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In the last decades, the thermal efficiency of Rankine cycles increased drastically, especially for large scale applications fueled by coal: for these power plants, the application of ultrasupercritical layouts was the main factor to achieve the goal, since the higher pressure ratio ensures higher cycle efficiencies.
The increment in thermal efficiency of power plants fueled by dirty fuels became crucial also in the reduction of the specific emissions of the plants, both in therms of greenhouse gas and for pollutant such as sulfur dioxide or NOx.
In large scale applications, ultrasupercritical Rankine cycles employ up to 10 feedwater heaters, five on the high pressure side and five on the low pressure side, including the deaerator, helping in the increment of the temperature at the inlet of the boiler up to 300°C, allowing a significant regenerative air preheating, thus reducing the fuel consumption. Studies on the best performant configurations of supercritical rankine cycles (300 bar of maximum pressure, 600°C of maximum temperature and two reheats) show that such layouts can achieve a cycle efficiency higher than 50%, about 6% higher than subcritical configurations. | 7 | Physical Chemistry |
CAM photosynthesis is also found in aquatic species in at least 4 genera, including: Isoetes, Crassula, Littorella, Sagittaria, and possibly Vallisneria, being found in a variety of species e.g. Isoetes howellii, Crassula aquatica.
These plants follow the same nocturnal acid accumulation and daytime deacidification as terrestrial CAM species. However, the reason for CAM in aquatic plants is not due to a lack of available water, but a limited supply of . is limited due to slow diffusion in water, 10000x slower than in air. The problem is especially acute under acid pH, where the only inorganic carbon species present is , with no available bicarbonate or carbonate supply.
Aquatic CAM plants capture carbon at night when it is abundant due to a lack of competition from other photosynthetic organisms. This also results in lowered photorespiration due to less photosynthetically generated oxygen.
Aquatic CAM is most marked in the summer months when there is increased competition for , compared to the winter months. However, in the winter months CAM still has a significant role. | 5 | Photochemistry |
Motexafin gadolinium (proposed tradename Xcytrin) is an inhibitor of thioredoxin reductase and ribonucleotide reductase. It has been proposed as a possible chemotherapeutic agent in the treatment of brain metastases. | 1 | Biochemistry |
Natural phenols are reactive species toward oxidation, notably the complex mixture of phenolics, found in food for example, can undergo autoxidation during the ageing process. Simple natural phenols can lead to the formation of B type proanthocyanidins in wines or in model solutions. This is correlated to the non-enzymatic browning color change characteristic of this process. This phenomenon can be observed in foods like carrot purees.
Browning associated with oxidation of phenolic compounds has also been given as the cause of cells death in calli formed in in vitro cultures. Those phenolics originate both from explant tissues and from explant secretions. | 0 | Organic Chemistry |
Following the invention of X-ray crystallography techniques in the 1910s, the atomic structure of many compounds was investigated. Most metals have relatively simple structures. However, in 1923 Linus Pauling reported on the structure of the intermetallic NaCd, which had such a complicated structure he was unable to fully explain it. Thirty years later, he concluded that NaCd contains 384 sodium and 768 cadmium atoms in each unit cell.
Most physical properties of CMAs show distinct differences with respect to the behavior of normal metallic alloys and therefore these materials possess a high potential for technological application.
The European Commission funded the Network of Excellence CMA from 2005 to 2010, uniting 19 core groups in 12 countries. From this emerged the European Integrated Center for the Development of New Metallic Alloys and Compounds (previously C-MAC, now ECMetAC), which connects researchers at 21 universities. | 8 | Metallurgy |
Thiosulfate (IUPAC-recommended spelling; sometimes thiosulphate in British English) is an oxyanion of sulfur with the chemical formula . Thiosulfate also refers to the compounds containing this anion, which are the salts of thiosulfuric acid, e.g. sodium thiosulfate . Thiosulfate also refers to the esters of thiosulfuric acid. The prefix thio- indicates that the thiosulfate is a sulfate with one oxygen replaced by sulfur. Thiosulfate is tetrahedral at the central S atom. Thiosulfate salts occur naturally. Thiosulfate ion has C symmetry, and is produced by certain biochemical processes. It rapidly dechlorinates water and is notable for its use to halt bleaching in the paper-making industry. Thiosulfate salts are mainly used in dying in textiles and the bleaching of natural substances.
Sodium thiosulfate, commonly called hypo (from "hyposulfite"), was widely used in photography to fix black and white negatives and prints after the developing stage; modern "rapid" fixers use ammonium thiosulfate as a fixing salt because it acts three to four times faster. Some bacteria can metabolise thiosulfates. | 8 | Metallurgy |
Physical biochemistry is a branch of biochemistry that deals with the theory, techniques, and methodology used to study the physical chemistry of biomolecules.
It also deals with the mathematical approaches for the analysis of biochemical reaction and the modelling of biological systems. It provides insight into the structure of macromolecules, and how chemical structure influences the physical properties of a biological substance.
It involves the use of physics, physical chemistry principles, and methodology to study biological systems. It employs various physical chemistry techniques such as chromatography, spectroscopy, Electrophoresis, X-ray crystallography, electron microscopy, and hydrodynamics. | 7 | Physical Chemistry |
Immediately prior to target introduction, the single stranded oligonucleotide library is often heated and cooled slowly to renature oligonucleotides into thermodynamically stable secondary and tertiary structures. Once prepared, the randomized library is incubated with immobilized target to allow oligonucleotide-target binding. There are several considerations for this target incubation step, including the target immobilization method and strategies for subsequent unbound oligonucleotide separation, incubation time and temperature, incubation buffer conditions, and target versus oligonucleotide concentrations. Examples of target immobilization methods include affinity chromatography columns, nitrocellulose binding assay filters, and paramagnetic beads. Recently, SELEX reactions have been developed where the target is whole cells, which are expanded near complete confluence and incubated with the oligonucleotide library on culture plates. Incubation buffer conditions are altered based on the intended target and desired function of the selected aptamer. For example, in the case of negatively charged small molecules and proteins, high salt buffers are used for charge screening to allow nucleotides to approach the target and increase the chance of a specific binding event. Alternatively, if the desired aptamer function is in vivo protein or whole cell binding for potential therapeutic or diagnostic application, incubation buffer conditions similar to in vivo plasma salt concentrations and homeostatic temperatures are more likely to generate aptamers that can bind in vivo. Another consideration in incubation buffer conditions is non-specific competitors. If there is a high likelihood of non-specific oligonucleotide retention in the reaction conditions, non specific competitors, which are small molecules or polymers other than the SELEX library that have similar physical properties to the library oligonucleotides, can be used to occupy these non-specific binding sites. Varying the relative concentration of target and oligonucleotides can also affect properties of the selected aptamers. If a good binding affinity for the selected aptamer is not a concern, then an excess of target can be used to increase the probability that at least some sequences will bind during incubation and be retained. However, this provides no selective pressure for high binding affinity, which requires the oligonucleotide library to be in excess so that there is competition between unique sequences for available specific binding sites. | 1 | Biochemistry |
The zeroth law of thermodynamics describes thermal equilibrium between thermodynamic systems in form of an equivalence relation. Accordingly, all thermal systems may be divided into a quotient set, denoted as M. If the set M has the cardinality of c, then one can construct an injective function , by which every thermal system has a parameter associated with it such that when two thermal systems have the same value of that parameter, they are in thermal equilibrium. This parameter is the property of temperature. The specific way of assigning numerical values for temperature is establishing a scale of temperature. In practical terms, a temperature scale is always based on usually a single physical property of a simple thermodynamic system, called a thermometer, that defines a scaling function for mapping the temperature to the measurable thermometric parameter. Such temperature scales that are purely based on measurement are called empirical temperature scales.
The second law of thermodynamics provides a fundamental, natural definition of thermodynamic temperature starting with a null point of absolute zero. A scale for thermodynamic temperature is established similarly to the empirical temperature scales, however, needing only one additional fixing point. | 7 | Physical Chemistry |
For the case of a relativistic incident electron, the "magic" angle is defined by the equality of two different functions
(denoted below by and ) of the collection angle :
and
where is the speed of the incoming electron divided by the speed of light (N.B., the symbol is also often used in the older literature to denote the collection angle instead of ).
