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Ultraviolet-visible(UV-Vis) absorption spectroelectrochemistry is a technique that studies the absorption of electromagnetic radiation in the UV-Vis regions of the spectrum, providing molecular information related to the electronic levels of molecules. It provides qualitative as well as quantitative information. UV-Vis spectroelectrochemistry helps to characterize compounds and materials, determines concentrations and different parameters such as absorptivity coefficients, diffusion coefficients, formal potentials or electron transfer rates. | 7 | Physical Chemistry |
Stereographic projection is also applied to the visualization of polytopes. In a Schlegel diagram, an -dimensional polytope in is projected onto an -dimensional sphere, which is then stereographically projected onto . The reduction from to can make the polytope easier to visualize and understand. | 3 | Analytical Chemistry |
In spectroscopy, the Dicke effect, also known as Dicke narrowing or sometimes collisional narrowing, named after Robert H. Dicke, refers to narrowing of the Doppler broadening of a spectral line due to collisions the emitting species (usually an atom or a molecule) experiences with other particles. | 7 | Physical Chemistry |
Mechanistically, oxidative addition is the step that determines which enantiomer is formed. Chiral ligands on the metal center along with low temperatures are the general tactics employed to produce an enantiopure product. In particular, the careful pairing of ligand classes with the type of nucleophile has proven to be essential. With Grignard reagents, ferrocenyl thiolate, phosphorus, and NHC ligands are typically used. There have also been several methods developed using diorganozinc nucleophiles coupled with phosphorus, amine, peptide, and NHC ligands. The scope of organoaluminium nucleophiles is comparatively smaller, but there have been a couple examples using NHC ligands. There is a need for more studies to better understand the mechanism of stereoinduction to expand the known set of reactions to encompass a larger overall substrate scope and to potentially allow for enantioselectivity at room temperature. | 0 | Organic Chemistry |
The non-recombinants are separated from recombinants; i.e., a r-DNA is introduced in bacteria, some bacteria are successfully transformed some remain non-transformed. When grown on medium containing ampicillin, bacteria die due to lack of ampicillin resistance. The position is later noted on nitrocellulose paper and separated out to move them to nutrient medium for mass production of required product.
An alternative to a selectable marker is a screenable marker which can also be denoted as a reporter gene, which allows the researcher to distinguish between wanted and unwanted cells, e.g. between blue and white colonies. These wanted or unwanted cells are simply un-transformed cells that were unable to take up the gene during the experiment. | 1 | Biochemistry |
Light-emitting diodes (LEDs) can be manufactured to emit radiation in the ultraviolet range. In 2019, following significant advances over the preceding five years, UV‑A LEDs of 365 nm and longer wavelength were available, with efficiencies of 50% at 1.0 W output. Currently, the most common types of UV LEDs are in 395 nm and 365 nm wavelengths, both of which are in the UV‑A spectrum. The rated wavelength is the peak wavelength that the LEDs put out, but light at both higher and lower wavelengths are present.
The cheaper and more common 395 nm UV LEDs are much closer to the visible spectrum, and give off a purple color. Other UV LEDs deeper into the spectrum do not emit as much visible light LEDs are used for applications such as UV curing applications, charging glow-in-the-dark objects such as paintings or toys, and lights for detecting counterfeit money and bodily fluids. UV LEDs are also used in digital print applications and inert UV curing environments. Power densities approaching 3 W/cm (30 kW/m) are now possible, and this, coupled with recent developments by photo-initiator and resin formulators, makes the expansion of LED cured UV materials likely.
UV‑C LEDs are developing rapidly, but may require testing to verify effective disinfection. Citations for large-area disinfection are for non-LED UV sources known as germicidal lamps. Also, they are used as line sources to replace deuterium lamps in liquid chromatography instruments. | 5 | Photochemistry |
A fluorophore's environment can impact quantum yield, usually resulting from changes in the rates of non-radiative decay. Many fluorophores used to label macromolecules are sensitive to solvent polarity. The class of 8-anilinonaphthalene-1-sulfonic acid (ANS) probe molecules are essentially non-fluorescent when in aqueous solution, but become highly fluorescent in nonpolar solvents or when bound to proteins and membranes. The quantum yield of ANS is ~0.002 in aqueous buffer, but near 0.4 when bound to serum albumin. | 7 | Physical Chemistry |
LAGP is one of the most studied solid-state electrolytes for lithium-ion batteries. The use of a solid-state electrolyte improves the battery safety eliminating liquid-based electrolytes, which are flammable and usually unstable above 4.3 V. In addition, it physically separates the anode from the cathode, reducing the risk of short-circuit, and strongly inhibits lithium dendrite growth. Finally, solid-state electrolytes can operate in a wide range of temperatures, with minimum conductivity loss and decomposition issues. Nevertheless, the ionic conductivity of solid-state electrolytes is some orders of magnitude lower than the one of conventional liquid-based electrolytes, therefore a thin electrolyte layer is preferred to reduce the overall internal impedance and to achieve a shorter diffusion path and larger energy densities. Therefore, LAGP is a suitable candidate for all-solid-state thin-film lithium-ion batteries, in which the electrolyte thickness ranges from 1 to some hundreds of micrometres. The good mechanical strength of LAGP effectively suppress lithium dendrites during lithium stripping and plating, reducing the risk of internal short-circuit and battery failure.
LAGP is applied as a solid-state electrolyte both as a pure material and as a component in organic-inorganic composite electrolytes. For example, LAGP can be composited with polymeric materials, like polypropylene (PP) or polyethylene oxide (PEO), to improve the ionic conductivity and to tune the electrochemical stability. Moreover, since LAGP is not fully stable against metallic lithium because of the electrochemical reactivity of Ge cations, additional interlayers can be introduced between the lithium anode and the solid electrolyte to improve the interfacial stability. The addition of a thin layer of metallic germanium inhibits the electrochemical reduction by lithium metal at very negative potentials and promotes the interfacial contact between the anode and the electrolyte, resulting in improved cycling performance and battery stability. The use of polymer-ceramic composite interlayers or the excess of LiO are alternative strategies to improve the electrochemical stability of LAGP at negative potentials.
LAGP has been also tested not only as a solid electrolyte, but also as an anode material in lithium-ion battery, showing high electrochemical stability and good cycling performance. | 7 | Physical Chemistry |
Methylglyoxal is involved in the formation of advanced glycation end products (AGEs). In this process, methylglyoxal reacts with free amino groups of lysine and arginine and with thiol groups of cysteine forming AGEs. Histones are also heavily susceptible to modification by methylglyoxal and these modifications are elevated in breast cancer.
DNA damages are induced by reactive carbonyls, principally methylglyoxal and glyoxal, at a frequency similar to that of oxidative DNA damages. Such damage, referred to as DNA glycation, can cause mutation, breaks in DNA and cytotoxicity. In humans, a protein DJ-1 (also named PARK7), has a key role in the repair of glycated DNA bases. | 1 | Biochemistry |
Transcriptomics is the quantitative science that encompasses the assignment of a list of strings ("reads") to the object ("transcripts" in the genome). To calculate the expression strength, the density of reads corresponding to each object is counted. Initially, transcriptomes were analyzed and studied using expressed sequence tags libraries and serial and cap analysis of gene expression (SAGE).
Currently, the two main transcriptomics techniques include DNA microarrays and RNA-Seq. Both techniques require RNA isolation through RNA extraction techniques, followed by its separation from other cellular components and enrichment of mRNA.
There are two general methods of inferring transcriptome sequences. One approach maps sequence reads onto a reference genome, either of the organism itself (whose transcriptome is being studied) or of a closely related species. The other approach, de novo transcriptome assembly, uses software to infer transcripts directly from short sequence reads and is used in organisms with genomes that are not sequenced. | 1 | Biochemistry |
Rabi resonance method is a technique developed by Isidor Isaac Rabi for measuring the nuclear spin. The atom is placed in a static magnetic field and a perpendicular rotating magnetic field.
We present a classical treatment in here. | 7 | Physical Chemistry |
Single-wavelength ellipsometry employs a monochromatic light source. This is usually a laser in the visible spectral region, for instance, a HeNe laser with a wavelength of 632.8 nm. Therefore, single-wavelength ellipsometry is also called laser ellipsometry. The advantage of laser ellipsometry is that laser beams can be focused on a small spot size. Furthermore, lasers have a higher power than broad band light sources. Therefore, laser ellipsometry can be used for imaging (see below). However, the experimental output is restricted to one set of and values per measurement. Spectroscopic ellipsometry (SE) employs broad band light sources, which cover a certain spectral range in the infrared, visible or ultraviolet spectral region. By that the complex refractive index or the dielectric function tensor in the corresponding spectral region can be obtained, which gives access to a large number of fundamental physical properties. Infrared spectroscopic ellipsometry (IRSE) can probe lattice vibrational (phonon) and free charge carrier (plasmon) properties. Spectroscopic ellipsometry in the near infrared, visible up to ultraviolet spectral region studies the refractive index in the transparency or below-band-gap region and electronic properties, for instance, band-to-band transitions or excitons. | 7 | Physical Chemistry |
Within set concrete there remains some free "calcium hydroxide" (Ca(OH)), which can further dissociate to form Ca and hydroxide (OH) ions". Any water which finds a seepage path through micro cracks and air voids present in concrete, will readily carry the (Ca(OH)) and Ca (depending on solution pH and chemical reaction at the time) to the underside of the structure where leachate solution contacts the atmosphere. Carbon dioxide (CO) from the atmosphere readily diffuses into the leachate and causes a chemical reaction, which precipitates (deposits) calcium carbonate (CaCO) on the outside of the concrete structure. Consisting primarily of CaCO this secondary deposit derived from concrete is known as "calthemite" and can mimic the shapes and forms of cave "speleothems", such as stalactites, stalagmites, flowstone etc. Other trace elements such as iron from rusting reinforcing steel bars may be transported and deposited by the leachate at the same time as the CaCO. This may colour the calthemites orange or red.
The chemistry involving the leaching of calcium hydroxide from concrete can facilitate the growth of calthemites up to ≈200 times faster than cave speleothems due to the different chemical reactions involved. The sight of calthemite is a visual sign that calcium is being leached from the concrete structure and the concrete is gradually degrading.
In very old concrete where the calcium hydroxide has been leached from the leachate seepage path, the chemistry may revert to that similar to "speleothem" chemistry in limestone cave. This is where carbon dioxide enriched rain or seepage water forms a weak carbonic acid, which leaches calcium carbonate (CaCO) from within the concrete structure and carries it to the underside of the structure. When it contacts the atmosphere, carbon dioxide degasses and calcium carbonate is precipitated to create calthemite deposits, which mimic the shapes and forms of speleothems. This degassing chemistry is not common in concrete structures as the leachate can often find new paths through the concrete to access free calcium hydroxide and this reverts the chemistry to that previously mentioned where CO is the reactant. | 8 | Metallurgy |
Prof. Blum began her independent research career in 2006 at the University of California, Irvine (UCI). Blum’s research focuses on the development and mechanistic study of reactions in organic, organometallic, catalytic, and materials chemistry, and on monitoring reaction intermediates by a combination of traditional spectroscopy and fluorescence microscopy methods. While many of her initial independent research publications were based on activated complexes of gold or palladium catalysts, she has more recently focused on borylation reactions to make advanced oxygen-, nitrogen-, or sulfur-containing heterocycles, amenable to pharmaceutical and agricultural derivation. Since starting her independent career, Blum developed single-molecule and single-particle techniques, often borrowed from biological or physical contexts, to study chemical processes, including to observe intermediates in "classical" reactions. Blum was elected Fellow of the American Association for the Advancement of Science (AAAS) in 2017 for distinguished contributions to molecular chemistry, particularly for the development of synthetic methods and of fluorescence microscopy tools to study chemical processes. | 0 | Organic Chemistry |
Smith continued his academic career as an assistant professor at the University of Minnesota in 1980, later becoming associate professor in 1986 and Professor in 2004. In 2011 he served as Distinguished Engineering Education Innovation (EI) Fellow at the Hong Kong University of Science and Technology. He retired from the University of Minnesota in 2011 and between 2006 and 2022 he served as Cooperative Learning Professor of Engineering Education at Purdue University's School of Engineering Education. Also since 2011, he has held positions as an emeritus Professor of Civil, Environmental, and Geo-Engineering, Morse-Alumni Distinguished University Teaching Professor, and Faculty Member at the Technological Leadership Institute at the University of Minnesota. Additionally, in collaboration with Tony Starfield, Alan Wassyng, Sam Sharp, and others, he developed the civil engineering systems and "How to model it" courses for upper division and first-year students, respectively, which, alongside his work in cooperative learning and teamwork with David W. and Roger T. Johnson, led to the creation of the Civil Engineering Project Management course and the Management of Technology Project and Knowledge Management course.
