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Bacterial transcription is the process in which a segment of bacterial DNA is copied into a newly synthesized strand of messenger RNA (mRNA) with use of the enzyme RNA polymerase.
The process occurs in three main steps: initiation, elongation, and termination; and the end result is a strand of mRNA that is complementary to a single strand of DNA. Generally, the transcribed region accounts for more than one gene. In fact, many prokaryotic genes occur in operons, which are a series of genes that work together to code for the same protein or gene product and are controlled by a single promoter. Bacterial RNA polymerase is made up of four subunits and when a fifth subunit attaches, called the sigma factor (σ-factor), the polymerase can recognize specific binding sequences in the DNA, called promoters. The binding of the σ-factor to the promoter is the first step in initiation. Once the σ-factor releases from the polymerase, elongation proceeds. The polymerase continues down the double stranded DNA, unwinding it and synthesizing the new mRNA strand until it reaches a termination site. There are two termination mechanisms that are discussed in further detail below. Termination is required at specific sites for proper gene expression to occur. Gene expression determines how much gene product, such as protein, is made by the gene. Transcription is carried out by RNA polymerase but its specificity is controlled by sequence-specific DNA binding proteins called transcription factors. Transcription factors work to recognize specific DNA sequences and based on the cells needs, promote or inhibit additional transcription. Similar to other taxa, bacteria experience bursts of transcription. The work of the Jones team in Jones et al 2014 explains some of the underlying causes of bursts and other variability, including stability of the resulting mRNA, the strength of promotion encoded in the relevant promoter and the duration of transcription due to strength of the TF binding site. They also found that bacterial TFs linger too briefly for TFs binding characteristics to explain the sustained transcription of bursts.
Bacterial transcription differs from eukaryotic transcription in several ways. In bacteria, transcription and translation can occur simultaneously in the cytoplasm of the cell, whereas in eukaryotes transcription occurs in the nucleus and translation occurs in the cytoplasm. There is only one type of bacterial RNA polymerase whereas eukaryotes have 3 types. Bacteria have a σ-factor that detects and binds to promoter sites but eukaryotes do not need a σ-factor. Instead, eukaryotes have transcription factors that allow the recognition and binding of promoter sites.
Overall, transcription within bacteria is a highly regulated process that is controlled by the integration of many signals at a given time. Bacteria heavily rely on transcription and translation to generate proteins that help them respond specifically to their environment. | 1 | Biochemistry |
Particles of refractory material in contact with aluminium can detach and become inclusions. We can find graphite inclusions (C), alumina inclusions (alpha-AlO), CaO, SiO, …
After some time, graphite refractory in contact with aluminium will react to create aluminum carbides (harder and more detrimental inclusions).
In aluminium alloy containing magnesium, the magnesium reacts with some refractories to create rather big and hard inclusions similar to spinels.
Unreacted refractory particles can originate from the degradation of refractory materials which comes in contact with the melt. | 8 | Metallurgy |
In general, polymeric mixtures are far less miscible than mixtures of small molecule materials. This effect results from the fact that the driving force for mixing is usually entropy, not interaction energy. In other words, miscible materials usually form a solution not because their interaction with each other is more favorable than their self-interaction, but because of an increase in entropy and hence free energy associated with increasing the amount of volume available to each component. This increase in entropy scales with the number of particles (or moles) being mixed. Since polymeric molecules are much larger and hence generally have much higher specific volumes than small molecules, the number of molecules involved in a polymeric mixture is far smaller than the number in a small molecule mixture of equal volume. The energetics of mixing, on the other hand, is comparable on a per volume basis for polymeric and small molecule mixtures. This tends to increase the free energy of mixing for polymer solutions and thereby making solvation less favorable, and thereby making the availability of concentrated solutions of polymers far rarer than those of small molecules.
Furthermore, the phase behavior of polymer solutions and mixtures is more complex than that of small molecule mixtures. Whereas most small molecule solutions exhibit only an upper critical solution temperature phase transition (UCST), at which phase separation occurs with cooling, polymer mixtures commonly exhibit a lower critical solution temperature phase transition (LCST), at which phase separation occurs with heating.
In dilute solutions, the properties of the polymer are characterized by the interaction between the solvent and the polymer. In a good solvent, the polymer appears swollen and occupies a large volume. In this scenario, intermolecular forces between the solvent and monomer subunits dominate over intramolecular interactions. In a bad solvent or poor solvent, intramolecular forces dominate and the chain contracts. In the theta solvent, or the state of the polymer solution where the value of the second virial coefficient becomes 0, the intermolecular polymer-solvent repulsion balances exactly the intramolecular monomer-monomer attraction. Under the theta condition (also called the Flory condition), the polymer behaves like an ideal random coil. The transition between the states is known as a coil–globule transition. | 7 | Physical Chemistry |
During the initial phases of glycolysis and the TCA cycle, cofactors such as NAD+ donate and accept electrons that aid in the electron transport chain's ability to produce a proton gradient across the inner mitochondrial membrane. The ATP synthase complex exists within the mitochondrial membrane (F portion) and protrudes into the matrix (F portion). The energy derived as a result of the chemical gradient is then used to synthesize ATP by coupling the reaction of inorganic phosphate to ADP in the active site of the ATP synthase enzyme; the equation for this can be written as ADP + P → ATP. | 1 | Biochemistry |
Along with the related organotantalum species, niobium alkylidenes were among the first Scrock carbenes studied. The first syntheses of these complexes involved addition of organolithium reagents lacking β-hydrogens into hindered Nb(V) complexes followed by α-proton elimination. As compared to tantalum alkylidenes, niobium alkylidenes are less thermally and hydrolytically stable. | 0 | Organic Chemistry |
The Shibasaki synthesis ((-) chiral, 2002) was a second published method in strychnine total synthesis using an asymmetric reaction step. Cyclohexenone 1 was reacted with dimethyl malonate 2 in an asymmetric Michael reaction using AlLibis(binaphthoxide) to form chiral diester 3. Its ketone group was protected as an acetal (2-ethyl-2-methyl-1,3-dioxolane, TsOH) and a carboxyl group was removed (LiCl, DMSO 140 °C) in monoester 4. A C2 fragment was added as Weinreb amide 5 to form PMB ether 6 using LDA. The ketone was then reduced to the alcohol (NaBHCN, TiCl) and then water was eliminated (DCC, CuCl) to form alkene 7. After ester reduction (DIBAL) to the alcohol and its TIPS protection (TIPSOTf, triethylamine), the acetal group was removed (catalytic CSA) in ketone 8. Enone 9 was then formed by Saegusa oxidation. The conversion to alcohol 10 was accomplished via a Mukaiyama aldol addition using formaldehyde, iodonation to 11 (iodine, DMAP) was followed by a Stille coupling (Pddba, PhAs, CuI) incorporating nitrobenzene unit 12. Alcohol 13 was formed after SEM protection (SEMCl,i-Pr2NEt) and TIPS removal (HF).
In the second part of the sequence alcohol 13 was converted to a triflate (triflic anhydride, N,N-diisopropylethylamine), then 2,2-bis(ethylthio)ethylamine 14 was added immediately followed by zinc powder, setting of a tandem reaction with nitro group reduction to the amine, 1,4-addition of the thio-amine group and amine-keto condensation to indole 16. Reaction with DMTSF gave thionium attack at C7 forming 17, the imine group was then reduced (NaBHCN, TiCl), the new amino group acylated (acetic anhydride, pyridine), both alcohol protecting groups removed (NaOMe / meOH) and the allyl alcohol group protected again (TIPS). This allowed removal of the ethylthio group (NiCl, NaBH, EtOH/MeOH) to 18. The alcohol was oxidized to the aldehyde using a Parikh-Doering oxidation and TIPS group removal gave hemiacetal 19 called (+)-diaboline which is acylated Wieland-Gumlich aldehyde. | 0 | Organic Chemistry |
Ampicillin overdose can cause behavioral changes, confusion, blackouts, and convulsions, as well as neuromuscular hypersensitivity, electrolyte imbalance, and kidney failure. | 4 | Stereochemistry |
Nanocrystalline materials can be prepared in several ways. Methods are typically categorized based on the phase of matter the material transitions through before forming the nanocrystalline final product. | 8 | Metallurgy |
EosFP emits a strong green fluorescence (516 nm) that changes irreversibly to red (581 nm) when irradiated with UV-light of 390 nm. This modification occurs due to a break in the peptide backbone next to the chromophore. This mechanism allows for localized tagging of the protein and makes EosFP an appropriate tool for tracking protein movement within living cells. Formation of the red chromophore involves cleaving the peptide backbone but includes almost no other changes in the protein structure.
According to single-molecule fluorescence spectroscopy, EosFP is tetrameric, and exhibits strong Forster resonance coupling within individual fluorophores. Like other fluorescent proteins, Eos can be used to report diverse signals in cells, tissues and organs without disturbing complex biological machinery. While the use of fluorescent proteins was once limited to the green fluorescent protein (GFP), in recent years many other fluorescent proteins have been cloned. Unlike GFPs, which are derived from the luminescent jellyfish Aequorea victoria, fluorescent proteins derived from anthozoa, including Eos, emit fluorescence in the red spectral range. The novel property of photoinduced green-to-red conversion in Eos is useful because it allows for localized tracking of proteins in living cells. EosFP is unique because it has a large separation in the wavelengths it can emit which allows for easy identification of peak colours. All green-to-red photoinducible fluorescent proteins, including Eos, contain a chromophoric unit derived from the tripeptide his-tyr-gly. This green-to-red conversion is completed by light rather than chemical oxidation such as in other FPs. | 1 | Biochemistry |
In order to survive, plants must be able to respond to many biotic and abiotic stresses, including pathogen attack, piercing/sucking insects, herbivory, and mechanical wounding. These stresses activate specialized signal transduction pathways, which are specific to the stressor and the amount of tissue damage inflicted. Similar to mechanical wounding, chewing insects, such as the tobacco hornworm (Manduca sexta, one of the major pests of tomato), cause extensive tissue damage activating the jasmonic acid (JA)-mediated response (Walling 2000). This JA-mediated response revolves around the octadecanoid pathway, which is responsible for the synthesis of JA and several other potent signaling molecules, and ends in the regulation of two sets of genes whose expression changes over time. The early genes amplify the wounding signal and can be detected 30 minutes to 2 hours after damage (Ryan 2000). Late gene expression can be seen 4–24 hours after wounding. Products of late-response genes act as deterrents to chewing-insect feeding, often by decreasing the nutritional value of the food ingested or interfering with insect gut function (Walling 2000). For example, serine proteinase inhibitors (Pins) interfere with digestive proteases in the insect gut and polyphenol oxidases (PPO) act to decrease the nutritive value of plant leaves after ingestion by herbivores (Johnson et al. 1989; Ryan 2000; Orozco-Cardenas 2001). Please see the Picture 3 for a summary of the wound response in tomato.
