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In organic chemistry, thiocarbamates (thiourethanes) are a family of organosulfur compounds. As the prefix thio- suggests, they are sulfur analogues of carbamates. There are two isomeric forms of thiocarbamates: O-thiocarbamates, (esters), and S-thiocarbamates, (thioesters). | 0 | Organic Chemistry |
Esters can also be derived from inorganic acids.
*Perchloric acid forms perchlorate esters, e.g., methyl perchlorate ()
*Sulfuric acid forms sulfate esters, e.g., dimethyl sulfate () and methyl bisulfate ()
*Nitric acid forms nitrate esters, e.g. methyl nitrate () and nitroglycerin ()
*Phosphoric acid forms phosphate esters, e.g. triphenyl phosphate () and methyl dihydrogen phosphate ()
*Carbonic acid forms carbonate esters, e.g. dimethyl carbonate () and 5-membered cyclic ethylene carbonate () (if one classifies carbonic acid as an inorganic compound)
*Trithiocarbonic acid forms trithiocarbonate esters, e.g. dimethyl trithiocarbonate () (if one classifies trithiocarbonic acid as an inorganic compound)
*Chloroformic acid forms chloroformate esters, e.g. methyl chloroformate () (if one classifies chloroformic acid as an inorganic compound)
*Boric acid forms borate esters , e.g. trimethyl borate ()
*Chromic acid forms di-tert-butyl chromate ()
Inorganic acids that exist as tautomers form two or more types of esters.
*Thiosulfuric acid forms two types of thiosulfate esters, e.g. O,O-dimethyl thiosulfate () and O,S-dimethyl thiosulfate ()
*Thiocyanic acid forms thiocyanate esters, e.g. methyl thiocyanate () (if one classifies thiocyanic acid as an inorganic compound), but forms isothiocyanate "esters" as well, e.g. methyl isothiocyanate (), although organyl isothiocyanates are not clasified as esters by the IUPAC
*Phosphorous acid forms two types of esters: phosphite esters, e.g. triethyl phosphite (), and phosphonate esters, e.g. diethyl phosphonate ()
Some inorganic acids that are unstable or elusive form stable esters.
*Sulfurous acid, which is unstable, forms stable dimethyl sulfite ()
In principle, a part of metal and metalloid alkoxides, of which many hundreds are known, could be classified as esters of the corresponding acids (e.g. aluminium triethoxide () could be classified as an ester of aluminic acid which is aluminium hydroxide, tetraethyl orthosilicate () could be classified as an ester of orthosilicic acid, and titanium ethoxide () could be classified as an ester of orthotitanic acid). | 0 | Organic Chemistry |
FAM227B is a protein that in humans is encoded by FAM227B gene. FAM227B stands for family with sequence similarity 227 member B and encodes protein FAM227B of the same name. Its aliases include C15orf33, MGC57432 and FLJ23800. | 1 | Biochemistry |
The Warburg hypothesis (), sometimes known as the Warburg theory of cancer, postulates that the driver of tumorigenesis is an insufficient cellular respiration caused by insult to mitochondria. The term Warburg effect in oncology describes the observation that cancer cells, and many cells grown in vitro, exhibit glucose fermentation even when enough oxygen is present to properly respire. In other words, instead of fully respiring in the presence of adequate oxygen, cancer cells ferment. The Warburg hypothesis was that the Warburg effect was the root cause of cancer. The current popular opinion is that cancer cells ferment glucose while keeping up the same level of respiration that was present before the process of carcinogenesis, and thus the Warburg effect would be defined as the observation that cancer cells exhibit glycolysis with lactate production and mitochondrial respiration even in the presence of oxygen. | 1 | Biochemistry |
For economic and other reasons, bitumen is sometimes sold combined with other materials, often without being labeled as anything other than simply "bitumen".
Of particular note is the use of re-refined engine oil bottoms – "REOB" or "REOBs"the residue of recycled automotive engine oil collected from the bottoms of re-refining vacuum distillation towers, in the manufacture of asphalt. REOB contains various elements and compounds found in recycled engine oil: additives to the original oil and materials accumulating from its circulation in the engine (typically iron and copper). Some research has indicated a correlation between this adulteration of bitumen and poorer-performing pavement. | 7 | Physical Chemistry |
*Materials Performance magazine
*CoatingsPro magazine
*CORROSION journal
*technical and reference books
*podcasts and webcasts | 8 | Metallurgy |
Transition metal benzyne complexes represent a special case of alkyne complexes since the free benzynes are not stable in the absence of the metal. | 0 | Organic Chemistry |
Clinopyroxene thermobarometry is a scientific method that uses the mineral clinopyroxene to determine the temperature and pressure of the magma when the mineral crystalized. Clinopyroxene is found in many igneous rocks, so the method can be used to determine information about the entire rock. Many different minerals can be used for geothermobarometry, but clinopyroxene is especially useful because it's a common phenocryst in igneous rocks and easy to identify, and the crystallization of jadeite, a type of clinopyroxene, implies a growth in molar volume, making it a good indicator of pressure.
The data given by this technique is used for understanding magmatic crystallization, prograde and retrograde metamorphism, and ore deposit formation. Understanding these processes can aid industries as well as the scientific community. With this data, information about the lithosphere composition can be extrapolated in more detail, and the diamond exploration industry can determine the probability that a kimberlite contains diamonds. | 9 | Geochemistry |
In stereochemistry, an epimer is one of a pair of diastereomers. The two epimers have opposite configuration at only one stereogenic center out of at least two. All other stereogenic centers in the molecules are the same in each. Epimerization is the interconversion of one epimer to the other epimer.
Doxorubicin and epirubicin are two epimers that are used as drugs. | 4 | Stereochemistry |
Triplet-triplet annihilation upconversion (TTA-UC) materials have the advantages of needing low excitation power and having changeable emission and excitation light wavelengths. Due to these advantages, many applications of TTA-UC materials have been explored. | 7 | Physical Chemistry |
When both steric and polar effects influence the reaction rate the Taft equation can be solved for both ρ* and δ through the use of standard least squares methods for determining a bivariant regression plane. Taft outlined the application of this method to solving the Taft equation in a 1957 paper. | 7 | Physical Chemistry |
The somatic fusion process occurs in four steps:
# The removal of the cell wall of one cell of each type of plant using cellulase enzyme to produce a somatic cell called a protoplast
# The cells are then fused using electric shock (electrofusion) or chemical treatment to join the cells and fuse together the nuclei. The resulting fused nucleus is called heterokaryon.
# The formation of the cell wall is then induced using hormones
# The cells are then grown into calluses which then are further grown to plantlets and finally to a full plant, known as a somatic hybrid.
The procedure for seed plants describe above, fusion of moss protoplasts can be initiated without electric shock but by the use of polyethylene glycol (PEG). Further, moss protoplasts do not need phytohormones for regeneration, and they do not form a callus. Instead, regenerating moss protoplasts behave like germinating moss spores. Of further note sodium nitrate and calcium ion at high pH can be used, although results are variable depending on the organism. | 1 | Biochemistry |
Computer simulations can only yield so much insight, as one would be required to run simulations on a wide range of parameter values, which can be unwieldy. A generally more powerful way to understand the properties of a model is to solve the differential equations analytically.
Analytical solutions are possible if simple mass-action kinetics on each reaction step are assumed:
where and are the forward and reverse rate-constants, respectively. is the substrate and the product. If the equilibrium constant for this reaction is:
The mass-action kinetic equation can be modified to be:
Given the reaction rates, the differential equations describing the rates of change of the species can be described. For example, the rate of change of will equal:
By setting the differential equations to zero, the steady-state concentration for the species can be derived. From here, the pathway flux equation can be determined. For the three-step pathway, the steady-state concentrations of and are given by:
Inserting either or into one of the rate laws will give the steady-state pathway flux, :
A pattern can be seen in this equation such that, in general, for a linear pathway of steps, the steady-state pathway flux is given by:
Note that the pathway flux is a function of all the kinetic and thermodynamic parameters. This means there is no single parameter that determines the flux completely. If is equated to enzyme activity, then every enzyme in the pathway has some influence over the flux. | 1 | Biochemistry |
All five families of luminescent beetle, Phengodidae, Rhagophthalidae, Elateridae, Sinopyrophoridae, and Lampyridae are categorized into the Lampyroid clade. It has been determined that the luciferases and luciferin protein expressed in the photocytes of all species of firefly is homologous with that expressed in beetle species within the families Phengodidae, Rhagophthalidae, and Elateridae. In fact, every bioluminescent beetle species studied has been shown to use very similar mechanisms for light production in the photocyte. The beetle genus, Sinopyrophoridae, has been shown to exhibit biolumiescence although the exact mechanism is not known. It is believed that it shares homology with other genera of beetles however. The first time the entire genome of a bioluminescent beetle was determined was in 2017 with Pyrocoelia pectoralis, a species of firefly, and in 2018, three more species of bioluminescent beetle had their genomes sequenced. Biolumiescence in beetles has been shown to serve multiple purposes including the deterrence of predators and the attraction of mates.
The variation in coloring among different species of firefly has been determined to be due to differences in the amino acid sequences of the luciferases expressed in their photocytes. Two luciferace genes have been identified in the genomes of fireflies. They are luc1-type and luc2-type. There is evidence that suggests that Luc1-type evolved from a gene duplication of the gene that encodes for acyl-CoA synthetase. It is hypothesized that the luciferase of click beetles evolved separately from that in fireflies being the result of two gene duplications of the acyl-CoA synthetase gene suggesting analogy instead of homology between the groups. Additional genes have been found to be related to the storage of luciferin. | 1 | Biochemistry |
* [https://books.google.com.ua/books/about/Le_fer_de_Dieu.html?id=urRyoAEACAAJ&redir_esc=y Le fer de Dieu : histoire de la météorite de Chinguetti], with Théodore Monod, Actes Sud, 2008, 152 pages. ISBN 978-2742775521.
* [https://agupubs.onlinelibrary.wiley.com/doi/full/10.1029/2011GL047173 Low temperature magnetic transition of chromite in ordinary chondrites], J. Gattacceca et al., 2011. | 9 | Geochemistry |
* CTDP1
* CTDSP1, CTDSP2, CTDSPL
* DULLARD
* EPM2A
* ILKAP
* MDSP
* PGAM5
* PHLPP1, PHLPP2
* PPEF1, PPEF2
* PPM1A, PPM1B, PPM1D, PPM1E, PPM1F, PPM1G, PPM1H, PPM1J, PPM1K, PPM1L, PPM1M, PPM1N
* PPTC7
* PTPMT1
* SSU72
* UBLCP1 | 1 | Biochemistry |
There are five main types of experimental data that are used for the determination of solution equilibrium constants. Potentiometric data obtained with a glass electrode are the most widely used with aqueous solutions. The others are Spectrophotometric, Fluorescence (luminescence) measurements and NMR chemical shift measurements; simultaneous measurement of K and ΔH for 1:1 adducts in biological systems is routinely carried out using Isothermal Titration Calorimetry.
The experimental data will comprise a set of data points. At the ith data point, the analytical concentrations of the reactants, T, T etc. will be experimentally known quantities and there will be one or more measured quantities, y', that depend in some way on the analytical concentrations and equilibrium constants. A general computational procedure has three main components.
# Definition of a chemical model of the equilibria. The model consists of a list of reagents, A, B, etc. and the complexes formed from them, with stoichiometries AB... Known or estimated values of the equilibrium constants for the formation of all complexes must be supplied.
# Calculation of the concentrations of all the chemical species in each solution. The free concentrations are calculated by solving the equations of mass-balance, and the concentrations of the complexes are calculated using the equilibrium constant definitions. A quantity corresponding to the observed quantity can then be calculated using physical principles such as the Nernst potential or Beer-Lambert law which relate the calculated quantity to the concentrations of the species.