Of course, the above integrals may easily be evaluated in terms of elementary functions, but they are presented as above because in the above form it is easier to see that the former integral is due to momentum transfers which are perpendicular to the beam direction, whereas the latter is due to momentum transfers parallel to the beam direction.
Using the above definition, it is then found that | 7 | Physical Chemistry |
Phycobilisomes are light-harvesting antennae that transmit the energy of harvested photons to photosystem II and photosystem I in cyanobacteria and in the chloroplasts of red algae and glaucophytes. They were lost during the evolution of the chloroplasts of green algae and plants. | 5 | Photochemistry |
Transfer RNA-like structures (tRNA-like structures) are RNA sequences, which have a similar tertiary structure to tRNA; they frequently contain a pseudoknot close to the 3' end. The presence of tRNA-like structures has been demonstrated in many plant virus RNA genomes. These tRNA-like structures are linked to regulation of plant virus replication.
tRNA-like structures mimic some tRNA function, such as aminoacylation. There are three aminoacylation specificities, valine, histidine and tyrosine. For example, valine binds to the tRNA-like structure of the turnip yellow mosaic virus genome whilst tyrosine binds to the tRNA-like structure of the barley stripe mosaic virus genome. tRNA-like structures which lack the 3' termini lack complete or partial tRNA mimicry.
tRNA-like structures are required for RNA encapsulation and increase RNA stability. They also act as 3'-translational enhancers and regulators of minus strand synthesis. | 1 | Biochemistry |
Dissimilatory nitrate reduction to ammonium (DNRA), or nitrate/nitrite ammonification, is an anaerobic respiration process. Microbes which undertake DNRA oxidise organic matter and use nitrate as an electron acceptor, reducing it to nitrite, then ammonium (). Both denitrifying and nitrate ammonification bacteria will be competing for nitrate in the environment, although DNRA acts to conserve bioavailable nitrogen as soluble ammonium rather than producing dinitrogen gas. | 1 | Biochemistry |
In molecular biology, linker DNA is double-stranded DNA (38-53 base pairs long) in between two nucleosome cores that, in association with histone H1, holds the cores together. Linker DNA is seen as the string in the "beads and string model", which is made by using an ionic solution on the chromatin. Linker DNA connects to histone H1 and histone H1 sits on the nucleosome core. Nucleosome is technically the consolidation of a nucleosome core and one adjacent linker DNA; however, the term nucleosome is used freely for solely the core. Linker DNA may be degraded by endonucleases.
The linkers are short double stranded DNA segments which are formed of oligonucleotides. These contain target sites for the action of one or more restriction enzymes. The linkers can be synthesized chemically and can be ligated to the blunt end of foreign DNA or vector DNA. These are then treated with restriction endonuclease enzyme to produce cohesive ends of DNA fragments. The commonly used linkers are EcoRI-linkers and sal-I linkers. | 7 | Physical Chemistry |
If multiplexed paired-end sequencing is used, then demultiplexing needs to be done to sort reads for different samples to different files. After the demultiplexing, error correction and read pair elimination based on unique identifier and barcode matching of pairs can be done. Developers adapt the demultiplexing and error correction steps from the CAPP-seq demultiplexing pipeline. | 1 | Biochemistry |
Most plastic items, like packaging materials, are used briefly and only once. These rarely experience polymer degradation during their service-lives. Other items experience only gradual degradation from the natural environment. Some plastic items, however, can experience long service-lives in aggressive environments, particularly those where they are subject to prolonged heat or chemical attack. Polymer degradation can be significant in these cases and, in practice, is often only held back by the use of advanced polymer stabilizers. Degradation arising from the effects of heat, light, air and water is the most common, but other means of degradation exist.
The in-service degradation of mechanical properties is an important aspect which limits the applications of these materials. Polymer degradation caused by in-service degradation can cause life threatening accidents. In 1996, a baby was fed via a Hickman line and suffered an infection, when new connectors were used by a hospital. The reason behind this infection was the cracking and erosion of the pipes from the inner side due to contact with liquid media. | 7 | Physical Chemistry |
The chromosome loops shown in the figure, bringing an enhancer to the promoter of its target gene, may be directed and formed by the eRNA transcribed from the enhancer after the enhancer is activated.
A transcribed enhancer RNA (eRNA) interacting with the complex of Mediator proteins (see Figure), especially Mediator subunit 12 (MED12), appears to be essential in forming the chromosome loop that brings the enhancer into close association with the promoter of the target gene of the enhancer in the case of five genes studied by Lai et al. Hou and Kraus, describe two other studies reporting similar results. Arnold et al. review another 5 instances where eRNA is active in forming the enhancer-promoter loop. | 1 | Biochemistry |
Titanium tetrachloride is a versatile reagent that forms diverse derivatives including those illustrated below. | 0 | Organic Chemistry |
Selegiline is metabolized by cytochrome P450 to -desmethylselegiline and levomethamphetamine. Desmethylselegiline has some activity against MAO-B, but much less than that of selegiline. It is thought to be further metabolized by CYP2C19. Levomethamphetamine (the less potent of the two enantiomers of methamphetamine) is converted to levoamphetamine (the less potent of the two enantiomers of amphetamine, with regards to psychological effects).
Due to the presence of these metabolites, people taking selegiline may test positive for "amphetamine" or "methamphetamine" on drug screening tests. While the amphetamine metabolites may contribute to selegiline's ability to inhibit reuptake of the neurotransmitters dopamine and norepinephrine, they have also been associated with orthostatic hypotension and hallucinations. The recovery of selegiline from urine is high at 87%, which has caused some researchers to question the clinical relevance of its amphetamine metabolites. The amphetamine metabolites are hydroxylated and, in phase II, conjugated by glucuronyltransferase.
A newer anti-Parkinson MAO-B inhibitor, rasagiline, metabolizes into 1(R)-aminoindan, which has no amphetamine-like characteristics. | 4 | Stereochemistry |
Lillie's trichrome is a combination of dyes used in histology.
It is similar to Massons trichrome stain, but it uses Biebrich scarlet for the plasma stain. It was initially published by Ralph D. Lillie in 1940. It is applied by submerging the fixated sample into the following three solutions: Weigerts iron hematoxylin working solution, Biebrich scarlet solution, and Fast Green FCF solution.
The resulting stains are black cell nuclei, brown cytoplasm, red muscle and myelinated fibers, blue collagen, and scarlet erythrocytes. | 1 | Biochemistry |
Like most amino acids, pipecolic acid is a chelating agent. One complex is Cu(HNCHCO)(HO).
Pipecolic acid was identified in the Murchison meteorite.
It also occurs in the leaves of the genus Myroxylon, a tree from South America. | 1 | Biochemistry |
β-TG levels may increase with age. It is elevated in diabetes mellitus.
β-TG levels have been found to be increased by treatment with the synthetic estrogen ethinylestradiol, though were not significantly increased by the natural estrogen estradiol valerate. Levels of β-TG have also been found to be increased or unchanged during normal pregnancy. | 1 | Biochemistry |
Lower-than-normal ceruloplasmin levels may indicate the following:
* Wilson disease (a rare [UK incidence 2/100,000] copper storage disease).
* Menkes disease (Menkes kinky hair syndrome) (rare – UK incidence 1/100,000)
* Copper deficiency
* Aceruloplasminemia
* Zinc toxicity | 1 | Biochemistry |
Reverberatory furnaces are long furnaces that can treat wet, dry, or roasted concentrate. Most of the reverberatory furnaces used in the latter years treated roasted concentrate because putting dry feed materials into the reverberatory furnace is more energy efficient, and because the elimination of some of the sulfur in the roaster results in higher matte grades.
The reverberatory furnace feed is added to the furnace through feed holes along the sides of the furnace, and the solid charge is melted. Additional silica is normally added to help form the slag. The furnace is fired with burners using pulverized coal, fuel oil or natural gas
Reverberatory furnaces can additionally be fed with molten slag from the later converting stage to recover the contained copper and other materials with a high copper content.
Because the reverberatory furnace bath is quiescent, very little oxidation of the feed occurs (and thus very little sulfur is eliminated from the concentrate). It is essentially a melting process. Consequently, wet-charged reverberatory furnaces have less copper in their matte product than calcine-charged furnaces, and they also have lower copper losses to slag. Gill quotes a copper in slag value of 0.23% for a wet-charged reverberatory furnace vs 0.37% for a calcine-charged furnace.