The plant response in this octadecanoid pathway is similar to mammalian prostaglandin and
leukotriene pathways (Ref Walling 2000). This particular pathway is inhibited by salicylic acid. | 1 | Biochemistry |
Irrespective of scan rate, the area under the peak (in units of AV) is equal to , where is the number of electrons exchanged in the oxidation/reduction of the center, is the electrode surface and is the electroactive coverage (in units of mol/cm). The latter can therefore be deduced from the area under the peak after subtraction of the capacitive current. | 7 | Physical Chemistry |
Emissive power is the rate at which radiation is emitted per unit area. It is a measure of heat flux. The total emissive power from a surface is denoted as and can be determined by,where is in units of steradians and is the total intensity.
The total emissive power can also be found by integrating the spectral emissive power over all possible wavelengths. This is calculated as,where represents wavelength.
The spectral emissive power can also be determined from the spectral intensity, as follows,
where both spectral emissive power and emissive intensity are functions of wavelength. | 7 | Physical Chemistry |
Directional freezing freezes from only one direction.
Directional freezing can freeze water, from only one direction or side of a container, into clear ice.
Directional freezing in a domestic freezer can be done by putting water in a insulated container so that the water freezes from the top down, and removing before fully frozen, so that the minerals in the water are not frozen.
F Hoffmann La Roche AG, Roche Diagnostics GmbH has a 2017 directional freezing patent for drying solid material. | 6 | Supramolecular Chemistry |
Kujawinski joined the faculty at Barnard College in 2002, and held an adjunct position at Columbia University. She spent two years at Barnard College before being awarded a National Science Foundation CAREER Award and returning to the Woods Hole Oceanographic Institution.
In an effort to understand how cellular metabolism impacts biogeochemical cycles, Kujawinski studies intra- and extracellular metabolic profiles. This information allows Kujawinski to identify which factors influence microbial interactions and the transformation of dissolved organic matter. Marine organic matter comprises carbon compounds that contain heteroatoms such as oxygen, nitrogen and sulphur. She makes use of high-resolution mass spectrometry and automated high through-put methods to analyze the low molecular waste organic materials in seawater. The majority of this organic matter is found deep within the ocean, where it serves as an energy source for microorganisms. Kujawinski is interested in the interplay between marine organisms releasing organic matter and organic matter serving as a food source for microorganisms. For example, Kujawinski identified that dihydrocypropanesulfonate and N-Acetyltaurine are released into the ocean by Phytoplankton and later removed by bacteria. She works alongside the Bermuda Institute of Ocean Sciences to establish which chemical compounds are produced by microorganisms. She is also interested in how these microorganisms evolve and how they interact via zooplankton and viruses.
Kujawinski worked on the Deepwater Horizon oil spill. During the ten years after the spill, Kujawinski analyzed what had been learnt in the time following the disaster. She found that the oil spill had helped scientists learn how bacteria are degrading fossil fuels released within the ocean, how the sun catalyzes the breakdown of crude oil, the impact of dispersants and how different parts of the ecosystem recovered.
Kujawinski was appointed Director of the National Science Foundation Center for Chemical Currencies of a Microbial Planet in 2021. The Center looks to understand the behaviour of bioreactive molecules and ocean microbes. | 9 | Geochemistry |
Fluorescent moieties emit photons several nanoseconds after absorption following an exponential decay curve, which differs between dyes and depends on the surrounding solvent. When the dye is attached to a macromolecules the decay curve becomes multiexponential. Conjugated dyes generally have a lifetime between 1–10 ns, a small amount of longer lived exceptions exist, notably pyrene with a lifetime of 400ns in degassed solvents or 100ns in lipids and coronene with 200ns. On a different category of fluorphores are the fluorescent organometals (lanthanides and transition metal-ligand complexes) which have been previously described, which have much longer lifetimes due to the restricted states: lanthanides have lifetimes of 0.5 to 3 ms, while transition metal-ligand complexes have lifetimes of 10 ns to 10 µs. Note that fluorescent lifetime should not be confused with the photodestruction lifetime or the "shelf-life" of a dye. | 1 | Biochemistry |
A wetting transition (Cassie–Wenzel transition) may occur during the process of wetting of a solid (or liquid) surface with a liquid. The transition corresponds to a certain change in contact angle, the macroscopic parameter characterizing wetting. Various contact angles can co-exist on the same solid substrate. Wetting transitions may occur in a different way depending on whether the surface is flat or rough. | 7 | Physical Chemistry |
The ARC gene, located on chromosome 15 in the mouse, chromosome 7 in the rat, and chromosome 8 in the human, is conserved across vertebrate species and has low sequence homology to spectrin, a cytoskeletal protein involved in forming the actin cellular cortex. A number of promoter and enhancer regions have been identified that mediate activity-dependent Arc transcription: a serum response element (SRE; see serum response factor) at ~1.5 kb upstream of the initiation site. a second SRE at ~6.5 kb; and a synaptic activity response element (SARE) sequence at ~7 kb upstream that contains binding sites for cyclic AMP response element-binding protein (CREB), myocyte enhancer factor 2 (MEF2), and SRF.
The 3' UTR of the mRNA contains a cis-acting element required for the localization of Arc to neuronal dendrites, as well as sites for two exon junction complexes (EJCs) that make Arc a natural target for nonsense mediated decay (NMD). Also important for translocation of cytoplasmic Arc mRNA to activated synapses is an 11 nucleotide binding site for heterogeneous nuclear ribonucleoprotein A2 (hnRNP A2).
It is suspected that the ARC gene originated from the gag gene of a Ty3/gypsy retrotransposon and was repurposed for mediating neuron-neuron communication. | 1 | Biochemistry |
Although usually the anion of the mineralizer is most active in dissolving the nutrient material, the cation also exerts an influence in some cases. The mineralizer can interact with impurities on the surface of the crystal and increase the growth rate. For example, the growth rate for sapphire (AlO) and zincite (ZnO) in potassium-containing solution (KOH, KCO) is higher in comparison to that in sodium-containing solution (NaOH, NaCO). This difference is not readily understood, but are attributed the interaction between potassium and an impurity absorbed on the surface. | 7 | Physical Chemistry |
Many applications have been considered, but few have been commercialized. ILs are used in the production of gasoline by catalyzing alkylation.
An IL based on tetraalkylphosphonium iodide is a solvent for tributyltin iodide, which functions as a catalyst to rearrange the monoepoxide of butadiene. This process was commercialized as a route to 2,5-dihydrofuran, but later discontinued. | 7 | Physical Chemistry |
The Kuwajima Taxol total synthesis by the group of Isao Kuwajima of the Tokyo Institute of Technology is one of several efforts in taxol total synthesis published in the 1990s. The total synthesis of Taxol is considered a landmark in organic synthesis.
This synthesis is truly synthetic without any help from small biomolecule precursors and also a linear synthesis with molecule ring construction in the order of A, B, C, D. At some point chirality is locked into the molecule via an asymmetric synthesis step which is unique compared to the other efforts. In common with the other efforts the tail addition is based on the Ojima lactam.
The 20 carbon frame is constructed from several pieces: propargyl alcohol (C1, C2, C14), propionaldehyde (C13, C12, C18), isobutyric acid (C15, C16, C17, C11), Trimethyl(phenylthiomethyl)silane (C10), 2-bromobenzaldehyde (C3 to C9), diethylaluminum cyanide (C19) and trimethylsilylmethyl bromide (C20) | 0 | Organic Chemistry |
Paints, inks, and dyes that are organic are more susceptible to photodegradation than those that are not. Ceramics are almost universally colored with non-organic origin materials so as to allow the material to resist photodegradation even under the most relentless conditions, maintaining its color. | 5 | Photochemistry |
The suffix -ene is used in organic chemistry to form names of organic compounds where the -C=C- group has been attributed the highest priority according to the rules of organic nomenclature. Sometimes a number between hyphens is inserted before it to say that the double bond is between that atom and the atom with the next number up. This suffix comes from the end of the word ethylene, which is the simplest alkene. The final "-e" disappears if it comes before by a suffix that starts with a vowel, e.g. "-enal", which is a compound that contains both a -C=C- bond and an aldehyde functional group. If the other suffix starts with a consonant or "y", the final "-e" remains, e.g. "-enediyne" (which has the "-ene" suffix and also the "-yne" suffix, for a compound with a double bond and two triple bonds.)
A Greek number prefix before the "-ene" indicates how many double bonds there are in the compound, e.g. butadiene.
The suffix "-ene" is also used in inorganic chemistry to indicate a one-atom thick two-dimensional layer of atoms, as in graphene, silicene, stanene, borophene, xenzophene, and germanene. | 0 | Organic Chemistry |
Tissue samples are lysed in buffer supplemented with leupeptin to maintain enzymatic activity. The samples are standardized for protein concentration and then loaded into a polyacrylamide gel for SDS-PAGE. After separation of proteins by molecular weight is complete, the gel is incubated in a renaturing buffer to restore enzymatic activity. During loading, a non-reducing buffer was used to preserve protein disulfide bonds. After the renaturing period, the gel is then incubated in assay buffer to allow the now active cathepsins to proteolyze the gelatin impregnated in the gel. This process takes place overnight. The next day, the gel is analyzed for regions of gelatin degradation by coomassie blue staining. Patches of gel that are no longer blue following a destain wash are noted. These bands are then correlated to their respective molecular weights in order to identify which cathepsins were active in the sample.
Cathepsin K detection by zymography | 1 | Biochemistry |
As a meal containing carbohydrates or protein is eaten and digested, blood glucose levels rise, and the pancreas secretes insulin. Blood glucose from the portal vein enters liver cells (hepatocytes). Insulin acts on the hepatocytes to stimulate the action of several enzymes, including glycogen synthase. Glucose molecules are added to the chains of glycogen as long as both insulin and glucose remain plentiful. In this postprandial or "fed" state, the liver takes in more glucose from the blood than it releases.
After a meal has been digested and glucose levels begin to fall, insulin secretion is reduced, and glycogen synthesis stops. When it is needed for energy, glycogen is broken down and converted again to glucose. Glycogen phosphorylase is the primary enzyme of glycogen breakdown. For the next 8–12 hours, glucose derived from liver glycogen is the primary source of blood glucose used by the rest of the body for fuel.