Between 1999 and 2004, he had a split appointment with Michigan State University where he served as a Senior Consultant to the Provost for Faculty Development. At the University of Minnesota, he was the Co-coordinator of the Bush Faculty Development Program for Excellence and Diversity in Teaching from 1996 to 1997, Director of undergraduate studies in the Department of Civil Engineering from 1999 to 2004, and executive co-director and researcher in the STEM Education Research Center from 2012 to 2018. He was inducted into the Michigan Technological University Academy for Engineering Education Leadership in 2018. | 8 | Metallurgy |
For an alternative proof, consider matrix properties. The sum of the diagonal elements of a matrix is called the trace of the matrix. In 2D and 3D every rotation is a planar rotation, and the trace is a function of the angle alone. For a 2D rotation, the trace is 2 cos θ; for a 3D rotation, 1 + 2 cos θ.
Examples
*Consider a 60° (6-fold) rotation matrix with respect to an orthonormal basis in 2D.
:The trace is precisely 1, an integer.
*Consider a 45° (8-fold) rotation matrix.
:The trace is 2/, not an integer.
Selecting a basis formed from vectors that spans the lattice, neither orthogonality nor unit length is guaranteed, only linear independence. However the trace of the rotation matrix is the same with respect to any basis. The trace is a similarity invariant under linear transformations. In the lattice basis, the rotation operation must map every lattice point into an integer number of lattice vectors, so the entries of the rotation matrix in the lattice basis – and hence the trace – are necessarily integers. Similar as in other proofs, this implies that the only allowed rotational symmetries correspond to 1,2,3,4 or 6-fold invariance. For example, wallpapers and crystals cannot be rotated by 45° and remain invariant, the only possible angles are: 360°, 180°, 120°, 90° or 60°.
Example
*Consider a 60° (360°/6) rotation matrix with respect to the oblique lattice basis for a tiling by equilateral triangles.
:The trace is still 1. The determinant (always +1 for a rotation) is also preserved.
The general crystallographic restriction on rotations does not guarantee that a rotation will be compatible with a specific lattice. For example, a 60° rotation will not work with a square lattice; nor will a 90° rotation work with a rectangular lattice. | 3 | Analytical Chemistry |
Consider the simpler case where there are two binding sites. See the scheme shown below. Each site is assumed to bind either molecule of substrate S or product P. The catalytic reaction is shown by the two reactions at the base of the scheme triangle, that is S to P and P to S. The model assumes the binding steps are always at equilibrium. The reaction rate is given by:
Invoking the rapid-equilibrium assumption we can write the various complexes in terms of equilibrium constants to give:
where . The and <math>
\pi and and
Using the author's own notation, if an enzyme has sites that can bind ligand, the form, in the general case, can be shown to be:
The non-cooperative reversible Michaelis-Menten equation can be seen to emerge when we set the Hill coefficient to one.
If the enzyme is irreversible the equation turns into the simple Michaelis-Menten equation that is irreversible. When setting the equilibrium constant to infinity, the equation can be seen to revert to the simpler case where the product inhibits the reverse step.
A comparison has been made between the MWC and reversible Hill equation.
A modification of the reversible Hill equation was published by Westermark et al where modifiers affected the catalytic properties instead. This variant was shown to provide a much better fit for describing the kinetics of muscle phosphofructokinase. | 7 | Physical Chemistry |
The second strategy attempts to deploy multiple NLR genes simultaneously, a breeding strategy known as stacking. Cultivars generated by either DNA-assisted molecular breeding or gene transfer will likely display more durable resistance, because pathogens would have to mutate multiple effector genes. DNA sequencing allows researchers to functionally “mine” NLR genes from multiple species/strains.
The avrBs2 effector gene from Xanthomona perforans is the causal agent of bacterial spot disease of pepper and tomato. The first “effector-rationalized” search for a potentially durable R gene followed the finding that avrBs2 is found in most disease-causing Xanthomonas species and is required for pathogen fitness. The Bs2 NLR gene from the wild pepper, Capsicum chacoense, was moved into tomato, where it inhibited pathogen growth. Field trials demonstrated robust resistance without bactericidal chemicals. However, rare strains of Xanthomonas overcame Bs2-mediated resistance in pepper by acquisition of avrBs2 mutations that avoid recognition but retain virulence. Stacking R genes that each recognize a different core effector could delay or prevent adaptation.
More than 50 loci in wheat strains confer disease resistance against wheat stem, leaf and yellow stripe rust pathogens. The Stem rust 35 (Sr35) NLR gene, cloned from a diploid relative of cultivated wheat, Triticum monococcum, provides resistance to wheat rust isolate Ug99. Similarly, Sr33, from the wheat relative Aegilops tauschii, encodes a wheat ortholog to barley Mla powdery mildew–resistance genes. Both genes are unusual in wheat and its relatives. Combined with the Sr2 gene that acts additively with at least Sr33, they could provide durable disease resistance to Ug99 and its derivatives. | 1 | Biochemistry |
Since it is not possible to measure K for all substances, various models have been developed to allow for their prediction, e.g. Quantitative structure–activity relationships (QSAR) or linear free energy relationships (LFER) such as the Hammett equation.
A variant of the UNIFAC system can also be used to estimate octanol-water partition coefficients. | 7 | Physical Chemistry |
The Ames process was used on August 3, 1942, by a group of chemists led by Frank Spedding and Harley Wilhelm at the Ames Laboratory as part of the Manhattan Project. It is a type of thermite-based purification, which was patented in 1895 by German chemist Hans Goldschmidt. Development of the Ames process came at a time of increased research into mass uranium-metal production. The desire for increased production was motivated by a fear of Nazi Germany's developing nuclear weapons before the Allies. The process originally involved mixing powdered uranium tetrafluoride and powdered magnesium together. This mixture was placed inside an iron pipe that was welded shut on one side and capped shut on another side. This container, called a "bomb" by Spedding, was placed into a furnace. When heated to a temperature of , the contents of the container reacted violently, leaving a 35-gram ingot of pure uranium metal. The process was quickly scaled up; by October 1942 the "Ames Project" was producing metal at a rate of per week. The uranium tetrafluoride and magnesium were sealed in a refractory-lined reactor vessel, still referred to as a "bomb". The thermite reaction was initiated by furnace heating the assembly to ; the large difference in density between slag and metal allowed complete separation in the liquid state, yielding slag-free metal. By July 1943, the production rate exceeded of uranium metal per month. Approximately 1000 tons of uranium ingots were produced at Ames before the process was transferred to industry.
The Ames project received the Army-Navy "E" Award for Excellence in Production on October 12, 1945, signifying 2.5 years of excellence in industrial production of metallic uranium as a vital war material. Iowa State University is unique among educational institutions to have received this award for outstanding service, an honor normally given to industry. | 8 | Metallurgy |
In general, electric (charge) radiation or magnetic (current, magnetic moment) radiation can be classified into multipoles E (electric) or M (magnetic) of order 2, e.g., E1 for electric dipole, E2 for quadrupole, or E3 for octupole. In transitions where the change in angular momentum between the initial and final states makes several multipole radiations possible, usually the lowest-order multipoles are overwhelmingly more likely, and dominate the transition.
The emitted particle carries away angular momentum, with quantum number , which for the photon must be at least 1, since it is a vector particle (i.e., it has total angular momentum quantum number| = 1). Thus, there is no radiation from E0 (electric monopoles) or M0 (magnetic monopoles, which do not seem to exist).
Since the total angular momentum has to be conserved during the transition, we have that
where and its z-projection is given by and where and are, respectively, the initial and final angular momenta of the atom.
The corresponding quantum numbers and (-axis angular momentum) must satisfy
and
Parity is also preserved. For electric multipole transitions
while for magnetic multipoles
Thus, parity does not change for E-even or M-odd multipoles, while it changes for E-odd or M-even multipoles.
These considerations generate different sets of transitions rules depending on the multipole order and type. The expression forbidden transitions is often used, but this does not mean that these transitions cannot occur, only that they are electric-dipole-forbidden. These transitions are perfectly possible; they merely occur at a lower rate. If the rate for an E1 transition is non-zero, the transition is said to be permitted; if it is zero, then M1, E2, etc. transitions can still produce radiation, albeit with much lower transitions rates. The transition rate decreases by a factor of about 1000 from one multipole to the next one, so the lowest multipole transitions are most likely to occur.
Semi-forbidden transitions (resulting in so-called intercombination lines) are electric dipole (E1) transitions for which the selection rule that the spin does not change is violated. This is a result of the failure of LS coupling. | 7 | Physical Chemistry |
* [https://web.archive.org/web/20110103135037/http://www.organicgardeninfo.com/feather-meal.html Organic gardening information] | 9 | Geochemistry |
Failure in the regulation of glyceroneogenesis may lead to type 2 diabetes, a metabolic disorder that results in high levels of blood glucose and blood lipid. Type 2 diabetes, in addition to a decreased sensitivity to insulin, is associated with the overproduction of triglycerides in the liver, due to excessively active glyceroneogenesis and excess release of fatty acids from adipose tissues. Glyceroneogenesis can be regulated by controlling the gene expression of PEPC-K.
Overexpressing PEPC-K in the liver will overproduce triglycerides and elevate the lipid level in the bloodstream, increasing the risk of fatty liver disease (hepatic steatosis). Conversely, in adipose tissue, down-regulated glyceroneogenesis may decrease de novo lipogenesis, increasing the export of free fatty acids to the bloodstream, leading to lipodystrophy. Both of these conditions are highly associated with type 2 diabetes. | 1 | Biochemistry |
The Rüchardt experiment, invented by Eduard Rüchardt, is a famous experiment in thermodynamics, which determines the ratio of the molar heat capacities of a gas, i.e. the ratio of (heat capacity at constant pressure) and (heat capacity at constant volume) and is denoted by (gamma, for ideal gas) or (kappa, isentropic exponent, for real gas). It arises because the temperature of a gas changes as pressure changes.
The experiment directly yields the heat capacity ratio or adiabatic index of the gas, which is the ratio of the heat capacity at constant pressure to heat capacity at constant volume. The results are sometimes also known as the isentropic expansion factor. | 7 | Physical Chemistry |
In the United States and in most European countries creatinine is usually reported in mg/dL, whereas in Canada, Australia, and a few European countries, μmol/L is the usual unit. One mg/dL of creatinine is 88.4 μmol/L.
The typical human reference ranges for serum creatinine are 0.5 mg/dL to 1.0 mg/dL (about 45 μmol/L to 90 μmol/L) for women and 0.7 mg/dL to 1.2 mg/dL (60 μmol/L to 110 μmol/L) for men. The significance of a single creatinine value must be interpreted in light of the patient's muscle mass. Patients with greater muscle mass have higher creatinine concentrations.
The trend of serum creatinine concentrations over time is more important than absolute creatinine concentration.
