radiative intensity they derive , the monochromatic vector flux density of radiation at each point in a region of space, which is equal to the time averaged monochromatic Poynting vector at that point (D. Mihalas 1978 on pages 9–11). They define the monochromatic volume-specific rate of gain of heat by matter from radiation as the negative of the divergence of the monochromatic flux density vector; it is a scalar function of the position of the point:
They define (pointwise) monochromatic radiative equilibrium by
: at every point of the region that is in radiative equilibrium.
They define (pointwise) radiative equilibrium by
: at every point of the region that is in radiative equilibrium.
This means that, at every point of the region of space that is in (pointwise) radiative equilibrium, the total, for all frequencies of radiation, interconversion of energy between thermal radiation and energy content in matter is nil(zero). Pointwise radiative equilibrium is closely related to Prevost's absolute radiative equilibrium.
D. Mihalas and B. Weibel-Mihalas (1984) emphasise that this definition applies to a static medium, in which the matter is not moving. They also consider moving media. | 7 | Physical Chemistry |
Attenuation was first observed by Charles Yanofsky in the trp operon of E. coli. The first observation was linked to two separate scientific facts. Mutations which knocked out the trp R (repressor) gene still showed some regulation of the trp operon (these mutants were not fully induced/repressed by tryptophan). The total range of trp operon regulation is about 700 X (on/off). When the trp repressor was knocked out, one still got about 10 X regulation by the absence or presence of trp. When the sequence of the beginning of the trp operon was determined an unusual open reading frame (ORF) was seen immediately preceding the ORFs for the known structural genes for the tryptophan biosynthetic enzymes. The general structural information shown below was observed from the sequence of the trp operon.
First, Yanofsky observed that the ORF contained two tandem Trp codons and the protein had a Trp percent composition which was about 10X normal. Second, the mRNA in this region contained regions of dyad symmetry which would allow it to form two mutually exclusive secondary structures. One of the structures looked exactly like a rho-independent transcription termination signal. The other secondary structure, if formed, would prevent the formation of this secondary structure and thus the terminator. This other structure is called the "preemptor". | 1 | Biochemistry |
The first transformation of metabolism of ZEN will reduce the ketone group to an alcohol via aliphatic hydroxylation and result in the formation of the two zearalenol metabolites. This process is catalyzed by 3 α- and 3 β-hydroxy steroid dehydrogenase (HSD). CYP450 enzymes will then catalyze aromatic hydroxylation at the 13 or 15 position resulting in 13- or 15- catechols. Steric hindrance of at the 13 position is suspected to be the reason that in humans and rats there is more of the 15-catechol present. The catechols are the processed into mono-ethyl esters by catechol-o-methyl transferase (COMT) and S-adenosyl methionine (SAM). After this transformation they may be metabolized further to quinones which can cause the formation of reactive oxygen species (ROS) and cause covalent modification of DNA. | 1 | Biochemistry |
Thomas Kurtzman is an American physical chemist most notable for his research into the use of convolutional neural networks (CNNs) to improve pharmaceutical design. According to Bioworld, Kurtzmans research "reached the devastating conclusion that the entirety" of apparent deep learning produced over the course of several years by a CNN dataset highly regarded in academia and industry was illusory. The perceived scientific progress, Kurtzman wrote, was due to CNNs effective learning of the deficiencies in the dataset. "This is alarming," the article continued, "as companies have been built on [https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220113 this research.]
During the COVID-19 pandemic, a computational tool Kurtzman developed, GIST, was used to research potential new drugs to treat the illness.
Kurtzman is a professor of chemistry at the Lehman College and the Graduate Center of the City University of New York. His research is conducted at the affiliated Kurtzman Lab and funded by the National Institutes of Health.
He is married to Mor Armony, vice dean for faculty and research at New York University's Stern School of Business. | 7 | Physical Chemistry |
Allelochemicals are a useful tool in sustainable farming due to their ability to control weeds. The possible application of allelopathy in agriculture is the subject of much research. Using allelochemical producing plants in agriculture results in significant suppression of weeds and various pests. Some plants will even reduce the germination rate of other plants by 50%. Current research is focused on the effects of weeds on crops, crops on weeds, and crops on crops. This research furthers the possibility of using allelochemicals as growth regulators and natural herbicides, to promote sustainable agriculture. Agricultural practices may be enhanced through the utilization of allelochemical producing plants. When used correctly, these plants can provide pesticide, herbicide, and antimicrobial qualities to crops. number of such allelochemicals are commercially available or in the process of large-scale manufacture. For example, leptospermone is an allelochemical in lemon bottlebrush (Callistemon citrinus). Although it was found to be too weak as a commercial herbicide, a chemical analog of it, mesotrione (tradename Callisto), was found to be effective. It is sold to control broadleaf weeds in corn but also seems to be an effective control for crabgrass in lawns. Sheeja (1993) reported the allelopathic interaction of the weeds Chromolaena odorata (Eupatorium odoratum) and Lantana camara on selected major crops.
Many crop cultivars show strong allelopathic properties, of which rice (Oryza sativa) has been most studied. Rice allelopathy depends on variety and origin: Japonica rice is more allelopathic than Indica and Japonica-Indica hybrid. More recently, critical review on rice allelopathy and the possibility for weed management reported that allelopathic characteristics in rice are quantitatively inherited and several allelopathy-involved traits have been identified. The use of allelochemicals in agriculture provide for a more environmentally friendly approach to weed control, as they do not leave behind residues. Currently used pesticides and herbicides leak into waterways and result in unsafe water qualities. This problem could be eliminated or significantly reduced by using allelochemicals instead of harsh herbicides. The use of cover crops also results in less soil erosion and lessens the need for nitrogen heavy fertilizers. | 1 | Biochemistry |
Radiation embrittlement, also known as neutron embrittlement, is a phenomenon more commonly observed in reactors and nuclear plants as these materials are constantly exposed to a steady amount of radiation. When a neutron irradiates the metal, voids are created in the material, which is known as void swelling. If the material is under creep (under low strain rate and high temperature condition), the voids will coalesce into vacancies which compromises the mechanical strength of the workpiece. | 8 | Metallurgy |
Petrobactin is a bis-catechol siderophore found in M. hydrocarbonoclasticus, A. macleodii, and the anthrax-producing B. anthracis. Like other siderophores petrobactin is a highly specific iron(III) transport ligand, contributing to the marine microbial uptake of environmental iron.
The iron-chelated petrobactin complex readily undergoes a photolytic oxidative decarboxylation due to its α-hydroxy carboxylate group, converting iron(III) to the more biologically useful iron(II). | 1 | Biochemistry |
Many columns of limestone rise above the surface of Mono Lake. These limestone towers consist primarily of calcium carbonate minerals such as calcite (CaCO). This type of limestone rock is referred to as tufa, which is a term used for limestone that forms in low to moderate temperatures. | 2 | Environmental Chemistry |
These polymers are commercially used in optical films, lenses, touch screens, light guide panels, reflection films, and other components for mobile devices, displays, cameras, copiers and other optical assemblies. | 7 | Physical Chemistry |
The Boom method (Boom nucleic acid extraction method)
is a solid phase extraction method for isolating nucleic acids (NA)
from biological samples. Silica beads are a key element to this method, which are capable of binding the nucleic acids in the presence of a chaotropic substance according to the chaotropic effect.
This method is one of the most widespread methods for isolating nucleic acids from biological samples and is known as a simple, rapid, and reliable method for the small-scale purification of nucleic acid from biological sample.
This method is said to have been developed and invented by Willem R. Boom et al. around 1990.
While the chaotropic effect was previously known and reported by other scientists,
Boom et al. contributed an optimization of the method to complex starting materials, such as body fluids and other biological starting materials, and provided a short procedure according to the Boom et al. US5234809. After the Boom et al. patent was filed,
similar applications were also filed by other parties.
In a narrow sense, the word "silica" meant SiO crystals; however, other forms of silica particles are available.
In particular, amorphous silicon oxide and glass powder, alkylsilica, aluminum silicate (zeolite), or, activated
silica with -NH, are all suitable as nucleic acid binding solid phase material according to this method.