In the case of calcine-charged furnaces, a significant portion of the sulfur has been eliminated during the roasting stage, and the calcine consists of a mixture of copper and iron oxides and sulfides. The reverberatory furnace acts to allow these species to approach chemical equilibrium at the furnace operating temperature (approximately 1600 °C at the burner end of the furnace and about 1200 °C at the flue end; the matte is about 1100 °C and the slag is about 1195 °C). In this equilibration process, oxygen associated with copper compounds exchanges with sulfur associated with iron compounds, increasing the iron oxide content of the furnace, and the iron oxides interact with silica and other oxide materials to form the slag.
The main equilibration reaction is:
:CuO + FeS → CuS + FeO
The slag and the matte form distinct layers that can be removed from the furnace as separate streams. The slag layer is periodically allowed to flow through a hole in the wall of the furnace above the height of the matte layer. The matte is removed by draining it through a hole into ladles for it to be carried by crane to the converters. This draining process is known as tapping the furnace. The matte taphole is normally a hole through a water-cooled copper block that prevents erosion of the refractory bricks lining the furnace. When the removal of the matte or slag is complete, the hole is normally plugged with clay, which is removed when the furnace is ready to be tapped again.
Reverberatory furnaces were often used to treat molten converter slag to recover contained copper. This would be poured into the furnaces from ladles carried by cranes. However, the converter slag is high in magnetite and some of this magnetite would precipitate from the converter slag (due to its higher melting point), forming an accretion on the hearth of the reverberatory furnace and necessitating shut downs of the furnace to remove the accretion. This accretion formation limits the quantity of converter slag that can be treated in a reverberatory furnace.
While reverberatory furnaces have very low copper losses to slag, they are not very energy-efficient and the low concentrations of sulfur dioxide in their off-gases make its capture uneconomic. Consequently, smelter operators devoted a lot of money in the 1970s and 1980s to developing new, more efficient copper smelting processes. In addition, flash smelting technologies had been developed in earlier years and began to replace reverberatory furnaces. By 2002, 20 of the 30 reverberatory furnaces still operating in 1994 had been shut down. | 8 | Metallurgy |
Although Unruh's prediction that an accelerating detector would see a thermal bath is not controversial, the interpretation of the transitions in the detector in the non-accelerating frame is. It is widely, although not universally, believed that each transition in the detector is accompanied by the emission of a particle, and that this particle will propagate to infinity and be seen as Unruh radiation.
The existence of Unruh radiation is not universally accepted. Smolyaninov claims that it has already been observed, while O'Connell and Ford claim that it is not emitted at all. While these skeptics accept that an accelerating object thermalizes at the Unruh temperature, they do not believe that this leads to the emission of photons, arguing that the emission and absorption rates of the accelerating particle are balanced. | 7 | Physical Chemistry |
The flame point of a material is a temperature value at which sustained flame can be supported on the material once ignited by an external source. Once the flame point of a material is reached, it produces enough fuel vapors or oils to support continuous burning. | 7 | Physical Chemistry |
Prp24 interacts with the U6 snRNA via its RRMs. It has been shown through chemical modification testing that nucleotides 39–57 of U6 (40–43 in particular) are involved in binding Prp24.
The LSm proteins are in a consistent configuration on the U6 RNA. It has been proposed that the LSm proteins and Prp24 interact both physically and functionally and the C-terminal motif of Prp24 is important for this interaction. The binding of Prp24 to U6 is enhanced by the binding of Lsm proteins to U6, as is binding of U4 and U6. It was revealed by electron microscopy that Prp24 may interact with the LSm protein ring at LSm2. | 1 | Biochemistry |
In ancient times, cinobufacini, which is extracted from the skin and the parotid venom glands of toad of the bufo genus was used to treat symptoms like swelling and pain. In the present time, cinobufacinin injections are used to achieve satisfactory effect on Hepatocellular carcinoma (HCC) in China. Bufothionine is a major active component of cinobufacini. Bufothionine has been shown to suppress growth of cancerous liver cells in vitro . In vivo, bufothionine has also been showing relieved symptoms and anti inflammatory activities in tumor bearing mice. Experiments were conducted in which cultured cancer cells were shown to have an increase in G2-M damage checkpoint, ensuring that growth of the cell will not continue until the damage to the DNA is corrected while also showing a drop in the G0 and G1 activity, which pertains to phase where there is cell growth and RNA production.
Bufothionine is shown to induce autophagy in hepatocellular carcinomas by inhibiting JAK2/STAT3 pathways, which may present possibilities of anti cancer mechanism in bufothionine through cinobufacini injections. Similarly, bufothionine has also been shown to increase the chances of cell death and decrease cell growth of gastric cancer related cells by inhibiting the PIM3 gene, which, in cancerous cells, increases the resistance of chemotherapeutic treatments. In glioblastoma multiforme (GBM), bufothionine presents anti-tumor activities in the GBM cells lines U87 and U373 by triggering endoplasmic reticulum stress to lead cell death in the U87 and U373 cells. | 1 | Biochemistry |
Radiolysis is the dissociation of molecules by ionizing radiation. It is the cleavage of one or several chemical bonds resulting from exposure to high-energy flux. The radiation in this context is associated with ionizing radiation; radiolysis is therefore distinguished from, for example, photolysis of the Cl molecule into two Cl-radicals, where (ultraviolet or visible spectrum) light is used.
The chemistry of concentrated solutions under ionizing radiation is extremely complex. Radiolysis can locally modify redox conditions, and therefore the speciation and the solubility of the compounds. | 5 | Photochemistry |
With the 2006 adoption of the Restriction of Hazardous Substances Directive (RoHS) regulations in the European Union, California banning most uses of lead, and similar regulations elsewhere, the problem of tin pest has returned, since some manufacturers which previously used tin/lead alloys now use predominately tin-based alloys. For example, the leads of some electrical and electronic components are plated with pure tin. In cold environments, this can change to α-modification grey tin, which is not electrically conductive, and falls off the leads. After reheating, it changes back to β-modification white tin, which is electrically conductive. This cycle can cause electrical short circuits and failure of equipment. Such problems can be intermittent as the powdered particles of tin move around. Tin pest can be avoided by alloying with small amounts of electropositive metals or semimetals soluble in tin's solid phase, e.g. antimony or bismuth, which prevent the phase change. | 8 | Metallurgy |
The Gaia hypothesis (), also known as the Gaia theory, Gaia paradigm, or the Gaia principle, proposes that living organisms interact with their inorganic surroundings on Earth to form a synergistic and self-regulating, complex system that helps to maintain and perpetuate the conditions for life on the planet.
The Gaia hypothesis was formulated by the chemist James Lovelock and co-developed by the microbiologist Lynn Margulis in the 1970s. Following the suggestion by his neighbour, novelist William Golding, Lovelock named the hypothesis after Gaia, the primordial deity who personified the Earth in Greek mythology. In 2006, the Geological Society of London awarded Lovelock the Wollaston Medal in part for his work on the Gaia hypothesis.
Topics related to the hypothesis include how the biosphere and the evolution of organisms affect the stability of global temperature, salinity of seawater, atmospheric oxygen levels, the maintenance of a hydrosphere of liquid water and other environmental variables that affect the habitability of Earth.