Serum creatinine concentrations may increase when an ACE inhibitor (ACEI) is taken for heart failure and chronic kidney disease. ACE inhibitors provide survival benefits for patients with heart failure and slow the disease progression in patients with chronic kidney disease. An increase not exceeding 30% is to be expected with ACEI use. Therefore, usage of ACEI should not be stopped unless an increase of serum creatinine exceeded 30% or hyperkalemia develops. | 1 | Biochemistry |
Asymmetric induction (also enantioinduction) describes the preferential formation in a chemical reaction of one enantiomer or diastereoisomer over the other as a result of the influence of a chiral feature present in the substrate, reagent, catalyst or environment. Asymmetric induction is a key element in asymmetric synthesis.
Asymmetric induction was introduced by Hermann Emil Fischer based on his work on carbohydrates. Several types of induction exist.
Internal asymmetric induction makes use of a chiral center bound to the reactive center through a covalent bond and remains so during the reaction. The starting material is often derived from chiral pool synthesis. In relayed asymmetric induction the chiral information is introduced in a separate step and removed again in a separate chemical reaction. Special synthons are called chiral auxiliaries. In external asymmetric induction chiral information is introduced in the transition state through a catalyst of chiral ligand. This method of asymmetric synthesis is economically most desirable. | 4 | Stereochemistry |
*Glutamate is the most common neurotransmitter. Most neurons secrete with glutamate or GABA. Glutamate is excitatory, meaning that the release of glutamate by one cell usually causes adjacent cells to fire an action potential. (Note: Glutamate is chemically identical to the MSG commonly used to flavor food.)
*GABA is an example of an inhibitory neurotransmitter.
* Monoamine neurotransmitters:
**Dopamine is a monoamine neurotransmitter. It plays a key role in the functioning of the limbic system, which is involved in emotional function and control. It also is involved in cognitive processes associated with movement, arousal, executive function, body temperature regulation, and pleasure and reward, and other processes.
**Norepinephrine, also known as noradrenaline, is a monoamine neurotransmitter that is involved in arousal, pain perception, executive function, body temperature regulation, and other processes.
**Epinephrine, also known as adrenaline, is a monoamine neurotransmitter that plays in fight-or-flight response, increases blood flow to muscles, output of the heart, pupil dilation, and glucose.
**Serotonin is a monoamine neurotransmitter that plays a regulatory role in mood, sleep, appetite, body temperature regulation, and other processes.
**Histamine is a monoamine neurotransmitter that is involved in arousal, pain, body temperature regulation, and appetite.
* Trace amines act as neuromodulators in monoamine neurons via binding to TAAR1.
*Acetylcholine assists motor function and is involved in memory.
*Nitric oxide functions as a neurotransmitter, despite being a gas. It is not grouped with the other neurotransmitters because it is not released in the same way.
*Endocannabinoids act in the endocannabinoid system to control neurotransmitter release in a host of neuronal tissues, including the hippocampus, amygdala, basal ganglia, and cerebellum.
* Eicosanoids act as neuromodulators via the Arachidonic acid cascade. | 1 | Biochemistry |
Consider a hydrogel made of polyelectrolytes decorated with weak acid groups that can ionize according to the reaction
is immersed in a salt solution of physiological concentration. The degree of ionization of the polyelectrolytes is then controlled by the and due to the charged nature of and , electrostatic interactions with other ions in the systems. This is effectively a reacting system governed by acid-base equilibrium modulated by electrostatic effects, and is relevant in drug delivery, sea water desalination and dialysis technologies. Due to the elastic nature of the gel, the dispersion of in the system is constrained and hence, there will be a partitioning of salts ions and inside and outside the gel, which is intimately coupled to the polyelectrolyte degree of ionization. This ion partitioning inside and outside the gel is analogous to the partitioning of ions across a semipemerable membrane in classical Donnan theory, but a membrane is not needed here because the gel volume constraint imposed by network elasticity effectively acts its role, in preventing the macroions to pass through the fictitious membrane while allowing ions to pass.
The coupling between the ion partitioning and polyelectrolyte ionization degree is only partially by the classical Donnan theory. As a starting point we can neglect the electrostatic interactions among ions. Then at equilibrium, some of the weak acid sites in the gel would dissociate to form that electrostatically attracts positive charged and salt cations leading to a relatively high concentration of and salt cations inside the gel. But because the concentration of is locally higher, it suppresses the further ionization of the acid sites. This phenomenon is the prediction of the classical Donnan theory. However, with electrostatic interactions, there are further complications to the picture. Consider the case of two adjacent, initially uncharged acid sites are both dissociated to form . Since the two sites are both negatively charged, there will be a charge-charge repulsion along the backbone of the polymer than tends to stretch the chain. This energy cost is high both elastically and electrostatically and hence suppress ionization. Even though this ionization suppression is qualitatively similar to that of Donnan prediction, it is absent without electrostatic consideration and present irrespective of ion partitioning. The combination of both effects as well as gel elasticity determines the volume of the gel at equilibrium. Due to the complexity of the coupled acid-base equilibrium, electrostatics and network elasticity, only recently has such system been correctly recreated in computer simulations. | 7 | Physical Chemistry |
The protein carbaminohemoglobin plays an important role in the transport of carbon dioxide in the blood, and its biologically important in many functions:
# Transport of Carbon Dioxide: This process allows for the transport of carbon dioxide from the tissues to the lungs. It is essential for maintaining the balance of gases in the bloodstream and to guarantee the removal of waste carbon dioxide from the body.
# Buffering Blood pH: The binding of carbon dioxide to hemoglobin plays a part in the buffering of blood pH. When tissues produce carbon dioxide, the increase in acidity is reduced by the formation of bicarbonate ions. This buffering process helps prevent a decrease in pH and helps maintain a stable environment.
# Facilitation of Gas Exchange: Hemoglobin facilitates the exchange of gases in the lungs and tissues. In the lungs, oxygen binds to hemoglobin and carbon dioxide is released. In the tissues, carbon dioxide binds to form carbaminohemoglobin and oxygen is released. This exchange process is important because tissues need oxygen and the removal of carbon dioxide is also necessary. | 1 | Biochemistry |
These multiple forms (isoforms or subtypes) of phosphodiesterase were isolated from rat brain using polyacrylamide gel electrophoresis in the early 1970s by Weiss and coworkers, and were soon afterward shown to be selectively inhibited by a variety of drugs in brain and other tissues, also by Weiss and coworkers.
The potential for selective phosphodiesterase inhibitors to be used as therapeutic agents was predicted in the 1970s by Weiss and coworkers. This prediction has now come to pass in a variety of fields (e.g. sildenafil as a PDE5 inhibitor and Rolipram as a PDE4 inhibitor). | 1 | Biochemistry |
The concept and use of the power spectrum of a signal is fundamental in electrical engineering, especially in electronic communication systems, including radio communications, radars, and related systems, plus passive remote sensing technology. Electronic instruments called spectrum analyzers are used to observe and measure the power spectra of signals.
The spectrum analyzer measures the magnitude of the short-time Fourier transform (STFT) of an input signal. If the signal being analyzed can be considered a stationary process, the STFT is a good smoothed estimate of its power spectral density. | 7 | Physical Chemistry |
* NDSC observations. The [http://www.ndsc.ncep.noaa.gov/ Network for the Detection for Stratospheric Change] (NDSC) is a set of high-quality remote-sounding research stations for observing and understanding the physical and chemical state of the stratosphere. Ozone and key ozone-related chemical compounds and parameters are targeted for measurement. The NDSC is a major component of the international upper atmosphere research effort and has been endorsed by national and international scientific agencies, including the International Ozone Commission, the United Nations Environment Programme (UNEP), and the World Meteorological Organization (WMO). The primary instruments and measurements are: Ozone lidar (vertical profiles of ozone from the tropopause to at least 40 km altitude; in some cases tropospheric ozone will also be measured). Temperature lidar (vertical profiles of temperature from about 30 to 80 km). Aerosol lidar (vertical profiles of aerosol optical depth in the lower stratosphere). Water vapor lidar (vertical profiles of water vapor in the lower stratosphere). Ozone microwave (vertical profiles of stratospheric ozone from 20 to 70 km). HO microwave (vertical profiles water vapor from about 20 to 80 km). ClO microwave (vertical profiles of ClO from about 25 to 45 km, depending on latitude). Ultraviolet/Visible spectrograph (column abundance of ozone, NO, and, at some latitudes, OClO and BrO). Fourier Transform Infrared spectrometer (column abundances of a broad range of species including ozone, HCl, NO, NO, ClONO, and HNO).
* MkIV observations. The [http://mark4sun.jpl.nasa.gov/ MkIV] Interferometer is a Fourier Transform Infra-Red (FTIR) Spectrometer, designed and built at the Jet Propulsion Laboratory in 1984, to remotely sense the composition of the Earth's atmosphere by the technique of solar absorption spectrometry. This was born out of concern that man-made pollutants (e.g. chlorofluorocarbons, aircraft exhaust) might perturb the ozone layer. Since 1984, the MkIV Interferometer has participated in 3 NASA DC-8 polar aircraft campaigns, and has successfully completed 15 balloon flights. In addition, the MkIV Interferometer made over 900 days of ground-based observations from many different locations, including McMurdo, Antarctica in 1986.
* Sonde observations. The [http://www.woudc.org/index_e.html World Ozone and Ultraviolet Radiation Data Centre] (WOUDC) is one of five World Data Centres which are part of the Global Atmosphere Watch (GAW) programme of the World Meteorological Organization (WMO). The WOUDC is operated by the Experimental Studies Division of the Meteorological Service of Canada (MSC) — formerly Atmospheric Environment Service (AES), Environment Canada and is located in Toronto. The WOUDC began as the World Ozone Data Centre (WODC) in 1960 and produced its first data publication of Ozone Data for the World in 1964. In June 1992, the AES agreed to a request from the WMO to add ultraviolet radiation data to the WODC. The Data Centre has since been renamed to the World Ozone and Ultraviolet Radiation Data Centre (WOUDC) with the two component parts: the WODC and the World Ultraviolet Radiation Data Centre (WUDC). | 2 | Environmental Chemistry |
Due to the high potency and clinical need for cancer treatments, epothilones have been the target of many total syntheses. The first group to publish the total synthesis of epothilones was S. J. Danishefsky et al. in 1996. This total synthesis of epothilone A was achieved via an intramolecular ester enolate-aldehyde condensation. Other syntheses of epothilones have been published by Nicolaou, Schinzer, Mulzer, and Carreira. In this approach, key building blocks aldehyde, glycidols, and ketoacid were constructed and coupled to the olefin metathesis precursor via an aldol reaction and then an esterification coupling. Grubbs' catalyst was employed to close the bis terminal olefin of the precursor compound. The resulting compounds were cis- and trans-macrocyclic isomers with distinct stereocenters. Epoxidation of cis- and trans-olefins yield epothilone A and its analogs.
One of the total syntheses of epothilone B is outlined below and was described by the laboratory of K. C. Nicolaou. The retrosynthetic analysis revealed 1, 2, and 3 as the building blocks (Figure 1).
As seen in Figure 2, keto acid 1 was generated from the keto aldehyde that was converted to the silyl ether via asymmetric allylboration and silylation of the resulting alcohol. Ozonolysis of the silyl ether and Lindgren–Pinnick oxidation of the aldehyde afforded the keto acid. Ketone 2 was constructed via Enders alkylation starting from the hydrazone. Ozonolysis, the last step of the Enders alkylation, was followed by reduction of the aldehyde and silylation of the resulting alcohol. Hydrogenolysis of the benzyl ether gave the alcohol, which was oxidized under Swern condition and alkylated with the Grignard reagent to yield the secondary alcohol. Oxidation of this alcohol with the Ley–Griffith reagent gave the desired ketone. Thiazole 3 was synthesized from the ester, which was reduced with diisobutylaluminium hydride, and the aldehyde was reacted with the stabilized ylide in the Wittig reaction. Asymmetric allylboration of the α,β-unsaturated aldehyde and protection of the hydroxy group gave the silyl ether, whose terminal olefin was reacted with osmium tetroxide to a diol that was cleaved with lead tetraacetate to furnish the aldehyde. Reduction, iodination, and treatment with triphenylphosphine led to phosphonium salt.