# Refinement of the equilibrium constants. Usually a Non-linear least squares procedure is used. A weighted sum of squares, U, is minimized. The weights, w and quantities y may be vectors. Values of the equilibrium constants are refined in an iterative procedure. | 7 | Physical Chemistry |
To form an A-B-A-B-... hexagonal close packing of spheres, the coordinate points of the lattice will be the spheres centers. Suppose, the goal is to fill a box with spheres according to HCP. The box would be placed on the x-y-z' coordinate space.
First form a row of spheres. The centers will all lie on a straight line. Their x-coordinate will vary by 2r since the distance between each center of the spheres are touching is 2r. The y-coordinate and z-coordinate will be the same. For simplicity, say that the balls are the first row and that their y- and z-coordinates are simply r, so that their surfaces rest on the zero-planes. Coordinates of the centers of the first row will look like (2r, r, r), (4r, r, r), (6r ,r, r), (8r ,r, r), ... .
Now, form the next row of spheres. Again, the centers will all lie on a straight line with x-coordinate differences of 2r, but there will be a shift of distance r in the x-direction so that the center of every sphere in this row aligns with the x-coordinate of where two spheres touch in the first row. This allows the spheres of the new row to slide in closer to the first row until all spheres in the new row are touching two spheres of the first row. Since the new spheres touch two spheres, their centers form an equilateral triangle with those two neighbors centers. The side lengths are all 2r, so the height or y-coordinate difference between the rows is r'. Thus, this row will have coordinates like this:
The first sphere of this row only touches one sphere in the original row, but its location follows suit with the rest of the row.
The next row follows this pattern of shifting the x-coordinate by r and the y-coordinate by . Add rows until reaching the x and y maximum borders of the box.
In an A-B-A-B-... stacking pattern, the odd numbered planes of spheres will have exactly the same coordinates save for a pitch difference in the z-coordinates and the even numbered planes of spheres will share the same x- and y-coordinates. Both types of planes are formed using the pattern mentioned above, but the starting place for the first row's first sphere will be different.
Using the plane described precisely above as plane #1, the A plane, place a sphere on top of this plane so that it lies touching three spheres in the A-plane. The three spheres are all already touching each other, forming an equilateral triangle, and since they all touch the new sphere, the four centers form a regular tetrahedron. All of the sides are equal to 2r because all of the sides are formed by two spheres touching. The height of which or the z-coordinate difference between the two "planes" is . This, combined with the offsets in the x and y-coordinates gives the centers of the first row in the B plane:
The second row's coordinates follow the pattern first described above and are:
The difference to the next plane, the A plane, is again in the z-direction and a shift in the x and y to match those x- and y-coordinates of the first A plane.
In general, the coordinates of sphere centers can be written as:
where i, j and k are indices starting at 0 for the x-, y- and z-coordinates. | 3 | Analytical Chemistry |
Archaerhodopsin 1 and 2 (AR1 and AR2) were the first archaerhodopsins to be identified and are expressed by Halobacterium sp. Aus-1 and Aus-2 respectively. Both species were first isolated in Western Australia in the late 1980s. The crystal structures of both proteins were solved by Kunio Ihara, Tsutomo Kouyama and co-workers at Nagoya University, together with collaborators at the Spring-8 synchrotron. | 5 | Photochemistry |
In epitranscriptomic sequencing, most methods focus on either (1) enrichment and purification of the modified RNA molecules before running on the RNA sequencer, or (2) improving or modifying bioinformatics analysis pipelines to call the modification peaks. Most methods have been adapted and optimized for mRNA molecules, except for modified bisulfite sequencing for profiling 5-methylcytidine which was optimized for tRNAs and rRNAs.
There are seven major classes of chemical modifications found in RNA molecules: N-methyladenosine, 2-O-methylation, N6,2-O-dimethyladenosine, 5-methylcytidine, 5-hydroxylmethylcytidine, inosine, and pseudouridine. Various sequencing methods have been developed to profile each type of modification. The scale, resolution, sensitivity, and limitations associated with each method and the corresponding bioinformatics tools used will be discussed. | 1 | Biochemistry |
Quinone molecules have been used as anolytes in alkaline AROFBs. Another anolyte candidate is fluorenone, reengineered to increase its water solubility. A reversible ketone (de)hydrogenation demonstration cell operated continuously for 120 days over 1,111 charging cycles at room temperature without a catalyst, retaining 97% percent capacity. The cell offers more than double the energy density of vanadium-based systems. The major challenge for alkaline AORFBs is the lack of a stable catholyte, holding their energy densities below 5 Wh/L. All reported alkaline AORFBs use excess potassium ferrocyanide catholyte because of the stability issue of ferrocyanide in alkaline solutions.
Metal-organic flow batteries use organic ligands to improve the properties of redox-active metals. The ligands can be chelates like EDTA, and can enable the electrolyte to be in neutral or alkaline conditions under which metal aquo complexes would otherwise precipitate. By blocking the coordination of water to the metal, organic ligands can inhibit metal-catalyzed water-splitting reactions, resulting in higher voltage all-aqueous systems. For example, the use of chromium coordinated to 1,3-propanediaminetetraacetate (PDTA), gave cell potentials of 1.62 V vs. ferrocyanide and a record 2.13 V vs. bromine. Metal-organic flow batteries may be known as coordination chemistry flow batteries, which represents the technology behind Lockheed Martin's Gridstar Flow technology. | 7 | Physical Chemistry |
A widely accepted explanation is that there is a stabilizing interaction (hyperconjugation) between the unshared electron pair on the endocyclic heteroatom (within the sugar ring) and the σ* orbital of the axial (exocyclic) C–X bond. This causes the molecule to align the donating lone pair of electrons antiperiplanar (180°) to the exocyclic C-X σ bond, lowering the overall energy of the system and causing more stability.
Some authors also question the validity of this hyperconjugation model based on results from the quantum theory of atoms in molecules. While most studies on the anomeric effects have been theoretical in nature, the n–σ* (hyperconjugation) hypothesis has also been extensively criticized on the basis that the electron density redistribution in acetals proposed by this hypothesis is not congruent with the known experimental chemistry of acetals and, in particular, the chemistry of monosaccharides. | 7 | Physical Chemistry |
Focusing his research on photochemistry, Natarajan studied various areas of the discipline such as polymer dynamics using fluorescence, flash photolysis studies using picosecond and femtosecond lasers and solar energy conversion. He demonstrated that micromolecular dye coatings of electrodes used in photoelectrochemical cells returned high current density. This led to his subsequent studies of solar energy conversion using chemically modified electrodes. He published his research in peer-reviewed journals including Nature, Journal of the American Chemical Society, Journal of Physical Chemistry A, Inorganic Chemistry and Chemical Communications for a total of 107 articles. He was granted patents for four of his findings. He mentored over 30 doctoral scholars and was associated with a number of journals as their editorial board member. He also was on a number of government committees including those of the Department of Science and Technology and the Council of Scientific and Industrial Research and delivered several featured talks and orations. | 5 | Photochemistry |
Inorganic nanoparticles, such as gold, silica, iron oxide (ex. magnetofection) and calcium phosphates have been shown to be capable of gene delivery. Some of the benefits of inorganic vectors is in their storage stability, low manufacturing cost and often time, low immunogenicity, and resistance to microbial attack. Nanosized materials less than 100 nm have been shown to efficiently trap the DNA or RNA and allows its escape from the endosome without degradation. Inorganics have also been shown to exhibit improved in vitro transfection for attached cell lines due to their increased density and preferential location on the base of the culture dish. Quantum dots have also been used successfully and permits the coupling of gene therapy with a stable fluorescence marker. Engineered organic nanoparticles are also under development, which could be used for co-delivery of genes and therapeutic agents. | 1 | Biochemistry |
Increasing levels of nitrogen deposition are shown to have a number of negative effects on both terrestrial and aquatic ecosystems. Nitrogen gases and aerosols can be directly toxic to certain plant species, affecting the aboveground physiology and growth of plants near large point sources of nitrogen pollution. Changes to plant species may also occur, as accumulation of nitrogen compounds increase its availability in a given ecosystem, eventually changing the species composition, plant diversity, and nitrogen cycling. Ammonia and ammonium – two reduced forms of nitrogen – can be detrimental over time due to an increased toxicity toward sensitive species of plants, particularly those that are accustomed to using nitrate as their source of nitrogen, causing poor development of their roots and shoots. Increased nitrogen deposition also leads to soil acidification, which increases base cation leaching in the soil and amounts of aluminum and other potentially toxic metals, along with decreasing the amount of nitrification occurring and increasing plant-derived litter. Due to the ongoing changes caused by high nitrogen deposition, an environment's susceptibility to ecological stress and disturbance – such as pests and pathogens – may increase, thus making it less resilient to situations that otherwise would have little impact to its long-term vitality.
Additional risks posed by increased availability of inorganic nitrogen in aquatic ecosystems include water acidification; eutrophication of fresh and saltwater systems; and toxicity issues for animals, including humans. Eutrophication often leads to lower dissolved oxygen levels in the water column, including hypoxic and anoxic conditions, which can cause death of aquatic fauna. Relatively sessile benthos, or bottom-dwelling creatures, are particularly vulnerable because of their lack of mobility, though large fish kills are not uncommon. Oceanic dead zones near the mouth of the Mississippi in the Gulf of Mexico are a well-known example of algal bloom-induced hypoxia. The New York Adirondack Lakes, Catskills, Hudson Highlands, Rensselaer Plateau and parts of Long Island display the impact of nitric acid rain deposition, resulting in the killing of fish and many other aquatic species.
Ammonia () is highly toxic to fish and the level of ammonia discharged from wastewater treatment facilities must be closely monitored. To prevent fish deaths, nitrification via aeration prior to discharge is often desirable. Land application can be an attractive alternative to the aeration. | 1 | Biochemistry |
Amorphous materials will have some degree of short-range order at the atomic-length scale due to the nature of intermolecular chemical bonding. Furthermore, in very small crystals, short-range order encompasses a large fraction of the atoms; nevertheless, relaxation at the surface, along with interfacial effects, distorts the atomic positions and decreases structural order. Even the most advanced structural characterization techniques, such as X-ray diffraction and transmission electron microscopy, have difficulty distinguishing amorphous and crystalline structures at short-length scales. | 7 | Physical Chemistry |
Once the fatty acid is inside the mitochondrial matrix, beta-oxidation occurs by cleaving two carbons every cycle to form acetyl-CoA. The process consists of 4 steps.
# A long-chain fatty acid is dehydrogenated to create a trans double bond between C2 and C3. This is catalyzed by acyl CoA dehydrogenase to produce trans-delta 2-enoyl CoA. It uses FAD as an electron acceptor and it is reduced to FADH.
# Trans-delta 2-enoyl CoA is hydrated at the double bond to produce L-3-hydroxyacyl CoA by enoyl-CoA hydratase.
# L-3-hydroxyacyl CoA is dehydrogenated again to create 3-ketoacyl CoA by 3-hydroxyacyl CoA dehydrogenase. This enzyme uses NAD as an electron acceptor.
# Thiolysis occurs between C2 and C3 (alpha and beta carbons) of 3-ketoacyl CoA. Thiolase enzyme catalyzes the reaction when a new molecule of coenzyme A breaks the bond by nucleophilic attack on C3. This releases the first two carbon units, as acetyl CoA, and a fatty acyl CoA minus two carbons. The process continues until all of the carbons in the fatty acid are turned into acetyl CoA.
This acetyl-CoA then enters the mitochondrial tricarboxylic acid cycle (TCA cycle). Both the fatty acid beta-oxidation and the TCA cycle produce NADH and FADH, which are used by the electron transport chain to generate ATP.