Glucagon, another hormone produced by the pancreas, in many respects serves as a countersignal to insulin. In response to insulin levels being below normal (when blood levels of glucose begin to fall below the normal range), glucagon is secreted in increasing amounts and stimulates both glycogenolysis (the breakdown of glycogen) and gluconeogenesis (the production of glucose from other sources). | 1 | Biochemistry |
In June 2020, the Cold Atom Laboratory experiment on board the International Space Station successfully created a BEC of rubidium atoms and observed them for over a second in free-fall. Although initially just a proof of function, early results showed that, in the microgravity environment of the ISS, about half of the atoms formed into a magnetically insensitive halo-like cloud around the main body of the BEC. | 7 | Physical Chemistry |
The steric isotope effect is a SKIE that does not involve bond breaking or formation. This effect is attributed to the different vibrational amplitudes of isotopologues. An example of such an effect is the racemization of 9,10-dihydro-4,5-dimethylphenanthrene. The smaller amplitude of vibration for deuterium as compared to hydrogen in C–H (carbon–hydrogen), C–D (carbon–deuterium) bonds results in a smaller van der Waals radius or effective size in addition to a difference in the ZPE between the two. When there is a greater effective bulk of molecules containing one over the other this may be manifested by a steric effect on the rate constant. For the example above deuterium racemizes faster than the hydrogen isotopologue resulting in a steric isotope effect. A model for the steric isotope effect was developed by Bartell. A steric isotope effect is usually small, unless the transformations passes through a transition state with severe steric encumbrance, as in the racemization process shown above.
Another example of the steric isotope effect is in the deslipping reaction of rotaxanes. The deuterium isotope, due to its smaller effective size, allows easier passage of the stoppers through the macrocycle, resulting in faster rates of deslipping for the deuterated rotaxanes. | 7 | Physical Chemistry |
In X-ray crystallography, a difference density map or Fo–Fc map shows the spatial distribution of the difference between the measured electron density of the crystal and the electron density explained by the current model.
A way to compute this map has been formulated for cyro-EM. | 3 | Analytical Chemistry |
The microbubbles used today are composed of a gas core and a surrounding shell. The makeup of these elements may vary depending on the preferred physical and chemical properties. Microbubble shells have been formed with lipids, galactose, albumin, or polymers. The gas core can be made up of air or heavy gases like nitrogen or perfluorocarbon. | 1 | Biochemistry |
TosMIC (toluenesulfonylmethyl isocyanide) is an organic compound with the formula CHCHSOCHNC. The molecule contains both sulfonyl and isocyanide groups. It is a colourless solid that, unlike many isocyanides, is odorless. It is prepared by dehydration of the related formamide derivative. It is used in the Van Leusen reaction which is used to convert ketones to nitriles or in the preparation of oxazoles and imidazoles. The versatility of TosMIC in organic synthesis has been documented. It is a fairly strong carbon acid, with an estimated pK of 14 (compared to 29 for methyl tolyl sulfone), the isocyano group acting as an electron acceptor of strength comparable to an ester group. | 0 | Organic Chemistry |
This is the hybrid of both of the above techniques. The upper part of ascending chromatography can be folded over a rod in order to allow the paper to become descending after crossing the rod. | 3 | Analytical Chemistry |
A sculpture titled Bamboozle, by Jacobus Verhoeff and his son Tom Verhoeff, is in the form of a fragment of the Laves graph, with its vertices represented by multicolored interlocking acrylic triangles. It was installed in 2013 at the Eindhoven University of Technology. | 3 | Analytical Chemistry |
In a common application, potassium thioacetate is combined with alkylating agents to give thioacetate esters (X = halide):
Hydrolysis of these esters affords thiols:
The thioacetate esters can also be cleaved with methanethiol in the presence of stoichiometric base, as illustrated in the preparation of pent-4-yne-1-thiol: | 0 | Organic Chemistry |
Negishi was born in Xinjing (today known as Changchun), the capital of Manchukuo, in July 1935. Following the transfer of his father who worked at the South Manchuria Railway in 1936, he moved to Harbin, and lived eight years there. In 1943, when he was nine, the Negishi family moved to Incheon, and a year later to Kyongsong Prefecture (now Seoul), both in Japanese-occupied Korea. In November 1945, three months after World War II ended, they moved to Japan. Since he excelled as a student, a year ahead of what would have been his graduation from grammar school, he was admitted to an elite secondary school, Shonan High School. At the age of 17, he gained admission to the University of Tokyo. After graduation from the University of Tokyo in 1958, Negishi did his internship at Teijin, where he conducted research on polymer chemistry. Later, he continued his studies in the United States after having won a Fulbright Scholarship and obtained his Ph.D. from the University of Pennsylvania in 1963, under the supervision of professor Allan R. Day. | 0 | Organic Chemistry |
In 1977, Edmonds et al. reported the identification, isolation, and synthesis of major arsenic-containing substance in sea organisms, the arsenobetaine. In 1999, NRC certified arsenobetaine in the dogfish muscle material DORM-2, which became the first matrix reference material certified for arsenobetaine. Before DORM-2, DORM-1 (issued in 1986) served as the reference material for which the concentration of arsenobetaine was widely reported in scientific literature. Besides arsenobetaine, NRC currently offers matrix reference materials certified for methylmercury (TORT-3), dibutyltin, and tributyltin (PACS-3).
* Biological tissues and sediments
** CARP, fish for dioxins, furans, and PCBs
** DOLT, dogfish liver for methylmercury
** DORM, fish protein for methylmercury
** TORT, lobster hepatopancreas for methylmercury and arsenobetaine
** PACS and SOPH, marine sediment for dibutyltin and tributyltin
** SELM, selenium-enriched yeast for methionine and selenomethionine | 1 | Biochemistry |
The clones that bind to a particular epitope with greater strength are more likely to be selected for further proliferation in the germinal centers of the follicles in various lymphoid tissues like the lymph nodes. This is not unlike natural selection: clones are selected for their fitness to attack the epitopes (strength of binding) on the encountered pathogen.
What makes the analogy even stronger is that the B lymphocytes have to compete with each other for signals that promote their survival in the germinal centers. | 1 | Biochemistry |
Next-generation sequencing has enabled a genome-wide approach to identify DNA footprints. Open chromatin assays such as DNase-Seq and FAIRE-Seq have proven to provide a robust regulatory landscape for many cell types. However, these assays require some downstream bioinformatics analyses in order to provide genome-wide DNA footprints. The computational tools proposed can be categorized in two classes: segmentation-based and site-centric approaches.
Segmentation-based methods are based on the application of Hidden Markov models or sliding window methods to segment the genome into open/closed chromatin region. Examples of such methods are: HINT, Boyle method and Neph method. Site-centric methods, on the other hand, find footprints given the open chromatin profile around motif-predicted binding sites, i.e., regulatory regions predicted using DNA-protein sequence information (encoded in structures such as position weight matrix). Examples of these methods are CENTIPEDE and Cuellar-Partida method. | 1 | Biochemistry |
The examples above define a standard drink as 0.6 fluid ounces (14 g or 17.7 mL) of ethanol, whereas other definitions exist, for example 10 grams of ethanol. | 1 | Biochemistry |
TIA1 or Tia1 cytotoxic granule-associated rna binding protein is a 3UTR mRNA binding protein that can bind the 5TOP sequence of 5'TOP mRNAs. It is associated with programmed cell death (apoptosis) and regulates alternative splicing of the gene encoding the Fas receptor, an apoptosis-promoting protein. Under stress conditions, TIA1 localizes to cellular RNA-protein conglomerations called stress granules. It is encoded by the TIA1 gene.
Mutations in the TIA1 gene have been associated with amyotrophic lateral sclerosis, frontotemporal dementia, and Welander distal myopathy. It also plays a crucial role in the development of toxic oligomeric tau in Alzheimer's disease. | 1 | Biochemistry |
Two systems exist for the asymmetric hydrogenation of 2-substituted quinolines with isolated yields generally greater than 80% and ee values generally greater than 90%. The first is an iridium(I)/chiral phosphine/I system, first reported by Zhou et al.. While the first chiral phosphine used in this system was MeOBiPhep, newer iterations have focused on improving the performance of this ligand. To this end, systems use phosphines (or related ligands) with improved air stability, recyclability, ease of preparation, lower catalyst loading and the potential role of achiral phosphine additives. As of October 2012 no mechanism appears to have been proposed, although both the necessity of I or a halogen surrogate and the possible role of the heteroaromatic N in assisting reactivity have been documented.
The second is an organocatalytic transfer hydrogenation system based on Hantzsch esters and a chiral Brønsted acid. In this case, the authors envision a mechanism where the isoquinoline is alternately protonated in an activating step, then reduced by conjugate addition of hydride from the Hantzsch ester.
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Much of the asymmetric hydrogenation chemistry of quinoxalines is closely related to that of the structurally similar quinolines. Effective (and efficient) results can be obtained with an Ir(I)/phophinite/I system and a Hantzsh ester-based organocatalytic system, both of which are similar to the systems discussed earlier with regards to quinolines. | 0 | Organic Chemistry |
Life requires a loss of entropy, or disorder, when molecules organize themselves into living matter. The emergence of life and increased complexity does not contradict the second law of thermodynamics, which states that overall entropy never decreases, since a living organism creates order in some places (e.g. its living body) at the expense of an increase of entropy elsewhere (e.g. heat and waste production).
Multiple sources of energy were available for chemical reactions on the early Earth. Heat from geothermal processes is a standard energy source for chemistry. Other examples include sunlight, lightning, atmospheric entries of micro-meteorites, and implosion of bubbles in sea and ocean waves. This has been confirmed by experiments and simulations.
Unfavorable reactions can be driven by highly favorable ones, as in the case of iron-sulfur chemistry. For example, this was probably important for carbon fixation. Carbon fixation by reaction of CO with HS via iron-sulfur chemistry is favorable, and occurs at neutral pH and 100 °C. Iron-sulfur surfaces, which are abundant near hydrothermal vents, can drive the production of small amounts of amino acids and other biomolecules. | 9 | Geochemistry |
There are a great variety of techniques to generate THz radiation and to detect THz fields. One can, e.g., use an antenna, a quantum-cascade laser, a free-electron laser, or optical rectification to produce well-defined THz sources. The resulting THz field can be characterized via its electric field E(t). Present-day experiments can already output E(t) that has a peak value in the range of MV/cm (megavolts per centimeter). To estimate how strong such fields are, one can compute the level of energy change such fields induce to an electron over microscopic distance of one nanometer (nm), i.e., L = 1 nm. One simply multiplies the peak E(t) with elementary charge e and L to obtain e E(t) L = 100 meV. In other words, such fields have a major effect on electronic systems because the mere field strength of E(t) can induce electronic transitions over microscopic scales. One possibility is to use such THz fields to study Bloch oscillations where semiconductor electrons move through the Brillouin zone, just to return to where they started, giving rise to the Bloch oscillations.