Today, the concepts of the Boom method, characterized by utilizing magnetic silica particles, are widely used. With this method, magnetic silica beads are captured by a magnetic bead collector, such as the Tajima pipette, Pick pen(R),
Quad Pole collector, and so on. | 1 | Biochemistry |
Aluminium surface composites with enhanced surface properties can be fabricated using FSP. Aluminium surface composites fabricated with the optimum friction stir processing parameters show better mechanical properties and corrosion resistance. The processing parameters such as tool rotational speed and tool shoulder diameter affects the surface properties. Higher surface hardness is exhibited by the surface composites fabricated at higher tool rotational speed and lower tool shoulder diameter. The properties of the composite materials can be altered by changing the type of reinforcement. Reinforcement particles aids in the grain size refinement as well as the property enhancement in the processed materials. The surface composite properties can be varied by changing the reinforcement particles based on the end application. The reinforcement phases can be metallic, ceramic, or polymer materials. | 8 | Metallurgy |
When referring to the genotype (the gene) the mnemonic is italicized and not capitalised. When referring to the gene product or phenotype, the mnemonic is first-letter capitalised and not italicized (e.g. DnaA – the protein produced by the dnaA gene; LeuA – the phenotype of a leuA mutant; Amp – the ampicillin-resistance phenotype of the β-lactamase gene bla). | 1 | Biochemistry |
The Qubit fluorometer method is to use fluorescent dyes to determine the concentration of either nucleic acids or proteins in a sample. Specialized fluorescent dyes bind specifically to the substances of interest. A spectrophotometer is used in this method to measure the natural absorbance of light at 260 nm (for DNA and RNA) or 280 nm (for proteins). | 7 | Physical Chemistry |
For all organic matter to be completely oxidized, an excess amount of potassium dichromate (or any oxidizing agent) must be present. Once oxidation is complete, the amount of excess potassium dichromate must be measured to ensure that the amount of Cr can be determined with accuracy. To do so, the excess potassium dichromate is titrated with ferrous ammonium sulfate (FAS) until all of the excess oxidizing agent has been reduced to Cr. Typically, the oxidation-reduction indicator ferroin is added during this titration step as well. Once all the excess dichromate has been reduced, the ferroin indicator changes from blue-green to a reddish brown. The amount of ferrous ammonium sulfate added is equivalent to the amount of excess potassium dichromate added to the original sample. Note: Ferroin indicator is bright red from commercially prepared sources, but when added to a digested sample containing potassium dichromate it exhibits a green hue. During the titration the color of the indicator changes from a green hue to a bright blue hue to a reddish brown upon reaching the endpoint. Ferroin indicator changes from red to pale blue when oxidized. | 9 | Geochemistry |
Bacteriorhodopsin in the ground state absorbs a photon and the retinal changes isomerization from all-trans 15-anti to the strained 13-cis 15-anti in the K state. The isomerisation reaction is fast and occurs in less than 1 ps. The retinal adopts a less strained conformation to form the L intermediate. | 5 | Photochemistry |
As polymers approach their ceiling temperature, thermal degradation gives way to complete decomposition. Certain polymers like PTFE, polystyrene and PMMA undergo depolymerization to give their starting monomers, whereas others like polyethylene undergo pyrolysis, with random chain scission giving a mixture of volatile products. Where monomers are obtained, they can be converted back into new plastic (chemical or feedstock recycling), whereas pyrolysis products are used as a type of synthetic fuel (energy recycling). In practice, even very efficient depolymerisation to monomers tends to see some competitive pyrolysis. Thermoset polymers may also be converted in this way, for instance, in tyre recycling. | 7 | Physical Chemistry |
There are several examples of covalently linked 2DPs which include the individual layers or sheets of graphite (called graphenes), MoS2, (BN)x and layered covalent organic frameworks. As required by the above definition, these sheets have a periodic internal structure.
A well-known example of a 2D polymer is graphene; whose optical, electronic and mechanical properties have been studied in depth. Graphene has a honeycomb lattice of carbon atoms that exhibit semiconducting properties. A potential repeat unit of graphene is a sp2-hybridized carbon atom. Individual sheets can in principle be obtained by exfoliation procedures, though in reality this is a non-trivial enterprise.
Molybdenumdisulfide can exist in two-dimensional, single or layered polymers where each Mo(IV) center occupies a trigonal prismatic coordination sphere.
Boron nitride polymers are stable in its crystalline hexagonal form where it has a two-dimensional layered structure similar to graphene. There are covalent bonds formed between boron and nitrogen atoms, yet the layers are held together by weak van der Waals interactions, in which the boron atoms are eclipsed over the nitrogen.
Two dimensional covalent organic frameworks (COFs) are one type of microporous coordination polymer that can be fabricated in the 2D plane. The dimensionality and topology of the 2D COFs result from both the shape of the monomers and the relative and dimensional orientations of their reactive groups. These materials contain desirable properties in fields of materials chemistry including thermal stability, tunable porosity, high specific surface area, and the low density of organic material. By careful selection of organic building units, long range π-orbital overlap parallel to the stacking direction of certain organic frameworks can be achieved.
Many covalent organic frameworks derive their topology from the directionality of the covalent linkages, thus small changes in organic linkers can dramatically affect their mechanical and electronic properties. Even small changes in their structure can induce dramatic changes in stacking behavior of molecular semiconductors.
Porphyrins are an additional class of conjugated, heterocyclic macrocycles. Control of monomer assembly through covalent assembly has also been demonstrated using covalent interactions with porphyrins. Upon thermal activation of porphyrin building blocks, covalent bonds form to create a conductive polymer, a versatile route for bottom-up construction of electronic circuits has been demonstrated. | 7 | Physical Chemistry |
Quantitative microbiological risk assessments (QMRAs) combine pathogen concentrations in water with dose-response relationships and data reflecting potential exposure to estimate the risk of infection.
Data on water exposure are generally collected using questionnaires, but may also be determined from actual measurements of water ingested, or estimated from previously published data. Respondents are asked to report the frequency and timing and location of exposures, detailed information about the amount of water swallowed and head submersion, and basic demographic characteristics such as age, gender, socioeconomic status and family composition. Once sufficient data are collected and determined to be representative of the general population, they are usually fit with distributions, and these distribution parameters are then used in the risk assessment equations. Monitoring data representing occurrence of pathogens, direct measurement of pathogen concentrations, or estimations deriving pathogen concentrations from indicator bacteria concentrations, are also fit with distributions. Dose is calculated by multiplying the concentration of pathogens per volume by volume. Dose-responses can also be fit with a distribution. | 3 | Analytical Chemistry |
Quorum quenching is the process of preventing quorum sensing by disrupting signalling. This is achieved by inactivating signalling enzymes, by introducing molecules that mimic signalling molecules and block their receptors, by degrading signalling molecules themselves, or by a modification of the quorum sensing signals due to an enzyme activity. | 1 | Biochemistry |
By oral route, phenethylamine's half-life is minutes; endogenously produced PEA in catecholamine neurons has a half-life of roughly 30 seconds. In humans, PEA is metabolized by phenylethanolamine N-methyltransferase (PNMT), monoamine oxidase A (), monoamine oxidase B (), the semicarbazide-sensitive amine oxidases (SSAOs) AOC2 and AOC3, flavin-containing monooxygenase 3 (FMO3), and aralkylamine N-acetyltransferase (AANAT). , an isomer of amphetamine, is produced in humans via the metabolism of phenethylamine by PNMT. β-Phenylacetic acid is the primary urinary metabolite of phenethylamine and is produced via monoamine oxidase metabolism and subsequent aldehyde dehydrogenase metabolism. Phenylacetaldehyde is the intermediate product which is produced by monoamine oxidase and then further metabolized into β-phenylacetic acid by aldehyde dehydrogenase.
When the initial phenylethylamine concentration in the brain is low, brain levels can be increased when taking a monoamine oxidase inhibitor (MAOI), particularly a MAO-B inhibitor, and by times when the initial concentration is high. | 1 | Biochemistry |
Metal carbonyls are important precursors for the synthesis of other organometallic complexes. Common reactions are the substitution of carbon monoxide by other ligands, the oxidation or reduction reactions of the metal center, and reactions at the carbon monoxide ligand. | 0 | Organic Chemistry |
Gravimetric analysis usually only provides for the analysis of a single element, or a limited group of elements, at a time. Comparing modern dynamic flash combustion coupled with gas chromatography with traditional combustion analysis will show that the former is both faster and allows for simultaneous determination of multiple elements while traditional determination allowed only for the determination of carbon and hydrogen. Methods are often convoluted and a slight mis-step in a procedure can often mean disaster for the analysis (colloid formation in precipitation gravimetry, for example). Compare this with hardy methods such as spectrophotometry and one will find that analysis by these methods is much more efficient. | 3 | Analytical Chemistry |
The Bellini–Tosi direction finder was a type of radio direction finder that was widely used from World War I to World War II. It used the signals from two crossed antennas, or four individual antennas simulating two crossed ones, to re-create the radio signal in a small area between two loops of wire. The operator could then measure the angle to the target radio source by performing direction finding within this small area. The advantage to the Bellini–Tosi system is that the antennas do not move, allowing them to be built at any required size.