Fatty acids are oxidized by most of the tissues in the body. However, some tissues such as the red blood cells of mammals (which do not contain mitochondria) and cells of the central nervous system do not use fatty acids for their energy requirements, but instead use carbohydrates (red blood cells and neurons) or ketone bodies (neurons only).
Because many fatty acids are not fully saturated or do not have an even number of carbons, several different mechanisms have evolved, described below. | 1 | Biochemistry |
Aluminium granules have been found safer and economical compared to atomized aluminium powder. Aluminium granules have lower explosion risk in production and in use of the product itself. | 8 | Metallurgy |
The columns are made of stainless steel. Conical vanes are attached alternately to the wall of the column and to a central rotating shaft. The product is poured in at the top under vacuum, and steam is pumped into the column from below. The vanes provide a large surface area over which volatile compounds can evaporate into the steam, and the rotation ensures a thin layer of the product is constantly moved over the moving cone. It typically takes 20 seconds for the liquid to move through the column, and industrial columns might process . The temperature and pressure can be adjusted depending on the compounds targeted. | 3 | Analytical Chemistry |
A transcriptome in vivo analysis tag (TIVA tag) is a multifunctional, photoactivatable mRNA-capture molecule designed for isolating mRNA from a single cell in complex tissues.
__TOC__ | 1 | Biochemistry |
A fresnel is a unit of frequency equal to 10 s. It was occasionally used in the field of spectroscopy, but its use has been superseded by terahertz (with the identical value 10 hertz). It is named for Augustin-Jean Fresnel the physicist whose expertise in optics led to the creation of Fresnel lenses. | 7 | Physical Chemistry |
Activated by calcium, the enzyme digests proteins preferentially after hydrophobic amino acids (aliphatic, aromatic and other hydrophobic amino acids). Although calcium ions do not affect the enzyme activity, they do contribute to its stability.
Proteins will be completely digested if the incubation time is long and the protease concentration high enough. Upon removal of the calcium ions, the stability of the enzyme is reduced, but the proteolytic activity remains. Proteinase K has two binding sites for Ca, which are located close to the active center, but are not directly involved in the catalytic mechanism. The residual activity is sufficient to digest proteins, which usually contaminate nucleic acid preparations. Therefore, the digestion with Proteinase K for the purification of nucleic acids is usually performed in the presence of EDTA (inhibition of metal-ion dependent enzymes such as nucleases).
Proteinase K is also stable over a wide pH range (4–12), with a pH optimum of pH 8.0.
An elevation of the reaction temperature from 37 °C to 50–60 °C may increase the activity several times, like the addition of 0.5–1% sodium dodecyl sulfate (SDS) or Guanidinium chloride (3 M), Guanidinium thiocyanate (1 M) and urea (4 M) . The above-mentioned conditions enhance proteinase K activity by making its substrate cleavage sites more accessible. Temperatures above 65 °C, trichloroacetic acid (TCA) or the serine protease-inhibitors AEBSF, PMSF or DFP inhibit the activity.
Proteinase K will not be inhibited by Guanidinium chloride, Guanidinium thiocyanate, urea, Sarkosyl, Triton X-100, Tween 20, SDS, citrate, iodoacetic acid, EDTA or by other serine protease inhibitors like Nα-Tosyl-Lys Chloromethyl Ketone (TLCK) and Nα-Tosyl-Phe Chloromethyl Ketone (TPCK).
Protease K activity in commonly used buffers | 1 | Biochemistry |
According to the IUPAC definition, in RRC(OH)OR R and R may or may not be a hydrogen. In a hemiketal, neither R-group can be a hydrogen. Hemiketals are regarded as hemiacetals where none of the R-groups are H, and are therefore a subclass of the hemiacetals. The Greek prefix hèmi means half, refers to the fact that a single alcohol has been added to the carbonyl group, in contrast to acetals or ketals, which are formed when a second alkoxy group has been added to the structure.
Cyclic hemiacetals and hemiketals are sometimes called lactols. They often form readily, especially when they are 5- and 6-membered rings. In this case an intramolecular OH group reacts with the carbonyl group. Glucose and many other aldoses exist as cyclic hemiacetals whereas fructose and similar ketoses exist as cyclic hemiketals. | 0 | Organic Chemistry |
The selection rule of electrocyclization reactions is given in the original statement of the Woodward–Hoffmann rules. If a generalized electrocyclic ring closure occurs in a polyene of 4n π-electrons, then it is conrotatory under thermal conditions and disrotatory under photochemical conditions. Conversely in a polyene of 4n + 2 π-electrons, an electrocyclic ring closure is disrotatory under thermal conditions and conrotatory under photochemical conditions.
This result can either be derived via an FMO analysis based upon the sign of p orbital lobes of the HOMO of the polyene or with correlation diagrams. Taking first the first possibility, in the ground state, if a polyene has 4n electrons, the outer p-orbitals of the HOMO that form the σ bond in the electrocyclized product are of opposite signs. Thus a constructive overlap is only produced under a conrotatory or antarafacial process. Conversely for a polyene with 4n + 2 electrons, the outer p-orbitals of the ground state HOMO are of the same sign. Thus constructive orbital overlap occurs with a disrotatory or suprafacical process.
Additionally, the correlation diagram for any 4n electrocyclic reaction will resemble the diagram for the 4 electron cyclization of 1,3-butadiene, while the correlation diagram any 4n + 2 electron electrocyclic reaction will resemble the correlation diagram for the 6 electron cyclization of 1,3,5-hexatriene.
This is summarized in the following table: | 7 | Physical Chemistry |
Indolicidin is an antimicrobial peptide isolated from neutrophil blood cells of cows. The mature peptide is just 13 amino acids, making it one of the smallest antimicrobial peptides known to be encoded as the primary product of the encoding antimicrobial peptide gene. Indolicidin is active against bacterial pathogens, but has also been shown to kill fungi and even HIV virus. | 0 | Organic Chemistry |
Modified aldol tandem reaction is a sequential chemical transformation that combines aldol reaction with other chemical reactions that generate enolates. Enolates are a common building block in chemical syntheses and are typically formed by the addition of base to a ketone or aldehyde. Modified Aldol tandem reactions allow similar reactivity to be produced without the need for a base which may have adverse effects in a given chemical synthesis. A representative example is the decarboxylative aldol reaction (Figure "Modified aldol tandem reaction, decarboxylative aldol reaction as an example"), where the enolate is generated via decarboxylation reaction mediated by either transition metals or organocatalysts. Key advantage of this reaction over other types of aldol reaction is the selective generation of an enolate in the presence of aldehydes. This allows for the directed aldol reaction to produce a desired cross aldol.
Transition metals have been used to mediate the modified aldol tandem reaction. Allyl β-keto carboxylates can be used as substrate for palladium-mediated decarboxylative aldol reaction (Figure "Palladium-mediated decarboxylative aldol reaction with allyl β-keto carboxylates"). The allyl group can be removed by palladium, following decarboxylation reaction selectively generates the enolate at the β-keto group, which could further react with aldehyde to generate aldols.
Using decarboxylation reaction to generate enolate is a common strategy in biosynthetic pathways such as polyketide synthesis, where malonic acid half thioester can be converted to the corresponding enolate for Claisen condensation reaction. Inspired by this, a modified tandem aldol reaction has been developed using the malonic acid half thioester as the enolate source. A copper based catalyst system has been developed for efficient aldol generation at mild conditions (Figure "Decarboxylative aldol reaction with malonic acid half thioester"). | 0 | Organic Chemistry |
Available coatings include polyesters, plastisols, polyurethanes, polyvinylidene fluorides (PVDF), epoxies, primers, backing coats and laminate films. For each product, the coating is built up in a number of layers.
Primer coatings form the essential link between the pretreatment and the finish coating. Essentially, a primer is required to provide inter-coat adhesion between the pretreatment and the finish coat and is also required to promote corrosion resistance in the total system. The composition of the primer will vary depending on the type of finish coat used. Primers require compatibility with various pretreatments and top coat paint systems; therefore, they usually comprise a mixture of resin systems to achieve this end.
Backing coats are applied to the underside of the strip with or without a primer. The coating is generally not as thick as the finish coating used for exterior applications. Backing coats are generally not exposed to corrosive environments and not visible in the end application. | 8 | Metallurgy |
The journal publishes the following types of articles
*Research Papers, original scientific work that has not been published previously
*Communications, original scientific work that has not been published previously and is of an urgent nature
*Perspectives, review articles of interest to a broad readership which are commissioned by the editorial board
*Comments, a medium for the discussion and exchange of scientific opinions, normally concerning material previously published in the journal | 7 | Physical Chemistry |
He was born on December 31, 1905, in Ordubad.
In 1923, he entered the higher pedagogical institute of Baku. In 1926, after successful graduation from the institute he taught at secondary school for 3 years. In 1929, he became a second-year student of chemistry faculty of MSU, from which he graduated in 1932. He was a student of Nikolay Zelinsky and Aleksei Balandin and one of the first seniors of the laboratory of organic chemistry of chemistry faculty's organic chemistry cathedra with “organocatalysis” speciality. On the termination of MSU he worked in Moscow at the chemical plant No.1, and then was transferred to Azerbaijan, where he managed the Cathedra of organic chemistry of the agricultural college of Azerbaijan at first. Then he worked (1933–1945) at the Azerbaijan Research Institute of Oil, where he became the manager of laboratory. His work was dedicated to scientific problems of petrochemistry and organocatalysis and was closely connected with the development of domestic oil-refining and petrochemical industry. Some developments assumed as the basis of new industrial processes.
Starting from 1934, he led the great pedagogical work at Azerbaijan University named after S.M.Kirov, sequentially holding the positions of associate professor, professor, head of a cathedra and rector (1954–1958). In 1933, Candidate of Chemistry was conferred on Yusif Mammadaliyev without defend of dissertation.
In 1942, he became a Doctor of Chemistry and in 1943, a professor; in 1945, the academician of the Academy of Sciences of the Azerbaijan SSR (from the establishment of academy). He was the director of Oil Academy of the Azerbaijan SSR. In 1946, he was nominated to the work in the Ministry of Oil Industry, where he became the chairman of scientific-technical council of the ministry. In 1951–1954, he was the academician-secretary of physics, chemistry and oil departments of the Academy of Sciences of the Azerbaijan SSR, in 1954–1958, the rector of Azerbaijan State University.
In 1947–1951 and 1958–1961 Mammadaliyev was chosen the president of the Academy of Sciences of the Azerbaijan SSR. The Institute of Petrochemical Processes was established in Baku on Mammadaliyev's initiative.
In 1958, Mammadaliyev was chosen as the corresponding member of the Academy of Sciences of the Azerbaijan SSR.
Mammadaliyev died in 1961. | 0 | Organic Chemistry |
Negative regulators act to prevent transcription or translation. Examples such as cFLIP suppress cell death mechanisms leading to pathological disorders like cancer, and thus play a crucial role in drug resistance. Circumvention of such actors is a challenge in cancer therapy.
Negative regulators of cell death in cancer include cFLIP, Bcl family, Survivin, HSP, IAP, NF-κB, Akt, mTOR, and FADD. | 1 | Biochemistry |
In the early days, Mander was involved in extracting chemicals in plants that might help fight against cancer. Eventually, he turned his research skills to “...the gibberellin family of plant bioregulators". He further developed his interest in this chemical group to include an understanding of their role in plant development. Professor Sir Alan R. Battersby said that Mander's “...synthesis of gibberellic acid was a brilliant landmark achievement. This molecule is of daunting complexity and he developed two flexible routes to it, both depending on many ingenious and novel synthetic procedures".