The THz sources can be also extremely short, down to single cycle of THz fields oscillation. For one THz, that means duration in the range of one picosecond (ps). Consequently, one can use THz fields to monitor and control ultrafast processes in semiconductors or to produce ultrafast switching in semiconductor components. Obviously, the combination of ultrafast duration and strong peak E(t') provides vast new possibilities to systematic studies in semiconductors.
Besides the strength and duration of E(t), the THz field's photon energy plays a vital role in semiconductor investigations because it can be made resonant with several intriguing many-body transitions. For example, electrons in conduction band and holes, i.e., electronic vacancies, in valence band attract each other via the Coulomb interaction. Under suitable conditions, electrons and holes can be bound to excitons that are hydrogen-like states of matter. At the same time, the exciton binding energy is few to hundreds of meV that can be matched energetically with a THz photon. Therefore, the presence of excitons can be uniquely detected based on the absorption spectrum of a weak THz field. Also simple states, such as plasma and correlated electron–hole plasma can be monitored or modified by THz fields. | 7 | Physical Chemistry |
In Ellman's original paper, he prepared this reagent by oxidizing 2-nitro-5-chlorobenzaldehyde to the carboxylic acid, introducing the thiol via sodium sulfide, and coupling the monomer by oxidization with iodine. Today, this reagent is readily available commercially. | 1 | Biochemistry |
Mapping the relative orientation of crystalline grains and/or phases helps understand material texture at the micro and nano scales. In a transmission electron microscope, this is accomplished by recording a diffraction pattern at a large number of points (pixels) over a region of the crystalline specimen. By comparing the recorded patterns to a database of known patterns (either previously indexed experimental patterns or simulated patterns), the relative orientation of grains in the field of view can be determined.
Because this process is highly automated, the quality of the recorded diffraction patterns is crucial to the software's ability to accurately compare and assign orientations to each pixel. Thus, the advantages of PED are well-suited for use with this scanning technique. By instead recording a PED pattern at each pixel, dynamical effects are reduced, and the patterns are more easily compared to simulated data, improving the accuracy of the automated phase/orientation assignment. | 3 | Analytical Chemistry |
In attempts to raise the chemical and quantum yields of nitrobenzyl-based PPGs, several beneficial modifications have been identified. The largest increase in quantum yield and reaction rate can be achieved through substitution at the benzylic carbon. However, potential substitutions must leave one hydrogen atom so the photodegradation can proceeded uninhibited.
Additional modifications have targeted the aromatic chromophore. Specifically, multiple studies have confirmed that the use of a 2,6-dinitrobenzyl PPG increases reaction yield. Additionally, depending on the leaving group, the presence of a second nitro-group may nearly quadruple the quantum yield (e.g. Φ = 0.033 to Φ = 0.12 when releasing a carbonate at 365 nm). While one may credit the increase in efficiency to the electronic effects of the second nitro group, this is not the case. Analogous systems with a 2-cyano-6-nitrobenzyl PPG exhibit similar electron-withdrawing effects, but do not provide such a large increase in efficiency. Therefore, the increase in efficiency is likely due to the increased probability of achieving the aci-nitro state; with two nitro groups, an incoming photon will be twice as likely to promote the compound into an excited state.
Finally, changing the excitation wavelength of the PPG may be advantageous. For example, if two PPGs have different excitation wavelengths one group may be removed while the other is left in place. To this end, several nitrobenzyl based PPGs display additional functionality. Common modifications include the use of 2-nitroveratryl (NV) or 6-nitropiperonulmethyl (NP). Both of these modifications induced red-shifting in the compounds' absorption spectra. | 5 | Photochemistry |
KREEP, an acronym built from the letters K (the atomic symbol for potassium), REE (rare-earth elements) and P (for phosphorus), is a geochemical component of some lunar impact breccia and basaltic rocks. Its most significant feature is somewhat enhanced concentration of a majority of so-called "incompatible" elements (those that are concentrated in the liquid phase during magma crystallization) and the heat-producing elements, namely radioactive uranium, thorium, and potassium (due to presence of the radioactive K). | 9 | Geochemistry |
In the chemical industry, the term intermediate may also refer to the (stable) product of a reaction that is itself valuable only as a precursor chemical for other industries. A common example is cumene which is made from benzene and propylene and used to make acetone and phenol in the cumene process. The cumene itself is of relatively little value in and of itself, and is typically only bought and sold by chemical companies. | 7 | Physical Chemistry |
Euhedral crystals (also known as idiomorphic or automorphic crystals) are those that are well-formed, with sharp, easily recognised faces. The opposite is anhedral (also known as xenomorphic or allotriomorphic): a rock with an anhedral texture is composed of mineral grains that have no well-formed crystal faces or cross-section shape in thin section. Anhedral crystal growth occurs in a competitive environment with no free space for the formation of crystal faces. An intermediate texture with some crystal face-formation is termed subhedral (also known as hypidiomorphic or hypautomorphic).
Crystals that grow from cooling liquid magma typically do not form smooth faces or sharp crystal outlines. As magma cools, the crystals grow and eventually touch each other, preventing crystal faces from forming properly or at all.
When snowflakes crystallize, they do not touch each other. Thus, snowflakes form euhedral, six-sided twinned crystals. In rocks, the presence of euhedral crystals may signify that they formed early in the crystallization of liquid magma or perhaps crystallized in a cavity or vug, without steric hindrance, or spatial restrictions, from other crystals. | 3 | Analytical Chemistry |
The experiment relies upon the interaction between optically-generated charge carriers and microwave frequency electromagnetic radiation. The most common approach is to use a resonant cavity. An oscillating voltage is produced using a signal generator such as a voltage controlled oscillator or a Gunn diode. The oscillating current is incident on an antenna, resulting in the emission of microwaves of the same frequency. These microwaves are then directed into a resonant cavity. Because they can transmit microwaves with lower loss than cables, metallic waveguides are often used to form the circuit. With the appropriate cavity dimensions and microwave frequency, a standing wave can be formed with 1 full wavelength filing the cavity.
The sample to be studied is placed at a maximum of the electric field component of the standing wave. Because metals act as cavity walls, the sample needs to have a relatively low free carrier concentration in the dark to be measurable. TRMC is hence best suited to the study of intrinsic or lightly doped semiconductors. Electrons and hole are generated by illuminating the sample with above band gap optical photons. Optical access to the sample is provided by a cavity wall which is both electrically conducting and optically transparent; for example a metallic grating or a transparent conducting oxide.
The photo-generated charge carriers move under the influence of the electric field component of the standing wave, resulting in a change in intensity of microwaves that leave the cavity. The intensity of microwaves out of the cavity is measured as a function of time using an appropriate detector and an oscilloscope. Knowledge of the properties of the cavity can be used to evaluate photoconductance from changes in microwave intensity. | 7 | Physical Chemistry |
Fungi are amongst the primary saprotrophic organisms in an ecosystem, as they are efficient in the decomposition of matter. Wood-decay fungi, especially white rot, secretes extracellular enzymes and acids that break down lignin and cellulose, the two main building blocks of plant fiber. These are long-chain organic (carbon-based) compounds, structurally similar to many organic pollutants. They achieve this using a wide array of enzymes. In the case of polycyclic aromatic hydrocarbons (PAHs), complex organic compounds with fused, highly stable, polycyclic aromatic rings, fungi are very effective in addition to marine environments. The enzymes involved in this degradation are ligninolytic and include lignin peroxidase, versatile peroxidase, manganese peroxidase, general lipase, laccase and sometimes intracellular enzymes, especially the cytochrome P450.
Other toxins fungi are able to degrade into harmless compounds include petroleum fuels, phenols in wastewater, polychlorinated biphenyl (PCB) in contaminated soils using Pleurotus ostreatus, polyurethane in aerobic and anaerobic conditions, such as conditions at the bottom of landfills using two species of the Ecuadorian fungus Pestalotiopsis, and more.
The mechanisms of degradation are not always clear, as the mushroom may be a precursor to subsequent microbial activity rather than individually effective in the removal of pollutants. | 2 | Environmental Chemistry |
The endophenotype concept has also been used in suicide studies. Personality characteristics can be viewed as endophenotypes that may exert a diathesis effect on an individual's susceptibility to suicidal behavior. Although the exact identification of these endophenotypes is controversial, certain traits such as impulsivity and aggression are commonly cited risk factors.
One such genetic basis for one of these at-risk endophenotypes has been suggested in 2007 to be the gene coding for the serotonin receptor 5-HT, known to be relevant in aggressive behaviors. | 2 | Environmental Chemistry |
Temperature ratings for insulations may vary based on what the overall thermocouple construction cable consists of.
Note: T300 is a new high-temperature material that was recently approved by UL for 300 °C operating temperatures. | 8 | Metallurgy |
The Bennett acceptance ratio method (BAR) is an algorithm for estimating the difference in free energy between two systems (usually the systems will be simulated on the computer).
It was suggested by Charles H. Bennett in 1976. | 7 | Physical Chemistry |
Dolly, a Finn-Dorset ewe, was the first mammal to have been successfully cloned from an adult somatic cell. Dolly was formed by taking a cell from the udder of her 6-year-old biological mother. Dollys embryo was created by taking the cell and inserting it into a sheep ovum. It took 435 attempts before an embryo was successful. The embryo was then placed inside a female sheep that went through a normal pregnancy. She was cloned at the Roslin Institute in Scotland by British scientists Sir Ian Wilmut and Keith Campbell and lived there from her birth in 1996 until her death in 2003 when she was six. She was born on 5 July 1996 but not announced to the world until 22 February 1997. Her stuffed remains were placed at Edinburghs Royal Museum, part of the National Museums of Scotland.
Dolly was publicly significant because the effort showed that genetic material from a specific adult cell, designed to express only a distinct subset of its genes, can be redesigned to grow an entirely new organism. Before this demonstration, it had been shown by John Gurdon that nuclei from differentiated cells could give rise to an entire organism after transplantation into an enucleated egg. However, this concept was not yet demonstrated in a mammalian system.