The basic technique remains in use, although the equipment has changed dramatically. Goniometers are widely used for military and civil purposes, e.g. interception of satellite and naval communications on the French warship Dupuy de Lôme uses multiple goniometers. | 7 | Physical Chemistry |
Isotopes with extremely long half-lives and their decay products can be used to study multi-million year processes, such as tectonics and extreme climate change. For example, in rubidium–strontium dating, the isotopic ratio of strontium (Sr/Sr) can be analyzed within ice cores to examine changes over the earths lifetime. Differences in this ratio within the ice core would indicate significant alterations in the earths geochemistry. | 7 | Physical Chemistry |
This process was the main process used in Britain from the mid-19th century until 1951. The process was very inefficient as it was designed as a small scale batch operation. Each retort only produced so companies would put them together in banks and used one large gas burner to heat all of them. The Belgian process requires redistillation to remove impurities of lead, cadmium, iron, copper, and arsenic. | 8 | Metallurgy |
Bond length is related to bond order: when more electrons participate in bond formation the bond is shorter. Bond length is also inversely related to bond strength and the bond dissociation energy: all other factors being equal, a stronger bond will be shorter. In a bond between two identical atoms, half the bond distance is equal to the covalent radius.
Bond lengths are measured in the solid phase by means of X-ray diffraction, or approximated in the gas phase by microwave spectroscopy. A bond between a given pair of atoms may vary between different molecules. For example, the carbon to hydrogen bonds in methane are different from those in methyl chloride. It is however possible to make generalizations when the general structure is the same. | 4 | Stereochemistry |
As noted above, by transitioning from one chair conformer to another, all axial positions become equatorial and all equatorial positions become axial. Substituent groups in equatorial positions roughly follow along the equator of the cyclohexane ring and are perpendicular to the axis, while substituents in axial positions roughly follow the imaginary axis of the carbon ring and are perpendicular to the equator.
Diaxial interactions or axial-axial interactions is what the steric strain between an axial substituent and another axial group, typically a hydrogen, on the same side of a chair conformation ring. The interaction is labeled by the carbon number they come from. A 1,3-diaxial interaction happens between the atoms connected to the first and third carbons. The more interactions the more strain on the molecule and the conformations with the most strain are less likely to be seen. An example is cyclopropane which, because of its planar geometry, has six fully eclipsed carbon and axial hydrogen bonds making the strain 116 kJ/mol (27.7 kcal/mol). Strain can also be decreased when the carbon-carbon bond angles are close or at the preferred bond angle of 109.5°, meaning a ring having six tetrahedral carbons is typically lower than that of most rings. | 4 | Stereochemistry |
Ted Ellis maintained a passion for art that preceded his professional art career; he painted throughout his time in the Army and as an environmental chemist, generally working out of a studio in his garage. His first commissions were produced for two co-workers at Rollins. They had wanted to purchase the piece that he was then working on, but he refused and instead offered to paint them two similar pieces, which they purchased for $40.
When he first got started, Ellis passed on an opportunity to do work for the J. C. Penney catalog because he was too busy, but ultimately found success in a similar publication.
Ellis published his first prints through Market Arts Dan Rose in Houston, but his art career took off when he noticed that his wifes Avon boutique magazine, targeted at African-Americans, lacked any art. He sent Avon a proposal which they accepted, and through the magazine he sold 42,610 signed prints of Thee Baptism. Since he was still working as an engineer at the time, he autographed the tens-of-thousands of prints during his lunch-break.
After quitting his job as an engineer in 1996, Ellis competed against 500 others for, and won, a 1998 Walt Disney Studios commission for art in honor of Black History Month. The piece was used in the 1999 celebration at Epcot Center and appeared on T-shirts, souvenir-mugs, and posters. | 3 | Analytical Chemistry |
Deoxyribozymes, also called DNA enzymes, DNAzymes, or catalytic DNA, are DNA oligonucleotides that are capable of performing a specific chemical reaction, often but not always catalytic. This is similar to the action of other biological enzymes, such as proteins or ribozymes (enzymes composed of RNA).
However, in contrast to the abundance of protein enzymes in biological systems and the discovery of biological ribozymes in the 1980s,
there is only little evidence for naturally occurring deoxyribozymes.
Deoxyribozymes should not be confused with DNA aptamers which are oligonucleotides that selectively bind a target ligand, but do not catalyze a subsequent chemical reaction.
With the exception of ribozymes, nucleic acid molecules within cells primarily serve as storage of genetic information due to its ability to form complementary base pairs, which allows for high-fidelity copying and transfer of genetic information. In contrast, nucleic acid molecules are more limited in their catalytic ability, in comparison to protein enzymes, to just three types of interactions: hydrogen bonding, pi stacking, and metal-ion coordination. This is due to the limited number of functional groups of the nucleic acid monomers: while proteins are built from up to twenty different amino acids with various functional groups, nucleic acids are built from just four chemically similar nucleobases. In addition, DNA lacks the 2'-hydroxyl group found in RNA which limits the catalytic competency of deoxyribozymes even in comparison to ribozymes.
In addition to the inherent inferiority of DNA catalytic activity, the apparent lack of naturally occurring deoxyribozymes may also be due to the primarily double-stranded conformation of DNA in biological systems which would limit its physical flexibility and ability to form tertiary structures, and so would drastically limit the ability of double-stranded DNA to act as a catalyst; though there are a few known instances of biological single-stranded DNA such as multicopy single-stranded DNA (msDNA), certain viral genomes, and the replication fork formed during DNA replication. Further structural differences between DNA and RNA may also play a role in the lack of biological deoxyribozymes, such as the additional methyl group of the DNA base thymidine compared to the RNA base uracil or the tendency of DNA to adopt the B-form helix while RNA tends to adopt the A-form helix. However, it has also been shown that DNA can form structures that RNA cannot, which suggests that, though there are differences in structures that each can form, neither is inherently more or less catalytic due to their possible structural motifs.
In 2021, the DNAmoreDB database for cataloguing known deoxyribozymes was released. | 7 | Physical Chemistry |
The structures of both eukaryotic and prokaryotic genes involve several nested sequence elements. Each element has a specific function in the multi-step process of gene expression. The sequences and lengths of these elements vary, but the same general functions are present in most genes. Although DNA is a double-stranded molecule, typically only one of the strands encodes information that the RNA polymerase reads to produce protein-coding mRNA or non-coding RNA. This sense or coding strand, runs in the 5 to 3 direction where the numbers refer to the carbon atoms of the backbone's ribose sugar. The open reading frame (ORF) of a gene is therefore usually represented as an arrow indicating the direction in which the sense strand is read.
Regulatory sequences are located at the extremities of genes. These sequence regions can either be next to the transcribed region (the promoter) or separated by many kilobases (enhancers and silencers). The promoter is located at the 5' end of the gene and is composed of a core promoter sequence and a proximal promoter sequence. The core promoter marks the start site for transcription by binding RNA polymerase and other proteins necessary for copying DNA to RNA. The proximal promoter region binds transcription factors that modify the affinity of the core promoter for RNA polymerase. Genes may be regulated by multiple enhancer and silencer sequences that further modify the activity of promoters by binding activator or repressor proteins. Enhancers and silencers may be distantly located from the gene, many thousands of base pairs away. The binding of different transcription factors, therefore, regulates the rate of transcription initiation at different times and in different cells.
Regulatory elements can overlap one another, with a section of DNA able to interact with many competing activators and repressors as well as RNA polymerase. For example, some repressor proteins can bind to the core promoter to prevent polymerase binding. For genes with multiple regulatory sequences, the rate of transcription is the product of all of the elements combined. Binding of activators and repressors to multiple regulatory sequences has a cooperative effect on transcription initiation.
Although all organisms use both transcriptional activators and repressors, eukaryotic genes are said to be default off, whereas prokaryotic genes are default on. The core promoter of eukaryotic genes typically requires additional activation by promoter elements for expression to occur. The core promoter of prokaryotic genes, conversely, is sufficient for strong expression and is regulated by repressors.
An additional layer of regulation occurs for protein coding genes after the mRNA has been processed to prepare it for translation to protein. Only the region between the start and stop codons encodes the final protein product. The flanking untranslated regions (UTRs) contain further regulatory sequences. The 3' UTR contains a terminator sequence, which marks the endpoint for transcription and releases the RNA polymerase. The 5’ UTR binds the ribosome, which translates the protein-coding region into a string of amino acids that fold to form the final protein product. In the case of genes for non-coding RNAs, the RNA is not translated but instead folds to be directly functional. | 1 | Biochemistry |
The Cossee–Arlman mechanism in polymer chemistry is the main pathway for the formation of C–C bonds in the polymerization of alkenes. The mechanism features an intermediate coordination complex that contains both the growing polymer chain and the monomer (alkene). These ligands combine within the coordination sphere of the metal to form a polymer chain that is elongated by two carbons.