Amongst his many scholarly activities, Mander contributed a chapter on Stereoselective Synthesis to the classic text Stereochemistry of Organic Compounds by Professors Ernest L. Eliel and Samuel H. Wilen.
Other interests include:
*Synthesis and preparation of semi-synthetic derivatives of gibberellins.
*Molecular basis of plant growth regulation with gibberellins.
*Synthesis of diterpenoid natural products with high bioactivity.
*Dissolving metal-mediated reductive alkylation of benzenoid synthons.
*C-selective acylation of enolates using methyl cyanoformate (Mander's reagent). | 0 | Organic Chemistry |
Stickland fermentation or The Stickland Reaction is the name for a chemical reaction that involves the coupled oxidation and reduction of amino acids to organic acids. The electron donor amino acid is oxidised to a volatile carboxylic acid one carbon atom shorter than the original amino acid. For example, alanine with a three carbon chain is converted to acetate with two carbons. The electron acceptor amino acid is reduced to a volatile carboxylic acid the same length as the original amino acid. For example, glycine with two carbons is converted to acetate.
In this way, amino acid fermenting microbes can avoid using hydrogen ions as electron acceptors to produce hydrogen gas. Amino acids can be Stickland acceptors, Stickland donors, or act as both donor and acceptor. Only histidine cannot be fermented by Stickland reactions, and is oxidised. With a typical amino acid mix, there is a 10% shortfall in Stickland acceptors, which results in hydrogen production. Under very low hydrogen partial pressures, increased uncoupled anaerobic oxidation has also been observed.
It occurs in proteolytic clostridiums such as:
C. perfringens,
C. difficile,
C. sporogenes,
and C. botulinum.
Additionally, sarcosine and betaine can act as electron acceptors. | 1 | Biochemistry |
A solution of methyl(cyano)cuprate (Solution A) was prepared as follows: to a suspension of 0.35 g (3.91 mmol) of copper(I) cyanide in 5 mL of tetrahydrofuran under argon at 0° was added dropwise over about 5 minutes 2.76 mL of a solution of methyllithium in ethyl ether (1.4 M, 3.86 mmol). The colorless solution was stirred for 10 minutes at 0°, warmed to 25° over 30 minutes, then cooled again to 0°. Separately, a solution of the lithium salt of (±)-cis-4-benzyloxy-2,3-epoxy-1-butanol (Solution B) was prepared as follows: to a solution of 0.5 g (2.58 mmol) of the epoxy alcohol and 0.90 g (21.4 mmol) of lithium chloride in 10 mL of tetrahydrofuran under argon at −78° was added dropwise 1.65 mL of a solution of n-butyllithium in hexane (1.56 M, 2.58 mmol). The solution was stirred for 5 minutes at −78°, allowed to warm to 0°, and then stirred at that temperature for 10 minutes. The reaction was effected by the addition of Solution A to Solution B via cannula at 0° followed by warming to room temperature over 2 hours. The reaction mixture was then stirred for a further 12 hours and then cautiously treated with 5 mL of saturated aqueous ammonium chloride. The mixture was stirred for 1–2 hours to aid removal of copper residues. Ethyl ether (20 mL) was then added, and the organic layer was separated. The aqueous phase was extracted twice with 20 mL of ethyl ether, and the combined organic phases were dried over magnesium sulfate, filtered, and concentrated to give 0.51 g of the product as a colorless oil (95%), IR (film) 3400, 3100, 3060, 3030, 2970, 2930, 2870, 1600, 1500, 1465, 1445, 1385, 1370, 1320, 1285, 1210, 1180, 1120, 1100, 1075, 1030, 1020, 980, 905, 830, 750, 730, 710, 695 cm–1; 1H NMR (CDCl) δ 0.90 (t, J = 6.0 Hz, 3 H), 1.37–1.53 (m, 2 H), 3.20 (br s, 2 H), 3.40–3.65 (m, 4 H), 4.48 (s, 2 H), 7.29 (s, 5 H). | 0 | Organic Chemistry |
In an anisotropic medium, such as a crystal, the polarisation field P is not necessarily aligned with the electric field of the light E. In a physical picture, this can be thought of as the dipoles induced in the medium by the electric field having certain preferred directions, related to the physical structure of the crystal. This can be written as:
Here χ is not a number as before but a tensor of rank 2, the electric susceptibility tensor. In terms of components in 3 dimensions:
or using the summation convention:
Since χ is a tensor, P is not necessarily colinear with E.
In nonmagnetic and transparent materials, χ = χ, i.e. the χ tensor is real and symmetric. In accordance with the spectral theorem, it is thus possible to diagonalise the tensor by choosing the appropriate set of coordinate axes, zeroing all components of the tensor except χ, χ and χ. This gives the set of relations:
The directions x, y and z are in this case known as the principal axes of the medium. Note that these axes will be orthogonal if all entries in the χ tensor are real, corresponding to a case in which the refractive index is real in all directions.
It follows that D and E are also related by a tensor:
Here ε is known as the relative permittivity tensor or dielectric tensor. Consequently, the refractive index of the medium must also be a tensor. Consider a light wave propagating along the z principal axis polarised such the electric field of the wave is parallel to the x-axis. The wave experiences a susceptibility χ and a permittivity ε. The refractive index is thus:
For a wave polarised in the y direction:
Thus these waves will see two different refractive indices and travel at different speeds. This phenomenon is known as birefringence and occurs in some common crystals such as calcite and quartz.
If χ = χ ≠ χ, the crystal is known as uniaxial. (See Optic axis of a crystal.) If χ ≠ χ and χ ≠ χ the crystal is called biaxial. A uniaxial crystal exhibits two refractive indices, an "ordinary" index (n) for light polarised in the x or y directions, and an "extraordinary" index (n) for polarisation in the z direction. A uniaxial crystal is "positive" if n > n and "negative" if n . Light polarised at some angle to the axes will experience a different phase velocity for different polarization components, and cannot be described by a single index of refraction. This is often depicted as an index ellipsoid. | 3 | Analytical Chemistry |
The probe to be detected is labeled with some biotin-molecules. After incubation with a gold-coupled anti-biotin conjugate, silver nitrate and a reducing agent are added. The reaction starts whereas the gold particle serves as a starting point for the silver precipitation.
The reaction needs to be stopped after a specific time. The constant reaction time is essential to obtain comparable results. | 1 | Biochemistry |
Mitochondria are commonly referred to as the cells "powerhouses" because of their capacity to effectively produce ATP which is essential to maintain cellular homeostasis and metabolism. Moreover, researchers have gained a better knowledge of mitochondrias significance in cell biology because of the discovery of cell signaling pathways by mitochondria which are crucial platforms for cell function regulation such as apoptosis. Its physiological adaptability is strongly linked to the cell mitochondrial channels ongoing reconfiguration through a range of mechanisms known as mitochondrial membrane dynamics, which include endomembrane fusion and fragmentation (separation) as well as ultrastructural membrane remodeling. As a result, mitochondrial dynamics regulate and frequently choreograph not only metabolic but also complicated cell signaling processes such as cell pluripotent stem cells, proliferation, maturation, aging, and mortality. Mutually, post-translational alterations of mitochondrial apparatus and the development of transmembrane contact sites among mitochondria and other structures, which both have the potential to link signals from diverse routes that affect mitochondrial membrane dynamics substantially, Mitochondria are wrapped by two membranes: an inner mitochondrial membrane (IMM) and an outer mitochondrial membrane (OMM), each with a distinctive function and structure, which parallels their dual role as cellular powerhouses and signaling organelles. The inner mitochondrial membrane divides the mitochondrial lumen into two parts: the inner border membrane, which runs parallel to the OMM, and the cristae, which are deeply twisted, multinucleated invaginations that give room for surface area enlargement and house the mitochondrial respiration apparatus. The outer mitochondrial membrane, on the other hand, is soft and permeable. It, therefore, acts as a foundation for cell signaling pathways to congregate, be deciphered, and be transported into mitochondria. Furthermore, the OMM connects to other cellular organelles, such as the endoplasmic reticulum (ER), lysosomes, endosomes, and the plasma membrane. Mitochondria play a wide range of roles in cell biology, which is reflected in their morphological diversity. Ever since the beginning of the mitochondrial study, it has been well documented that mitochondria can have a variety of forms, with both their general and ultra-structural morphology varying greatly among cells, during the cell cycle, and in response to metabolic or cellular cues. Mitochondria can exist as independent organelles or as part of larger systems; they can also be unequally distributed in the cytosol through regulated mitochondrial transport and placement to meet the cells localized energy requirements. Mitochondrial dynamics refers to the adaptive and variable aspect of mitochondria, including their shape and subcellular distribution. | 1 | Biochemistry |
Ribosomal frameshifting may be controlled by mechanisms found in the mRNA sequence (cis-acting). This generally refers to a slippery sequence, a RNA secondary structure, or both. A −1 frameshift signal consists of both elements separated by a spacer region typically 5–9 nucleotides long. Frameshifting may also be induced by other molecules which interact with the ribosome or the mRNA (trans-acting). | 1 | Biochemistry |
One of the most time-consuming aspects of endotoxin testing using LAL is pretreating samples to overcome assay inhibition that may interfere with the LAL test such that the recovery of endotoxin is affected. If the product being tested causes the endotoxin recovery to be less than expected, the product is inhibitory to the LAL test. Products which cause higher than expected values are enhancing. Overcoming the inhibition and enhancement properties of a product is required by the FDA as part of the validation of the LAL test for use in the final release testing of injectables and medical devices. Proper endotoxin recovery must be proven before LAL can be used to release product. | 3 | Analytical Chemistry |
: This type of reactor contains several tubes with small diameters. These tubes contain catalysts and are surrounded by cooling water which removes the heat of the reaction. A fixed-bed reactor is suitable for operation at low temperatures and has an upper-temperature limit of 257 °C (530 K). Excess temperature leads to carbon deposition and hence blockage of the reactor. Since large amounts of the products formed are in liquid state, this type of reactor can also be referred to as a trickle flow reactor system. | 0 | Organic Chemistry |
The study of MA structure and function is challenging, in particular because of their megadalton size, but also because of their complex compositions and varying dynamic natures. Most have had standard chemical and biochemical methods applied (methods of protein purification and centrifugation, chemical and electrochemical characterization, etc.). In addition, their methods of study include modern proteomic approaches, computational and atomic-resolution structural methods (e.g., X-ray crystallography), small-angle X-ray scattering (SAXS) and small-angle neutron scattering (SANS), force spectroscopy, and transmission electron microscopy and cryo-electron microscopy. Aaron Klug was recognized with the 1982 Nobel Prize in Chemistry for his work on structural elucidation using electron microscopy, in particular for protein-nucleic acid MAs including the tobacco mosaic virus (a structure containing a 6400 base ssRNA molecule and >2000 coat protein molecules). The crystallization and structure solution for the ribosome, MW ~ 2.5 MDa, an example of part of the protein synthetic machinery of living cells, was object of the 2009 Nobel Prize in Chemistry awarded to Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada E. Yonath. | 1 | Biochemistry |
The C-terminus of RPB1 is appended to form the C-terminal domain (CTD). The carboxy-terminal domain of RNA polymerase II typically consists of up to 52 repeats of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser. The domain stretches from the core of the RNAPII enzyme to the exit channel, this placement is effective due to its inductions of "RNA processing reactions, through direct or indirect interactions with components of the RNA processing machinery". The CTD domain does not exist in RNA Polymerase I or RNA Polymerase III. The RNA Polymerase CTD was discovered first in the laboratory of C.J.Ingles at the University of Toronto and also in the laboratory of J Corden at Johns Hopkins University during the processes of sequencing the DNA encoding the RPB1 subunit of RNA polymerase from Yeast and Mice respectively. Other proteins often bind the C-terminal domain of RNA polymerase in order to activate polymerase activity. It is the protein domain that is involved in the initiation of transcription, the capping of the RNA transcript, and attachment to the spliceosome for RNA splicing. | 1 | Biochemistry |
The innate immune system has evolved to protect against infection by detecting pathogen-associated molecular patterns (PAMPs), and triggering a complex set of responses collectively known as "inflammation". Many cells express specific pattern recognition receptors (PRRs) for exogenous RNA including toll-like receptor 3,7,8 (TLR3, TLR7, TLR8), the RNA helicase RIG1 (RARRES3), protein kinase R (PKR, a.k.a. EIF2AK2), members of the oligoadenylate synthetase family of proteins (OAS1, OAS2, OAS3), and others. All of these proteins can specifically bind to exogenous RNA molecules and trigger an immune response.