The first mammalian cloning (resulting in Dolly) had a success rate of 29 embryos per 277 fertilized eggs, which produced three lambs at birth, one of which lived. In a bovine experiment involving 70 cloned calves, one-third of the calves died quite young. The first successfully cloned horse, Prometea, took 814 attempts. Notably, although the first clones were frogs, no adult cloned frog has yet been produced from a somatic adult nucleus donor cell.
There were early claims that Dolly had pathologies resembling accelerated aging. Scientists speculated that Dollys death in 2003 was related to the shortening of telomeres, DNA-protein complexes that protect the end of linear chromosomes. However, other researchers, including Ian Wilmut who led the team that successfully cloned Dolly, argue that Dollys early death due to respiratory infection was unrelated to problems with the cloning process. This idea that the nuclei have not irreversibly aged was shown in 2013 to be true for mice.
Dolly was named after performer Dolly Parton because the cells cloned to make her were from a mammary gland cell, and Parton is known for her ample cleavage. | 1 | Biochemistry |
Brain-derived neurotrophic factor (BDNF) is also a myokine, though BDNF produced by contracting muscle is not released into circulation. Rather, BDNF produced in skeletal muscle appears to enhance the oxidation of fat. Skeletal muscle activation through exercise also contributes to an increase in BDNF secretion in the brain. A beneficial effect of BDNF on neuronal function has been noted in multiple studies. Dr. Pedersen writes, "Neurotrophins are a family of structurally related growth factors, including brain-derived neurotrophic factor (BDNF), which exert many of their effects on neurons primarily through Trk receptor tyrosine kinases. Of these, BDNF and its receptor TrkB are most widely and abundantly expressed in the brain. However, recent studies show that BDNF is also expressed in non-neurogenic tissues, including skeletal muscle. BDNF has been shown to regulate neuronal development and to modulate synaptic plasticity. BDNF plays a key role in regulating survival, growth and maintenance of neurons, and BDNF has a bearing on learning and memory. However, BDNF has also been identified as a key component of the hypothalamic pathway that controls body mass and energy homeostasis.
With respect to studies of exercise and brain function, a 2010 report is of particular interest. Erickson et al. have shown that the volume of the anterior hippocampus increased by 2% in response to aerobic training in a randomized controlled trial with 120 older adults. The authors also summarize several previously-established research findings relating to exercise and brain function: (1) Aerobic exercise training increases grey and white matter volume in the prefrontal cortex of older adults and increases the functioning of key nodes in the executive control network. (2) Greater amounts of physical activity have been associated with sparing of prefrontal and temporal brain regions over a 9-y period, which reduces the risk for cognitive impairment. (3) Hippocampal and medial temporal lobe volumes are larger in higher-fit older adults (larger hippocampal volumes have been demonstrated to mediate improvements in spatial memory). (4) Exercise training increases cerebral blood volume and perfusion of the hippocampus.
Regarding the 2010 study, the authors conclude: "We also demonstrate that increased hippocampal volume is associated with greater serum levels of BDNF, a mediator of neurogenesis in the dentate gyrus. Hippocampal volume declined in the control group, but higher preintervention fitness partially attenuated the decline, suggesting that fitness protects against volume loss. Caudate nucleus and thalamus volumes were unaffected by the intervention. These theoretically important findings indicate that aerobic exercise training is effective at reversing hippocampal volume loss in late adulthood, which is accompanied by improved memory function." | 1 | Biochemistry |
In a hydrogen bond, the electronegative atom not covalently attached to the hydrogen is named the proton acceptor, whereas the one covalently bound to the hydrogen is named the proton donor. This nomenclature is recommended by the IUPAC. The hydrogen of the donor is protic and therefore can act as a Lewis acid and the acceptor is the Lewis base. Hydrogen bonds are represented as system, where the dots represent the hydrogen bond. Liquids that display hydrogen bonding (such as water) are called associated liquids.
Hydrogen bonds arise from a combination of electrostatics (multipole-multipole and multipole-induced multipole interactions), covalency (charge transfer by orbital overlap), and dispersion (London forces).
In weaker hydrogen bonds, hydrogen atoms tend to bond to elements such as sulfur (S) or chlorine (Cl); even carbon (C) can serve as a donor, particularly when the carbon or one of its neighbors is electronegative (e.g., in chloroform, aldehydes and terminal acetylenes). Gradually, it was recognized that there are many examples of weaker hydrogen bonding involving donor other than N, O, or F and/or acceptor Ac with electronegativity approaching that of hydrogen (rather than being much more electronegative). Although weak (≈1 kcal/mol), "non-traditional" hydrogen bonding interactions are ubiquitous and influence structures of many kinds of materials.
The definition of hydrogen bonding has gradually broadened over time to include these weaker attractive interactions. In 2011, an IUPAC Task Group recommended a modern evidence-based definition of hydrogen bonding, which was published in the IUPAC journal Pure and Applied Chemistry. This definition specifies: | 6 | Supramolecular Chemistry |
Surprisal analysis was extended to better characterize and understand cellular processes, see figure, biological phenomena and human disease with reference to personalized diagnostics. Surprisal analysis was first utilized to identify genes implicated in the balance state of cells in vitro; the genes mostly present in the balance state were genes directly responsible for the maintenance of cellular homeostasis. Similarly, it has been used to discern two distinct phenotypes during the EMT of cancer cells. | 7 | Physical Chemistry |
Whiting events have a unique effect on the waters around them. The fact that calcium carbonate clouds increase turbidity and light reflectance holds implications for organisms and processes that depend on light. In addition, whiting events can function as a transport mechanism for organic carbon to the benthic zone, which is relevant to nutrient cycling. The cyanobacteria abundant clouds also hold the potential to act as a means to study the microorganism's role in carbon cycling (especially in relation to climate change) and their possible role in finding petroleum source rocks. | 9 | Geochemistry |
The members of the order Pasteurellales are currently distinguished mainly based on their position in the branching of the 16srRNA tree. There are currently very few molecular markers known that can distinguish members of this order from other bacteria. A CSI approach was recently used to elucidate the phylogenetic relationships between the species in this order; more than 40 CSIs were discovered that were uniquely shared by all or most of the species. Two major clades are formed within this Pasteurellales: Clade I, encompassing Aggregatibacter, Pasteurella, Actinobacillus succinogenes, Mannheimia succiniciproducens, Haemophilus influenzae and Haemophilus somnus, was supported by 13 CSIs. Clade II, encompassing Actinobacillus pleuropneumoniae, Actinobacillus minor, Haemophilus ducreyi, Mannheimia haemolytica and Haemophilus parasuis, was supported by 9 CSIs. Based on these results, it was proposed that Pasteurellales be divided from its current one family into two different ones. Additionally, the signatures described would provide novel means of identifying undiscovered Pasteurellales species. | 1 | Biochemistry |
Common roll-to-roll coating processes include:
* Air knife coating
* Anilox coater
* Flexo coater
* Gap Coating
** Knife-over-roll coating
* Gravure coating
* Hot melt coating- when the necessary coating viscosity is achieved by temperature rather than solution of the polymers etc. This method commonly implies slot-die coating above room temperature, but it also is possible to have hot-melt roller coating; hot-melt metering-rod coating, etc.
* Immersion dip coating
* Kiss coating
* Metering rod (Meyer bar) coating
* Roller coating
** Forward roller coating
** Reverse roll coating
* Silk Screen coater
** Rotary screen
*Slot Die coating - Slot die coating was originally developed in the 1950s. Slot die coating has a low operational cost and is an easily scaled processing technique for depositing thin and uniform films rapidly, while minimizing material waste. Slot die coating technology is used to deposit a variety of liquid chemistries onto substrates of various materials such as glass, metal, and polymers by precisely metering the process fluid and dispensing it at a controlled rate while the coating die is precisely moved relative to the substrate. The complex inner geometry of conventional slot dies require machining or can be accomplished with 3-D printing.
*Extrusion coating - generally high pressure, often high temperature, and with the web travelling much faster than the speed of the extruded polymer
**Curtain coating- low viscosity, with the slot vertically above the web and a gap between slot-die and web.
** Slide coating- bead coating with an angled slide between the slot-die and the bead. Commonly used for multilayer coating in the photographic industry.
** Slot die bead coating- typically with the web backed by a roller and a very small gap between slot-die and web.
** Tensioned-web slot-die coating- with no backing for the web.
* Inkjet printing
* Lithography
* Flexography | 8 | Metallurgy |
The raw sequencing data is then processed through bioinformatics (e.g., the GemCode analysis software developed by 10x Genomics) to remove low-quality reads and to assign reads to their respective barcodes. Reads can be aligned to a reference genome or assembled de novo to generate long-range contigs. The read alignment step is important for determining the order and orientation of the long DNA fragments, and for identifying genomic variations, such as insertions or deletions. | 1 | Biochemistry |
One of the most important advantages of Fourier-transform spectroscopy was shown by P. B. Fellgett, an early advocate of the method. The Fellgett advantage, also known as the multiplex principle, states that when obtaining a spectrum when measurement noise is dominated by detector noise (which is independent of the power of radiation incident on the detector), a multiplex spectrometer such as a Fourier-transform spectrometer will produce a relative improvement in signal-to-noise ratio, compared to an equivalent scanning monochromator, of the order of the square root of m, where m is the number of sample points comprising the spectrum. However, if the detector is shot-noise dominated, the noise will be proportional to the square root of the power, thus for a broad boxcar spectrum (continuous broadband source), the noise is proportional to the square root of m, thus precisely offset the Fellgetts advantage. For line emission sources the situation is even worse and there is a distinct `multiplex disadvantage as the shot noise from a strong emission component will overwhelm the fainter components of the spectrum. Shot noise is the main reason Fourier-transform spectrometry was never popular for ultraviolet (UV) and visible spectra. | 7 | Physical Chemistry |
While the JamesonCell continued to expand in base metals concentrate cleaning, SX–EW electrolyte cleaning and coal fines recovery applications, it also found new applications in cleaning potash slimes and was adopted by the Philex Mining Corporation as the sole flotation machine for its Benguet copper concentrator. This is not the normal application for the Cell. No other metals concentrator operates solely using Jameson Cells. | 8 | Metallurgy |
In organic chemistry, isothiouronium is a functional group with the formula [RSC(NH)] (R = alkyl, aryl) and is the acid salt of isothiourea. The H centres can also be replaced by alkyl and aryl. Structurally, these cations resemble guanidinium cations. The CNS core is planar and the C–N bonds are short. | 0 | Organic Chemistry |
Contrary to the abundance of theoretical and experimental work on the MPI of rare gas atoms, the amount of research on the prediction of the rate of MPI of neutral molecules was scarce until recently. Walsh et al. have measured the MPI rate of some diatomic molecules interacting with a CO laser. They found that these molecules are tunnel-ionized as if they were structureless atoms with an ionization potential equivalent to that of the molecular ground state. A. Talebpour et al. were able to quantitatively fit the ionization yield of diatomic molecules interacting with a Ti:sapphire laser pulse. The conclusion of the work was that the MPI rate of a diatomic molecule can be predicted from the PPT model by assuming that the electron tunnels through a barrier given by instead of barrier which is used in the calculation of the MPI rate of atoms. The importance of this finding is in its practicality; the only parameter needed for predicting the MPI rate of a diatomic molecule is a single parameter, . Using the semi-empirical model for the MPI rate of unsaturated hydrocarbons is feasible. This simplistic view ignores the ionization dependence on orientation of molecular axis with respect to polarization of the electric field of the laser, which is determined by the symmetries of the molecular orbitals. This dependence can be used to follow molecular dynamics using strong field multiphoton ionization. | 7 | Physical Chemistry |
The chemical reaction for the dissolution of gold, the "Elsner equation", follows:
: 4Au + 8NaCN + O + 2HO → 4Na[Au(CN)] + 4NaOH
Potassium cyanide and calcium cyanide are sometimes used in place of sodium cyanide.