The Gaia hypothesis was initially criticized for being teleological and against the principles of natural selection, but later refinements aligned the Gaia hypothesis with ideas from fields such as Earth system science, biogeochemistry and systems ecology. Even so, the Gaia hypothesis continues to attract criticism, and today many scientists consider it to be only weakly supported by, or at odds with, the available evidence. | 9 | Geochemistry |
The HUGO Gene Nomenclature Committee is responsible for providing human gene naming guidelines and approving new, unique human gene names and symbols (short identifiers typically created by abbreviating). For some nonhuman species, model organism databases serve as central repositories of guidelines and help resources, including advice from curators and nomenclature committees. In addition to species-specific databases, approved gene names and symbols for many species can be located in the National Center for Biotechnology Information's "Entrez Gene" database. | 1 | Biochemistry |
Let us consider the example of a system of charged particles subject to a constant external magnetic field: in this case the canonical time reversal operation that reverses the velocities and the time and keeps the coordinates untouched is no more a symmetry for the system. Under this consideration, it seems that only Onsager–Casimir reciprocal relations could hold; these equalities relate two different systems, one subject to and another to , and so their utility is limited. However, there was proved that it is possible to find other time reversal operations which preserve the dynamics and so Onsager reciprocal relations; in conclusion, one cannot state that the presence of a magnetic field always breaks T-symmetry. | 7 | Physical Chemistry |
Allyltrimethylsilane is the organosilicon compound with the formula (CH)SiCHCH=CH. The molecule consists of the trimethylsilyl group attached to allyl group. This colorless liquid is used in organic synthesis. | 0 | Organic Chemistry |
5-Methylcytosine (5-mC) is a methylated form of the DNA base cytosine (see figure). 5-mC is an epigenetic marker found predominantly on cytosines within CpG dinucleotides, which consist of a cytosine is followed by a guanine reading in the 5′ to 3′ direction along the DNA strand (CpG sites). About 28 million CpG dinucleotides occur in the human genome. In most tissues of mammals, on average, 70% to 80% of CpG cytosines are methylated (forming 5-methyl-CpG, or 5-mCpG). Methylated cytosines within CpG sequences often occur in groups, called CpG islands. About 59% of promoter sequences have a CpG island while only about 6% of enhancer sequences have a CpG island. CpG islands constitute regulatory sequences, since if CpG islands are methylated in the promoter of a gene this can reduce or silence gene expression.
DNA methylation regulates gene expression through interaction with methyl binding domain (MBD) proteins, such as MeCP2, MBD1 and MBD2. These MBD proteins bind most strongly to highly methylated CpG islands. These MBD proteins have both a methyl-CpG-binding domain and a transcriptional repression domain. They bind to methylated DNA and guide or direct protein complexes with chromatin remodeling and/or histone modifying activity to methylated CpG islands. MBD proteins generally repress local chromatin by means such as catalyzing the introduction of repressive histone marks or creating an overall repressive chromatin environment through nucleosome remodeling and chromatin reorganization.
Transcription factors are proteins that bind to specific DNA sequences in order to regulate the expression of a given gene. The binding sequence for a transcription factor in DNA is usually about 10 or 11 nucleotides long. There are approximately 1,400 different transcription factors encoded in the human genome and they constitute about 6% of all human protein coding genes. About 94% of transcription factor binding sites that are associated with signal-responsive genes occur in enhancers while only about 6% of such sites occur in promoters.
EGR1 is a transcription factor important for regulation of methylation of CpG islands. An EGR1 transcription factor binding site is frequently located in enhancer or promoter sequences. There are about 12,000 binding sites for EGR1 in the mammalian genome and about half of EGR1 binding sites are located in promoters and half in enhancers. The binding of EGR1 to its target DNA binding site is insensitive to cytosine methylation in the DNA.
While only small amounts of EGR1 protein are detectable in cells that are un-stimulated, EGR1 translation into protein at one hour after stimulation is markedly elevated. Expression of EGR1 in various types of cells can be stimulated by growth factors, neurotransmitters, hormones, stress and injury. In the brain, when neurons are activated, EGR1 proteins are upregulated, and they bind to (recruit) pre-existing TET1 enzymes, which are highly expressed in neurons. TET enzymes can catalyze demethylation of 5-methylcytosine. When EGR1 transcription factors bring TET1 enzymes to EGR1 binding sites in promoters, the TET enzymes can demethylate the methylated CpG islands at those promoters. Upon demethylation, these promoters can then initiate transcription of their target genes. Hundreds of genes in neurons are differentially expressed after neuron activation through EGR1 recruitment of TET1 to methylated regulatory sequences in their promoters. | 1 | Biochemistry |
This book covers underground mining and surveying. When a vein below ground is to be exploited a shaft is begun and a wooden shed with a windlass is placed above it. The tunnel dug at the bottom follows the vein and is just big enough for a man. The entire vein should be removed. Sometimes the tunnel eventually connects with a tunnel mouth in a hill side. Stringers and cross veins should be explored with cross tunnels or shafts when they occur. Agricola next describes that gold, silver, copper and mercury can be found as native metals, the others very rarely. Gold and silver ores are described in detail. Agricola then states that it is rarely worthwhile digging for other metals unless the ores are rich. Gems are found in some mines, but rarely have their own veins, lodestone is found in iron mines and emery in silver mines. Various minerals and colours of earths can be used to give indications of the presence of metal ores. The actual mineworking varies with the hardness of the rock, the softest is worked with a pick and requires shoring with wood, the hardest is usually broken with fire. Iron wedges, hammers and crowbars are used to break other rocks. Noxious gases and the ingress of water are described. Methods for lining tunnels and shafts with timber are described. The book concludes with a long treatise on surveying, showing the instruments required and techniques for determining the course of veins and tunnels. Surveyors allow veins to be followed, but also prevent mines removing ore from other claims and stop mine workings from breaking into other workings. | 8 | Metallurgy |
Parts-per notation is often used describing dilute solutions in chemistry, for instance, the relative abundance of dissolved minerals or pollutants in water. The quantity "1 ppm" can be used for a mass fraction if a water-borne pollutant is present at one-millionth of a gram per gram of sample solution. When working with aqueous solutions, it is common to assume that the density of water is 1.00 g/mL. Therefore, it is common to equate 1 kilogram of water with 1 L of water. Consequently, 1 ppm corresponds to 1 mg/L and 1 ppb corresponds to 1 μg/L.
Similarly, parts-per notation is used also in physics and engineering to express the value of various proportional phenomena. For instance, a special metal alloy might expand 1.2 micrometers per meter of length for every degree Celsius and this would be expressed as Parts-per notation is also employed to denote the change, stability, or uncertainty in measurements. For instance, the accuracy of land-survey distance measurements when using a laser rangefinder might be 1 millimeter per kilometer of distance; this could be expressed as "Accuracy = 1 ppm."
Parts-per notations are all dimensionless quantities: in mathematical expressions, the units of measurement always cancel. In fractions like "2 nanometers per meter" so the quotients are pure-number coefficients with positive values less than or equal to 1. When parts-per notations, including the percent symbol (%), are used in regular prose (as opposed to mathematical expressions), they are still pure-number dimensionless quantities. However, they generally take the literal "parts per" meaning of a comparative ratio (e.g. "2 ppb" would generally be interpreted as "two parts in a billion parts").
Parts-per notations may be expressed in terms of any unit of the same measure. For instance, the expansion coefficient of some brass alloy, may be expressed as 18.7 (μm/m)/°C, or as 18.7 (μ in/in)/°C; the numeric value representing a relative proportion does not change with the adoption of a different unit of length.
Similarly, a metering pump that injects a trace chemical into the main process line at the proportional flow rate is doing so at a rate that may be expressed in a variety of volumetric units, including 125 cm/m, etc.
In nuclear magnetic resonance spectroscopy (NMR), chemical shift is usually expressed in ppm. It represents the difference of a measured frequency in parts per million from the reference frequency. The reference frequency depends on the instruments magnetic field and the element being measured. It is usually expressed in MHz. Typical chemical shifts are rarely more than a few hundred Hz from the reference frequency, so chemical shifts are conveniently expressed in ppm (Hz/MHz). Parts-per notation gives a dimensionless quantity that does not depend on the instruments field strength. | 2 | Environmental Chemistry |
Dynamic covalent reactions have recently been used in Systems chemistry to initiate signaling cascades by reversibly releasing protons. The dynamic nature of the reactions provides a suitable "on-off" switch-like nature to the cascade systems. | 6 | Supramolecular Chemistry |
Acicular ferrite is a microstructure of ferrite in steel that is characterised by needle-shaped crystallites or grains when viewed in two dimensions. The grains, actually three-dimensional in shape, have a thin lenticular shape. This microstructure is advantageous over other microstructures for steel because of its chaotic ordering, which increases toughness.
Acicular ferrite is formed in the interior of the original austenitic grains by direct nucleation on the inclusions, resulting in randomly oriented short ferrite needles with a basket weave appearance. Acicular ferrite is also characterised by high angle boundaries between the ferrite grains. This further reduces the chance of cleavage, because these boundaries impede crack propagation.
In C-Mn steel weld metals, it is reported that nucleation of various ferrite morphologies is aided by non-metallic inclusion; in particular oxygen-rich inclusions of a certain type and size are associated with the intragranular nucleation of acicular ferrite, as observed, for example, by,. Acicular ferrite is a fine Widmanstätten constituent, which is nucleated by an optimum intragranular dispersion of oxide/sulfide/silicate particles. The interlocking nature of acicular ferrite, together with its fine grain size (0.5 to 5 μm with aspect ratio from 3:1 to 10:1), provides maximum resistance to crack propagation by cleavage.