The specific chemical, structural or other characteristics of long RNA molecules that are required for recognition by PRRs remain largely unknown despite intense study. At any given time, a typical mammalian cell may contain several hundred thousand mRNA and other, regulatory long RNA molecules. How cells distinguish exogenous long RNA from the large amount of endogenous long RNA is an important open question in cell biology. Several reports suggest that phosphorylation of the 5-end of a long RNA molecule can influence its immunogenicity, and specifically that 5-triphosphate RNA, which can be produced during viral infection, is more immunogenic than 5-diphosphate RNA, 5-monophosphate RNA or RNA containing no 5 phosphate. However, in vitro-transcribed (ivT) long RNA containing a 7-methylguanosine cap (present in eukaryotic mRNA) is also highly immunogenic despite having no 5 phosphate, suggesting that characteristics other than 5'-phosphorylation can influence the immunogenicity of an RNA molecule.
Eukaryotic mRNA contains chemically modified nucleotides such as N-methyladenosine, 5-methylcytidine, and 2'-O-methylated nucleotides. Although only a very small number of these modified nucleotides are present in a typical mRNA molecule, they may help prevent mRNA from activating the innate immune system by disrupting secondary structure that would resemble double-stranded RNA (dsRNA), a type of RNA thought to be present in cells only during viral infection.
The immunogenicity of long RNA has been used to study both innate and adaptive immunity. | 1 | Biochemistry |
The discovery of oncometabolites has ushered in a new era in cancer biology, one that has the potential to improve patient care. The discovery of new therapeutic and reliable markers that exploit vulnerabilities of cancer cells, are being used to targeting either upstream or downstream effectors of these pathways. Oncometabolites can be used as diagnostic biomarkers and may be able to assist oncologists in making more precise decisions in early stages of tumorigenesis, particularly in predicting more aggressive tumor behavior. | 1 | Biochemistry |
In eukaryotic somatic cells, the poly(A) tails of most mRNAs in the cytoplasm gradually get shorter, and mRNAs with shorter poly(A) tail are translated less and degraded sooner. However, it can take many hours before an mRNA is degraded. This deadenylation and degradation process can be accelerated by microRNAs complementary to the 3′ untranslated region of an mRNA. In immature egg cells, mRNAs with shortened poly(A) tails are not degraded, but are instead stored and translationally inactive. These short tailed mRNAs are activated by cytoplasmic polyadenylation after fertilisation, during egg activation.
In animals, poly(A) ribonuclease (PARN) can bind to the 5′ cap and remove nucleotides from the poly(A) tail. The level of access to the 5′ cap and poly(A) tail is important in controlling how soon the mRNA is degraded. PARN deadenylates less if the RNA is bound by the initiation factors 4E (at the 5′ cap) and 4G (at the poly(A) tail), which is why translation reduces deadenylation. The rate of deadenylation may also be regulated by RNA-binding proteins. Additionally, RNA triple helix structures and RNA motifs such as the poly(A) tail 3’ end binding pocket retard deadenylation process and inhibit poly(A) tail removal. Once the poly(A) tail is removed, the decapping complex removes the 5′ cap, leading to a degradation of the RNA. Several other proteins are involved in deadenylation in budding yeast and human cells, most notably the CCR4-Not complex. | 1 | Biochemistry |
The mature mRNA finds its way to a ribosome, where it gets translated. In prokaryotic cells, which have no nuclear compartment, the processes of transcription and translation may be linked together without clear separation. In eukaryotic cells, the site of transcription (the cell nucleus) is usually separated from the site of translation (the cytoplasm), so the mRNA must be transported out of the nucleus into the cytoplasm, where it can be bound by ribosomes. The ribosome reads the mRNA triplet codons, usually beginning with an AUG (adenine−uracil−guanine), or initiator methionine codon downstream of the ribosome binding site. Complexes of initiation factors and elongation factors bring aminoacylated transfer RNAs (tRNAs) into the ribosome-mRNA complex, matching the codon in the mRNA to the anti-codon on the tRNA. Each tRNA bears the appropriate amino acid residue to add to the polypeptide chain being synthesised. As the amino acids get linked into the growing peptide chain, the chain begins folding into the correct conformation. Translation ends with a stop codon which may be a UAA, UGA, or UAG triplet.
The mRNA does not contain all the information for specifying the nature of the mature protein. The nascent polypeptide chain released from the ribosome commonly requires additional processing before the final product emerges. For one thing, the correct folding process is complex and vitally important. For most proteins it requires other chaperone proteins to control the form of the product. Some proteins then excise internal segments from their own peptide chains, splicing the free ends that border the gap; in such processes the inside "discarded" sections are called inteins. Other proteins must be split into multiple sections without splicing. Some polypeptide chains need to be cross-linked, and others must be attached to cofactors such as haem (heme) before they become functional. | 1 | Biochemistry |
DNA in solution does not take a rigid structure but is continually changing conformation due to thermal vibration and collisions with water molecules, which makes classical measures of rigidity impossible to apply. Hence, the bending stiffness of DNA is measured by the persistence length, defined as:
This value may be directly measured using an atomic force microscope to directly image DNA molecules of various lengths. In an aqueous solution, the average persistence length is 46–50 nm or 140–150 base pairs (the diameter of DNA is 2 nm), although can vary significantly. This makes DNA a moderately stiff molecule.
The persistence length of a section of DNA is somewhat dependent on its sequence, and this can cause significant variation. The variation is largely due to base stacking energies and the residues which extend into the minor and major grooves. | 4 | Stereochemistry |
Hypothermia has played a major role in the success or failure of many military campaigns, from Hannibals loss of nearly half his men in the Second Punic War (218 B.C.) to the near destruction of Napoleons armies in Russia in 1812. Men wandered around confused by hypothermia, some lost consciousness and died, others shivered, later developed torpor, and tended to sleep. Others too weak to walk fell on their knees; some stayed that way for some time resisting death. The pulse of some was weak and hard to detect; others groaned; yet others had eyes open and wild with quiet delirium. Deaths from hypothermia in Russian regions continued through the first and second world wars, especially in the Battle of Stalingrad.
Civilian examples of deaths caused by hypothermia occurred during the sinkings of the RMS Titanic and RMS Lusitania, and more recently of the MS Estonia.
Antarctic explorers developed hypothermia; Ernest Shackleton and his team measured body temperatures "below 94.2°, which spells death at home", though this probably referred to oral temperatures rather than core temperature and corresponded to mild hypothermia. One of Scott's team, Atkinson, became confused through hypothermia.
Nazi human experimentation during World War II amounting to medical torture included hypothermia experiments, which killed many victims. There were 360 to 400 experiments and 280 to 300 subjects, indicating some had more than one experiment performed on them. Various methods of rewarming were attempted: "One assistant later testified that some victims were thrown into boiling water for rewarming". | 1 | Biochemistry |
The simplest and most commonly encountered of the phosphoric acids is orthophosphoric acid, . Indeed, the term phosphoric acid often means this compound specifically (and this is also the current IUPAC nomenclature). | 0 | Organic Chemistry |
As much as 25% of the primary production from phytoplankton in the global oceans may be recycled within the microbial loop through viral shunting. The viral shunt is a mechanism whereby marine viruses prevent microbial particulate organic matter (POM) from migrating up trophic levels by recycling them into dissolved organic matter (DOM), which can be readily taken up by microorganisms. The DOM recycled by the viral shunt pathway is comparable to the amount generated by the other main sources of marine DOM. Viruses can easily infect microorganisms in the microbial loop due to their relative abundance compared to microbes. Prokaryotic and eukaryotic mortality contribute to carbon nutrient recycling through cell lysis. There is evidence as well of nitrogen (specifically ammonium) regeneration. This nutrient recycling helps stimulates microbial growth. | 9 | Geochemistry |
Urea is basic and is protonated readily. It is also a Lewis base, forming metal complexes of the type .
Urea reacts with malonic esters to make barbituric acids. | 0 | Organic Chemistry |
The strength of a material is dependent on how easily dislocations in its crystal lattice can be propagated. These dislocations create stress fields within the material depending on their character. When solute atoms are introduced, local stress fields are formed that interact with those of the dislocations, impeding their motion and causing an increase in the yield stress of the material, which means an increase in strength of the material. This gain is a result of both lattice distortion and the modulus effect.
When solute and solvent atoms differ in size, local stress fields are created that can attract or repel dislocations in their vicinity. This is known as the size effect. By relieving tensile or compressive strain in the lattice, the solute size mismatch can put the dislocation in a lower energy state. In substitutional solid solutions, these stress fields are spherically symmetric, meaning they have no shear stress component. As such, substitutional solute atoms do not interact with the shear stress fields characteristic of screw dislocations. Conversely, in interstitial solid solutions, solute atoms cause a tetragonal distortion, generating a shear field that can interact with edge, screw, and mixed dislocations. The attraction or repulsion of the dislocation to the solute atom depends on whether the atom sits above or below the slip plane. For example, consider an edge dislocation encountering a smaller solute atom above its slip plane. In this case, the interaction energy is negative, resulting in attraction of the dislocation to the solute. This is due to the reduced dislocation energy by the compressed volume lying above the dislocation core. If the solute atom were positioned below the slip plane, the dislocation would be repelled by the solute. However, the overall interaction energy between an edge dislocation and a smaller solute is negative because the dislocation spends more time at sites with attractive energy. This is also true for solute atom with size greater than the solvent atom. Thus, the interaction energy dictated by the size effect is generally negative.
The elastic modulus of the solute atom can also determine the extent of strengthening. For a “soft” solute with elastic modulus lower than that of the solvent, the interaction energy due to modulus mismatch (U) is negative, which reinforce the size interaction energy (U). In contrast, U is positive for a “hard” solute, which results in lower total interaction energy than a soft atom. Even though the interaction force is negative (attractive) in both cases when the dislocation is approaching the solute. The maximum force (F) necessary to tear dislocation away from the lowest energy state (i.e. the solute atom) is greater for the soft solute than the hard one. As a result, a soft solute will strengthen a crystal more than a hard solute due to the synergistic strengthening by combining both size and modulus effects.
The elastic interaction effects (i.e. size and modulus effects) dominate solid-solution strengthening for most crystalline materials. However, other effects, including charge and stacking fault effects, may also play a role. For ionic solids where electrostatic interaction dictates bond strength, charge effect is also important. For example, addition of divalent ion to a monovalent material may strengthen the electrostatic interaction between the solute and the charged matrix atoms that comprise a dislocation. However, this strengthening is to a less extent than the elastic strengthening effects. For materials containing a higher density of stacking faults, solute atoms may interact with the stacking faults either attractively or repulsively. This lowers the stacking fault energy, leading to repulsion of the partial dislocations, which thus makes the material stronger.