The details of this mechanism can be used to explain the stereoregularity of the polymerisation of alkenes using Ziegler–Natta or metallocene catalysts. Stereoregularity is relevant for unsymmetrical alkenes such as propylene. The coordination sphere of the metal ligands sterically influences which end of the propylene attaches to the growing polymer chain and the relative stereochemistry of the methyl groups on the polymer. The stereoregularity is influenced by the ligands. For the metallocene catalysts, the cyclopentadienyl ligands (or their surrogates) fulfill this role. For heterogeneous catalysts, the stereoregularity is determined by the surface structure around the active site on the catalyst particle, and can be influenced by additives such as succinates or phthalates, which tend to block specific sites, while leaving others (with different stereoreactivity) to catalyse the polymerization. | 7 | Physical Chemistry |
The Swain equation relates the kinetic isotope effect for the protium/tritium combination with that of the protium/deuterium combination according to:
where k are the reaction rate constants for the protonated, deuterated and tritiated reactants respectively. | 7 | Physical Chemistry |
Exposure of a positive resist to radiation changes the chemical structure such that it becomes a liquid or more soluble. These changes in chemical structure are often rooted in the cleavage of specific linkers in the polymer. Once irradiated, the "decomposed" polymers can be washed away using a developer solvent leaving behind the polymer that was not exposed to light. This type of technology allows the production of very fine stencils for applications such as microelectronics. In order to have these types of qualities, positive resists utilize polymers with labile linkers in their back bone that can be cleaved upon irradiation, or use a photo-generated acid to hydrolyze bonds in the polymer. A polymer that decomposes upon irradiation to a liquid or more soluble product is referred to as a positive tone resist. Common functional groups that can be hydrolyzed by a photo-generated acid catalyst include polycarbonates and polyesters. | 5 | Photochemistry |
Desymmetrization in stereochemistry is the modification of a molecule that results in the loss of one or more symmetry elements. A common application of this class of reactions involves the introduction of chirality. Formally, such conversions required the loss of an improper axis of rotation (mirror plane, center of inversion, rotation-reflection axis). In other words, desymmetrisations convert prochiral precursors into chiral products. | 4 | Stereochemistry |
Spot analysis, spot test analysis, or spot test is a chemical test, a simple and efficient technique where analytic assays are executed in only one, or a few drops, of a chemical solution, preferably in a great piece of filter paper, without using any sophisticated instrumentation. The development and popularization of the test is credited to Fritz Feigl.
A spot test or spot assay can also refer to a test often used in microbiology. | 3 | Analytical Chemistry |
Nettle agents (named after stinging nettles) or urticants are a variety of chemical warfare agents that produce corrosive skin and tissue injury upon contact, resulting in erythema, urticaria, intense itching, and a hive-like rash.
Most nettle agents, such as the best known and studied nettle agent, phosgene oxime, are often grouped with the vesicant (blister agent) chemical agents. However, because nettle agents do not cause blisters, they are not true vesicants. | 1 | Biochemistry |
Molecular propeller is a molecule that can propel fluids when rotated, due to its special shape that is designed in analogy to macroscopic propellers: it has several molecular-scale blades attached at a certain pitch angle around the circumference of a shaft, aligned along the rotational axis.
The molecular propellers designed in the group of Prof. Petr Král from the University of Illinois at Chicago have their blades formed by planar aromatic molecules and the shaft is a carbon nanotube. Molecular dynamics simulations show that these propellers can serve as efficient pumps in the bulk and at the surfaces of liquids. Their pumping efficiency depends on the chemistry of the interface between the blades and the liquid. For example, if the blades are hydrophobic, water molecules do not bind to them, and the propellers can pump them well. If the blades are hydrophilic, water molecules form hydrogen bonds with the atoms in the polar blades. This can largely block the flow of other water molecules around the blades and significantly slow down their pumping. | 6 | Supramolecular Chemistry |
Soil biota affect soil pH directly through excretion, and indirectly by acting on the physical environment. Many soil fungi, although not all of them, acidify the soil by excreting oxalic acid, a product of their respiratory metabolism. Oxalic acid precipitates calcium, forming insoluble crystals of calcium oxalate and thus depriving the soil solution from this necessary element. On the opposite side, earthworms exert a buffering effect on soil pH through their excretion of mucus, endowed with amphoteric properties.
By mixing organic matter with mineral matter, in particular clay particles, and by adding mucus as a glue for some of them, burrowing soil animals, e.g. fossorial rodents, moles, earthworms, termites, some millipedes and fly larvae, contribute to decrease the natural acidity of raw organic matter, as observed in mull humus forms. | 9 | Geochemistry |
The Norrish type I reaction is the photochemical cleavage or homolysis of aldehydes and ketones into two free radical intermediates (α-scission). The carbonyl group accepts a photon and is excited to a photochemical singlet state. Through intersystem crossing the triplet state can be obtained. On cleavage of the α-carbon bond from either state, two radical fragments are obtained. The size and nature of these fragments depends upon the stability of the generated radicals; for instance, the cleavage of 2-butanone largely yields ethyl radicals in favor of less stable methyl radicals.
Several secondary reaction modes are open to these fragments depending on the exact molecular structure.
* The fragments can simply recombine to the original carbonyl compound, with racemisation at the α-carbon.
* The acyl radical can lose a molecule of carbon monoxide, forming a new carbon radical at the other α-carbon, followed by formation of a new carbon–carbon bond between the radicals. The ultimate effect is simple extraction of the carbonyl unit from the carbon chain. The rate and yield of this product depends upon the bond-dissociation energy of the ketone's α substituents. Typically the more α substituted a ketone is, the more likely the reaction will yield products in this way.
* The abstraction of an α-proton from the carbonyl fragment may form a ketene and an alkane.
* The abstraction of a β-proton from the alkyl fragment may form an aldehyde and an alkene.
The synthetic utility of this reaction type is limited, for instance it often is a side reaction in the Paternò–Büchi reaction. One organic synthesis based on this reaction is that of bicyclohexylidene. | 5 | Photochemistry |
Cannabinoid binding sites exist throughout the central and peripheral nervous systems. The two most relevant receptors for cannabinoids are the CB and CB receptors, which are expressed predominantly in the brain and immune system respectively. Density of expression varies based on species and correlates with the efficacy that cannabinoids will have in modulating specific aspects of behavior related to the site of expression. For example, in rodents, the highest concentration of cannabinoid binding sites are in the basal ganglia and cerebellum, regions of the brain involved in the initiation and coordination of movement. In humans, cannabinoid receptors exist in much lower concentration in these regions, which helps explain why cannabinoids possess a greater efficacy in altering rodent motor movements than they do in humans.
A recent analysis of cannabinoid binding in CB and CB receptor knockout mice found cannabinoid responsiveness even when these receptors were not being expressed, indicating that an additional binding receptor may be present in the brain. Binding has been demonstrated by 2-arachidonoylglycerol (2-AG) on the TRPV1 receptor suggesting that this receptor may be a candidate for the established response.
In addition to CB1 and CB2, certain orphan receptors are known to bind endocannabinoids as well, including GPR18, GPR55 (a regulator of neuroimmune function), and GPR119. CB1 has also been noted to form a functional human receptor heterodimer in orexin neurons with OX1, the CB1–OX1 receptor, which mediates feeding behavior and certain physical processes such as cannabinoid-induced pressor responses which are known to occur through signaling in the rostral ventrolateral medulla. | 1 | Biochemistry |
Lipofuscin accumulation in the eye, is a major risk factor implicated in macular degeneration, a degenerative disease, and Stargardt disease, an inherited juvenile form of macular degeneration.
In the peripheral nervous system, abnormal accumulation of lipofuscin known as lipofuscinosis is associated with a family of neurodegenerative disorders – neuronal ceroid lipofuscinoses, the most common of these is Batten disease.
Also, pathological accumulation of lipofuscin is implicated in Alzheimers disease, Parkinsons disease, amyotrophic lateral sclerosis, certain lysosomal diseases, acromegaly, denervation atrophy, lipid myopathy, chronic obstructive pulmonary disease, and centronuclear myopathy. Accumulation of lipofuscin in the colon is the cause of the condition melanosis coli.