Composition control of weld metal is often performed to maximise the volume fraction of acicular ferrite due to the toughness it imparts. During continuous cooling, higher alloy contents or faster cooling generally delay transformation, which will then take place at lower temperatures, below the bainite start temperature, and lead to higher hardness. The efficacy of inclusions as nucleation sites in modern low alloy steel weld metals is such that fine-scale intragranular bainite can nucleate on them, both by continuous cooling and by isothermal transformation below the bainite start temperature. Some confusion has arisen in the literature, as this fine-scale intragranular bainite, which can resemble acicular ferrite in appearance in the optical microscope, has been called acicular ferrite by some researchers. See, for example. | 8 | Metallurgy |
Clathrate hydrates were discovered in 1810 by Humphry Davy. Clathrates were studied by P. Pfeiffer in 1927 and in 1930, E. Hertel defined "molecular compounds" as substances decomposed into individual components following the mass action law in solution or gas state. Clathrate hydrates were discovered to form blockages in gas pipelines in 1934 by Hammerschmidt that led to increase in research to avoid hydrate formation. In 1945, H. M. Powell analyzed the crystal structure of these compounds and named them clathrates. Gas production through methane hydrates has since been realized and has been tested for energy production in Japan and China. | 6 | Supramolecular Chemistry |
Like the ALR genes, the MRS2 gene was cloned and sequenced before it was identified as a Mg transporter. The MRS2 gene was identified in the nuclear genome of yeast in a screen for suppressors of a mitochondrial gene RNA splicing mutation, and was cloned and sequenced by Wiesenberger et al. (1992). Mrs2p was not identified as a putative Mg transporter until Bui et al. (1999). Gregan et al. (2001a) identified LPE10 by homology to MRS2 and showed that both LPE10 and MRS2 mutants altered the Mg content of yeast mitochondria and affected RNA splicing activity in the organelle. Mg transport has been shown to be directly mediated by Mrs2p, but not for Lpe10p.
The Mrs2p and Lpe10p proteins are 470 and 413 amino acid residues in size, respectively, and a 250–300 amino acid region in the middle of the proteins shows a weak similarity to the full CorA protein. The TM topologies of the Mrs2p and Lpe10p proteins have been assessed using a protease protection assay and are shown in the figure. TM 1 and 2 correspond to TM 2 and 3 in the CorA protein. The conserved GMN motif is at the outside end of the first TM domain, and when the glycine (G) in this motif was mutated to a cysteine (C) in Mrs2p, Mg transport was strongly reduced.
The figure shows the experimentally determined topology of Mrs2p and Lpe10p as adapted from Bui et al. (1999) and Gregan et al. (2001a). The GMN motif location is indicated in red and the TM domains in light blue. The orientation in the membrane and the positions of the N- and C-termini are indicated. The various sizes of the soluble domains are given in amino acids (AA), TM domains are numbered, and the figure is not drawn to scale.
Mrs2p has been localised to the mitochondrial inner membrane by subcellular fractionation and immunodetection and Lpe10p to the mitochondria. Mitochondria lacking Mrs2p do not show a fast Mg uptake, only a slow ‘leak’, and overaccumulation of Mrs2p leads to an increase in the initial rate of uptake. Additionally, CorA, when fused to the mitochondrial leader sequence of Mrs2p, can partially complement the mitochondrial defect conferred by the loss of either Mrs2p or Lpe10p. Hence, Mrs2p and/or Lpe10p may be the major Mg uptake system for mitochondria. A possibility is that the proteins form heterodimers, as neither protein (when overexpressed) can fully complement the loss of the other.
The characteristics of Mg uptake in isolated mitochondria by Mrs2p were quantified using mag-fura 2. The uptake of Mg by Mrs2p shared a number of attributes with CorA. First, Mg uptake was directly dependent on the electric potential (ΔΨ) across the boundary membrane. Second, the uptake is saturated far below that which the ΔΨ theoretically permits, so the transport of Mg by Mrs2p is likely to be regulated in a similar manner to CorA, possibly by the inactivation of the protein. Third, Mg efflux was observed via Mrs2p upon the artificial depolarisation of the mitochondrial membrane by valinomycin. Finally, the Mg fluxes through Mrs2p are inhibited by cobalt (III) hexaammine.
The kinetics of Mg uptake by Mrs2p were determined in the Froschauer et al. (2004) paper on CorA in bacteria. The initial change in free Mg concentration was 150 μM s-1 for wild type and 750 μM s-1 for mitochondria from yeast overexpressing MRS2. No attempt was made to scale the observed transport to the amount of transporter present. | 1 | Biochemistry |
Oxygen-18 (, Ω) is a natural, stable isotope of oxygen and one of the environmental isotopes.
is an important precursor for the production of fluorodeoxyglucose (FDG) used in positron emission tomography (PET). Generally, in the radiopharmaceutical industry, enriched water () is bombarded with hydrogen ions in either a cyclotron or linear accelerator, producing fluorine-18. This is then synthesized into FDG and injected into a patient. It can also be used to make an extremely heavy version of water when combined with tritium (hydrogen-3): or . This compound has a density almost 30% greater than that of natural water.
The accurate measurements of rely on proper procedures of analysis, sample preparation and storage. | 9 | Geochemistry |
Normality is defined as the number of gram or mole equivalents of solute present in one litre of solution. The SI unit of normality is equivalents per litre (Eq/L).
where is normality, is the mass of solute in grams, is the equivalent weight of solute, and is the volume of the entire solution in litres. | 3 | Analytical Chemistry |
There are many fish oil dietary supplements on the market. Evidence suggests that marine based omega-3 dietary supplements are able to reduce cardiovascular disease, and premature death. These effects may not carry over in other populations such as people who have diabetes. The ingredients of dietary supplements are not as carefully controlled as prescription products and have not been fixed and tested in clinical trials, as prescription drugs have, and the prescription forms are more concentrated, requiring fewer capsules to be taken and increasing the likelihood of compliance. | 1 | Biochemistry |
The L-arabinose operon houses genes coding for arabinose-digesting enzymes. These function to break down arabinose as an alternative source for energy when glucose is low or absent. The operon consists of a regulatory repressor gene (araC), three control sites (ara02, ara01, araI1, and araI2), two promoters (Parac/ParaBAD) and three structural genes (araBAD). Once produced, araC acts as repressor by binding to the araI region to form a loop which prevents polymerases from binding to the promotor and transcribing the structural genes into proteins.
In the absence of Arabinose and araC (repressor), loop formation is not initiated and structural gene expression will be lower. In the absence of Arabinose but presence of araC, araC regions form dimers, and bind to bring ara02 and araI1 domains closer by loop formation. In the presence of both Arabinose and araC, araC binds with the arabinose and acts as an activator. This conformational change in the araC no longer can form a loop, and the linear gene segment promotes RNA polymerase recruitment to the structural araBAD region. | 1 | Biochemistry |
The reactions that occur with permeable reactive barriers and ferrous iron are surface based. The surface reactions take three different forms: direct reduction, electron shunting through ferrous iron, and reduction by production and reaction of hydrogen. Pathway A represents direct electron transfer (ET) for Fe to the adsorbed halocarbon (RX) at the metal/water point of contact, resulting in dechlorination and production of Fe. Pathway B shows that Fe (resulting from corrosion of Fe) may also dechlorinate RX, producing Fe. Pathway C shows that H from the anaerobic corrosion of Fe might react with RX if a catalyst is present. | 2 | Environmental Chemistry |
During the Song Dynasty, Chinese copper output from domestic mining was in decline and the resulting shortages caused miners to seek alternative methods for extracting copper. The discovery of a new “wet process” for extracting copper from mine water was introduced between the eleventh and twelfth century, which helped to mitigate their loss of supply.