Surface carburizing, or case hardening, is one example of solid solution strengthening in which the density of solute carbon atoms is increased close to the surface of the steel, resulting in a gradient of carbon atoms throughout the material. This provides superior mechanical properties to the surface of the steel without having to use a higher-cost material for the component. | 8 | Metallurgy |
In the developed world, the estimated daily intake of CoQ has been determined at 3–6 mg per day, derived primarily from meat.
South Koreans have an estimated average daily CoQ (Q + Q) intake of 11.6 mg/d, derived primarily from kimchi. | 1 | Biochemistry |
Many solvents can lead to a sudden loss of consciousness if inhaled in large amounts. Solvents like diethyl ether and chloroform have been used in medicine as anesthetics, sedatives, and hypnotics for a long time. Many solvents (e.g. from gasoline or solvent-based glues) are abused recreationally in glue sniffing, often with harmful long-term health effects such as neurotoxicity or cancer. Fraudulent substitution of 1,5-pentanediol by the psychoactive 1,4-butanediol by a subcontractor caused the Bindeez product recall.
Ethanol (grain alcohol) is a widely used and abused psychoactive drug. If ingested, the so-called "toxic alcohols" (other than ethanol) such as methanol, 1-propanol, and ethylene glycol metabolize into toxic aldehydes and acids, which cause potentially fatal metabolic acidosis. The commonly available alcohol solvent methanol can cause permanent blindness or death if ingested. The solvent 2-butoxyethanol, used in fracking fluids, can cause hypotension and metabolic acidosis. | 2 | Environmental Chemistry |
In sporadic cancers, a DNA repair deficiency is occasionally found to be due to a mutation in a DNA repair gene. However, much more frequently, reduced or absent expression of a DNA repair gene in cancer is due to methylation of its promoter. For example, of 113 colorectal cancers examined, only four had a missense mutation in the DNA repair gene MGMT, while the majority had reduced MGMT expression due to methylation of the MGMT promoter region. Similarly, among 119 cases of mismatch repair-deficient colorectal cancers that lacked DNA repair gene PMS2 expression, 6 had a mutation in the PMS2 gene, while for 103 PMS2 was deficient because its pairing partner MLH1 was repressed due to promoter methylation (PMS2 protein is unstable in the absence of MLH1). In the remaining 10 cases, loss of PMS2 expression was likely due to epigenetic overexpression of the microRNA, miR-155, which down-regulates MLH1. | 1 | Biochemistry |
TLRs are present in vertebrates as well as invertebrates. Molecular building blocks of the TLRs are represented in bacteria and in plants, and plant pattern recognition receptors are well known to be required for host defence against infection. The TLRs thus appear to be one of the most ancient, conserved components of the immune system.
In recent years TLRs were identified also in the mammalian nervous system. Members of the TLR family were detected on glia, neurons and on neural progenitor cells in which they regulate cell-fate decision.
It has been estimated that most mammalian species have between ten and fifteen types of toll-like receptors. Thirteen TLRs (named simply TLR1 to TLR13) have been identified in humans and mice together, and equivalent forms of many of these have been found in other mammalian species. However, equivalents of certain TLR found in humans are not present in all mammals. For example, a gene coding for a protein analogous to TLR10 in humans is present in mice, but appears to have been damaged at some point in the past by a retrovirus. On the other hand, mice express TLRs 11, 12, and 13, none of which is represented in humans. Other mammals may express TLRs that are not found in humans. Other non-mammalian species may have TLRs distinct from mammals, as demonstrated by the anti-cell-wall TLR14, which is found in the Takifugu pufferfish. This may complicate the process of using experimental animals as models of human innate immunity.
Vertebrate TLRs are divided by similarity into the families of TLR 1/2/6/10/14/15, TLR 3, TLR 4, TLR 5, TLR 7/8/9, and TLR 11/12/13/16/21/22/23. | 1 | Biochemistry |
The formation of amide is promoted by CDI. Although the reactivity of CDI is less than acid chlorides, it is more easily handled and avoids the use of thionyl chloride in acid chloride formation, which can cause side reactions. An early application of this type of reaction was noted in the formation of peptide bonds (with CO formation as a driving force). The proposed mechanism for the reaction between a carboxylic acid and CDI is presented below.
In the realm of peptide synthesis, this product may be treated with an amine such as that found on an amino acid to release the imidazole group and couple the peptides. The side products, carbon dioxide and imidazole, are relatively innocuous. Racemization of the amino acids also tends to be minimal, reflecting the mild reaction conditions.
CDI can also be used for esterification, although alcoholysis requires heat or the presence of a potent nucleophiles as sodium ethoxide, or other strong bases like NaH. This reaction has generally good yield and wide scope, although forming the ester from tertiary alcohols when the acid reagent has a relatively acidic α-proton is troublesome, since C-C condensations can occur, though this itself may be a desirable reaction. A similar reaction involving thiols and selenols can yield the corresponding esters. The alcohol reaction can also be used to form glycosidic bonds.
Similarly, an acid can be used in the place of an alcohol to form the anhydride, although dicyclohexylcarbodiimide is a more typical reagent. The equilibrium can be shifted in the favor of the anhydride by utilizing an acid in a 2:1 ratio that forms an insoluble salt with the imidazole. Typical acids are trifluoro- and trichloroacetic acids. Symmetric anhydrides can thus be formed by replacing this trifluoro- or trichloroacetyl group with the acid that was used to form the original reagent.
Another related reaction is the reaction of formic acid with CDI to form the formylized imidazole. This reagent is a good formylating agent and can regenerate the unsubstituted imidazole (with formation of carbon monoxide) upon heating.
Yet another reaction involves the acylation of triphenylalkelynephosphoranes.
::(CH)P=CHR + R-CO-Im → (CH)P-CHR-COR + ImH)P-CHR-COR + (CH)P=CHR → (CH)P=CR-COR + (CH)P-CHR
These can undergo the Wittig reaction to form α,β unsaturated ketones or aldehydes.
The reagent can even undergo reaction with peroxide to form the peroxycarboxylic acid, which can react further to form diacyl peroxides. The imidazole group is also reduced by LiAlH to form aldehydes from the carboxylic acid (rather than amines or alcohols). The reagent can also be reacted with Grignard reagents to form ketones.
A C-C acylation reaction can occur with a malonic ester-type compound, in the following scheme useful for syntheses of macrolide antibiotics. | 0 | Organic Chemistry |
British physician George Oliver and physiologist Edward Albert Schäfer, professor at University College London, collaborated on the physiological effects of adrenal extracts. They first published their findings in two reports in 1894, a full publication followed in 1895. Though frequently falsely attributed to secretin, found in 1902 by Bayliss and Starling, Oliver and Schäfer's adrenal extract containing adrenaline, the substance causing the physiological changes, was the first hormone to be discovered. The term hormone would later be coined by Starling. | 1 | Biochemistry |
Three explanations are frequently used to explain the series:
#The ionic radius is expected to decrease regularly from Mn(II) to Zn(II). This is the normal periodic trend and would account for the general increase in stability.
#The crystal field stabilization energy (CFSE) increases from zero for Mn(II) to a maximum at Ni(II). This makes the complexes increasingly stable. CFSE for Zn(II) is zero.
#Although the CFSE of Cu(II) is less than that of Ni(II), octahedral Cu(II) complexes are subject to the Jahn–Teller effect, which affords octahedral Cu(II) complexes additional stability.
However, none of the above explanations can satisfactorily explain the success of the Irving–Williams series in predicting the relative stabilities of transition metal complexes. A recent study of metal-thiolate complexes indicates that an interplay between covalent and electrostatic contributions in metal–ligand binding energies might result in the Irving–Williams series.
Some actual CFSE values for octahedral complexes of first-row transition metals (∆) are 0.4Δ (4 Dq) for iron, 0.8Δ (8 Dq) for cobalt and 1.2Δ (12 Dq) for nickel. When the stability constants are quantitatively adjusted for these values they follow the trend that is predicted, in the absence of crystal field effects, between manganese and zinc. This was an important factor contributing to the acceptance of crystal field theory, the first theory to successfully account for the thermodynamic, spectroscopic and magnetic properties of complexes of the transition metal ions and precursor to ligand field theory.
Natural proteins affinities for metal binding also follow the Irving–Williams series. However, in a recent study published in the journal Nature', researchers have reported a protein-design approach to overcome the Irving-Williams series restriction, allowing proteins to bind other metals over copper ions vice versa to Irving–Williams series. | 7 | Physical Chemistry |
TGA can be used to evaluate the thermal stability of a material. In a desired temperature range, if a species is thermally stable, there will be no observed mass change. Negligible mass loss corresponds to little or no slope in the TGA trace. TGA also gives the upper use temperature of a material. Beyond this temperature the material will begin to degrade.
TGA is used in the analysis of polymers. Polymers usually melt before they decompose, thus TGA is mainly used to investigate the thermal stability of polymers. Most polymers melt or degrade before 200 °C. However, there is a class of thermally stable polymers that are able to withstand temperatures of at least 300 °C in air and 500 °C in inert gases without structural changes or strength loss, which can be analyzed by TGA. | 7 | Physical Chemistry |
The synthesis of the pyrimidines CTP and UTP occurs in the cytoplasm and starts with the formation of carbamoyl phosphate from glutamine and CO. Next, aspartate carbamoyltransferase catalyzes a condensation reaction between aspartate and carbamoyl phosphate to form carbamoyl aspartic acid, which is cyclized into 4,5-dihydroorotic acid by dihydroorotase. The latter is converted to orotate by dihydroorotate oxidase. The net reaction is:
:(S)-Dihydroorotate + O → Orotate + HO
Orotate is covalently linked with a phosphorylated ribosyl unit. The covalent linkage between the ribose and pyrimidine occurs at position C of the ribose unit, which contains a pyrophosphate, and N of the pyrimidine ring. Orotate phosphoribosyltransferase (PRPP transferase) catalyzes the net reaction yielding orotidine monophosphate (OMP):
:Orotate + 5-Phospho-α-D-ribose 1-diphosphate (PRPP) → Orotidine 5'-phosphate + Pyrophosphate
Orotidine 5-monophosphate is decarboxylated by orotidine-5-phosphate decarboxylase to form uridine monophosphate (UMP). PRPP transferase catalyzes both the ribosylation and decarboxylation reactions, forming UMP from orotic acid in the presence of PRPP. It is from UMP that other pyrimidine nucleotides are derived. UMP is phosphorylated by two kinases to uridine triphosphate (UTP) via two sequential reactions with ATP. First, the diphosphate from UDP is produced, which in turn is phosphorylated to UTP. Both steps are fueled by ATP hydrolysis:
:ATP + UMP → ADP + UDP
:UDP + ATP → UTP + ADP
CTP is subsequently formed by the amination of UTP by the catalytic activity of CTP synthetase. Glutamine is the NH donor and the reaction is fueled by ATP hydrolysis, too:
:UTP + Glutamine + ATP + HO → CTP + ADP + P
Cytidine monophosphate (CMP) is derived from cytidine triphosphate (CTP) with subsequent loss of two phosphates. | 1 | Biochemistry |
In general, photosynthesis in cyanobacteria uses water as an electron donor and produces oxygen as a byproduct, though some may also use hydrogen sulfide a process which occurs among other photosynthetic bacteria such as the purple sulfur bacteria.
Carbon dioxide is reduced to form carbohydrates via the Calvin cycle. The large amounts of oxygen in the atmosphere are considered to have been first created by the activities of ancient cyanobacteria. They are often found as symbionts with a number of other groups of organisms such as fungi (lichens), corals, pteridophytes (Azolla), angiosperms (Gunnera), etc. The carbon metabolism of cyanobacteria include the incomplete Krebs cycle, the pentose phosphate pathway, and glycolysis.