Gold is one of the few metals that dissolves in the presence of cyanide ions and oxygen. The soluble gold species is dicyanoaurate. from which it can be recovered by adsorption onto activated carbon. | 8 | Metallurgy |
The Creighton process involves the hydrogenation of a 6 carbon chain aldehyde. The reactant is 2,3,4,5,6-pentahydroxyhexanal (an aldehyde) and the product is 1,2,3,4,5,6-hexanehexol (an alcohol). The product thus has two more hydrogen atoms than the reactant: -CHO is replaced by -CHOH.
The Creighton process was patented in the 1920s. | 0 | Organic Chemistry |
Trace elements serve as regulators of biological processes in the ocean, influencing marine ecosystem dynamics and the carbon cycle. Despite this significance, knowledge of the marine biogeochemical cycles of these essential micronutrients is surprisingly incomplete. GEOTRACES is quantifying the supply, removal, internal cycling, chemical form and distribution of essential micronutrients and other trace elements. Understanding the sensitivity of these biogeochemical cycles to changing environmental conditions will improve projections of the ocean’s response to global change.
The cycles of many trace elements and isotopes have been impacted significantly by human activity, which has increased the discharge of harmful elements into the ocean. GEOTRACES’ emphasis on understanding the processes regulating the marine biogeochemical cycles of trace elements will improve prediction of the transport and fate of contaminants in the ocean and thereby help to protect the ocean environment.
Much of what is known about ocean conditions in the past and, therefore, about the ocean’s role in climate variability is derived from trace element and isotope patterns recorded in marine archives (sediments, corals, etc.). Greater knowledge of the processes governing these tracers in the modern ocean will improve interpretation of ocean conditions in the past, from which more reliable prediction of future changes can be made. | 9 | Geochemistry |
The ammonia produced in neurons is fixed into α-ketoglutarate by the glutamate-dehydrogenase reaction to form glutamate, then transaminated by alanine aminotransferase into lactate-derived pyruvate to form alanine, which is exported to astrocytes. In the astrocytes, this process is then reversed, and lactate is transported in the other direction. | 1 | Biochemistry |
Several single nucleotide polymorphisms within the TCF7L2 gene have been associated with type 2 diabetes. Studies conducted by Ravindranath Duggirala and Michael Stern at The University of Texas Health Science Center at San Antonio were the first to identify strong linkage for type 2 diabetes at a region on Chromosome 10 in Mexican Americans This signal was later refined by Struan Grant and colleagues at DeCODE genetics and isolated to the TCF7L2 gene. The molecular and physiological mechanisms underlying the association of TCF7L2 with type 2 diabetes are under active investigation, but it is likely that TCF7L2 has important biological roles in multiple metabolic tissues, including the pancreas, liver and adipose tissue. TCF7L2 polymorphisms can increase susceptibility to type 2 diabetes by decreasing the production of glucagon-like peptide-1 (GLP-1). | 1 | Biochemistry |
The term antiaromaticity was first proposed by Ronald Breslow in 1967 as "a situation in which a cyclic delocalisation of electrons is destabilising". The IUPAC criteria for antiaromaticity are as follows:
#The molecule must be cyclic.
#The molecule must be planar.
#The molecule must have a complete conjugated π-electron system within the ring.
#The molecule must have 4n π-electrons where n is any integer within the conjugated π-system.
This differs from aromaticity only in the fourth criterion: aromatic molecules have 4n +2 π-electrons in the conjugated π system and therefore follow Hückel’s rule. Non-aromatic molecules are either noncyclic, nonplanar, or do not have a complete conjugated π system within the ring.
Having a planar ring system is essential for maximizing the overlap between the p orbitals which make up the conjugated π system. This explains why being a planar, cyclic molecule is a key characteristic of both aromatic and antiaromatic molecules. However, in reality, it is difficult to determine whether or not a molecule is completely conjugated simply by looking at its structure: sometimes molecules can distort in order to relieve strain and this distortion has the potential to disrupt the conjugation. Thus, additional efforts must be taken in order to determine whether or not a certain molecule is genuinely antiaromatic.
An antiaromatic compound may demonstrate its antiaromaticity both kinetically and thermodynamically. As will be discussed later, antiaromatic compounds experience exceptionally high chemical reactivity (being highly reactive is not “indicative” of an antiaromatic compound, it merely suggests that the compound could be antiaromatic). An antiaromatic compound may also be recognized thermodynamically by measuring the energy of the cyclic conjugated π electron system. In an antiaromatic compound, the amount of conjugation energy in the molecule will be significantly higher than in an appropriate reference compound.
In reality, it is recommended that one analyze the structure of a potentially antiaromatic compound extensively before declaring that it is indeed antiaromatic. If an experimentally determined structure of the molecule in question does not exist, a computational analysis must be performed. The potential energy of the molecule should be probed for various geometries in order to assess any distortion from a symmetric planar conformation.
This procedure is recommended because there have been multiple instances in the past where molecules which appear to be antiaromatic on paper turn out to be not truly so in actuality. The most famous (and heavily debated) of these molecules is cyclobutadiene, as is discussed later.
Examples of antiaromatic compounds are pentalene (A), biphenylene (B), cyclopentadienyl cation (C). The prototypical example of antiaromaticity, cyclobutadiene, is the subject of debate, with some scientists arguing that antiaromaticity is not a major factor contributing to its destabilization. Cyclooctatetraene appears at first glance to be antiaromatic, but is an excellent example of a molecule adopting a non-planar geometry to avoid the destabilization that results from antiaromaticity. Because antiaromatic compounds are often short-lived and difficult to work with experimentally, antiaromatic destabilization energy is often modeled by simulation rather than by experimentation. | 7 | Physical Chemistry |
Human milk oligosaccharides can be synthesized in large quantities using precision industrial fermentation methods e.g. by the commonly used, non-pathogenic bacteria Escherichia coli. During the fermentation process the bacteria are fed with a carbon-source (e.g. glucose), salts, minerals and trace elements under aseptic conditions in a stainless steel bioreactor, while lactose is added to the process as precursor molecule. Bacteria are then converting the lactose into human milk oligosaccharides by decorating it with other sugar monomers. After the fermentation process the HMOs are completely separated from the bacteria, proteins and DNA using different filtration techniques. Subsequently the HMOs are purified, crystallized, dried, packaged and delivered to infant formula manufacturers where they are mixed with other components of infant formula. | 0 | Organic Chemistry |
TNP-ATP should be stored at −20 degrees Celsius, in the dark, and used under minimal lighting conditions. When in solution, TNP-ATP has a shelf-life of about 30 days. | 7 | Physical Chemistry |
Through the process of alternative splicing, the CKLF gene encodes 4 CKLF protein isoforms, i.e. proteins made from different areas of the same gene. These isoforms are 1) CKLF1 and CKLF3 proteins that consist of 99 and 67 amino acids, respectively, and are secreted from their parent cells and 2) CKLF2 (which is the full-length product of the CKLF gene) and CKLF4 proteins which consist of 152 and 120 amino acids, respectively, and are located in the membranes of their parent cells. | 1 | Biochemistry |
Cytochrome c is an essential component of the respiratory electron transport chain in mitochondria. The heme group of cytochrome c accepts electrons from the bc Complex III and transports them to Complex IV, while it transfers energy in the opposite direction.
Cytochrome c can also catalyze several redox reactions such as hydroxylation and aromatic oxidation, and shows peroxidase activity by oxidation of various electron donors such as 2,2-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS), 2-keto-4-thiomethyl butyric acid and 4-aminoantipyrine.
A bacterial cytochrome c functions as a nitrite reductase. | 1 | Biochemistry |
In 2016, microcystin had been found in San Francisco Bay Area shellfish in seawater, apparently from freshwater runoff, exacerbated by drought. | 2 | Environmental Chemistry |
Theories for the origin of homochirality in the molecules of life can be classified as deterministic or based on chance depending on their proposed mechanism. If there is a relationship between cause and effect — that is, a specific chiral field or influence causing the mirror symmetry breaking — the theory is classified as deterministic; otherwise it is classified as a theory based on chance (in the sense of randomness) mechanisms.
Another classification for the different theories of the origin of biological homochirality could be made depending on whether life emerged before the enantiodiscrimination step (biotic theories) or afterwards (abiotic theories). Biotic theories claim that homochirality is simply a result of the natural autoamplification process of life—that either the formation of life as preferring one chirality or the other was a chance rare event which happened to occur with the chiralities we observe, or that all chiralities of life emerged rapidly but due to catastrophic events and strong competition, the other unobserved chiral preferences were wiped out by the preponderance and metabolic, enantiomeric enrichment from the winning chirality choices. If this was the case, remains of the extinct chirality sign should be found. Since this is not the case, nowadays biotic theories are no longer supported.
The emergence of chirality consensus as a natural autoamplification process has also been associated with the 2nd law of thermodynamics. | 4 | Stereochemistry |
The screw axis appears in the dual quaternion formulation of a spatial displacement . The dual quaternion is constructed from the dual vector defining the screw axis and the dual angle , where φ is the rotation about and d the slide along this axis, which defines the displacement D to obtain,
A spatial displacement of points q represented as a vector quaternion can be defined using quaternions as the mapping
where d is translation vector quaternion and S is a unit quaternion, also called a versor, given by
that defines a rotation by 2θ around an axis S.