Similar to the Anglo-Saxon method for cupellation, the Chinese employed the use of a base metal to extract the target metal from its impurities. First, the base metal, iron, is hammered into thin sheets. The sheets are then placed into a trough filled with “vitriol water” i.e., copper mining water which is then left to steep for several day. The mining water contains copper salts in the form of copper sulfate . The iron then reacts with the copper, displacing it from the sulfate ions, causing the copper to precipitate onto the iron sheets, forming a "wet" powder. Finally, the precipitated copper is collected and refined further through the traditional smelting process. This is the first large-scale use of a hydrometallurgical process. | 8 | Metallurgy |
Vitamin B, CHCoNOP, is the most complex of all known vitamins. Its chemical structure had been determined by x-ray crystal structure analysis in 1956 by the research group of Dorothy Hodgkin (Oxford University) in collaboration with Kenneth N. Trueblood at UCLA and John G. White at Princeton University.
Core of the molecule is the corrin structure, a nitrogenous tetradentate ligand system. This is biogenetically related to porphyrins and chlorophylls, yet differs from them in important respects: the carbon skeleton lacks one of the four meso carbons between the five-membered rings, two rings (A and D, fig. 1) being directly connected by a carbon-carbon single bond. The corrin chromophore system is thus non-cyclic and expands over three meso positions only, incorporating three vinylogous amidine units. Lined up at the periphery of the macrocyclic ring are eight methyl groups and four propionic and three acetic acid side chains. Nine carbon atoms on the corrin periphery are chirogenic centers. The tetradentate, monobasic corrin ligand is equatorially coordinated with a trivalent cobalt ion which bears two additional axial ligands.
Several natural variants of the B structure exist that differ in these axial ligands. In the vitamin itself, the cobalt bears a cyano group on the top side of the corrin plane (cyanocobalamin), and a nucleotide loop on the other. This loop is connected on its other end to the peripheral propionic amide group at ring D and consists of structural elements derived from aminopropanol, phosphate, ribose, and 5,6-dimethylbenzimidazole. One of the nitrogen atoms of the imidazole ring is axially coordinated to the cobalt, the nucleotide loop thus forming a nineteen-membered ring. All side chain carboxyl groups are amides.
Cobyric acid, one of the natural derivatives of vitamin B, lacks the nucleotide loop; depending on the nature of the two axial ligands, it displays instead its propionic acid function at ring D as carboxylate (as shown in fig. 1), or carboxylic acid (with two cyanide ligands at cobalt). | 0 | Organic Chemistry |
Perovskite structures are adopted by many oxides that have the chemical formula ABO. The idealized form is a cubic structure (space group Pmm, no. 221) which is rarely encountered. The orthorhombic (e.g. space group Pnma, no. 62, or Amm2, no. 68) and tetragonal (e.g. space group I4/mcm, no. 140, or P4mm, no. 99) phases are the most common non-cubic variants. Although the perovskite structure is named after CaTiO, this mineral forms a non-idealized form. SrTiO and CaRbF are examples of cubic perovskites. Barium titanate is an example of a perovskite which can take on the rhombohedral (space group R3m, no. 160), orthorhombic, tetragonal and cubic forms depending on temperature.
In the idealized cubic unit cell of such a compound, the type A atom sits at cube corner position (0, 0, 0), the type B atom sits at the body-center position (1/2, 1/2, 1/2) and oxygen atoms sit at face centered positions (1/2, 1/2, 0), (1/2, 0, 1/2) and (0, 1/2, 1/2). The diagram to the right shows edges for an equivalent unit cell with A in the cube corner position, B at the body center, and O at face-centered positions.
Four general categories of cation-pairing are possible: ABX, or 1:2 perovskites; ABX, or 2:4 perovskites; ABX, or 3:3 perovskites; and ABX, or 1:5 perovskites.
The relative ion size requirements for stability of the cubic structure are quite stringent, so slight buckling and distortion can produce several lower-symmetry distorted versions, in which the coordination numbers of A cations, B cations or both are reduced. Tilting of the BO octahedra reduces the coordination of an undersized A cation from 12 to as low as 8. Conversely, off-centering of an undersized B cation within its octahedron allows it to attain a stable bonding pattern. The resulting electric dipole is responsible for the property of ferroelectricity and shown by perovskites such as BaTiO that distort in this fashion.
Complex perovskite structures contain two different B-site cations. This results in the possibility of ordered and disordered variants. | 3 | Analytical Chemistry |
Signal transduction is regulated in various ways and one of the ways is translocation. Regulated translocation generates ultrasensitive response in mainly three ways:
#Regulated translocation increases the local concentration of the signaling protein. When concentration of the signaling protein is high enough to partially saturate the enzyme that inactivates it, ultrasensitive response is generated.
#Translocation of multiple components of the signaling cascade, where stimulus (input signal) causes translocation of both signaling protein and its activator in the same subcellular compartment and thereby generates ultrasensitive response which increases speed and accuracy of the signal.
#Translocation to the compartment which contains stoichiometric inhibitors.
Translocation is one way of regulating signal transduction, and it can generate ultrasensitive switch-like responses or multistep-feedback loop mechanisms. A switch-like response will occur if translocation raises the local concentration of a signaling protein. For example, epidermal growth factor (EGF) receptors can be internalized through clathrin-independent endocytosis (CIE) and/or clathrin-dependent endocytosis (CDE) in ligand concentration-dependent manner. The distribution of receptors into the two pathways was shown to be EGF concentration-dependent. In the presence of low concentrations of EGF, the receptor was exclusively internalized via CDE, whereas at high concentrations, receptors were equally distributed between CDE and CIE. | 1 | Biochemistry |
*Oxygen (O)
*Ozone (O)
*Hydrogen peroxide (HO) and other inorganic peroxides, Fenton's reagent
*Fluorine (F), chlorine (Cl), and other halogens
*Nitric acid (HNO) and nitrate compounds such as potassium nitrate (KNO), the oxidizer in black powder
*Potassium chlorate (KClO)
*Peroxydisulfuric acid (HSO)
*Peroxymonosulfuric acid (HSO)
*Hypochlorite, chlorite, chlorate, perchlorate, and other analogous halogen oxyanions
*Fluorides of chlorine, bromine, and iodine
*Hexavalent chromium compounds such as chromic and dichromic acids and chromium trioxide, pyridinium chlorochromate (PCC), and chromate/dichromate compounds such as Sodium dichromate (NaCrO)
*Permanganate compounds such as potassium permanganate (KMnO)
*Sodium perborate (·)
*Nitrous oxide (NO), Nitrogen dioxide/Dinitrogen tetroxide (NO / NO)
*Sodium bismuthate (NaBiO)
*Cerium (IV) compounds such as ceric ammonium nitrate and ceric sulfate
*Lead dioxide (PbO) | 7 | Physical Chemistry |
Lamina-associated domains (LADs) are parts of the chromatin that heavily interact with the lamina, a network-like structure at the inner membrane of the nucleus. LADs consist mostly of transcriptionally silent chromatin, being enriched with trimethylated Lys27 on histone H3, (i.e. H3K27me3); which is a common posttranslational histone modification of heterochromatin. LADs have CTCF-binding sites at their periphery. | 1 | Biochemistry |
Enzymatic browning affects the color, flavor, and nutritional value of foods, causing huge economic loss when not sold to consumers on time. It is estimated that more than 50% of produce is lost as a result of enzymatic browning. The increase in human population and consequential depletion in natural resources has prompted many biochemists and food engineers alike to find new or improved techniques to preserve food and for longer by using methods to inhibit the browning reaction. This effectively increases the shelf life of foods, solving this part of the waste problem. A better understanding of the enzymatic browning mechanisms, specifically, understanding the properties of the enzymes and substrates that are involved in the reaction may help food technologists to control certain stages in the mechanism and ultimately apply that knowledge to inhibit browning.
Apples are fruits commonly studied by researchers due to their high phenolic content, which make them highly susceptible to enzymatic browning. In accordance with other findings regarding apples and browning activity, a correlation has been found between higher phenolic quantities and increased enzymatic activity in apples. This provides a potential target and thus hope for food industries wishing to genetically modify foods to decrease polyphenol oxidase activity and thus decrease browning. An example of such accomplishments in food engineering is in the production of Arctic apples. These apples, engineered by Okanagan Specialty Fruits Inc, are a result of applying gene splicing, a laboratory technique that has allowed for the reduction in polyphenol oxidase.