On the other hand, myocardial lipofuscin accumulation more directly reflects chronological ageing rather than human cardiac pathology. | 1 | Biochemistry |
Selection of an appropriate DNA polymerase is critical to the efficiency of the base addition step and must meet several criteria:
* Ability to efficiently incorporate FdNTP at consecutive positions
* Lack of 3–5 exonuclease and proofreading activity to prevent the removal newly incorporated FdNTP
* High fidelity to minimize mis-incorporations
* Good activity on templates which are mounted to surfaces (e.g. optical mapping surface)
In addition, different polymerase preference for different fluorochromes, linker length on fluorochrome-nucleotides, and buffer compositions are also important factors to be considered to optimize the base addition process and maximize number of consecutive FdNTP incorporations. | 1 | Biochemistry |
Manganese is found in leafy green vegetables, fruits, nuts, cinnamon and whole grains. The nutritious kernel, called wheat germ, which contains the most minerals and vitamins of the grain, has been removed from most processed grains (such as white bread). The wheat germ is often sold as livestock feed. Many common vitamin and mineral supplement products fail to include manganese in their compositions. Relatively high dietary intake of other minerals such as iron, magnesium, and calcium may inhibit the proper intake of manganese. | 1 | Biochemistry |
Antisense oligonucleotides were discovered in 1978 by Paul Zamecnik and Mary Stephenson. Oligonucleotides, which are short nucleic acid fragments, bind to complementary target mRNA molecules when added to the cell. These molecules can be composed of single-stranded DNA or RNA and are generally 13–25 nucleotides long. The antisense oligonucleotides can affect gene expression in two ways: by using an RNase H-dependent mechanism or by using a steric blocking mechanism. RNase H-dependent oligonucleotides cause the target mRNA molecules to be degraded, while steric-blocker oligonucleotides prevent translation of the mRNA molecule. The majority of antisense drugs function through the RNase H-dependent mechanism, in which RNase H hydrolyzes the RNA strand of the DNA/RNA heteroduplex. expression. | 1 | Biochemistry |
In molecular biology, a guanine tetrad (also known as a G-tetrad or G-quartet) is a structure composed of four guanine bases in a square planar array. They most prominently contribute to the structure of G-quadruplexes, where their hydrogen bonding stabilizes the structure. Usually, there are at least two guanine tetrads in a G-quadruplex, and they often feature Hoogsteen-style hydrogen bonding.
Guanine tetrads are formed by sequences rich in guanine, such as GGGGC. They may also play a role in the dimerization of non-endogenous RNAs to facilitate the replication of some viruses. Guanine tetrads dimerize through their 5' ends since it is more energetically favorable.
They can be stabilized by central cations, such as lithium, sodium, potassium, rubidium, or caesium. However, they still form a variety of different structures. Guanine tetrads are not always stable, but the sugar-phosphate backbone of DNA can assist in stability of the guanine tetrads themselves. Guanine tetrads are more stable when stacked, as intermolecular forces between each layers help stabilize them.
Guanine tetrads can also influence recombination, replication, and transcription. For instance, guanine tetrads are found in the promoter region of the Myc family of oncogenes. They also function in immunoglobulin class switching and may play a role in the genome of HIV. Guanine tetrads appear frequently in the telomeric regions of DNA. | 1 | Biochemistry |
The chemical properties of RNA make large RNA molecules inherently fragile, and they can easily be broken down into their constituent nucleotides through hydrolysis. These limitations do not make use of RNA as an information storage system impossible, simply energy intensive (to repair or replace damaged RNA molecules) and prone to mutation. While this makes it unsuitable for current DNA optimised life, it may have been acceptable for more primitive life. | 9 | Geochemistry |
TLR3 does not use the MyD88 dependent pathway. Its ligand is retroviral double-stranded RNA (dsRNA), which activates the TRIF dependent signalling pathway. To explore the role of this pathway in retroviral reprograming, knock down techniques of TLR3 or TRIF were prepared, and results showed that only the TLR3 pathway is required for full induction of target gene expression by the retrovirus expression vector. This retroviral expression of four transcriptional factors (Oct4, Sox2, Klf4 and c-Myc; OSKM) induces pluripotency in somatic cells. This is supported by study, which shows, that efficiency and amount of human iPSC generation, using retroviral vectors, is reduced by knockdown of the pathway with peptide inhibitors or shRNA knockdown of TLR3 or its adaptor protein TRIF. Taken together, stimulation of TLR3 causes great changes in chromatin remodeling and nuclear reprogramming, and activation of inflammatory pathways is required for these changes, induction of pluripotency genes and generation of human induced pluripotent stem cells (iPSC) colonies. | 1 | Biochemistry |
The reactions of the glutaminolytic pathway take place partly in the mitochondria and to some extent in the cytosol (compare the metabolic scheme of the glutaminolytic pathway). | 1 | Biochemistry |
Boronic esters are oxidized to the corresponding alcohols with base and hydrogen peroxide (for an example see: carbenoid) | 0 | Organic Chemistry |
In geometric phase analysis, crystallographic quantities are not determined at one particular point of the input image. Instead, they are quantified across the whole image resulting in a two-dimensional map of given quantity. Quantities which can be mapped with geometric phase analysis include interplanar distances (d-spacing), strain tensor and displacement vector.
Since the calculations are performed in frequential domain, the input image of crystal lattice must be transformed into frequential representation using Fourier transform. From mathematical point of view, the frequential image is a complex matrix with the size equal to the original image. From crystallographic point of view, it can be seen as an artificial diffraction pattern or reciprocal image as it depicts reciprocal lattice. In this representation, the intensity peaks (or power peaks) correspond to the crystallographic planes depicted in the original image.
Due to the complex nature of the frequential image, it can be used to calculate amplitude and phase. Together with a vector of one crystallographic plane depicted in the image, the amplitude and phase can be used to generate a 2D map of d-spacing. If two vectors of non-parallel planes are known, the method can be used to generate maps of strain and displacement. | 3 | Analytical Chemistry |
Browning is the process of food turning brown due to the chemical reactions that take place within. The process of browning is one of the chemical reactions that take place in food chemistry and represents an interesting research topic regarding health, nutrition, and food technology. Though there are many different ways food chemically changes over time, browning in particular falls into two main categories: enzymatic versus non-enzymatic browning processes.
Browning has many important implications on the food industry relating to nutrition, technology, and economic cost. Researchers are especially interested in studying the control (inhibition) of browning and the different methods that can be employed to maximize this inhibition and ultimately prolong the shelf life of food. | 1 | Biochemistry |
Phosphonates are one of the three sources of phosphate intake in biological cells. The other two are inorganic phosphate and organophosphates.
The naturally occurring phosphonate 2-aminoethylphosphonic acid was first identified in 1959 in plants and many animals, where it is localized in membranes. Phosphonates are quite common among different organisms, from prokaryotes to eubacteria and mushrooms, mollusks, insects and others. They were first reported in natural soils by Newman and Tate (1980). The biological role of the natural phosphonates is still poorly understood. Bis- or polyphosphonates have not been found to occur naturally.
A number of natural product phosphonate substances with antibiotic properties have been identified. Phosphonate natural product antibiotics include fosfomycin which is approved by FDA for the treatment of non-complicated urinary tract infection as well as several pre-clinically investigated substances such as Fosmidomycin (inhibitor isoprenyl synthase), SF-2312 (inhibitor of the glycolytic enzyme enolase, and substances of unknown mode of actions such as alahopcin. Although phosphonates are profoundly cell impermeable, natural product phosphonate antibiotics are effective against a number of organisms, because many bacterial species express glycerol-3-phosphate and glucose-6-phosphate importers, which can be hijacked by phosphonate antibiotics. Fosfomycin resistant bacterial strains frequently have mutations that inactivate these transporters; however, such mutations are not maintained in the absence of antibiotic because of the fitness cost they impose. | 0 | Organic Chemistry |
The propagation of radiation in a medium that is assumed to be homogeneous, isotropic, and at rest takes place in straight lines and has the same velocity in all directions. Unless if propagating through a vacuum, thermal radiation does decay over time as energy is scattered.
Scattering occurs due to the presence of discontinuities in every medium that arise from their atomic structure. An example of scattering is when thermal radiation from the sun scatters after entering the earth's atmosphere. On a clear day at noon, only about two-thirds of this radiation actually reaches the surface. The rest is intercepted by particles in the air and changed into heat in the process. Scattering is noticeably larger for rays of shorter wave length; hence the blue color of skylight. | 7 | Physical Chemistry |
The mechanism involves the addition of amine to dichlorocarbene, a reactive intermediate generated by the dehydrohalogenation of chloroform. Two successive base-mediated dehydrochlorination steps result in formation of the isocyanide. | 0 | Organic Chemistry |
For small spots of vitiligo, it is possible to use psoralen as drops, applied only on the spots. This method does not have side effects since the amount is very low.
For larger area, the psoralen is taken as a pill, and the amount is high (10 mg); some patients experience nausea and itching after ingesting the psoralen compound. For these patients PUVA bath therapy may be a good option.
Long term use of PUVA therapy with a pill has been associated with higher rates of skin cancer.