In the proper Euclidean group E(3) a rotation may be conjugated with a translation to move it to a parallel rotation axis. Such a conjugation, using quaternion homographies, produces the appropriate screw axis to express the given spatial displacement as a screw displacement, in accord with Chasles’ theorem. | 3 | Analytical Chemistry |
Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. These representations include closely packed spheres (CPK models) made of plastic, metal wires for skeletal models, graphic computations and animations by computers, artistic rendering. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
The more advanced, computer-based molecular models of DNA involve molecular dynamics simulations and quantum mechanics computations of vibro-rotations, delocalized molecular orbitals (MOs), electric dipole moments, hydrogen-bonding, and so on. DNA molecular dynamics modeling involves simulating deoxyribonucleic acid (DNA) molecular geometry and topology changes with time as a result of both intra- and inter- molecular interactions of DNA. Whereas molecular models of DNA molecules such as closely packed spheres (CPK models) made of plastic or metal wires for skeletal models are useful representations of static DNA structures, their usefulness is very limited for representing complex DNA dynamics. Computer molecular modeling allows both animations and molecular dynamics simulations that are very important to understand how DNA functions in vivo. | 4 | Stereochemistry |
Although Golden Gate Cloning speeds up multisegment cloning, careful design of donor and recipient plasmids is required. Scientists at New England Biolabs have successfully demonstrated the assembly of 35 fragments via a single-tube Golden Gate Assembly reaction. Critical to this method of assembly, the vector backbone of the destination plasmid and all the assembly fragments are flanked by Type IIS restriction enzyme recognition sites, as this subtype of restriction enzymes cut downstream from their recognition sites. After cutting, each assembly active piece of DNA has unique overhangs that anneal to the next fragment of DNA in the planned assembly and become ligated, building the assembly. While it is also possible for an overhang to anneal back to its original complementary overhang associated with the upstream recognition site and become ligated, re-forming the original sequence, this will be susceptible to further cutting throughout the assembly reaction. | 1 | Biochemistry |
During DNA damage or cellular stress PARPs are activated, leading to an increase in the amount of poly(ADP-ribose) and a decrease in the amount of NAD. For over a decade it was thought that PARP1 was the only poly(ADP-ribose)polymerase in mammalian cells, therefore this enzyme has been the most studied. Caspases are a family of cysteine proteases that are known to play an essential role in programmed cell death. This protease cleaves PARP-1 into two fragments, leaving it completely inactive, to limit poly(ADP-ribose) production. One of its fragments migrates from the nucleus to the cytoplasm and is thought to become a target of autoimmunity.
During caspase-independent apoptosis, also called parthanatos, poly(ADP-ribose) accumulation can occur due to activation of PARPs or inactivation of poly(ADP-ribose)glycohydrolase, an enzyme that hydrolyses poly(ADP-ribose) to produce free ADP-ribose. Studies have shown poly(ADP-ribose) drives the translocation of the apoptosis inducing factor protein to the nucleus where it will mediate DNA fragmentation. It has been suggested that if a failure of caspase activation under stress conditions were to occur, necroptosis would take place. Overactivation of PARPs has led to a necrotic cell death regulated by the tumor necrosis factor protein. Though the mechanism is not yet understood, PARP inhibitors have been shown to affect necroptosis. | 1 | Biochemistry |
A selenonic acid is an organoselenium compound containing the SeOH functional group. Selenonic acids are the selenium analogs of sulfonic acids. Examples of the acid are rare. Benzeneselenonic acid is a white solid. It can be prepared by the oxidation of benzeneselenol. | 0 | Organic Chemistry |
In silico experiments with Monte Carlo simulations demonstrated that both SPINA-GT and SPINA-GD can be estimated with sufficient reliability, even if laboratory assays have limited accuracy. This was confirmed by longitudinal in vivo studies that showed that GT has lower intraindividual variation (i.e. higher reliability) than TSH, FT4 or FT3. | 1 | Biochemistry |
Several techniques exist to produce pre-alloyed powder, such as Grade 5. In the hydride-dehydride process feedstock such as solid scrap, billet or machined turnings are processed to remove contaminants, hydrogenated to produce brittle material then ground under argon in a vibratory ball mill, typically at 400 °C for 4 hours at a pressure of 1 psi for Ti Grade 5. The resulting particles are angular and measure between 50 and 300 μm. Cold compaction after dehydrogenation of the powder, followed by either vacuum hot pressing (in this case the dehydrogenation process can be bypassed as hydrogen is removed under vacuum) or HIP and a final vacuum anneal, produces powders with hydrogen below 125 ppm. The possible presence of contaminants makes these powders unsuitable for use in critical aircraft applications.
In the plasma rotating electrode process (PREP), the feedstock, such as Ti Grade 5, is in the form of a rotating bar which is arced with gas plasma. The molten metal is centrifugally flung off the bar, cools down and is collected. The powders produced are spherical; between 100 and 300 μm is size, with good packing and flow characteristics, making the powder ideal for high quality, near net shapes produced by HIP, such as aviation parts and porous coatings on hip prostheses.
In the titanium gas atomisation (TGA) process, titanium is vacuum induction skull melted in a water cooled copper crucible, the metal tapped and the molten metal stream atomized with a stream of high pressure inert gas. The tiny droplets are spherical and measure between 50 and 350 μm. The TGA process has been used to produce a wide variety of materials such as commercially pure (CP) titanium, conventional alpha-beta and beta alloys.
In plasma atomization (PA) process, a titanium wire is atomized by 3 inert gas plasma jets to form spherical metal powders. The distribution of diameter obtained in the PA process ranges between 0–200 μm and the powders obtained is very pure. The PA process specializes in the production of high temperature melting material as titanium (CP-Ti, Ti-6Al-4V), niobium, molybdenum, tantalum and many more. | 8 | Metallurgy |
As indicated in the Figure above, captioned "Demethylation of 5-methylcytosine," the first step in active demethylation is a TET oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). The demethylation process, in some tissues and at some genome locations, may stop at that point. As reviewed by Uribe-Lewis et al., in addition to being an intermediate in active DNA demethylation, 5hmC is often a stable DNA modification. Within the genome, 5hmC is located at transcriptionally active genes, regulatory elements and chromatin associated complexes. In particular, 5hmC is dynamically changed and positively correlated with active gene transcription during cell lineage specification, and high levels of 5hmC are found in embryonic stem cells and in the central nervous system. In humans, defective 5-hydroxymethylating activity is associated with a phenotype of lymphoproliferation, immunodeficiency and autoimmunity. | 1 | Biochemistry |
Andesitic magma is an intermediate magma and is approximately evenly dispersed regarding iron, magnesium, calcium, sodium, and potassium. The silica composition of andesitic magma ranges from 55 - 65 wt.%. It forms in temperatures ranging from approximately 1470 °F to 1830 °F. Andesitic magma has an intermediate viscosity and volatiles content. It forms minerals such as plagioclase feldspar, mica, and amphibole. | 9 | Geochemistry |
In DVD drives, the signal produced from the disc is a reflection of the addressing laser beam, and is therefore very intense. For 3D optical storage however, the signal must be generated within the tiny volume that is addressed, and therefore it is much weaker than the laser light. In addition, fluorescence is radiated in all directions from the addressed point, so special light collection optics must be used to maximize the signal. | 5 | Photochemistry |
In the 1950s, Norwegian scientist Scholander set out to explain how Arctic fish can survive in water colder than the freezing point of their blood. His experiments led him to believe there was “antifreeze” in the blood of Arctic fish. Then in the late 1960s, animal biologist Arthur DeVries was able to isolate the antifreeze protein through his investigation of Antarctic fish. These proteins were later called antifreeze glycoproteins (AFGPs) or antifreeze glycopeptides to distinguish them from newly discovered nonglycoprotein biological antifreeze agents (AFPs). DeVries worked with Robert Feeney (1970) to characterize the chemical and physical properties of antifreeze proteins. In 1992, Griffith et al. documented their discovery of AFP in winter rye leaves. Around the same time, Urrutia, Duman and Knight (1992) documented thermal hysteresis protein in angiosperms. The next year, Duman and Olsen noted AFPs had also been discovered in over 23 species of angiosperms, including ones eaten by humans. They reported their presence in fungi and bacteria as well. | 1 | Biochemistry |
In 1967, Charles Pedersen, who was a chemist working at DuPont, discovered a simple method of synthesizing a crown ether when he was trying to prepare a complexing agent for divalent cations. His strategy entailed linking two catecholate groups through one hydroxyl on each molecule. This linking defines a polydentate ligand that could partially envelop the cation and, by ionization of the phenolic hydroxyls, neutralize the bound dication. He was surprised to isolate a by-product that strongly complexed potassium cations. Citing earlier work on the dissolution of potassium in 16-crown-4, he realized that the cyclic polyethers represented a new class of complexing agents that were capable of binding alkali metal cations. He proceeded to report systematic studies of the synthesis and binding properties of crown ethers in a seminal series of papers. The fields of organic synthesis, phase transfer catalysts, and other emerging disciplines benefited from the discovery of crown ethers. Pedersen particularly popularized the dibenzo crown ethers.
Pedersen shared the 1987 Nobel Prize in Chemistry for the discovery of the synthetic routes to, and binding properties of, crown ethers. | 6 | Supramolecular Chemistry |
:The following carbon numbering system of porphyrins is an older numbering used by biochemists and not the 1–24 numbering system recommended by IUPAC, which is shown in the table above.
*Heme l is the derivative of heme B which is covalently attached to the protein of lactoperoxidase, eosinophil peroxidase, and thyroid peroxidase. The addition of peroxide with the glutamyl-375 and aspartyl-225 of lactoperoxidase forms ester bonds between these amino acid residues and the heme 1- and 5-methyl groups, respectively. Similar ester bonds with these two methyl groups are thought to form in eosinophil and thyroid peroxidases. Heme l is one important characteristic of animal peroxidases; plant peroxidases incorporate heme B. Lactoperoxidase and eosinophil peroxidase are protective enzymes responsible for the destruction of invading bacteria and virus. Thyroid peroxidase is the enzyme catalyzing the biosynthesis of the important thyroid hormones. Because lactoperoxidase destroys invading organisms in the lungs and excrement, it is thought to be an important protective enzyme.