Another type of issue that is closely studied is the browning of seafood. Seafood, in particular shrimp, is a staple consumed by people all over the world. The browning of shrimp, which is actually referred to as melanosis, creates a great concern for food handlers and consumers. Melanosis mainly occurs during postmortem handling and refrigerated storage. Recent studies have found a plant extract that acts as an anti-melatonin polyphenol oxidase inhibitor serves the same function as sulfites but without the health risks. | 1 | Biochemistry |
Müllerian mimicry need not involve visual mimicry; it may employ any of the senses. For example, many snakes share the same auditory warning signals, forming an auditory Müllerian mimicry ring. More than one signal may be shared: snakes can make use of both auditory signals and warning coloration. | 1 | Biochemistry |
All of the basic information regarding the target is necessary here, including the gene symbol, the accession database number for the sequence in question, the length of the sequence being amplified, information about the specificity screen used such as BLAST, what splicing variants exist for the sequence, and where the exon or intron for each primer is. There are several desired, but not required information pieces for this section, such as the location of the amplicon, whether any pseudogenes or homologs exist, whether a sequence alignment was done and the data obtained from it, and any data on the secondary structure of the amplified sequence. | 1 | Biochemistry |
In the U.S. MTBE has been used in gasoline at low levels since 1979, replacing tetraethyllead (TEL) as an antiknock (octane rating) additive to prevent engine knocking. Oxygenates also help gasoline burn more completely, reducing tailpipe emissions. Oxygenates also dilute or displace gasoline components such as aromatics (e.g., benzene). Before the introduction of other oxygenates and octane enhancers, refiners chose MTBE for its blending characteristics and low cost. | 2 | Environmental Chemistry |
Artificial restriction enzymes can be generated by fusing a natural or engineered DNA-binding domain to a nuclease domain (often the cleavage domain of the type IIS restriction enzyme FokI). Such artificial restriction enzymes can target large DNA sites (up to 36 bp) and can be engineered to bind to desired DNA sequences. Zinc finger nucleases are the most commonly used artificial restriction enzymes and are generally used in genetic engineering applications, but can also be used for more standard gene cloning applications. Other artificial restriction enzymes are based on the DNA binding domain of TAL effectors.
In 2013, a new technology CRISPR-Cas9, based on a prokaryotic viral defense system, was engineered for editing the genome, and it was quickly adopted in laboratories. For more detail, read CRISPR (Clustered regularly interspaced short palindromic repeats).
In 2017, a group from University of Illinois reported using an Argonaute protein taken from Pyrococcus furiosus (PfAgo) along with guide DNA to edit DNA in vitro as artificial restriction enzymes.
Artificial ribonucleases that act as restriction enzymes for RNA have also been developed. A PNA-based system, called a PNAzyme, has a Cu(II)-2,9-dimethylphenanthroline group that mimics ribonucleases for specific RNA sequence and cleaves at a non-base-paired region (RNA bulge) of the targeted RNA formed when the enzyme binds the RNA. This enzyme shows selectivity by cleaving only at one site that either does not have a mismatch or is kinetically preferred out of two possible cleavage sites. | 1 | Biochemistry |
In recent years a mammalian two hybrid (M2H) system has been designed to study mammalian protein-protein interactions in a cellular environment that closely mimics the native protein environment. Transiently transfected mammalian cells are used in this system to find protein-protein interactions.
Using a mammalian cell line to study mammalian protein-protein interactions gives the advantage of working in a more native context.
The post-translational modifications, phosphorylation, acylation and glycosylation are similar. The intracellular localization of the proteins is also more correct compared to using a yeast two hybrid system.
It is also possible with the mammalian two-hybrid system to study signal inputs.
Another big advantage is that results can be obtained within 48 hours after transfection. | 1 | Biochemistry |
Spin-polarized electron energy loss spectroscopy or SPEELS is a technique that is mainly used to measure the dispersion relation of the collective excitations, over the whole Brillouin zone.
Spin waves are collective perturbations in a magnetic solid. Their properties depend on their wavelength (or wave vector). For long wavelength (short wave vector) spin wave the resulting spin precession has a very low frequency and the spin waves can be treated classically. Ferromagnetic resonance (FMR) and Brillouin light scattering (BLS) experiments provide information about the long wavelength spin waves in ultrathin magnetic films and nanostructures. If the wavelength is comparable to the lattice constant, the spin waves are governed by the microscopic exchange coupling and a quantum mechanical description is needed. Therefore, experimental information on these short wavelength (large wave vector) spin waves in ultrathin films is highly desired and may lead to fundamentally new insights into the spin dynamics in reduced dimensions in the future.
SPEELS is the one of the few techniques that can be used to measure the dispersion of such short wavelength spin waves in ultrathin films and nanostructures. | 7 | Physical Chemistry |
A preform is a pre-made shape of solder specially designed for the application where it is to be used. Many methods are used to manufacture the solder preform, stamping being the most common. The solder preform may include the solder flux needed for the soldering process. This can be an internal flux, inside the solder preform, or external, with the solder preform coated. | 8 | Metallurgy |
The solvent used in substitution reactions inherently determines the nucleophilicity of the nucleophile; this fact has become increasingly more apparent as more reactions are performed in the gas phase.
As such, solvent conditions significantly affect the performance of a reaction with certain solvent conditions favoring one reaction mechanism over another. For S1 reactions the solvents ability to stabilize the intermediate carbocation is of direct importance to its viability as a suitable solvent. The ability of polar solvents to increase the rate of S1 reactions is a result of the polar solvents solvating the reactant intermediate species, i.e., the carbocation, thereby decreasing the intermediate energy relative to the starting material. The following table shows the relative solvolysis rates of tert-butyl chloride with acetic acid (CHCOH), methanol (CHOH), and water (HO).
The case for S2 reactions is quite different, as the lack of solvation on the nucleophile increases the rate of an S2 reaction. In either case (S1 or S2), the ability to either stabilize the transition state (S1) or destabilize the reactant starting material (S2) acts to decrease the ΔG and thereby increase the rate of the reaction. This relationship is according to the equation ΔG = –RT ln K (Gibbs free energy). The rate equation for S2 reactions are bimolecular being first order in Nucleophile and first order in Reagent. The determining factor when both S2 and S1 reaction mechanisms are viable is the strength of the Nucleophile. Nuclephilicity and basicity are linked and the more nucleophilic a molecule becomes the greater said nucleophile's basicity. This increase in basicity causes problems for S2 reaction mechanisms when the solvent of choice is protic. Protic solvents react with strong nucleophiles with good basic character in an acid/base fashion, thus decreasing or removing the nucleophilic nature of the nucleophile. The following table shows the effect of solvent polarity on the relative reaction rates of the S2 reaction of 1-bromobutane with azide (N). There is a noticeable increase in reaction rate when changing from a protic solvent to an aprotic solvent. This difference arises from acid/base reactions between protic solvents (not aprotic solvents) and strong nucleophiles. While it is true that steric effects also affect the relative reaction rates, however, for demonstration of principle for solvent polarity on S2 reaction rates, steric effects may be neglected.
A comparison of S1 to S2 reactions is to the right. On the left is an S1 reaction coordinate diagram. Note the decrease in ΔG for the polar-solvent reaction conditions. This arises from the fact that polar solvents stabilize the formation of the carbocation intermediate to a greater extent than the non-polar-solvent conditions. This is apparent in the ΔE, ΔΔG. On the right is an S2 reaction coordinate diagram. Note the decreased ΔG for the non-polar-solvent reaction conditions. Polar solvents stabilize the reactants to a greater extent than the non-polar-solvent conditions by solvating the negative charge on the nucleophile, making it less available to react with the electrophile. | 7 | Physical Chemistry |
Exposure to ultraviolet radiation (UVR), whether from the sun or tanning devices is known to be a major cause of the three main types of skin cancer: non-melanoma skin cancer (basal cell carcinoma and squamous cell carcinoma) and melanoma. Overexposure to UVR induces at least two types of DNA damage: cyclobutane–pyrimidine dimers (CPDs) and 6–4 photoproducts (6–4PPs). While DNA repair enzymes can fix some mutations, if they are not sufficiently effective, a cell will acquire genetic mutations which may cause the cell to die or become cancerous. These mutations can result in cancer, aging, persistent mutation and cell death. For example, squamous cell carcinoma can be caused by a UVB-induced mutation in the p53 gene.
Non-melanoma skin cancer includes squamous cell carcinoma (SCC) and basal cell carcinoma (BCC), and is more common than melanoma. With early detection and treatment, it is typically not life-threatening. Prevalence increases with age, cumulative exposure to UV, and proximity to the equator. It is most prevalent in Australia, where the rate is 1,000 in 100,000 and where, as of 2000, it represented 75 percent of all cancers.