Fragments 1, 2, and 3 were reacted with each other to deliver epothilone B in an approach including Wittig reaction, aldol reaction, and Yamaguchi esterification (Figure 3). Preparative thin-layer chromatography was used to separate the diastereomers. | 0 | Organic Chemistry |
Before a PSD can be determined, it is vital that a representative sample is obtained. In the case where the material to be analysed is flowing, the sample must be withdrawn from the stream in such a way that the sample has the same proportions of particle sizes as the stream. The best way to do this is to take many samples of the whole stream over a period, instead of taking a portion of the stream for the whole time. In the case where the material is in a heap, scoop or thief sampling needs to be done, which is inaccurate: the sample should ideally have been taken while the powder was flowing towards the heap. After sampling, the sample volume typically needs to be reduced. The material to be analysed must be carefully blended, and the sample withdrawn using techniques that avoid size segregation, for example using a rotary divider. Particular attention must be paid to avoidance of loss of fines during manipulation of the sample. | 7 | Physical Chemistry |
Organic acid anhydrides are prepared in industry by diverse means. Acetic anhydride is mainly produced by the carbonylation of methyl acetate. Maleic anhydride is produced by the oxidation of benzene or butane. Laboratory routes emphasize the dehydration of the corresponding acids. The conditions vary from acid to acid, but phosphorus pentoxide is a common dehydrating agent:
:2 CHCOOH + PO → CHC(O)OC(O)CH + "PO(OH)"
Acid chlorides are also effective precursors:
:CHC(O)Cl + HCONa → HCOCOCH + NaCl
Mixed anhydrides containing the acetyl group are prepared from ketene:
:RCOH + HC=C=O → RCOC(O)CH | 0 | Organic Chemistry |
In the 19th century, a number of people had employed an electric arc to melt iron. Sir Humphry Davy conducted an experimental demonstration in 1810; welding was investigated by Pepys in 1815; Pinchon attempted to create an electrothermic furnace in 1853; and, in 1878–79, Sir William Siemens took out patents for electric furnaces of the arc type.
The first successful and operational furnace was invented by James Burgess Readman in Edinburgh, Scotland, in 1888 and patented in 1889. This was specifically for the creation of phosphorus.
Further electric arc furnaces were developed by Paul Héroult, of France, with a commercial plant established in the United States in 1907. The Sanderson brothers formed The Sanderson Brothers Steel Co. in Syracuse, New York, installing the first electric arc furnace in the U.S. This furnace is now on display at Station Square, Pittsburgh, Pennsylvania.
Initially "electric steel" produced by an electric arc furnace was a specialty product for such uses as machine tools and spring steel. Arc furnaces were also used to prepare calcium carbide for use in carbide lamps. The Stassano electric furnace is an arc type furnace that usually rotates to mix the bath. The Girod furnace is similar to the Héroult furnace.
While EAFs were widely used in World War II for production of alloy steels, it was only later that electric steelmaking began to expand. The low capital cost for a mini-mill—around US$140–200 per ton of annual installed capacity, compared with US$1,000 per ton of annual installed capacity for an integrated steel mill—allowed mills to be quickly established in war-ravaged Europe, and also allowed them to successfully compete with the big United States steelmakers, such as Bethlehem Steel and U.S. Steel, for low-cost, carbon steel "long products" (structural steel, rod and bar, wire, and fasteners) in the U.S. market.
When Nucor—now one of the largest steel producers in the US — entered the market for long steel products in 1969, they used a mini-mill with an EAF as its steelmaking furnace, soon followed by other manufacturers. Whilst Nucor expanded rapidly in the Eastern US, the companies that followed them into mini-mill operations concentrated on local markets for long products, where the EAF allowed the plants to vary production according to local demand. This pattern was followed globally, with EAF steel production primarily used for long products, while integrated mills, using blast furnaces and basic oxygen furnaces, cornered the markets for "flat products"—sheet steel and heavier steel plate. In 1987, Nucor expanded into the flat products market, still using the EAF production method. | 8 | Metallurgy |
Silica gel particles are commonly used as a stationary phase in high-performance liquid chromatography (HPLC) for several reasons, including:
# High surface area: Silica gel particles have a high surface area, allowing direct interactions with solutes or after bonding of variety of ligands for versatile interactions with the sample molecules, leading to better separations.
# Chemical and thermal stability and inertness: Silica gel is chemically stable, as it usually does not react with either the solvents of the mobile phase nor the compounds being separated, resulting in accurate, repeatable and reliable analyses.
# Wide applicability: Silica gel is versatile and can be modified with various functional groups, making it suitable for a wide range of analytes and applications.
# Efficient separation: The unique properties of silica gel particles, combined with their high surface area and controlled average particle diameter pore size, facilitate efficient and precise separation of compounds in HPLC.
# Reproducibility: Silica gel particles can offer high batch-to-batch reproducibility, which is crucial for consistent and reliable HPLC analyses throughout decades.
# Particle diameter and pore size control: Silica gel can be engineered to have specific pore sizes, enabling precise control over separation based on molecular size.
# Cost-effectiveness: Silica is the most abundant element on earth, hence its gel is a cost-effective choice for HPLC applications, making it widely adopted in laboratories.
The United States Pharmacopoeia (USP) has classified HPLC columns by L# types. The most popular column in this classification is an octadecyl carbon chain (C18)-bonded silica (USP classification L1). This is followed by C8-bonded silica (L7), pure silica (L3), cyano-bonded silica (CN) (L10) and phenyl-bonded silica (L11). Note that C18, C8 and phenyl are dedicated reversed-phase stationary phases, while CN columns can be used in a reversed-phase mode depending on analyte and mobile phase conditions. Not all C18 columns have identical retention properties. Surface functionalization of silica can be performed in a monomeric or a polymeric reaction with different short-chain organosilanes used in a second step to cover remaining silanol groups (end-capping). While the overall retention mechanism remains the same, subtle differences in the surface chemistries of different stationary phases will lead to changes in selectivity.
Modern columns have different polarity depending on the ligand bonded to the stationary phase. PFP is pentafluorphenyl. CN is cyano. NH2 is amino. ODS is octadecyl or C18. ODCN is a mixed mode column consisting of C18 and nitrile.
Recent developments in chromatographic supports and instrumentation for liquid chromatography (LC) facilitate rapid and highly efficient separations, using various stationary phases geometries. Various analytical strategies have been proposed, such as the use of silica-based monolithic supports, elevated mobile phase temperatures, and columns packed with sub-3 μm superficially porous particles (fused or solid core) or with sub-2 μm fully porous particles for use in ultra-high-pressure LC systems (UHPLC). | 3 | Analytical Chemistry |
Human endogenous retroviruses (HERV) comprise a significant part of the human genome, with approximately 98,000 ERV elements and fragments making up 5–8%. According to a study published in 2005, no HERVs capable of replication had been identified; all appeared to be defective, containing major deletions or nonsense mutations (not true for HERV-K). This is because most HERVs are merely traces of original viruses, having first integrated millions of years ago. An analysis of HERV integrations is ongoing as part of the 100,000 Genomes Project.
A 2023 study found HERV can become awakened from dormant states and contribute to aging which could be blocked by neutralizing antibodies.
Human endogenous retroviruses were originally discovered when human genomic libraries were screened under low-stringency conditions using either probes from animal retroviruses or by using oligonucleotides with similarity to virus sequences. | 1 | Biochemistry |
A number of examples of molecular mimicry by pathogens, emulating natural endogenous ligands of paired receptors for immune evasion, have been described in the literature. Such interactions are particularly common with the inhibitory members of receptor pairs, bolstering the hypothesis that activating partners are a later evolutionary response to this immune escape strategy.
The first described interaction between a paired receptor and a viral protein identified ILT-2 and ILR-4 (LILRB1 and LILRB2) as targets for herpes simplex virus UL18 protein, which resembles an MHC-I molecule. Variations in susceptibility to mouse cytomegalovirus infection due to differences in Ly49-family paired receptors among mouse strains are well-characterized, and are attributed to the structural resemblance between the viral protein m157 and MHC-I molecules. The pathogenic bacterium Escherichia coli K1 exposes surface polysialic acid molecules that serve as a molecular mimic for the native ligand of the inhibitory receptor Siglec-11, but induces an opposing response through interactions with the paired activating receptor Siglec-16, exemplifying the benefit of activating receptors as defense mechanisms against molecular mimicry by pathogens.
Paired receptors are also used as viral entry receptors by a number of viruses and occasionally as entry mechanisms for other pathogens. Sialylation is common among mammalian cell-surface proteins and a number of pathogens use sialic acid - either self-synthesized or obtained from the host cell - to evade host immunity, including by interacting with inhibitory siglec receptors. | 1 | Biochemistry |
Gaps often remain after initial BAC contig construction. These gaps occur if the Bacterial Artificial Chromosome (BAC) library screened has low complexity, meaning it does not contain a high number of STS or restriction sites, or if certain regions were less stable in cloning hosts and thus underrepresented in the library. If gaps between contigs remain after STS landmark mapping and restriction fingerprinting have been performed, the sequencing of contig ends can be used to close these gaps. This end-sequencing strategy essentially creates a novel STS with which to screen the other contigs. Alternatively, the end sequence of a contig can be used as a primer to primer walk across the gap. | 1 | Biochemistry |
There are several national and international bioanalytical organisations active throughout the world. Often they are part of a bigger organisation, e.g. Bioanalytical Focus Group and Ligand Binding Assay Bioanalytical Focus Group, which are both within the American Association of Pharmaceutical Scientists (AAPS) and FABIAN, a working group of the Analytical Chemistry Section of the Royal Netherlands Chemical Society. The European Bioanalysis Forum (EBF), on the other hand, is independent of any larger society or association. | 3 | Analytical Chemistry |
Some of Naim's recent publications include (but are not limited to):
* Maalouf K, Jia J, Rizk S, Brogden G, Keiser M, Das A, Naim HY A modified lipid composition in Fabry disease leads to an intracellular block of the detergent-resistant membrane-associated dipeptidyl peptidase IV
* Sim L, Willemsma C, Mohan S, Naim HY, Pinto BM, Rose DR Structural basis for substrate selectivity in human maltase-glucoamylase and sucrase-isomaltase N-terminal domains
* Krahn MP, Rizk S, Alfalah M, Behrendt M, Naim HY Protocadherin of the liver, kidney and colon associates with detergent-resistant membranes during cellular differentiation
* Zimmer KP, Fischer I, Mothes T, Weissen-Plenz G, Schmitz M, Wieser H, Mendez E, Buening J, Lerch MM, Ciclitira PC, Weber P, Naim HY Endocytotic Segregation of Gliadin Peptide 31-49 in Enterocytes
* Behrendt M, Polaina J, Naim HY Structural hierarchy of regulatory elements in the folding and transport of an intestinal multi-domain protein | 1 | Biochemistry |
The steric factor, usually denoted ρ, is a quantity used in collision theory.
Also called the probability factor, the steric factor is defined as the ratio between the experimental value of the rate constant and the one predicted by collision theory. It can also be defined as the ratio between the pre-exponential factor and the collision frequency, and it is most often less than unity. Physically, the steric factor can be interpreted as the ratio of the cross section for reactive collisions to the total collision cross section.
Usually, the more complex the reactant molecules, the lower the steric factors. Nevertheless, some reactions exhibit steric factors greater than unity: the harpoon reactions, which involve atoms that exchange electrons, producing ions. The deviation from unity can have different causes: the molecules are not spherical, so different geometries are possible; not all the kinetic energy is delivered into the right spot; the presence of a solvent (when applied to solutions); and so on.