There are some groups capable of heterotrophic growth, while others are parasitic, causing diseases in invertebrates or algae (e.g., the black band disease). | 5 | Photochemistry |
For a given cation, Pauling defined the electrostatic bond strength to each coordinated anion as , where z is the cation charge and ν is the cation coordination number. A stable ionic structure is arranged to preserve local electroneutrality, so that the sum of the strengths of the electrostatic bonds to an anion equals the charge on that anion.
where is the anion charge and the summation is over the adjacent cations. For simple solids, the are equal for all cations coordinated to a given anion, so that the anion coordination number is the anion charge divided by each electrostatic bond strength. Some examples are given in the table.
Pauling showed that this rule is useful in limiting the possible structures to consider for more complex crystals such as the aluminosilicate mineral orthoclase, , with three different cations. However, from data analysis of oxides from the Inorganic Crystal Structure Database (ICSD), the result showed that only 20% of all oxygen atoms matched with the prediction from second rule (using a cutoff of 0.01). | 4 | Stereochemistry |
AMPylation is involved in bacterial homeostasis. The most famous example is AMPylator GS-ATase (GlnE), which contributes in complex regulation of nitrogen metabolism through AMPylation of glutamine synthetase that was introduced in the AMPylation and DeAMPylation parts.
Another example of AMPylators that play a role in bacterial homeostasis is the class I Fic AMPylators (FicT), which modifies the GyrB subunit of DNA gyrase, the conserved tyrosine residue for ATP binding of ParE subunit at Topoisomerase IV. This DNA gyrase inactivation by AMPylation leads to the activation of SOS response, which is the cellular response to DNA damage. The activity of FicT AMPylation is reversible and only leads to growth arrest, but not cell death. Therefore, FicT AMPylation plays a role in regulating cell stress, which is shown in the Wolbachia bacteria that the level of FicT increases in response to doxycycline.
A Class III Fic AMPylator NmFic of N. meningtidis is also found to modify AMPylate GyrB at the conserved tyrosine for ATP binding. This shows that Fic domains are highly conserved that indicates the important role of AMPylation in regulating cellular stress in bacteria. The regulation of NmFic involves the concentration-dependent monomerization and autoAMPylation for activation of NmFic activity. | 1 | Biochemistry |
The organization of the DNA that is achieved by the nucleosome cannot fully explain the packaging of DNA observed in the cell nucleus. Further compaction of chromatin into the cell nucleus is necessary, but it is not yet well understood. The current understanding is that repeating nucleosomes with intervening "linker" DNA form a 10-nm-fiber, described as "beads on a string", and have a packing ratio of about five to ten. A chain of nucleosomes can be arranged in a 30 nm fiber, a compacted structure with a packing ratio of ~50 and whose formation is dependent on the presence of the H1 histone.
A crystal structure of a tetranucleosome has been presented and used to build up a proposed structure of the 30 nm fiber as a two-start helix.
There is still a certain amount of contention regarding this model, as it is incompatible with recent electron microscopy data. Beyond this, the structure of chromatin is poorly understood, but it is classically suggested that the 30 nm fiber is arranged into loops along a central protein scaffold to form transcriptionally active euchromatin. Further compaction leads to transcriptionally inactive heterochromatin. | 1 | Biochemistry |
The principal components of volcanic gases are water vapor (HO), carbon dioxide (CO), sulfur either as sulfur dioxide (SO) (high-temperature volcanic gases) or hydrogen sulfide (HS) (low-temperature volcanic gases), nitrogen, argon, helium, neon, methane, carbon monoxide and hydrogen. Other compounds detected in volcanic gases are oxygen (meteoric), hydrogen chloride, hydrogen fluoride, hydrogen bromide, sulfur hexafluoride, carbonyl sulfide, and organic compounds. Exotic trace compounds include mercury, halocarbons (including CFCs), and halogen oxide radicals.
The abundance of gases varies considerably from volcano to volcano, with volcanic activity and with tectonic setting. Water vapour is consistently the most abundant volcanic gas, normally comprising more than 60% of total emissions. Carbon dioxide typically accounts for 10 to 40% of emissions.
Volcanoes located at convergent plate boundaries emit more water vapor and chlorine than volcanoes at hot spots or divergent plate boundaries. This is caused by the addition of seawater into magmas formed at subduction zones. Convergent plate boundary volcanoes also have higher HO/H, HO/CO, CO/He and N/He ratios than hot spot or divergent plate boundary volcanoes. | 2 | Environmental Chemistry |
For symmetric rotors a quantum number J is associated with the total angular momentum of the molecule. For a given value of J, there is a 2J+1- fold degeneracy with the quantum number, M taking the values +J ...0 ... -J. The third quantum number, K is associated with rotation about the principal rotation axis of the molecule. In the absence of an external electrical field, the rotational energy of a symmetric top is a function of only J and K and, in the rigid rotor approximation, the energy of each rotational state is given by
where and for a prolate symmetric top molecule or for an oblate molecule.
This gives the transition wavenumbers as
which is the same as in the case of a linear molecule. With a first order correction for centrifugal distortion the transition wavenumbers become
The term in D has the effect of removing degeneracy present in the rigid rotor approximation, with different K values. | 7 | Physical Chemistry |
As thiolated polymers exhibit biocompatibility, cellular mimicking properties and efficiently support proliferation and differentiation of various cell types, they are used as scaffolds for tissue engineering. Furthermore thiolated polymers such as thiolated hyaluronic acid and thiolated chitosan were shown to exhibit wound healing properties. | 7 | Physical Chemistry |
AFM operation is usually described as one of three modes, according to the nature of the tip motion: contact mode, also called static mode (as opposed to the other two modes, which are called dynamic modes); tapping mode, also called intermittent contact, AC mode, or vibrating mode, or, after the detection mechanism, amplitude modulation AFM; and non-contact mode, or, again after the detection mechanism, frequency modulation AFM.
Despite the nomenclature, repulsive contact can occur or be avoided both in amplitude modulation AFM and frequency modulation AFM, depending on the settings. | 6 | Supramolecular Chemistry |
The Gilman test is a chemical test for the detection of Grignard reagents and organolithium reagents.
A 0.5 mL sample is added to a 1% solution of Mischler's ketone in benzene or toluene. To this solution is added 1 mL of water for hydrolysis to take place and then several drops of 0.2% iodine in glacial acetic acid. If the color of the resulting solution becomes a greenish-blue then the original sample did contain the organometallic species. | 3 | Analytical Chemistry |
Phenol extraction is a processing technology used to prepare phenols as raw materials, compounds or additives for industrial wood processing and for chemical industries.
Extraction can be performed using different solvents. There is a risk that polyphenol oxidase (PPO) degrades the phenolic content of the sample therefore there is a need to use PPO inhibitors like potassium dithionite (KSO) or to perform experiment using liquid nitrogen or to boil the sample for a few seconds (blanching) to inactivate the enzyme. Further fractionation of the extract can be achieved using solid phase extraction columns, and may lead to isolation of individual compounds.
The recovery of natural phenols from biomass residue is part of biorefining. | 0 | Organic Chemistry |
Most aquatic habitats are occupied by fish or other animals requiring certain minimum dissolved oxygen concentrations to survive. Dissolved oxygen concentrations may be measured directly in wastewater, but the amount of oxygen potentially required by other chemicals in the wastewater is termed as oxygen demand. Dissolved or suspended oxidizable organic material in wastewater will be used as a food source. Finely divided material is readily available to microorganisms whose populations will increase to digest the amount of food available. Digestion of this food requires oxygen, so the oxygen content of the water will ultimately be decreased by the amount required to digest the dissolved or suspended food. Oxygen concentrations may fall below the minimum required by aquatic animals if the rate of oxygen utilization exceeds replacement by atmospheric oxygen.
Basically, the reaction for biochemical oxidation may be written as:
:Oxidizable material + bacteria + nutrient + O → CO + HO + oxidized inorganics such as or
Oxygen consumption by reducing chemicals such as sulfides and nitrites is typified as follows:
:S + 2 O →
: + O → | 3 | Analytical Chemistry |
Rutledge received his BSc in chemistry and biochemistry from the University of Auckland in 1993. He received his MSc from the same institution with first class honours in chemistry in 1995. He left New Zealand in 1995 and obtained his DPhil at Magdalen College, Oxford working with Jack Edward Baldwin in 1999. He was a postdoctoral research fellow at the same institution until 2003. | 0 | Organic Chemistry |
In molecular genetics, an untranslated region (or UTR) refers to either of two sections, one on each side of a coding sequence on a strand of mRNA. If it is found on the 5 side, it is called the 5 UTR (or leader sequence), or if it is found on the 3 side, it is called the 3 UTR (or trailer sequence). mRNA is RNA that carries information from DNA to the ribosome, the site of protein synthesis (translation) within a cell. The mRNA is initially transcribed from the corresponding DNA sequence and then translated into protein. However, several regions of the mRNA are usually not translated into protein, including the 5 and 3 UTRs.
Although they are called untranslated regions, and do not form the protein-coding region of the gene, uORFs located within the 5' UTR can be translated into peptides.
The 5 UTR is upstream from the coding sequence. Within the 5 UTR is a sequence that is recognized by the ribosome which allows the ribosome to bind and initiate translation. The mechanism of translation initiation differs in prokaryotes and eukaryotes. The 3 UTR is found immediately following the translation stop codon. The 3 UTR plays a critical role in translation termination as well as post-transcriptional modification.
These often long sequences were once thought to be useless or junk mRNA that has simply accumulated over evolutionary time. However, it is now known that the untranslated region of mRNA is involved in many regulatory aspects of gene expression in eukaryotic organisms. The importance of these non-coding regions is supported by evolutionary reasoning, as natural selection would have otherwise eliminated this unusable RNA.
It is important to distinguish the 5 and 3 UTRs from other non-protein-coding RNA. Within the coding sequence of pre-mRNA, there can be found sections of RNA that will not be included in the protein product. These sections of RNA are called introns. The RNA that results from RNA splicing is a sequence of exons. The reason why introns are not considered untranslated regions is that the introns are spliced out in the process of RNA splicing. The introns are not included in the mature mRNA molecule that will undergo translation and are thus considered non-protein-coding RNA. | 1 | Biochemistry |
To produce a ton of steel in an electric arc furnace requires approximately 400 kilowatt-hours (1.44 gigajoules) per short ton or about 440 kWh (1.6 GJ) per tonne. The theoretical minimum amount of energy required to melt a tonne of scrap steel is 300 kWh (1.09 GJ) (melting point ). Therefore, a 300-tonne, 300 MVA EAF will require approximately 132 MWh of energy to melt the steel, and a "power-on time" (the time that steel is being melted with an arc) of approximately 37 minutes.
Electric arc steelmaking is only economical where there is plentiful, reliable electricity, with a well-developed electrical grid. In many locations, mills operate during off-peak hours when utilities have surplus power generating capacity and the price of electricity is less. This compares very favourably with energy consumption of global steel production by all methods estimated at some 5,555 kWh (20 GJ) per tonne (1 gigajoule is equal to approximately 270 kWh). | 8 | Metallurgy |
Plasma electron temperatures can range between ~6,000 K and ~10,000 K and are usually several orders of magnitude greater than the temperature of the neutral species. Argon ICP plasma discharge temperatures are typically ~5,500 to 6,500 K and are therefore comparable to that reached at the surface (photosphere) of the sun (~4,500 K to ~6,000 K). ICP discharges are of relatively high electron density, on the order of 10 cm. As a result, ICP discharges have wide applications where a high-density plasma (HDP) is needed.
* ICP-AES, a type of atomic emission spectroscopy.
* ICP-MS, a type of mass spectrometry.
* ICP-RIE, a type of reactive-ion etching.