The most significant complication of PUVA therapy for psoriasis is squamous cell skin cancer. Two carcinogenic components of the therapy include the nonionizing radiation of UVA light as well as the psoralen intercalation with DNA. Both processes negatively contribute to genome instability. | 5 | Photochemistry |
Monitoring the biological pump is critical to understanding how the Earth's carbon cycle is changing. A variety of techniques are used to monitor the biological pump, which can be deployed from various platforms such as ships, autonomous vehicles, and satellites. At present, satellite remote sensing is the only tool available for viewing the entire surface ocean at high temporal and spatial scales. | 9 | Geochemistry |
This term refers to the apparent preference of positively charged nitrogen substituents for the equatorial conformation beyond what normal steric interactions would predict in rings containing an electronegative atom, such as oxygen. Substituents containing carbons with partial positive charges are not seen to exhibit the same effect. Theoretical explanations for the reverse anomeric effect include an electrostatic explanation and the delocalization of the sp electrons of the anomeric carbon and oxygen lone pair. There is some debate as to whether or not this is a real phenomenon. The nitrogen containing substituents it has been reported with are quite bulky, making it hard to separate the normal effects of steric bulk and the reverse anomeric effect, if it does exist. For example, in the molecule shown below, the pyridinium substituent strongly prefers the equatorial position, as steric factors would predict, but actually shows a stronger preference for this conformation than predicted, suggesting the reverse anomeric effect is contributing. | 7 | Physical Chemistry |
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The P promoter allows for tight regulation and control of a target gene in vivo. As explained above, P is regulated by the addition and absence of arabinose. As tested, the promoter can be further repressed with reduced levels of cAMP through the addition of glucose. Plasmid vectors have been constructed and tested with a selectable marker (Cm in this case), origin of replication, araC and operons, multiple cloning site and P promoter. Studies show that vectors are highly expressed and can be used, in combination with chromosomal null alleles, to study loss of function of essential genes. | 1 | Biochemistry |
Darken's first equation is:
where:
* is the marker velocity of inert markers showing the diffusive flux.
* and are the diffusion coefficients of the two components.
* and are the atomic fractions of the two components.
* represents the direction in which the diffusion is measured.
It is important to note that this equation only holds in situations where the total concentration remains constant.
Darken's second equation is:
where:
* is the activity coefficient of the first component.
* is the overall diffusivity of the binary solution. | 7 | Physical Chemistry |
In 1954 and 1958 Krishna Bahadur and co-workers published the successful synthesis of amino acids from a mixture of paraformaldehyde, colloidal molybdenum oxide or potassium nitrate and ferric chloride under sunlight. It appears that this experimental approach was seminal for the assays to produce Jeewanu, which he first reported in 1963 in an obscure Indian journal, Vijnana Parishad Anusandhan Patrika. His detailed syntheses were published in Germany in 1964 in a series of articles.
Their initial experiment consisted of a sterilised apparatus in which inorganic nitrogenous compounds (such as ammonium phosphate and ammonium molybdate) and organic compounds such as citric acid (CHO), paraformaldehyde (OH(CHO)H) and formaldehyde (CHO) for carbon sources were mixed with minerals commonly found in living cells. Inorganic substances such as colloidal ferric chloride or molybdenum compounds supposedly acted as cofactors and catalysts.
When the apparatus was exposed to sunlight for several days and constantly shaken, microscopic spherical particles were formed. The interesting features of these particles were that they were enclosed in a semipermeable membrane, like the typical cell membrane. Like living cells, they were reported to contain amino acids, phospholipid membrane and carbohydrates. In addition, they were claimed to have reproductive capability by budding, much like unicellular organisms, but did not grow on any bacterial culture medium. Bahadur reported that the Jeewanu exhibited various catalytic properties and produced their own peptides by metabolic reactions. Bahadur's later work on the Jeewanu also detected the presence of amino acids in peptide form and sugars in the form of ribose, deoxyribose, fructose and glucose, as well as nucleic acid bases (DNA and RNA building blocks) including adenine, guanine, cytosine, thymine and uracil. Bahadur also reported having detected ATPase-like and peroxidase-like activity. Bahadur stated that by using molybdenum as a cofactor, the Jeewanu showed capability of reversible photochemical electron transfer, and released a gas mixture of oxygen and hydrogen at a 1:2 ratio. | 9 | Geochemistry |
In organometallic chemistry, the activation of cyclopropanes by transition metals is a research theme with implications for organic synthesis and homogeneous catalysis. Being highly strained, cyclopropanes are prone to oxidative addition to transition metal complexes. The resulting metallacycles are susceptible to a variety of reactions. These reactions are rare examples of C-C bond activation. The rarity of C-C activation processes has been attributed to Steric effects that protect C-C bonds. Furthermore, the directionality of C-C bonds as compared to C-H bonds makes orbital interaction with transition metals less favorable. Thermodynamically, C-C bond activation is more favored than C-H bond activation as the strength of a typical C-C bond is around 90 kcal per mole while the strength of a typical unactivated C-H bond is around 104 kcal per mole.
Two main approaches achieve C-C bond activation using a transition metal. One strategy is to increase the ring strain and the other is to stabilize the resulting cleaved C-C bond complex (e.g. through aromatization or chelation). Because of the large ring strain energy of cyclopropanes (29.0 kcal per mole), they are often used as substrates for C-C activation through oxidative addition of a transition metal into one of the three C-C bonds leading to a metallacyclobutane intermediate.
Substituents on the cyclopropane affect the course of its activation. | 0 | Organic Chemistry |
Chromatin immunoprecipitation (ChIP) techniques have been in use since 1984 to detect protein-DNA interactions. There have been many variations on ChIP to improve the quality of results. One such improvement, ChIP-on-chip (ChIP-chip), combines ChIP with microarray technology. This technique has limited sensitivity and specificity, especially in vivo where microarrays are constrained by thousands of proteins present in the nuclear compartment, resulting in a high rate of false positives. Next came ChIP-sequencing (ChIP-seq), which combines ChIP with high-throughput sequencing. However, the heterogeneous nature of sheared DNA fragments maps binding sites to within ±300 base pairs, limiting specificity. Secondly, contaminating DNA presents a grave problem since so few genetic loci are cross-linked to the protein of interest, making any non-specific genomic DNA a significant source of background noise.
To address these problems, Rhee and Pugh revised the classic nuclease protection assay to develop ChIP-exo. This new ChIP technique relies on a lambda exonuclease that degrades only, and all, unbound double-stranded DNA in the 5′-3′ direction. Briefly, a protein of interest (engineering one with an epitope tag can be useful for immunoprecipitation) is crosslinked in vivo to its natural binding locations across a genome using formaldehyde.
Cells are then collected, broken open, and the chromatin sheared and solubilized by sonication. An antibody is then used to immunoprecipitate the protein of interest, along with the crosslinked DNA. DNA PCR adaptors are then ligated to the ends, which serve as a priming point for second strand DNA synthesis after the exonuclease digestion. Lambda exonuclease then digests double DNA strands from the 5′ end until digestion is blocked at the border of the protein-DNA covalent interaction. Most contaminating DNA is degraded by the addition of a second single-strand specific exonuclease. After the cross-linking is reversed, the primers to the PCR adaptors are extended to form double stranded DNA, and a second adaptor is ligated to 5′ ends to demarcate the precise location of exonuclease digestion cessation. The library is then amplified by PCR, and the products are identified by high throughput sequencing. This method allows for resolution of up to a single base pair for any protein binding site within any genome, which is a much higher resolution than either ChIP-chip or ChIP-seq. | 1 | Biochemistry |
Frequency modulation atomic force microscopy, introduced by Albrecht, Grütter, Horne and Rugar in 1991,
is a mode of nc-AFM where the change in resonant frequency of the sensor is tracked directly, by always exciting the sensor on resonance. To maintain excitation on resonance the electronics must keep a 90° phase difference between the excitation and response of the sensor. This is either done by driving the sensor with the deflection signal phase shifted by 90°, or by using an advanced phase-locked loop which can lock to a specific phase. The microscope can then use the change in resonant frequency (f) as the SPM reference channel, either in feedback mode, or it can be recorded directly in constant height mode.
While recording frequency-modulated images, an additional feedback loop is normally used to keep the amplitude of resonance constant, by adjusting the drive amplitude. By recording the drive amplitude during the scan (usually referred to as the damping channel as the need for a higher drive amplitude corresponds to more damping in the system) a complementary image is recorded showing only non-conservative forces. This allows conservative and non-conservative forces in the experiment to be separated. | 6 | Supramolecular Chemistry |
Sigma-2 receptors have been found to be highly expressed in proliferating cells, including tumor cells, and to play a role in the differentiation, morphology, and survival of those cells. By interacting with EGFR membrane proteins sigma-2 receptors play a role in the regulation of signals further downstream such as PKC and RAF. Both PKC and Raf kinase up regulate transcription and cell proliferation. | 1 | Biochemistry |
Peripheral node addressin, often referred to as PNAd, are glycoprotein ligands. More formally, the term includes "lymph" to specify the node: peripheral lymph node addressin.