When collision theory is applied to reactions in solution, the solvent cage has an effect on the reactant molecules, as several collisions can take place in a single encounter, which leads to predicted preexponential factors being too large. ρ values greater than unity can be attributed to favorable entropic contributions.
Usually there is no simple way to accurately estimate steric factors without performing trajectory or scattering calculations. It is also more commonly known as the frequency factor. | 7 | Physical Chemistry |
In coordination chemistry, the ligand cone angle (θ) is a measure of the steric bulk of a ligand in a transition metal coordination complex. It is defined as the solid angle formed with the metal at the vertex of a cone and the outermost edge of the van der Waals spheres of the ligand atoms at the perimeter of the base of the cone. Tertiary phosphine ligands are commonly classified using this parameter, but the method can be applied to any ligand. The term cone angle was first introduced by Chadwick A. Tolman, a research chemist at DuPont. Tolman originally developed the method for phosphine ligands in nickel complexes, determining them from measurements of accurate physical models. | 4 | Stereochemistry |
Unlike denitrification, which removes reactive nitrogen from the system under gaseous form (as N or NO), dissimilatory nitrate reduction to ammonium conserves nitrogen as dissolved species within the system. Since DNRA takes nitrate and converts it into ammonium, it does not produce N or NO gases. Consequently, DNRA recycles nitrogen rather than causing gaseous-N loss, which leads to more sustainable primary production and nitrification.
Within an ecosystem, denitrification and DNRA can occur simultaneously. Usually DNRA is about 15% of the total nitrate reduction rate, which includes both DNRA and denitrification. However, the relative importance of each process is influenced by environmental variables. For example, DNRA is found to be three to seven times higher in sediments under fish cages than nearby sediments due to the accumulation of organic carbon.
Conditions where dissimilatory nitrate reduction to ammonium is favoured over denitrification in marine coastal ecosystems include the following:
* High carbon loads and high sulfate reduction rates (e.g. areas of coastal or river runoff)
* Unvegetated subtidal sediment
* Marshes with high temperatures and sulfate reduction rates (producing high levels of sulfides), e.g. mangroves
* High organic matter deposition (e.g. aquacultures)
* Ecosystems where organic matter has a high C/N ratio
* High electron donor (organic carbon) to acceptor (nitrate) ratio
* High summer temperatures and low NO concentrations
High sulfide concentration can inhibit the processes of nitrification and denitrification. Meanwhile, it can also enhance dissimilatory nitrate reduction to ammonium since high sulfide concentration provides more electron donors.
Ecosystems where DNRA is dominant have less nitrogen loss, resulting in higher levels of preserved nitrogen in the system. Within sediments, the total dissimilatory nitrate reduction to ammonium rate is higher in spring and summer compared to autumn. Prokaryotes are the major contributors for DNRA during summer, while eukaryotes and prokaryotes contribute similarly to DNRA during spring and autumn.
Potential benefits of using dissimilatory nitrate reduction to ammonium for individual organisms may include the following:
* Detoxification of accumulated nitrite: if an enzyme uses nitrate as an electron acceptor and produces nitrite, it can result in high levels of intracellular nitrite concentrations that can be toxic to the cell. DNRA does not store nitrite within the cell, reducing the level of toxicity.
* DNRA produces an electron sink that can be used for NADH re-oxidation into NAD: the need for having an electron sink is more apparent when the environment is nitrate-limited. | 1 | Biochemistry |
When α chains of laminin-111 bind to cell surface receptors integrins α1β1, α3β1, α4β1, α6β1 and Cdc42 GTPase are activated. The activated GTPase then activates Cdc42 which further activates c-Jun kinases and phosphorylation of Jun. Activation of c-Jun kinases leads to high levels of c-Jun expression which results in neurite outgrowth. The synthesis of Nitric Oxides resides somewhere in the pathway and is yet to be determined. Weston et al. (2000) proposed that the synthesis of Nitric Oxide may be upstream to the activation of Cdc42. Nonetheless, Nitric Oxide synthesis is shown to be an important element in laminin-mediated neurite outgrowth. | 0 | Organic Chemistry |
Bawendi received both an A.B. in 1982 and an A.M. in 1983 from Harvard University. He earned a Ph.D. in chemistry in 1988 from the University of Chicago, under the supervision of Karl Freed and Takeshi Oka.
With Freed, Bawendi worked on theoretical polymer physics, and with Oka, Bawendi worked on experiments on hot-bands of H, which played a role in deciphering the emission spectrum of Jupiter observed in 1989.
During his graduate studies, Oka recommended Bawendi to a summer program in Bell Labs, where Louis E. Brus introduced Bawendi to the research on quantum dots. Upon graduation, Bawendi went to work with Brus at Bell Labs as a postdoctoral researcher.
Bawendi joined Massachusetts Institute of Technology (MIT) in 1990 and became professor in 1996. | 7 | Physical Chemistry |
The corrosion resistance of a stainless steel is dependent on the presence of an ultra-thin protective oxide film (passive film) on its surface, but it is possible under certain conditions for this oxide film to break down, for example in halide solutions or reducing acids. Areas where the oxide film can break down can also sometimes be the result of the way components are designed, for example under gaskets, in sharp re-entrant corners or associated with incomplete weld penetration or overlapping surfaces. These can all form crevices which can promote corrosion. To function as a corrosion site, a crevice has to be of sufficient width to permit entry of the corrodent, but narrow enough to ensure that the corrodent remains stagnant. Accordingly crevice corrosion usually occurs in gaps a few micrometres wide, and is not found in grooves or slots in which circulation of the corrodent is possible. This problem can often be overcome by paying attention to the design of the component, in particular to avoiding formation of crevices or at least keeping them as open as possible. Crevice corrosion is a very similar mechanism to pitting corrosion; alloys resistant to one are generally resistant to both. Crevice corrosion can be viewed as a less severe form of localized corrosion when compared with pitting. The depth of penetration and the rate of propagation in pitting corrosion are significantly greater than in crevice corrosion.
Crevices can develop a local chemistry which is very different from that of the bulk fluid. For example, in boilers, concentration of non-volatile impurities may occur in crevices near heat-transfer surfaces because of the continuous water vaporization. "Concentration factors" of many millions are not uncommon for common water impurities like sodium, sulfate or chloride ions. The concentration process is often referred to as "hideout" (HO), whereas the opposite process, whereby the concentrations tend to even out (e.g., during shutdown) is called "hideout return" (HOR). In a neutral pH solution, the pH inside the crevice can drop to 2, a highly acidic condition that accelerates the corrosion of most metals and alloys.
For a given crevice type, two factors are important in the initiation of crevice corrosion: the chemical composition of the electrolyte in the crevice and the electrical potential drop into the crevice. Researchers had previously claimed that either one or the other of the two factors was responsible for initiating crevice corrosion, but recently it has been shown that it is a combination of the two that causes active crevice corrosion. Both the drop of potential and the change in composition of the crevice electrolyte are produced by the oxygen depletion of the solution inside the crevice (oxygen consumption caused by the metal oxidation at the inner surface of the occluded cavity) and the separation of electroactive areas, with net anodic reactions (oxidation) occurring within the crevice and net cathodic reactions (reduction) occurring at the exterior of the crevice (on the bold surface). The ratio of the surface areas between the cathodic and anodic region is significant.
Some of the phenomena occurring within the crevice may be somewhat reminiscent of galvanic corrosion:
;galvanic corrosion: two connected metals + single environment
;crevice corrosion: one metal part + two connected environments
The mechanism of crevice corrosion can be (but is not always) similar to that of pitting corrosion. However, there are sufficient differences to warrant a separate treatment. For example, in crevice corrosion, one has to consider the geometry of the crevice and the nature of the concentration process leading to the development of the differential local chemistry. The extreme and often unexpected local chemistry conditions inside the crevice need to be considered. Galvanic effects can play a role in crevice degradation. | 8 | Metallurgy |
Compounds containing fluorine-18, a radioactive isotope that emits positrons, are often used in positron emission tomography (PET) scanning, because the isotopes half-life of about 110 minutes is usefully long by positron-emitter standards. One such radiopharmaceutical is 2-deoxy-2-(F)fluoro-D-glucose (generically referred to as fludeoxyglucose), commonly abbreviated as F-FDG, or simply FDG. In PET imaging, FDG can be used for assessing glucose metabolism in the brain and for imaging cancer tumors. After injection into the blood, FDG is taken up by "FDG-avid" tissues with a high need for glucose, such as the brain and most types of malignant tumors. Tomography, often assisted by a computer to form a PET/CT (CT stands for "computer tomography") machine, can then be used to diagnose or monitor treatment of cancers, especially Hodgkins lymphoma, lung cancer, and breast cancer.
Natural fluorine is monoisotopic, consisting solely of fluorine-19. Fluorine compounds are highly amenable to nuclear magnetic resonance (NMR), because fluorine-19 has a nuclear spin of , a high nuclear magnetic moment, and a high magnetogyric ratio. Fluorine compounds typically have a fast NMR relaxation, which enables the use of fast averaging to obtain a signal-to-noise ratio similar to hydrogen-1 NMR spectra. Fluorine-19 is commonly used in NMR study of metabolism, protein structures and conformational changes. In addition, inert fluorinated gases have the potential to be a cheap and efficient tool for imaging lung ventilation. | 1 | Biochemistry |
The surface deformation of hydrogels is important because it can result in self-induced cracking. Each hydrogel has a characteristic wavelength of instability (λ) that depends on elastocapillary length. This length is calculated by dividing the surface tension (γ) by the elasticity (μ) of the hydrogel. The greater the wavelength of instability, the greater the elastocapillary length of instability, which makes a material more prone to cracking. The characteristic wavelength of instability can be modeled by:
Where H is the thickness of the hydrogel. | 7 | Physical Chemistry |
Sedimentation in potable water treatment generally follows a step of chemical coagulation and flocculation, which allows grouping particles together into flocs of a bigger size. This increases the settling speed of suspended solids and allows settling colloids. | 3 | Analytical Chemistry |
Depending on the quality of the result produced, assays may be classified into:
# Qualitative assays, i.e. assays which generally give just a pass or fail, or positive or negative or some such sort of only small number of qualitative gradation rather than an exact quantity.
#Semi-quantitative assays, i.e. assays that give the read-out in an approximate fashion rather than an exact number for the quantity of the substance. Generally they have a few more gradations than just two outcomes, positive or negative, e.g. scoring on a scale of 1+ to 4+ as used for blood grouping tests based on RBC agglutination in response to grouping reagents (antibody against blood group antigens).
# Quantitative assays, i.e. assays that give accurate and exact numeric quantitative measure of the amount of a substance in a sample. An example of such an assay used in coagulation testing laboratories for the most common inherited bleeding disease - Von Willebrand disease is VWF antigen assay where the amount of VWF present in a blood sample is measured by an immunoassay.