Another benefit of ICP discharges is that they are relatively free of contamination, because the electrodes are completely outside the reaction chamber. By contrast, in a capacitively coupled plasma (CCP), the electrodes are often placed inside the reactor and are thus exposed to the plasma and subsequent reactive chemical species. | 7 | Physical Chemistry |
Dechelation (or de-chelation) is a reverse process of the chelation in which the chelating agent is recovered by acidifying solution with a mineral acid to form a precipitate. | 7 | Physical Chemistry |
Some countries use the International Maximum Residue Limits -Codex Alimentarius to define the residue limits; this was established by Food and Agriculture Organization of the United Nations (FAO) and World Health Organization (WHO) in 1963 to develop international food standards, guidelines codes of practices, and recommendation for food safety. Currently the CODEX has 185 Member Countries and 1 member organization (EU).
The following is the list of maximum residue limits (MRLs) for spices adopted by the commission. | 2 | Environmental Chemistry |
* pentacyanopyridine -
* tetracyanopyrazine -
* tricyanotriazine -
* tetracyano-bitriazine -
* dicyanotetrazine -
* hexacyanotrisimidazole -
* hexacyanohexaazatriphenylene - | 0 | Organic Chemistry |
These methods are referred to as reverse genetics. Reverse genetics is an approach to discover the function of a gene by analyzing the phenotypic effects of specific gene sequences obtained by DNA sequencing | 1 | Biochemistry |
In 1999 the laboratory of Prof. Dr. Ben L. Feringa at the University of Groningen, The Netherlands, reported the creation of a unidirectional molecular rotor. Their 360° molecular motor system consists of a bis-helicene connected by an alkene double bond displaying axial chirality and having two stereocenters.
One cycle of unidirectional rotation takes 4 reaction steps. The first step is a low temperature endothermic photoisomerization of the trans (P,P) isomer 1 to the cis (M,M) 2 where P stands for the right-handed helix and M for the left-handed helix. In this process, the two axial methyl groups are converted into two less sterically favorable equatorial methyl groups.
By increasing the temperature to 20 °C these methyl groups convert back exothermally to the (P,P) cis axial groups (3) in a helix inversion. Because the axial isomer is more stable than the equatorial isomer, reverse rotation is blocked. A second photoisomerization converts (P,P) cis 3 into (M,M) trans 4, again with accompanying formation of sterically unfavorable equatorial methyl groups. A thermal isomerization process at 60 °C closes the 360° cycle back to the axial positions.
A major hurdle to overcome is the long reaction time for complete rotation in these systems, which does not compare to rotation speeds displayed by motor proteins in biological systems. In the fastest system to date, with a fluorene lower half, the half-life of the thermal helix inversion is 0.005 seconds. This compound is synthesized using the Barton-Kellogg reaction. In this molecule the slowest step in its rotation, the thermally induced helix-inversion, is believed to proceed much more quickly because the larger tert-butyl group makes the unstable isomer even less stable than when the methyl group is used. This is because the unstable isomer is more destabilized than the transition state that leads to helix-inversion. The different behaviour of the two molecules is illustrated by the fact that the half-life time for the compound with a methyl group instead of a tert-butyl group is 3.2 minutes.
The Feringa principle has been incorporated into a prototype nanocar. The car synthesized has a helicene-derived engine with an oligo (phenylene ethynylene) chassis and four carborane wheels and is expected to be able to move on a solid surface with scanning tunneling microscopy monitoring, although so far this has not been observed. The motor does not perform with fullerene wheels because they quench the photochemistry of the motor moiety. Feringa motors have also been shown to remain operable when chemically attached to solid surfaces. The ability of certain Feringa systems to act as an asymmetric catalyst has also been demonstrated.
In 2016, Feringa was awarded a Nobel prize for his work on molecular motors. | 6 | Supramolecular Chemistry |
The method uses scattering parameters of a material sample embedded in a waveguide, namely and , to calculate permittivity and permeability data. and correspond to the cumulative reflection and transmission coefficient of the sample that are referenced to the each sample end, respectively: these parameters account for the multiple internal reflections inside the sample, which is considered to have a thickness of . The reflection coefficient of the bulk sample is:
where
The sign of the root for the reflection coefficient is chosen appropriately to ensure its passivity (). Similarly, the transmission coefficient of the bulk sample can be written as:
Thus, the effective permeability () and permittivity () of the material can be written as:
where
and
* is the free-space wavelength.
* is the guided mode wavelength of the unfilled transmission line.
* is the cutoff wavelength of the unfilled transmission line
The constitutive relation for admits an infinite number of solutions due to the branches of the complex logarithm. The ambiguity regarding its result can be resolved by taking the group delay into account. | 7 | Physical Chemistry |
Transcriptomics studies generate large amounts of data that have potential applications far beyond the original aims of an experiment. As such, raw or processed data may be deposited in public databases to ensure their utility for the broader scientific community. For example, as of 2018, the Gene Expression Omnibus contained millions of experiments. | 1 | Biochemistry |
Alkenyl- and alkynylaluminates are most commonly generated through the addition of n-butyllithium to the alkenylalane. The alkenyl and alkynyl groups, which are better able to stabilize negative charge, are transferred in preference to the alkyl group. When these intermediates react with alkyl halides, functionalized olefins are produced.
Treatment of alkenylaluminates with halogen electrophiles such as N-bromosuccinimide (NBS) and iodine leads to the formation of halogenated olefins. These products are useful for cross-coupling reactions.
Zirconium-catalyzed carboalumination of alkynes by trimethylalane is a convenient method for accessing substituted alkenylalanes stereoselectively. Upon exposure to aldehydes and ketones, alkenylalanes form secondary or tertiary allylic alcohols. Formaldehyde is a useful reagent in this context for the introduction of a hydroxymethyl unit.
Alkynylalanes are primarily used in place of the corresponding alkali metal acetylides when the latter reagents are ineffective. The coupling of an acetylide and tertiary alkyl halide is an example of a reaction that cannot be accomplished with alkali metal acetylides, which displace halides in an S2 fashion. The corresponding alkynylalanes are able to couple to tertiary halides via an S1-like mechanism.
Alkynyl- and alkenylalanes add in a conjugate fashion to enones in the s-cis conformation without nucleophilic activation. Enones locked in an s-trans conformation, such as cyclohexenone, are unreactive. The coordination of oxygen to aluminium is believed to be necessary for this reaction.
When alkynes and dialkylalanes are combined in a 2:1 ratio, 1,3-dienes result. The aluminium-carbon bond of the initially formed alkenylalane adds across a second molecule of alkyne, forming a conjugated dienylalane. Protonolysis provides the metal-free diene product.
Alkenyl- and alkynylalanes undergo transmetalation to a variety of metals, including boron, zirconium, and mercury. | 0 | Organic Chemistry |
Host response is defined as the "response of the host organism (local and systemic) to the implanted material or device". Most materials will have a reaction when in contact with the human body. The success of a biomaterial relies on the host tissue's reaction with the foreign material. Specific reactions between the host tissue and the biomaterial can be generated through the biocompatibility of the material. | 1 | Biochemistry |
Between 1986 and 1989, she was a post-doctoral fellow at the University of California, San Francisco where she researched prion diseases and published with Stanley Prusiner. In 1989, she was the first author on a paper published in Nature, entitled "Linkage of a prion protein missense variant to Gerstmann‑Sträussler syndrome", describing the discovery of a mutation linked to a neurodegenerative disease. She was the first author on a paper published in 1990 in Science, entitled "Spontaneous neurodegeneration in transgenic mice with mutant prion protein", describing the creation of a transgenic mouse modeling a neurodegenerative disease. According to the Minneapolis Star Tribune, she helped prove Prusiner's theory that prions cause neurodegenerative diseases. Prusiner recognized her contribution towards the Nobel Prize he won for that work, saying that Karen Hsiao "discovered a mutation in the PrP gene that caused familial disease and reproduced the disease in transgenic mice". | 1 | Biochemistry |
The butyrate or butanoate ion, , is the conjugate base of butyric acid. It is the form found in biological systems at physiological pH. A butyric (or butanoic) compound is a carboxylate salt or ester of butyric acid. | 1 | Biochemistry |
Poolman has made seminal contributions to the understanding of the dynamics and permeability of biological membranes and to the field of vectorial biochemistry, that is, the role of electrochemical gradients in the fuelling and regulation of membrane transport. He demonstrated that the exchange of different sugars can be more advantageous for a cell than sugar-proton symport, and showed that cells exploit the coupling of substrate import to product exchange to conserve metabolic energy.
He is an expert in the field of ATP-binding cassette transporters, one of the largest known protein families, by combining functional and structural studies. Highlights include: discovery of export of hydrophobic compounds from the inner leaflet of the lipid bilayer; elucidation of sensing and gating mechanism of ABC importers involved in cell volume regulation; single-molecule fluorescence studies to elucidate the mechanism of solute capture and translocation; structural basis for peptide selection by receptors involved in nitrogen uptake; structural basis for vitamin recognition and transport by a new class of ABC importers; and the energy coupling stoichiometry of ABC importers.
Poolman has advanced of membrane transport by combining mechanistic in vitro studies with in vivo analyses of transporter regulation. His group has developed innovative technologies in membrane reconstitution and the probing of the physicochemical state of both the cytoplasm and the cell membrane. His group was the first to show that changes in the ionic strength are used to gate the activity of osmoregulatory transporters, providing the cell with a simple on/off switch to control its cytoplasmic volume. In parallel, his group developed sensors to quantify changes in ionic strength and excluded volume (macromolecular crowding). | 0 | Organic Chemistry |
RNA molecules that do not code for any proteins still maintain a function in the cell. The function of the RNA depends on its classification. These roles include:
* aiding protein synthesis
* catalyzing reactions
* regulating various processes.
Protein synthesis is aided by functional RNA molecules such as tRNA, which helps add the correct amino acid to a polypeptide chain during translation, rRNA, a major component of ribosomes (which guide protein synthesis), as well as mRNA which carry the instructions for creating the protein product.
One type of functional RNA involved in regulation are microRNA (miRNA), which works by repressing translation. These miRNAs work by binding to a complementary target mRNA sequence to prevent translation from occurring. Short-interfering RNA (siRNA) also work by negative regulation of transcription. These siRNA molecules work in RNA-induced silencing complex (RISC) during RNA interference by binding to a target DNA sequence to prevent transcription of a specific mRNA. | 1 | Biochemistry |
The relationship below provides a way to determine the volume-based concentration of any individual gaseous component
where c is the concentration of component i.
Dalton's law is not strictly followed by real gases, with the deviation increasing with pressure. Under such conditions the volume occupied by the molecules becomes significant compared to the free space between them. In particular, the short average distances between molecules increases intermolecular forces between gas molecules enough to substantially change the pressure exerted by them, an effect not included in the ideal gas model. | 7 | Physical Chemistry |
* Association studies can determine whether a genetic variant is associated with a disease or trait.
* A tag SNP is a representative single-nucleotide polymorphism in a region of the genome with high linkage disequilibrium (the non-random association of alleles at two or more loci). Tag SNPs are useful in whole-genome SNP association studies, in which hundreds of thousands of SNPs across the entire genome are genotyped.
* Haplotype mapping: sets of alleles or DNA sequences can be clustered so that a single SNP can identify many linked SNPs.
* Linkage disequilibrium (LD), a term used in population genetics, indicates non-random association of alleles at two or more loci, not necessarily on the same chromosome. It refers to the phenomenon that SNP allele or DNA sequence that are close together in the genome tend to be inherited together. LD can be affected by two parameters (among other factors, such as population stratification): 1) The distance between the SNPs [the larger the distance, the lower the LD]. 2) Recombination rate [the lower the recombination rate, the higher the LD].
* In genetic epidemiology SNPs are used to estimate transmission clusters. | 1 | Biochemistry |
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