*Heme m is the derivative of heme B covalently bound at the active site of myeloperoxidase. Heme m contains the two ester bonds at the heme 1- and 5-methyl groups also present in heme l of other mammalian peroxidases, such as lactoperoxidase and eosinophil peroxidase. In addition, a unique sulfonamide ion linkage between the sulfur of a methionyl amino-acid residue and the heme 2-vinyl group is formed, giving this enzyme the unique capability of easily oxidizing chloride and bromide ions to hypochlorite and hypobromite. Myeloperoxidase is present in mammalian neutrophils and is responsible for the destruction of invading bacteria and viral agents. It perhaps synthesizes hypobromite by "mistake". Both hypochlorite and hypobromite are very reactive species responsible for the production of halogenated nucleosides, which are mutagenic compounds.
*Heme D is another derivative of heme B, but in which the propionic acid side chain at the carbon of position 6, which is also hydroxylated, forms a γ-spirolactone. Ring III is also hydroxylated at position 5, in a conformation trans to the new lactone group. Heme D is the site for oxygen reduction to water of many types of bacteria at low oxygen tension.
*Heme S is related to heme B by having a formyl group at position 2 in place of the 2-vinyl group. Heme S is found in the hemoglobin of a few species of marine worms. The correct structures of heme B and heme S were first elucidated by German chemist Hans Fischer.
The names of cytochromes typically (but not always) reflect the kinds of hemes they contain: cytochrome a contains heme A, cytochrome c contains heme C, etc. This convention may have been first introduced with the publication of the structure of heme A. | 1 | Biochemistry |
The L-alanine derivative β-methylamino-L-alanine (BMAA) has long been identified as a neurotoxin which was first associated with the amyotrophic lateral sclerosis/parkinsonism–dementia complex (Lytico-bodig disease) in the Chamorro people of Guam. The widespread occurrence of BMAA can be attributed to cyanobacteria which produce BMAA as a result of complex reactions under nitrogen stress. Following research, excitotoxicity appears to be the likely mode of action for BMAA which acts as a glutamate agonist, activating AMPA and NMDA receptors and causing damage to cells even at relatively low concentrations of 10 μM. The subsequent uncontrolled influx of Ca then leads to the pathophysiology described above. Further evidence of the role of BMAA as an excitotoxin is rooted in the ability of NMDA antagonists like MK801 to block the action of BMAA. More recently, evidence has been found that BMAA is misincorporated in place of L-serine in human proteins. A considerable portion of the research relating to the toxicity of BMAA has been conducted on rodents. A study published in 2016 with vervets (Chlorocebus sabaeus) in St. Kitts, which are homozygous for the apoE4 (APOE-ε4) allele (a condition which in humans is a risk factor for Alzheimers disease), found that vervets orally administered BMAA developed hallmark histopathology features of Alzheimers Disease including amyloid beta plaques and neurofibrillary tangle accumulation. Vervets in the trial fed smaller doses of BMAA were found to have correlative decreases in these pathology features. This study demonstrates that BMAA, an environmental toxin, can trigger neurodegenerative disease as a result of a gene/environment interaction. While BMAA has been detected in brain tissue of deceased ALS/PDC patients, further insight is required to trace neurodegenerative pathology in humans to BMAA. | 1 | Biochemistry |
Because gas molecules diffract electrons and affect the quality of the electron gun, RHEED experiments are performed under vacuum. The RHEED system must operate at a pressure low enough to prevent significant scattering of the electron beams by gas molecules in the chamber. At electron energies of 10keV, a chamber pressure of 10 mbar or lower is necessary to prevent significant scattering of electrons by the background gas. In practice, RHEED systems are operated under ultra high vacuums. The chamber pressure is minimized as much as possible in order to optimize the process. The vacuum conditions limit the types of materials and processes that can be monitored in situ with RHEED. | 3 | Analytical Chemistry |
The neuroprostanes are prostaglandin-like compounds formed in vivo from the free radical-catalyzed peroxidation
of essential fatty acids (primarily docosahexaenoic acid) without the direct action of cyclooxygenase (COX) enzymes. The result is the formation of isoprostane-like compounds F4-, D4-, E4-, A4-, and J4-neuroprostanes which have been shown to be produced in vivo. These oxygenated essential fatty acids possess potent biological activity as anti-inflammatory mediators inhibiting the response of human macrophages that augment the perception of pain. | 1 | Biochemistry |
The mechanism of the Kröhnke pyridine synthesis begins with enolization of α-pyridinium methyl ketone 4 followed by 1,4-addition to the α, β-unsaturated ketone 5 to form the Michael adduct 6, which immediately tautomerizes to the 1,5-dicarbonyl 7. Addition of ammonia to 7 followed by dehydration via 8 generates the imine intermediate 9., The imine intermediate is then deprotonated to enamine 10 and cyclizes with the carbonyl to generate intermediate 11. The pyridinium cation is then eliminated to form hydroxy-dienamine 12. Aromatization of 12 via subsequent loss of water generates the desired pyridine heterocycle 13. | 0 | Organic Chemistry |
The TET enzymes are a family of ten-eleven translocation (TET) methylcytosine dioxygenases. They are instrumental in DNA demethylation. 5-Methylcytosine (see first Figure) is a methylated form of the DNA base cytosine (C) that often regulates gene transcription and has several other functions in the genome.
Demethylation by TET enzymes (see second Figure), can alter the regulation of transcription. The TET enzymes catalyze the hydroxylation of DNA 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and can further catalyse oxidation of 5hmC to 5-formylcytosine (5fC) and then to 5-carboxycytosine (5caC). 5fC and 5caC can be removed from the DNA base sequence by base excision repair and replaced by cytosine in the base sequence.
TET enzymes have central roles in DNA demethylation required during embryogenesis, gametogenesis, memory, learning, addiction and pain perception. | 1 | Biochemistry |
The first isolation of deoxyribonucleic acid (DNA) was done in 1869 by Friedrich Miescher. DNA extraction is the process of isolating DNA from the cells of an organism isolated from a sample, typically a biological sample such as blood, saliva, or tissue. It involves breaking open the cells, removing proteins and other contaminants, and purifying the DNA so that it is free of other cellular components. The purified DNA can then be used for downstream applications such as PCR, sequencing, or cloning. Currently, it is a routine procedure in molecular biology or forensic analyses.
This process can be done in several ways, depending on the type of the sample and the downstream application, the most common methods are: mechanical, chemical and enzymatic lysis, precipitation, purification, and concentration. The specific method used to extract the DNA, such as phenol-chloroform extraction, alcohol precipitation, or silica-based purification.
For the chemical method, many different kits are used for extraction, and selecting the correct one will save time on kit optimization and extraction procedures. PCR sensitivity detection is considered to show the variation between the commercial kits.
There are many different methods for extracting DNA, but some common steps include:
# Lysis: This step involves breaking open the cells to release the DNA. For example, in the case of bacterial cells, a solution of detergent and salt (such as SDS) can be used to disrupt the cell membrane and release the DNA. For plant and animal cells, mechanical or enzymatic methods are often used.
# Precipitation: Once the DNA is released, proteins and other contaminants must be removed. This is typically done by adding a precipitating agent, such as alcohol (such as ethanol or isopropanol), or a salt (such as ammonium acetate). The DNA will form a pellet at the bottom of the solution, while the contaminants will remain in the liquid.
# Purification: After the DNA is precipitated, it is usually further purified by using column-based methods. For example, silica-based spin columns can be used to bind the DNA, while contaminants are washed away. Alternatively, a centrifugation step can be used to purify the DNA by spinning it down to the bottom of a tube.
# Concentration: Finally, the amount of DNA present is usually increased by removing any remaining liquid. This is typically done by using a vacuum centrifugation or a lyophilization (freeze-drying) step.
It's worth noting that some variations on these steps may be used depending on the specific DNA extraction protocol. Additionally, some kits are commercially available that include reagents and protocols specifically tailored to a specific type of sample. | 1 | Biochemistry |
Alkynylation finds use in synthesis of pharmaceuticals, particularly in the preparation of steroid hormones. For example, ethynylation of 17-ketosteroids produces important contraceptive medications known as progestins. Examples include drugs such as Norethisterone, Ethisterone, and Lynestrenol. Hydrogenation of these compounds produces anabolic steroids with oral bioavailability, such as Norethandrolone.
Alkynylation is used to prepare commodity chemicals such as propargyl alcohol, butynediol, 2-methylbut-3-yn-2-ol (a precursor to isoprenes such as vitamin A), 3-hexyne-2,5-diol (a precursor to Furaneol), and sulcatone (a precursor to Linalool). | 0 | Organic Chemistry |
The chloroplast stroma contains many proteins, though the most common and important is RuBisCO, which is probably also the most abundant protein on the planet. RuBisCO is the enzyme that fixes CO into sugar molecules. In plants, RuBisCO is abundant in all chloroplasts, though in plants, it is confined to the bundle sheath chloroplasts, where the Calvin cycle is carried out in plants. | 5 | Photochemistry |
Nevertheless, it was known that yeast extracts can ferment sugar even in the absence of living yeast cells. While studying this process in 1897, the German chemist and zymologist Eduard Buchner of Humboldt University of Berlin, Germany, found that sugar was fermented even when there were no living yeast cells in the mixture, by an enzyme complex secreted by yeast that he termed zymase. In 1907 he received the Nobel Prize in Chemistry for his research and discovery of "cell-free fermentation".
One year earlier, in 1906, ethanol fermentation studies led to the early discovery of oxidized nicotinamide adenine dinucleotide (NAD). | 1 | Biochemistry |
In organic chemistry, the Cieplak effect is a predictive model to rationalize why nucleophiles preferentially add to one face of a carbonyl over another. Proposed by Andrzej Stanislaw Cieplak in 1980, it correctly predicts results that could not be justified by the other standard models at the time, such as the Cram and Felkin–Anh models. In the Cieplak model, electrons from a neighboring bond delocalize into the forming carbon–nucleophile (C–Nuc) bond, lowering the energy of the transition state and accelerating the rate of reaction. Whichever bond can best donate its electrons into the C–Nuc bond determines which face of the carbonyl the nucleophile will add to. The nucleophile may be any of a number of reagents, most commonly organometallic or reducing agents. The Cieplak effect is subtle, and often competes with sterics, solvent effects, counterion complexation of the carbonyl oxygen, and other effects to determine product distribution. Subsequent work has questioned its legitimacy (see Criticisms). | 0 | Organic Chemistry |
Anabolism () is the set of metabolic pathways that construct macromolecules like DNA or RNA from smaller units. These reactions require energy, known also as an endergonic process. Anabolism is the building-up aspect of metabolism, whereas catabolism is the breaking-down aspect. Anabolism is usually synonymous with biosynthesis. | 1 | Biochemistry |
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