# Functional assays, i.e. an assay that tries to quantify functioning of an active substance rather than just its quantity. The functional counterpart of the VWF antigen assay is Ristocetin Cofactor assay, which measures the functional activity of the VWF present in a patient's plasma by adding exogenous formalin-fixed platelets and gradually increasing quantities of drug named ristocetin while measuring agglutination of the fixed platelets. A similar assay but used for a different purpose is called Ristocetin Induced Platelet Aggregation or RIPA, which tests response of endogenous live platelets from a patient in response to Ristocetin (exogenous) & VWF (usually endogenous). | 1 | Biochemistry |
Pneumatic fracturing is a method that has become very popular in the last ten years used to remediate contaminated sites. The method consists of injecting gas into a contaminated subsurface at a pressure higher than that of the gases that are present. By doing this fractures "spider-web" throughout the subsurface so that pumps may be placed in the ground to suck out the contaminated water through these cracks. Substrates may also be injected into the soil through the cracks to further the remediation of the soil and ground water. The clean-up technique was developed and patented through the research of various professors at the New Jersey Institute of Technology in 1996 with hopes of cleaning up various United States Environmental Protection Agency (EPA) Superfund sites which are some of the most heavily contaminated sites in the country. The patent is held by John R. Schuring, PhD and PE, professor of civil and environmental engineering at the New Jersey Institute of Technology, developed in conjunction with Thomas M. Boland, Trevor C. King, Sean T. McGonigal, David S. Kosson, Conan D. Fitzgerald, and Sankar Venkatraman. This method has been adopted by environmental contractors all over the country since it has been patented. | 2 | Environmental Chemistry |
Permutation re-sampling requires a computationally demanding number of permutations to get reliable estimates of the p-values for the most differentially expressed genes, if n is large. Eisinga, Breitling and Heskes (2013) provide the exact probability mass distribution of the rank product statistic. Calculation of the exact p-values offers a substantial improvement over permutation approximation, most significantly for that part of the distribution rank product analysis is most interested in, i.e., the thin right tail. However, exact statistical significance of large rank products may take unacceptable long amounts of time to compute. Heskes, Eisinga and Breitling (2014) provide a method to determine accurate approximate p-values of the rank product statistic in a computationally fast manner. | 1 | Biochemistry |
In 2009, the Zimmerman group discovered a compound to target the trinucleotide repeat expanded RNA and DNA that cause DM1. Through rational design, they utilized a triaminotriazine recognition unit to target TT or UU mismatches through a Janus Wedge type binding mode, creating a base triplet with the mismatch. The combined use of an acridine intercalator to pi-pi stack on the target gave a nanomolar binding affinity for TT or UU mismatches over others. Along with high binding affinity, this molecule was shown to displace MBNL from the complex with r(CUG) with a micromolar K Additionally, HIV-1 RNA has been targeted extensively in vitro by RNA-binding small molecules. In 2007, Miller and coworkers used dynamic combinatorial chemistry to screen a compound library against HIV-1 frameshift regulatory stem-loop RNA. They identified a hit compound that was selective for the regulatory sequence with micromolar binding affinity.
In 2011, Butcher and colleagues discovered a frameshifting stimulator (DB213) which bound to HIV-1 FS RNA with moderate binding affinity. An NMR structure of the RNA in complex with DB213, showed that the small molecule bound to the major groove of the RNA duplex. [https://scholar.google.com/citations?hl=en&user=ViAlX_kAAAAJ Schneekloth] and Hargrove have taken a different approach by targeting the HIV-1 TAR RNA hairpin. In a small molecule microarray screening, the Schneekloth group identified a thienopyridine derivative that interacts with HIV-1 TAR RNA hairpin. Further SAR studies provided more information on the structure and binding mode. The lead analogue was found to bind to the 5’-UTR of HIV with an IC of 40 μM for displacing a Tat-derived peptide. The Hargrove group developed a small library of amiloride derivatives with changes at the C(5) and C(6) positions to improve the binding affinity of amiloride to the loop and bulge of the HIV-1 TAR RNA. Using in vitro studies and modeling, they found a hit compound whose inhibition activity was increased by more than 100x compared to the parent amiloride. This compound is reported to be one of the tightest non-aminoglycoside TAR ligands reported to date. | 1 | Biochemistry |
A detailed mechanism for the Murai reaction has not been elucidated. Experimental and computational studies give evidence for at least two different mechanisms, depending on the catalyst. For catalysts such as [Ru(H)(CO)(PR)] which are active as Ru, a combination of computational density functional studies and experimental evidence has resulted in the following proposed mechanism:
It is proposed that at high temperatures RuH(CO)(PPh) converts to an unsaturated Ru(CO)(PPh) species. The catalytic cycle is proposed to begins with coordination of the ketone followed by oxidative addition of a C-H bond. The resulting five-coordinated metallocycle is stabilized by an agostic interaction. The C-C bond formation is the rate limiting step. | 0 | Organic Chemistry |
Zintl phases are intermetallic compounds that have a pronounced ionic bonding character. They are made up of a polyanionic substructure and group 1 or 2 counter ions, and their structure can be understood by a formal electron transfer from the electropositive element to the more electronegative element in their composition. Thus, the valence electron concentration (VEC) of the anionic element is increased, and it formally moves to the right in its row of the periodic table. Generally the anion does not reach an octet, so to reach that closed shell configuration, bonds are formed. The structure can be explained by the 8-N rule (replacing the number of valence electrons, N, by VEC), making it comparable to an isovalent element. The formed polyanionic substructures can be chains (two-dimensional), rings, and other two-or three-dimensional networks or molecule-like entities.
The Zintl line is a hypothetical boundary drawn between groups 13 and 14. It separates the columns based on the tendency for group 13 elements to form metals when reacted with electropositive group 1 or 2 elements and for group 14 and above to form ionic solids. The typical salts formed in these reactions become more metallic as the main group element becomes heavier. | 7 | Physical Chemistry |
Carbon-14, C-14, or radiocarbon, is a radioactive isotope of carbon with an atomic nucleus containing 6 protons and 8 neutrons. Its presence in organic materials is the basis of the radiocarbon dating method pioneered by Willard Libby and colleagues (1949) to date archaeological, geological and hydrogeological samples. Carbon-14 was discovered on February 27, 1940, by Martin Kamen and Sam Ruben at the University of California Radiation Laboratory in Berkeley, California. Its existence had been suggested by Franz Kurie in 1934.
There are three naturally occurring isotopes of carbon on Earth: carbon-12 (), which makes up 99% of all carbon on Earth; carbon-13 (), which makes up 1%; and carbon-14 (), which occurs in trace amounts, making up about 1 or 1.5 atoms per 10 atoms of carbon in the atmosphere. Carbon-12 and carbon-13 are both stable, while carbon-14 is unstable and has a half-life of years. Carbon-14 has a maximum specific activity of 62.4 mCi/mmol (2.31 GBq/mmol), or 164.9 GBq/g. Carbon-14 decays into nitrogen-14 () through beta decay. A gram of carbon containing 1 atom of carbon-14 per 10 atoms will emit ~0.2 beta particles per second. The primary natural source of carbon-14 on Earth is cosmic ray action on nitrogen in the atmosphere, and it is therefore a cosmogenic nuclide. However, open-air nuclear testing between 1955 and 1980 contributed to this pool.
The different isotopes of carbon do not differ appreciably in their chemical properties. This resemblance is used in chemical and biological research, in a technique called carbon labeling: carbon-14 atoms can be used to replace nonradioactive carbon, in order to trace chemical and biochemical reactions involving carbon atoms from any given organic compound. | 9 | Geochemistry |
Alkaline phosphatase from E. coli can be purified using a DEAE-Cellulose matrix. A. phosphatase has a slight negative charge, allowing it to weakly bind to the positively charged amine groups in the matrix. The enzyme can then be eluted out by adding buffer with higher salt concentrations. | 3 | Analytical Chemistry |
Phillips was born 3 December 1939 in Kendal, lived in South Shields and attended the Grammar School. He studied at the University of Birmingham attaining a BSc and PhD. | 5 | Photochemistry |
The usage of SABIO-RK is free of charge. Commercial users need a license.
SABIO-RK offers several ways for data access:
* a browser-based interface
* RESTful-based web services for programmatic access
Result data sets can be exported in different formats including SBML, BioPAX/SBPAX, and table format. | 1 | Biochemistry |
Chloride inclusions (MgCl, NaCl, CaCl, …) are a special type of inclusion as they are liquid in liquid metal. When aluminium solidifies, they form spherical voids similar to hydrogen gas porosity but the void contains a chloride crystal formed when aluminium became colder. | 8 | Metallurgy |
Chemical potential was first described by the American engineer, chemist and mathematical physicist Josiah Willard Gibbs. He defined it as follows:
Gibbs later noted also that for the purposes of this definition, any chemical element or combination of elements in given proportions may be considered a substance, whether capable or not of existing by itself as a homogeneous body. This freedom to choose the boundary of the system allows the chemical potential to be applied to a huge range of systems. The term can be used in thermodynamics and physics for any system undergoing change. Chemical potential is also referred to as partial molar Gibbs energy (see also partial molar property). Chemical potential is measured in units of energy/particle or, equivalently, energy/mole.
In his 1873 paper A Method of Geometrical Representation of the Thermodynamic Properties of Substances by Means of Surfaces, Gibbs introduced the preliminary outline of the principles of his new equation able to predict or estimate the tendencies of various natural processes to ensue when bodies or systems are brought into contact. By studying the interactions of homogeneous substances in contact, i.e. bodies, being in composition part solid, part liquid, and part vapor, and by using a three-dimensional volume–entropy–internal energy graph, Gibbs was able to determine three states of equilibrium, i.e. "necessarily stable", "neutral", and "unstable", and whether or not changes will ensue. In 1876, Gibbs built on this framework by introducing the concept of chemical potential so to take into account chemical reactions and states of bodies that are chemically different from each other. In his own words from the aforementioned paper, Gibbs states:
In this description, as used by Gibbs, ε refers to the internal energy of the body, η refers to the entropy of the body, and ν is the volume of the body. | 7 | Physical Chemistry |
In biochemistry, steady state refers to the maintenance of constant internal concentrations of molecules and ions in the cells and organs of living systems. Living organisms remain at a dynamic steady state where their internal composition at both cellular and gross levels are relatively constant, but different from equilibrium concentrations. A continuous flux of mass and energy results in the constant synthesis and breakdown of molecules via chemical reactions of biochemical pathways. Essentially, steady state can be thought of as homeostasis at a cellular level. | 7 | Physical Chemistry |
A Gran plot (also known as Gran titration or the Gran method) is a common means of standardizing a titrate or titrant by estimating the equivalence volume or end point in a strong acid-strong base titration or in a potentiometric titration. Such plots have been also used to calibrate glass electrodes, to estimate the carbonate content of aqueous solutions, and to estimate the K values (acid dissociation constants) of weak acids and bases from titration data.
Gran plots use linear approximations of the a priori non-linear relationships between the measured quantity, pH or electromotive potential (emf), and the titrant volume. Other types of concentration measures, such as spectrophotometric absorbances or NMR chemical shifts, can in principle be similarly treated. These approximations are only valid near, but not at, the end point, and so the method differs from end point estimations by way of first- and second-derivative plots, which require data at the end point. Gran plots were originally devised for graphical determinations in pre-computer times, wherein an x-y plot on paper would be manually extrapolated to estimate the x-intercept. The graphing and visual estimation of the end point have been replaced by more accurate least-squares analyses since the advent of modern computers and enabling software packages, especially spreadsheet programs with built-in least-squares functionality. | 3 | Analytical Chemistry |
The cyano group in HCN can add to the carbonyl group to form cyanohydrins, . In this reaction the ion is the nucleophile that attacks the partially positive carbon atom of the carbonyl group. The mechanism involves a pair of electrons from the carbonyl-group double bond transferring to the oxygen atom, leaving it single-bonded to carbon and giving the oxygen atom a negative charge. This intermediate ion rapidly reacts with , such as from the HCN molecule, to form the alcohol group of the cyanohydrin.
Organometallic compounds, such as organolithium reagents, Grignard reagents, or acetylides, undergo nucleophilic addition reactions, yielding a substituted alcohol group. Related reactions include organostannane additions, Barbier reactions, and the Nozaki–Hiyama–Kishi reaction.
In the aldol reaction, the metal enolates of ketones, esters, amides, and carboxylic acids add to aldehydes to form β-hydroxycarbonyl compounds (aldols). Acid or base-catalyzed dehydration then leads to α,β-unsaturated carbonyl compounds. The combination of these two steps is known as the aldol condensation.