PNAd is a critical component of the immune system, enabling the targeted migration of lymphocytes to the lymph nodes and facilitating an effective immune response. PNAd's role in lymphocyte homing is essential for the proper functioning of the immune system, as it ensures that lymphocytes can efficiently enter the lymph nodes to encounter and respond to foreign antigens, such as viruses and bacteria.
PNAd is a type of cell adhesion molecule found on the surface of high endothelial venules (HEVs) in lymph nodes. It plays a crucial role in the immune system by facilitating the migration of lymphocytes, a type of white blood cell, from the bloodstream to the lymph nodes where they participate in immune responses.
The process of lymphocyte migration from the bloodstream to the lymph nodes is called lymphocyte homing. PNAd plays a key role in this process by interacting with L-selectin, which is present on the surface of lymphocytes. The adhesion molecule L-selectin binds to sulfated carbohydrate ligands on high endothelial venules (HEV). The binding between PNAd and L-selectin allows lymphocytes to slow down and roll along the inner surface of HEVs. This rolling action enables lymphocytes to come into close contact with other molecules called chemokines, which trigger the firm adhesion and subsequent transmigration of lymphocytes across the endothelial cells and into the lymph node. | 1 | Biochemistry |
Changes to the surface of the planet, such as an absence of volcanoes or higher sea levels, which would reduce the amount of land surface exposed to weathering can change the rates at which different processes in this cycle take place. Over tens to hundreds of millions of years, carbon dioxide levels in the atmosphere may vary due to natural perturbations in the cycle but even more generally, it serves as a critical negative feedback loop between carbon dioxide levels and climate changes. For example, if CO builds up in the atmosphere, the greenhouse effect will serve to increase the surface temperature, which will in turn increase the rate of rainfall and silicate weathering, which will remove carbon from the atmosphere. In this way, over long timescales, the carbonate-silicate cycle has a stabilizing effect on the Earths climate, which is why it has been called the Earths thermostat. | 9 | Geochemistry |
Chloroeremomycin is a member of the glycopeptide family of antibiotics, such as vancomycin. The molecule is a non-ribosomal polypeptide that has been glycosylated. It is composed of seven amino acids and three saccharide units. Although chloroeremomycin has never been in clinical phases, oritavancin, a semi-synthetic derivative of chloroeremomycin, has been investigated.
Chloroeremomycin is a type of glycopeptide antibiotic and works by blocking the construction of a cell wall. Chloroeremomycin is naturally produced by Amycolatopsis orientalis. | 0 | Organic Chemistry |
Only 20.35% of the catchment of the lake is covered by forest.
Demographic growth and lack of employment are some of the factors that have promoted conversion of forested areas into subsistence agriculture, especially following the coffee price crisis.
The loss of forest cover is particularly critical on steep terrains, which are most susceptible to overland flow and erosion. Soil loss results in siltation farther downslope, as well as in streams and in the lake. It also decreases water recharge of the deep aquifers. | 2 | Environmental Chemistry |
Diethyl azodicarboxylate, conventionally abbreviated as DEAD and sometimes as DEADCAT, is an organic compound with the structural formula . Its molecular structure consists of a central azo functional group, RN=NR, flanked by two ethyl ester groups. This orange-red liquid is a valuable reagent but also quite dangerous and explodes upon heating. Therefore, commercial shipment of pure diethyl azodicarboxylate is prohibited in the United States and is carried out either in solution or on polystyrene particles.
DEAD is an aza-dienophile and an efficient dehydrogenating agent, converting alcohols to aldehydes, thiols to disulfides and hydrazo groups to azo groups; it is also a good electron acceptor. While DEAD is used in numerous chemical reactions it is mostly known as a key component of the Mitsunobu reaction, a common strategy for the preparation of an amine, azide, ether, thioether, or ester from the corresponding alcohol. It is used in the synthesis of various natural products and pharmaceuticals such as zidovudine, an AIDS drug; FdUMP, a potent antitumor agent; and procarbazine, a chemotherapy drug. | 0 | Organic Chemistry |
Andreas Hierlemann (17 August 1964) is a German chemist and professor of Biosystems Engineering at ETH Zurich. He is known for his work in the field of CMOS-based chemical and biomicrosensors and high-density microelectrode arrays. | 7 | Physical Chemistry |
Born in Nantes in Brittany, France, Dauphas received a B.Sc. degree from in 1998. The same year, he obtained an M.Sc. from , at the National Polytechnic Institute of Lorraine (; INPL). In 2002, also from INPL, he was awarded a Ph.D. in geochemistry and cosmochemistry, working with Bernard Marty and Laurie Reisberg. He then completed his postdoctoral research at the Enrico Fermi Institute of the University of Chicago and the Field Museum of Natural History from 2002 to 2004, before joining the faculty at the University of Chicago in 2004. | 9 | Geochemistry |
In nature bacteria play a major role in the degradation of phosphonates. Due to the presence of natural phosphonates in the environment, bacteria have evolved the ability to metabolize phosphonates as nutrient sources. Some bacteria use phosphonates as a phosphorus source for growth. Aminophosphonates can also be used as sole nitrogen source by some bacteria. The polyphosphonates used in industry differ greatly from natural phosphonates such as 2-aminoethylphosphonic acid, because they are much larger, carry a high negative charge and are complexed with metals. Biodegradation tests with sludge from municipal sewage treatment plants with HEDP and NTMP showed no indication for any degradation. An investigation of HEDP, NTMP, EDTMP and DTPMP in standard biodegradation tests also failed to identify any biodegradation. It was noted, however, that in some tests due to the high sludge to phosphonate ratio, removal of the test substance from solution observed as loss of DOC was observed. This factor was attributed to adsorption rather than biodegradation. However, bacterial strains capable of degrading aminopolyphosphonates and HEDP under P-limited conditions have been isolated from soils, lakes, wastewater, activated sludge and compost.
"No biodegradation of phosphonates during water treatment is observed but photodegradation of the Fe(III)-complexes is rapid. Aminopolyphosphonates are also rapidly oxidized in the presence of Mn(II) and oxygen and stable breakdown products are formed that have been detected in wastewater. The lack of information about phosphonates in the environment is linked to analytical problems of their determination at trace concentrations in natural waters. Phosphonates are present mainly as Ca and Mg-complexes in natural waters and therefore do not affect metal speciation or transport." Phosphonates interact strongly with some surfaces, which results in a significant removal in technical and natural systems. | 0 | Organic Chemistry |
Decantation is a process for the separation of mixtures of immiscible liquids or of a liquid and a solid mixture such as a suspension. The layer closer to the top of the container—the less dense of the two liquids, or the liquid from which the precipitate or sediment has settled out—is poured off, leaving denser liquid or the solid behind. The process typically is unable to remove all of the top layer, meaning the separation is incomplete or at least one of the two separated components is still contaminated by the other one. | 3 | Analytical Chemistry |
An early model for the role of substituents in pi stacking interactions was proposed by Hunter and Sanders. They used a simple mathematical model based on sigma and pi atomic charges, relative orientations, and van der Waals interactions to qualitatively determine that electrostatics are dominant in substituent effects. According to their model, electron-withdrawing groups reduce the negative quadrupole of the aromatic ring and thereby favor parallel displaced and sandwich conformations. Contrastingly, electron donating groups increase the negative quadrupole, which may increase the interaction strength in a T-shaped configuration with the proper geometry. Based on this model, the authors proposed a set of rules governing pi stacking interactions which prevailed until more sophisticated computations were applied.
Experimental evidence for the Hunter–Sanders model was provided by Siegel et al. using a series of substituted syn- and . In these compounds the aryl groups "face-off" in a stacked geometry due to steric crowding, and the barrier to epimerization was measured by nuclear magnetic resonance spectroscopy. The authors reported that aryl rings with electron-withdrawing substituents had higher barriers to rotation. The interpretation of this result was that these groups reduced the electron density of the aromatic rings, allowing more favorable sandwich pi stacking interactions and thus a higher barrier. In other words, the electron-withdrawing groups resulted in "less unfavorable" electrostatic interactions in the ground state.
Hunter et al. applied a more sophisticated chemical double mutant cycle with a hydrogen-bonded "zipper" to the issue of substituent effects in pi stacking interactions. This technique has been used to study a multitude of noncovalent interactions. The single mutation, in this case changing a substituent on an aromatic ring, results in secondary effects such as a change in hydrogen bond strength. The double mutation quantifies these secondary interactions, such that even a weak interaction of interest can be dissected from the array. Their results indicate that more electron-withdrawing substituents have less repulsive pi stacking interactions. Correspondingly, this trend was exactly inverted for interactions with pentafluorophenylbenzene, which has a quadrupole moment equal in magnitude but opposite in sign as that of benzene. The findings provide direct evidence for the Hunter–Sanders model. However, the stacking interactions measured using the double mutant method were surprisingly small, and the authors note that the values may not be transferable to other systems.