The Prins reaction occurs when a nucleophilic alkene or alkyne reacts with an aldehyde as electrophile. The product of the Prins reaction varies with reaction conditions and substrates employed. | 0 | Organic Chemistry |
The GLODAPv1.1 climatology contains analysed fields of "present day" (1990s) dissolved inorganic carbon (DIC), alkalinity, carbon-14 (C), CFC-11 and CFC-12. The fields consist of three-dimensional, objectively-analysed global grids at 1° horizontal resolution, interpolated onto 33 standardised vertical intervals from the surface (0 m) to the abyssal seafloor (5500 m). In terms of temporal resolution, the relative scarcity of the source data mean that, unlike the World Ocean Atlas, averaged fields are only produced for the annual time-scale. The GLODAP climatology is missing data in certain oceanic provinces including the Arctic Ocean, the Caribbean Sea, the Mediterranean Sea and Maritime Southeast Asia.
Additionally, analysis has attempted to separate natural from anthropogenic DIC, to produce fields of pre-industrial (18th century) DIC and "present day" anthropogenic . This separation allows estimation of the magnitude of the ocean sink for anthropogenic , and is important for studies of phenomena such as ocean acidification. However, as anthropogenic DIC is chemically and physically identical to natural DIC, this separation is difficult. GLODAP used a mathematical technique known as C* (C-star) to deconvolute anthropogenic from natural DIC (there are a number of alternative methods). This uses information about ocean biogeochemistry and surface disequilibrium together with other ocean tracers including carbon-14, CFC-11 and CFC-12 (which indicate water mass age) to try to separate out natural from that added during the ongoing anthropogenic transient. The technique is not straightforward and has associated errors, although it is gradually being refined to improve it. Its findings are generally supported by independent predictions made by dynamic models.
The GLODAPv2 climatology largely repeats the earlier format, but makes use of the large number of observations of the oceans carbon cycle made over the intervening period (2000–2013). The analysed "present-day" fields in the resulting dataset are normalised to year 2002. Anthropogenic carbon was estimated in GLODAPv2 using a "transit-time distribution" (TTD) method (an approach using a Greens function). In addition to updated fields of DIC (total and anthropogenic) and alkalinity, GLODAPv2 includes fields of seawater pH and calcium carbonate saturation state (Ω; omega). The latter is a non-dimensional number calculated by dividing the local carbonate ion concentration by the ambient saturation concentration for calcium carbonate (for the biomineral polymorphs calcite and aragonite), and relates to an oceanographic property, the carbonate compensation depth. Values of this below 1 indicate undersaturation, and potential dissolution, while values above 1 indicate supersaturation, and relative stability. | 9 | Geochemistry |
The shikimate pathway is a seven-step metabolic route used by bacteria, fungi, algae, parasites, and plants for the biosynthesis of aromatic amino acids (phenylalanine, tyrosine, and tryptophan). This pathway is not found in animals; therefore, phenylalanine and tryptophan represent essential amino acids that must be obtained from the animal's diet (animals can synthesise tyrosine from phenylalanine, and therefore is not an essential amino acid except for individuals unable to hydroxylate phenylalanine to tyrosine).
The seven enzymes involved in the shikimate pathway are DAHP synthase, 3-dehydroquinate synthase, 3-dehydroquinate dehydratase, shikimate dehydrogenase, shikimate kinase, EPSP synthase, and chorismate synthase. The pathway starts with two substrates, phosphoenol pyruvate and erythrose-4-phosphate and ends with chorismate, a substrate for the three aromatic amino acids. The fifth enzyme involved is the shikimate kinase, an enzyme that catalyzes the ATP-dependent phosphorylation of shikimate to form shikimate 3-phosphate (shown in the figure below). Shikimate 3-phosphate is then coupled with phosphoenol pyruvate to give 5-enolpyruvylshikimate-3-phosphate via the enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase.
Then 5-enolpyruvylshikimate-3-phosphate is transformed into chorismate by a chorismate synthase.
Prephenic acid is then synthesized by a Claisen rearrangement of chorismate by chorismate mutase.
Prephenate is oxidatively decarboxylated with retention of the hydroxyl group to give p-hydroxyphenylpyruvate, which is transaminated using glutamate as the nitrogen source to give tyrosine and α-ketoglutarate. | 1 | Biochemistry |
Depending on the purpose of the analysis, RNA-seq can be performed using different approaches:
* Ion Torrent sequencing: NGS technology based on the use of a semiconductor chip where the sample is loaded integrated with an ion-sensitive field-effect transistor able to sensitively detect reductions of the pH value due to the release of one or more protons after the incorporation of one or more dNTPs during sequencing by synthesis: the signal is, then, transmitted to a machine composed of an electronic reading board to interface with the chip, a microprocessor for signal processing and a fluidics system to control the flow of reagents over the chip.
* Illumina sequencing: it offers a good method for small RNA sequencing and it is the most widely used approach. After the library preparation and amplification steps, the sequencing (based on the use of reversible dye-terminators) can be performed by using different systems, such as Miseq System, Miseq Series, NextSeq Series and many others, according to the applications | 1 | Biochemistry |
Sacrificial metals are widely used to prevent other metals from corroding: for example in galvanised steel. Many steel objects are coated with a layer of zinc, which is more electronegative than iron, and thus oxidises in preference to the iron, preventing the iron from rusting. Similarly, sacrificial bars of a metal such as aluminium or aluminium alloys can be attached to an oil rig or to the hull of a ship to prevent it from rusting and breaking down. Magnesium may similarly be used on dry land for installations such as pipelines and oil refineries, where its high driving voltage is better for overcoming the resistance of soils found on dry land. | 7 | Physical Chemistry |
Glycoproteins and glycolipids are by definition covalently bonded to carbohydrates. They are very abundant on the surface of the cell, and their interactions contribute to the overall stability of the cell. | 0 | Organic Chemistry |
Because of its potent biological activities, kendomycin has attracted interest as a target of total synthesis. The first total synthesis of kendomycin was accomplished by Lee and Yuan in 2004. The total number of syntheses stands at 6. | 0 | Organic Chemistry |
Criegee intermediates are formed by the gas-phase reactions of alkenes and ozone in the Earths atmosphere. Ozone adds across the carbon–carbon double bond of the alkene to form a molozonide, which then decomposes to produce a carbonyl (RRCO) and a carbonyl oxide. The latter is known as the Criegee intermediate.
The alkene ozonolysis reaction is extremely exothermic, releasing about of excess energy. Therefore, the Criegee intermediates are formed with a large amount of internal energy. | 2 | Environmental Chemistry |
In some snails, the protein component of the egg yolk is primarily ferritin. This is a different ferritin, with a different genetic sequence, from the somatic ferritin. It is produced in the midgut glands and secreted into the haemolymph, whence it is transported to the eggs. | 1 | Biochemistry |
In chemical physics and physical chemistry, chemical affinity is the electronic property by which dissimilar chemical species are capable of forming chemical compounds. Chemical affinity can also refer to the tendency of an atom or compound to combine by chemical reaction with atoms or compounds of unlike composition. | 7 | Physical Chemistry |
Ribozymes have been proposed and developed for the treatment of disease through gene therapy. One major challenge of using RNA-based enzymes as a therapeutic is the short half-life of the catalytic RNA molecules in the body. To combat this, the 2’ position on the ribose is modified to improve RNA stability. One area of ribozyme gene therapy has been the inhibition of RNA-based viruses.
A type of synthetic ribozyme directed against HIV RNA called gene shears has been developed and has entered clinical testing for HIV infection.
Similarly, ribozymes have been designed to target the hepatitis C virus RNA, SARS coronavirus (SARS-CoV), Adenovirus and influenza A and B virus RNA. The ribozyme is able to cleave the conserved regions of the virus's genome, which has been shown to reduce the virus in mammalian cell culture. Despite these efforts by researchers, these projects have remained in the preclinical stage. | 7 | Physical Chemistry |
It is theorized that the process of making testosterone from cholesterol, needs magnesium to function properly.
Studies have shown that significant gains in testosterone occur after taking 8-10 mg magnesium/kg body weight/day. | 1 | Biochemistry |
In gamma spectrometry, the Compton edge is a feature of a detector output spectrum that results from Compton scattering in such as a scintillation detector or Photodiode detector. It occurs when a gamma-ray scatters within the detector and some of the interaction energy escapes so that only a fraction is detected. The amount of energy deposited in the detector depends on the scattering angle of the photon, leading to a spectrum of energies each corresponding to a different scattering angle. The highest energy that can be deposited, corresponding to full backscatter, is called the Compton edge. In mathematical terms, the Compton edge is the inflection point of the high-energy side of the Compton region. | 7 | Physical Chemistry |
White adipose tissue, also known as white fat, is one two types of adipose tissue in mammals. White adipose tissue stores energy in the form of triglycerides, which can be broken down to free fatty acids on demand. Its normal function is to store free fatty acids as triglycerides within the tissue. When glucose is deficient, in situations like fasting, white adipose tissue generates glycerol 3-phosphate. | 1 | Biochemistry |
Supermicelle is a hierarchical micelle structure (supramolecular assembly) where individual components are also micelles. Supermicelles are formed via bottom-up chemical approaches, such as self-assembly of long cylindrical micelles into radial cross-, star- or dandelion-like patterns in a specially selected solvent; solid nanoparticles may be added to the solution to act as nucleation centers and form the central core of the supermicelle. The stems of the primary cylindrical micelles are composed of various block copolymers connected by strong covalent bonds; within the supermicelle structure they are loosely held together by hydrogen bonds, electrostatic or solvophobic interactions. | 6 | Supramolecular Chemistry |
The reaction has the following mechanism:
The rate of each species are:
These equations cannot be solved, because each one has values that change with time. For example, the first equation contains the concentrations of [Br], and , which depend on time, as can be seen in their respective equations.
To solve the rate equations the steady state approximation can be used. The reactants of this reaction are and , the intermediates are H and Br, and the product is HBr.
For solving the equations, the rates of the intermediates are set to 0 in the steady state approximation:
From the reaction rate of H, , so the reaction rate of Br can be simplified:
The reaction rate of HBr can also be simplifed, changing to , since both values are equal.
The concentration of H from equation 1 can be isolated:
The concentration of this intermediate is small and changes with time like the concentrations of reactants and product. It is inserted into the last differential equation to give
Simplifying the equation leads to
The experimentally observed rate is
The experimental rate law is very similar to the rate obtained with the steady state approximation, if is and is . | 7 | Physical Chemistry |
When electromagnetic radiation is absorbed by an atom or molecule, the energy of the radiation changes the state of the atom or molecule from an initial state to a final state. The number of states in a specific energy range is discrete for gaseous or diluted systems, with discrete energy levels. Condensed systems, like liquids or solids, have a continuous density of states distribution and often possess continuous energy bands. In order for a substance to change its energy it must do so in a series of "steps" by the absorption of a photon. This absorption process can move a particle, like an electron, from an occupied state to an empty or unoccupied state. It can also move a whole vibrating or rotating system, like a molecule, from one vibrational or rotational state to another or it can create a quasiparticle like a phonon or a plasmon in a solid. | 7 | Physical Chemistry |
Grant McDonald Wilson (May 24, 1931 – September 10, 2012) was a notable American thermodynamicist. He is widely known to the fields of chemical engineering and physical chemistry for having developed the Wilson equation, one of the first attempts of practical importance to model nonideal behavior in liquid mixtures as observed in practice with common polar compounds such as alcohols, amines, etc. The equation has been in use in all commercial chemical process simulators to predict phase behavior and produce safe process designs of commercial and environmental protection importance to the chemical industry. He founded the company Wilco (now Wiltec) in 1977 to research, measure, commercialize, and publish thermophysical property data for numerous chemical mixtures of interest to the industry. The Journal of Chemical & Engineering Data published a posthumous issue in honor of Wilson in April 2014 in recognition of his extensive contributions to the field. | 7 | Physical Chemistry |
A Winkler bottle is a piece of laboratory glassware specifically made for carrying out the Winkler test. These bottles have conical tops and a close fitting stopper to aid in the exclusion of air bubbles when the top is sealed. This is important because oxygen in trapped air would be included in the measurement and would affect the accuracy of the test. | 3 | Analytical Chemistry |
Bacterial initiation factor-2 is a bacterial initiation factor.