In a follow-up study, Hunter et al. verified to a first approximation that the interaction energies of the interacting aromatic rings in a double mutant cycle are dominated by electrostatic effects. However, the authors note that direct interactions with the ring substituents, discussed below, also make important contributions. Indeed, the interplay of these two factors may result in the complicated substituent- and geometry-dependent behavior of pi stacking interactions. | 6 | Supramolecular Chemistry |
Modern two-dimensional chromatographic techniques are based on the results of the early developments of paper chromatography and thin-layer chromatography (TLC) which involved liquid mobile phases and solid stationary phases. These techniques would later generate modern gas chromatography (GC) and liquid chromatography (LC) analysis. Different combinations of one-dimensional GC and LC produced the analytical chromatographic technique that is known as two-dimensional chromatography.
The earliest form of 2D-chromatography came in the form of a multi-step TLC separation in which a thin sheet of cellulose is used first with one solvent in one direction, then, after the paper has been dried, another solvent is run in a direction at right angles to the first. This methodology first appeared in the literature with a 1944 publication by A. J. P. Martin and coworkers detailing an efficient method for separating amino acids – "...but the two-dimensional chromatogram is especially convenient, in that it shows at a glance information that can be gained otherwise only as the result of numerous experiments" (Biochem J., 1944, 38, 224). | 3 | Analytical Chemistry |
There is evidence that use during pregnancy may result in harm to the baby. Teratogenic and embryotoxic effects were shown on four animal species. In one case report, a 6-month old infant developed benign bright blue discolouration of the cornea after treatment with favipiravir which resolved after treatment cessation. | 4 | Stereochemistry |
Supplemental potassium decreases the risk of experiencing a life-threatening heart rhythm problem from arsenic trioxide. | 1 | Biochemistry |
Harold Scott MacDonald "Donald" Coxeter (9 February 1907 – 31 March 2003) was a British-Canadian geometer and mathematician. | 4 | Stereochemistry |
The pillar carries a number of inscriptions of different dates, some of which have not been studied systematically despite the pillar's prominent location and easy access. | 8 | Metallurgy |
The convention for a polypeptide is to list its constituent amino acid residues as they occur from the amino terminus to the carboxylic acid terminus. The amino acid residues are always joined by peptide bonds. Protein, though used colloquially to refer to any polypeptide, refers to larger or fully functional forms and can consist of several polypeptide chains as well as single chains. Proteins can also be modified to include non-peptide components, such as saccharide chains and lipids. | 1 | Biochemistry |
The first structure of a creatine kinase solved by X-ray protein crystallography was that of the octameric, sarcomeric muscle-type mitochondrial CK (s-mtCK) in 1996., followed by the structure of ubiquitous mitochondrial CK (u-mtCK) in 2000. Both mt-CK isoforms form octameric structures (built of 4 banana-like dimers) with a four-fold symmetry and a central channel.
The atomic structure of the banana-shaped, dimeric cytosolic brain-type BB-CK was solved in 1999 at a resolution of 1,4 Å. Cytosolic BB-CK, as well as muscle-type MM-CK both form banana-shaped symmetric dimers, with one catalytic active site in each subunit. | 1 | Biochemistry |
Both the structure of ATP synthase and its underlying gene are remarkably similar in all known forms of life. ATP synthase is powered by a transmembrane electrochemical potential gradient, usually in the form of a proton gradient. In all living organisms, a series of redox reactions is used to produce a transmembrane electrochemical potential gradient, or a so-called proton motive force (pmf).
Redox reactions are chemical reactions in which electrons are transferred from a donor molecule to an acceptor molecule. The underlying force driving these reactions is the Gibbs free energy of the reactants relative to the products. If donor and acceptor (the reactants) are of higher free energy than the reaction products, the electron transfer may occur spontaneously. The Gibbs free energy is the energy available ("free") to do work. Any reaction that decreases the overall Gibbs free energy of a system will proceed spontaneously (given that the system is isobaric and also at constant temperature), although the reaction may proceed slowly if it is kinetically inhibited.
The fact that a reaction is thermodynamically possible does not mean that it will actually occur. A mixture of hydrogen gas and oxygen gas does not spontaneously ignite. It is necessary either to supply an activation energy or to lower the intrinsic activation energy of the system, in order to make most biochemical reactions proceed at a useful rate. Living systems use complex macromolecular structures to lower the activation energies of biochemical reactions.
It is possible to couple a thermodynamically favorable reaction (a transition from a high-energy state to a lower-energy state) to a thermodynamically unfavorable reaction (such as a separation of charges, or the creation of an osmotic gradient), in such a way that the overall free energy of the system decreases (making it thermodynamically possible), while useful work is done at the same time. The principle that biological macromolecules catalyze a thermodynamically unfavorable reaction if and only if a thermodynamically favorable reaction occurs simultaneously, underlies all known forms of life.
The transfer of electrons from a donor molecule to an acceptor molecule can be spatially separated into a series of intermediate redox reactions. This is an electron transport chain (ETC). Electron transport chains often produce energy in the form of a transmembrane electrochemical potential gradient. The gradient can be used to transport molecules across membranes. Its energy can be used to produce ATP or to do useful work, for instance mechanical work of a rotating bacterial flagella. | 5 | Photochemistry |
Phosphine gas is denser than air and hence may collect in low-lying areas. It can form explosive mixtures with air, and may also self-ignite. | 0 | Organic Chemistry |
In DNA, the coding region is flanked by the promoter sequence on the 5 end of the template strand and the termination sequence on the 3 end. During transcription, the RNA Polymerase (RNAP) binds to the promoter sequence and moves along the template strand to the coding region. RNAP then adds RNA nucleotides complementary to the coding region in order to form the mRNA, substituting uracil in place of thymine. This continues until the RNAP reaches the termination sequence.
After transcription and maturation, the mature mRNA formed encompasses multiple parts important for its eventual translation into protein. The coding region in an mRNA is flanked by the 5 untranslated region (5-UTR) and 3 untranslated region (3-UTR), the 5' cap, and Poly-A tail. During translation, the ribosome facilitates the attachment of the tRNAs to the coding region, 3 nucleotides at a time (codons). The tRNAs transfer their associated amino acids to the growing polypeptide chain, eventually forming the protein defined in the initial DNA coding region. | 1 | Biochemistry |
The ion vibration current (IVI) and the associated ion vibration potential is an electric signal that arises when an acoustic wave propagates through a homogeneous fluid.
Historically, the IVI was the first known electroacoustic phenomenon. It was predicted by Peter Debye in 1933.
When a longitudinal sound wave travels through a solvent, the associated pressure gradients push the fluid particles back and forth, and it is easy in practice to create such accelerations that measure thousands or millions of gs. If a solute molecule is more dense or less dense than the surrounding liquid, then in this accelerating environment, the molecule will move relative to the surrounding liquid. This relative motion is essentially the same phenomenon that occurs in a centrifuge, or more simply, it is essentially the same phenomenon that occurs when low-density objects float to the top of a glass of water, and high-density particles sink to the bottom (see the equivalence principle, which states that gravity is just like any other acceleration). The amount of relative motion depends on the balance between the molecules effective mass (which includes both the mass of the molecule itself and any solvent molecules that are so tightly bound to the molecule that they follow along with the molecule's motion), its effective volume (related to buoyant force), and the viscous drag (friction) between the molecule and the surrounding fluid.
IVI concerns the case where the particles in question are anions and cations. In general, they will have different amounts of motion relative to the fluid during the sound wave oscillations, and that discrepancy creates an alternating electric potential between various points in a sound wave.
This effect was extensively used in the 1950s and 1960s for characterizing ion solvation. These works are mostly associated with the names of Zana and Yaeger, who published a review of their studies in 1982.
This effect can be studied with modern devices that employ electroacoustics for studying zeta potential, as described in the book. | 7 | Physical Chemistry |
MEGAN analysis starts with collecting reads from any shotgun platform. Then, the reads are compared with sequence databases using BLAST or similar. Third, MEGAN assigns a taxon ID to processed read results based on NCBI taxonomy which creates a MEGAN file that contains required information for statistical and graphical analysis. Lastly, lowest common ancestor (LCA) algorithm can be run to inspect assignments, to analyze data and to create summaries of data based on different NCBI taxonomy levels. LCA algorithm simply finds the lowest common ancestor of different species. | 1 | Biochemistry |
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