IF2 binds to an initiator tRNA and controls the entry of tRNA onto the ribosome. IF2, bound to GTP, binds to the 30S P site. After associating with the 30S subunit, fMet-tRNA binds to the IF2 then IF2 transfers the tRNA into the partial P site. When the 50S subunit joins, it hydrolyzes GTP to GDP and P, causing a conformational change in the IF2 that causes IF2 to release and allow the 70S ribosome to form.
Human mitochondria use a nuclear-encoded homolog, MTIF2, for translation initiation. | 1 | Biochemistry |
These materials are prepared by treating graphite with a strong oxidant or a strong reducing agent:
The reaction is reversible.
The host (graphite) and the guest X interact by charge transfer. An analogous process is the basis of commercial lithium-ion batteries.
In a graphite intercalation compound not every layer is necessarily occupied by guests. In so-called stage 1 compounds, graphite layers and intercalated layers alternate and in stage 2 compounds, two graphite layers with no guest material in between alternate with an intercalated layer. The actual composition may vary and therefore these compounds are an example of non-stoichiometric compounds. It is customary to specify the composition together with the stage. The layers are pushed apart upon incorporation of the guest ions. | 6 | Supramolecular Chemistry |
In 1989 the U.S. Environmental Protection Agency (EPA) published its Total Coliform Rule (TCR) which imposed major monitoring changes for public water systems nationwide. The testing requirements under the 1989 TCR were more thorough than the previous requirements. The required number of routine coliform tests was increased, especially for smaller water utilities. The regulation also required automatic repeat testing from all sources that show a total coliform positive (known as triggered source water monitoring). In 2013 EPA revised the TCR, with minor corrections in 2014. | 3 | Analytical Chemistry |
Hemolithin is the name given to a protein molecule isolated from two CV3 meteorites, Allende and Acfer-086. Its deuterium to hydrogen ratio is 26 times terrestrial which is consistent with it having formed in an interstellar molecular cloud, or later in the protoplanetary disk at the start of the Solar System 4.567 billion years ago. The elements hydrogen, lithium, carbon, oxygen, nitrogen and iron that it is composed of, were all available for the first time 13 billion years ago after the first generation of massive stars ended in nucleosynthetic events.
The research leading to the discovery of Hemolithin started in 2007 when another protein, one of the first to form on Earth, was observed to entrap water. That property being useful to chemistry before biochemistry on earth developed, theoretical enthalpy calculations on the condensation of amino acids were performed in gas phase space asking: "whether amino acids could polymerize to protein in space?" - they could, and their water of condensation aided their polymerization. This led to several manuscripts of isotope and mass information on Hemolithin. | 9 | Geochemistry |
Baculovirus-infected insect cells (Sf9, Sf21, High Five strains) or mammalian cells (HeLa, HEK 293) allow production of glycosylated or membrane proteins that cannot be produced using fungal or bacterial systems. It is useful for production of proteins in high quantity. Genes are not expressed continuously because infected host cells eventually lyse and die during each infection cycle. | 1 | Biochemistry |
DNA circularization depends on both the axial (bending) stiffness and torsional (rotational) stiffness of the molecule. For a DNA molecule to successfully circularize it must be long enough to easily bend into the full circle and must have the correct number of bases so the ends are in the correct rotation to allow bonding to occur. The optimum length for circularization of DNA is around 400 base pairs (136 nm), with an integral number of turns of the DNA helix, i.e., multiples of 10.4 base pairs. Having a non integral number of turns presents a significant energy barrier for circularization, for example a 10.4 x 30 = 312 base pair molecule will circularize hundreds of times faster than 10.4 x 30.5 ≈ 317 base pair molecule.
The bending of short circularized DNA segments is non-uniform. Rather, for circularized DNA segments less than the persistence length, DNA bending is localised to 1-2 kinks that form preferentially in AT-rich segments. If a nick is present, bending will be localised to the nick site. | 4 | Stereochemistry |
Thermal transport in non-metal solids was usually considered to be governed by the three-phonon scattering process, and the role of four-phonon and higher-order scattering processes was believed to be negligible. Recent studies have shown that the four-phonon scattering can be important for nearly all materials at high temperature and for certain materials at room temperature. The predicted significance of four-phonon scattering in boron arsenide was confirmed by experiments. | 7 | Physical Chemistry |
* James, Rachael and Open University (2005) [https://books.google.com/books?id=jiQ6Gjdn_7oC&q=%22marine+biogeochemical+cycles%22 Marine Biogeochemical Cycles] Butterworth-Heinemann. . | 9 | Geochemistry |
The 2nd analytical group of cations consists of ions which form acid-insoluble sulfides. Cations in the 2nd group include: Cd, Bi, Cu, As, As, Sb, Sb, Sn, Sn and Hg. Pb is usually also included here in addition to the first group. Although these methods refer to solutions that contain sulfide (S), these solutions actually only contain HS and bisulfide (HS). Sulfide (S) does not exist in appreciable concentrations in water.
The reagent used can be any substance that gives S ions in such solutions; most commonly used are hydrogen sulfide (at 0.2-0.3 M), thioacetamide (at 0.3-0.6 M), addition of hydrogen sulfide can often prove to be a lumbersome process and therefore sodium sulfide can also serve the purpose. The test with the sulfide ion must be conducted in the presence of dilute HCl. Its purpose is to keep the sulfide ion concentration at a required minimum, so as to allow the precipitation of 2nd group cations alone. If dilute acid is not used, the early precipitation of 4th group cations (if present in solution) may occur, thus leading to misleading results. Acids beside HCl are rarely used. Sulfuric acid may lead to the precipitation of the 5th group cations, whereas nitric acid oxidises the sulfide ion in the reagent, forming colloidal sulfur.
The precipitates of these cations are almost indistinguishable, except for CdS, which is yellow. All the precipitates, except for HgS, are soluble in dilute nitric acid. HgS is soluble only in aqua regia, which can be used to separate it from the rest. The action of ammonia is also useful in differentiating the cations. CuS dissolves in ammonia forming an intense blue solution, whereas CdS dissolves forming a colourless solution. The sulfides of As, As, Sb, Sb, Sn, Sn are soluble in yellow ammonium sulfide, where they form polysulfide complexes.
This group is determined by adding the salt in water and then adding dilute hydrochloric acid (to make the medium acidic) followed by hydrogen sulfide gas. Usually it is done by passing hydrogen sulfide over the test tube for detection of 1st group cations. If it forms a reddish-brown or black precipitate then Bi, Cu, Hg or Pb is present. Otherwise, if it forms a yellow precipitate, then Cd or Sn is present; or if it forms a brown precipitate, then Sn must be present; or if a red orange precipitate is formed, then Sb is present.
:Pb + KCrO → PbCrO + 2 K
Confirmation test for copper:
:2 Cu + K[Fe(CN)] + CHCOOH → Cu[Fe(CN)] + 4 K
:Cu + 2 NaOH → Cu(OH) + 2 Na
:Cu(OH) → CuO + HO (endothermic)
Confirmation test for bismuth:
:Bi + 3 KI (in excess) → BiI + 3 K
:BiI + KI → K[BiI]
:Bi + HO (in excess) → BiO + 2 H
Confirmation test for mercury:
:Hg + 2 KI (in excess) → HgI + 2 K
:HgI + 2 KI → K[HgI] (red precipitate dissolves)
:2 Hg + SnCl → 2 Hg + SnCl (white precipitate turns gray) | 3 | Analytical Chemistry |
While it is a common and wide-ranging species throughout eastern North America, insular populations on the eastern periphery of the species' range are at risk from invasive species, with the extinction of the Gull Island vole being a notable example of this. In addition, due to its dependence on mesic habitats, populations of the species on the mainland periphery of its range in the Southeastern United States may be at potential risk from climate change-induced aridification. | 2 | Environmental Chemistry |
The Fischer–Tropsch process (FT) is a collection of chemical reactions that converts a mixture of carbon monoxide and hydrogen, known as syngas, into liquid hydrocarbons. These reactions occur in the presence of metal catalysts, typically at temperatures of and pressures of one to several tens of atmospheres. The Fischer–Tropsch process is an important reaction in both coal liquefaction and gas to liquids technology for producing liquid hydrocarbons.
In the usual implementation, carbon monoxide and hydrogen, the feedstocks for FT, are produced from coal, natural gas, or biomass in a process known as gasification. The process then converts these gases into synthetic lubrication oil and synthetic fuel. This process has received intermittent attention as a source of low-sulfur diesel fuel and to address the supply or cost of petroleum-derived hydrocarbons. Fischer–Tropsch process is discussed as a step of producing carbon-neutral liquid hydrocarbon fuels from CO and hydrogen.
The process was first developed by Franz Fischer and Hans Tropsch at the Kaiser Wilhelm Institute for Coal Research in Mülheim an der Ruhr, Germany, in 1925. | 0 | Organic Chemistry |
Johnson et al. describe two isoforms of succinyl-CoA synthetase in amniotes, one that specifies synthesis of ATP, and one that synthesises GTP.
* - ATP-forming - SUCLA2
* - GTP-forming - SUCLG2
In amniotes, the enzyme is a heterodimer of an α- and a β-subunit. The specificity for either adenosine or guanosine phosphates is defined by the β-subunit, which is encoded by 2 genes. SUCLG2 is GTP-specific and SUCLA2 is ATP-specific, while SUCLG1 encodes the common α-subunit. β variants are produced at different amounts in different tissues, causing GTP or ATP substrate requirements.
Mostly consuming tissues such as heart and brain have more ATP-specific succinyl-CoA synthetase (ATPSCS), while synthetic tissues such as kidney and liver have the more GTP-specific form (GTPSCS). Kinetics analysis of ATPSCS from the breast muscle of pigeons and GTPSCS from pigeon liver showed that their apparent Michaelis constants were similar for CoA, but different for the nucleotides, phosphate, and succinate. The largest difference was for succinate: Kapp of ATPSCS = 5mM versus that of GTPSCS = 0.5mM. | 1 | Biochemistry |
Given that there is no need for restriction enzymes other than for generating the linearized vector, the procedure is much simpler and faster than traditional subcloning. There is also no need to add restriction sites when designing primers and thus shorter primers can be used saving time and money. In addition, in instances where there are no viable restriction sites that can be used for traditional cloning, TA cloning is often used as an alternative. The major downside of TA cloning is that directional cloning is not possible, so the gene has a 50% chance of getting cloned in the reverse direction. | 1 | Biochemistry |
Thermodynamically, a smooth surface is the lowest ever configuration, which has the smallest surface area. However, it requires a kinetic process such as surface and bulk diffusion to create a perfectly flat surface.
Conclusion: enhancing surface and bulk diffusion will help create a smoother surface. | 7 | Physical Chemistry |
Even though the sequencing accuracy for each individual nucleotide is very high, the very large number of nucleotides in the genome means that if an individual genome is only sequenced once, there will be a significant number of sequencing errors. Furthermore, many positions in a genome contain rare single-nucleotide polymorphisms (SNPs). Hence to distinguish between sequencing errors and true SNPs, it is necessary to increase the sequencing accuracy even further by sequencing individual genomes a large number of times. | 1 | Biochemistry |
V̇O may also be calculated by the Fick equation:
, when these values are obtained during exertion at a maximal effort. Here Q is the cardiac output of the heart, CO is the arterial oxygen content, and CO is the venous oxygen content. (CO – CO) is also known as the arteriovenous oxygen difference.
The Fick equation may be used to measure V̇O in critically ill patients, but its usefulness is low even in non-exerted cases. Using a breath-based VO to estimate cardiac output, on the other hand, seems to be reliable enough. | 1 | Biochemistry |
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