Melanoma accounts for approximately one percent of skin cancer, and causes most of skin cancer-related deaths. The average age of diagnosis is 63, and it is the most common cancer in the 25–29 age group and the second most common in the 15-29 group, which may be due in part to the increased UV exposure and use of indoor tanning observed in this population. In the United States, the melanoma incidence rate was 22.3 per 100,000, based on 2010–2014 data from the National Institutes of Health Surveillance, Epidemiology and End Results (SEER) Program, and the death rate was 2.7 per 100,000. 9,730 people were estimated to die of melanoma in the United States in 2017, and these numbers are anticipated to continue rising. Although 91.7% of patients diagnosed with melanoma survive beyond 5-years, advanced melanoma is largely incurable, and only 19.9% percent of patients with metastatic disease survive beyond 5 years. An international meta-analysis performed in 2014 estimates that annually, 464,170 cases of skin cancer can be attributed to exposure to indoor tanning.
A 2012 analysis of epidemiological studies found a 20% increase in the risk of melanoma (a relative risk of 1.20) among those who had ever used a tanning device compared to those who had not, and a 59% percent increase (a relative risk of 1.59) among those who had used one before age 35. Additionally, a 2014 systematic review and meta-analysis found that indoor tanners had a 16 percent increased risk of developing melanoma, which increased to 23 percent for North Americans. For those who started tanning indoors before age 25, their risk further increased to 35% compared to those who began after age 25. | 5 | Photochemistry |
Sulfonamides can be prepared in the laboratory in many ways. The classic approach entails the reaction of sulfonyl chlorides with an amine.
A base such as pyridine is typically added to absorb the HCl that is generated. Illustrative is the synthesis of sulfonylmethylamide.
The reaction of primary and secondary amines with benzenesulfonyl chloride is the basis of the Hinsberg reaction, a method for detecting primary and secondary amines.
Sulfonamides undergo a variety of acid-base reactions. The N-H bond can be deprotonated. The alkylsulfonamides can be deprotonated at carbon. Arylsulfonamides undergo ortho-lithiation. | 0 | Organic Chemistry |
Several methods are available for the preparation of palladacycles. A simple and direct method is C–H activation. The cyclopalladation of aromatic derivatives is usually considered to go through an electrophilic aromatic substitution pathway. The oxidative addition of aryl halides is another useful method. However, the accessibility of the aryl halides starting material is a major drawback.
Other types of reactions such as transmetalation and nucleopalladation also turned out to be effective methods in the synthesis of palladacycles. | 0 | Organic Chemistry |
Chlorophyll fluorescence is light re-emitted by chlorophyll molecules during return from excited to non-excited states. It is used as an indicator of photosynthetic energy conversion in plants, algae and bacteria. Excited chlorophyll dissipates the absorbed light energy by driving photosynthesis (photochemical energy conversion), as heat in non-photochemical quenching or by emission as fluorescence radiation. As these processes are complementary processes, the analysis of chlorophyll fluorescence is an important tool in plant research with a wide spectrum of applications. | 5 | Photochemistry |
In chromatography, endcapping refers to the replacement of accessible silanol groups in a bonded stationary phase by trimethylsilyl groups. End-capped columns have much lower residual silanol group activity compared to non-endcapped columns. Endcapped columns show decreased retention for hydrogen bond acceptors, such as ionized bases, and increased retention for protonated bases. | 3 | Analytical Chemistry |
Almost all transgenic plants contain a few common building blocks that make unknown GMOs easier to find. Even though detecting a novel gene in a GMO can be like finding a needle in a haystack, the fact that the needles are usually similar makes it much easier. To trigger gene expression, scientists couple the gene they want to add with what is known as a transcription promoter. The high-performing 35S promoter is a common feature to many GMOs. In addition, the stop signal for gene transcription in most GMOs is often the same: the NOS terminator. Researchers now compile a set of genetic sequences characteristic of GMOs. After genetic elements characteristic of GMOs are selected, methods and tools are developed for detecting them in test samples. Approaches being considered include microarrays and anchor PCR profiling. | 1 | Biochemistry |
Complex glycans possess a multitude of overlapping signals, especially in a proton spectrum. Therefore, it is advantageous to utilize 2D experiments for the assignment of signals.
The table and figures below list most widespread NMR techniques used in carbohydrate studies. | 0 | Organic Chemistry |
Hydrogen damage is caused by hydrogen atoms (as opposed to hydrogen molecules in the gaseous state), interacting with metal. | 8 | Metallurgy |
KRP stands for kinesin related proteins. bimC is a subfamily of KRPs and its function is to separate the duplicated centrosomes during mitosis. | 1 | Biochemistry |
The ridges enhance the quantum reflection from the surface, reducing the effective constant of the van der Waals attraction of atoms to the surface. Such interpretation leads to the estimate of the reflectivity
where is width of the ridges, is distance between ridges, is grazing angle, and is wavenumber and is coefficient of reflection of atoms with wavenumber from a flat surface at the normal incidence. Such estimate predicts the enhancement of the reflectivity at the increase of period ; this estimate is valid at . See quantum reflection for the approximation (fit) of the function . | 7 | Physical Chemistry |
SLC18A2 is essential for enabling the release of neurotransmitters from the axon terminals of monoamine neurons into the synaptic cleft. If SLC18A2 function is inhibited or compromised, monoamine neurotransmitters such as dopamine cannot be released into the synapse via typical release mechanisms (i.e., exocytosis resulting from action potentials).
Cocaine users display a marked reduction in SLC18A2 immunoreactivity. Those with cocaine-induced mood disorders displayed a significant loss of SLC18A2 immunoreactivity; this might reflect damage to dopamine axon terminals in the striatum. These neuronal changes could play a role in causing disordered mood and motivational processes in more severely addicted users. | 1 | Biochemistry |
BD angle theory was developed based on "frozen" interactions in crystals where the impacts of dynamics at play in the system (e.g., easily changed torsional angles) may be negligible. However, much of the chemistry of general interest and use takes place via collisions of molecules tumbling in solution; accordingly, dynamics are taken into account in such cases. | 7 | Physical Chemistry |
The synapse contains at least two clusters of synaptic vesicles, the readily releasable pool and the reserve pool. The readily releasable pool is located within the active zone and connected directly to the presynaptic membrane while the reserve pool is clustered by cytoskeletal and is not directly connected to the active zone. | 1 | Biochemistry |
Sulfinic acids are oxoacids of sulfur with the structure RSO(OH). In these organosulfur compounds, sulfur is pyramidal. | 0 | Organic Chemistry |
Photorespiration can occur when the oxygen concentration is too high. RuBisCO cannot distinguish between oxygen and carbon dioxide very well, so it can accidentally add O instead of CO to RuBP. This process reduces the efficiency of photosynthesis—it consumes ATP and oxygen, releases CO, and produces no sugar. It can waste up to half the carbon fixed by the Calvin cycle. Several mechanisms have evolved in different lineages that raise the carbon dioxide concentration relative to oxygen within the chloroplast, increasing the efficiency of photosynthesis. These mechanisms are called carbon dioxide concentrating mechanisms, or CCMs. These include Crassulacean acid metabolism, carbon fixation, and pyrenoids. Chloroplasts in plants are notable as they exhibit a distinct chloroplast dimorphism. | 5 | Photochemistry |
Rhizobia bind to host specific lectins present in root hairs which together with Nod factors lead to the formation of nodulation. Nod factors are recognized by a specific class of receptor kinases that have LysM domains in their extracellular domains. The two LysM (lysin motif) receptor kinases (NFR1 and NFR5) that appear to make up the Nod factor receptor were first isolated in the model legume Lotus japonicus in 2003. They now have been isolated also from soybean and the model legume Medicago truncatula. NFR5 lacks the classical activation loop in the kinase domain. The NFR5 gene lacks introns. First the cell membrane is depolarized and the root hairs start to swell and cell division stops. Nod factor cause the fragmentation and rearrangement of actin network, which coupled with the reinstitution of cell growth lead to the curling of the root hair around the bacteria. This is followed by the localized breakdown of the cell wall and the invagination of the plant cell membrane, allowing the bacterium to form an infection thread. As the infection thread grows the rhizobia travel down its length towards the site of the nodule. During this process the pericycle cells in plants become activated and cells in the inner cortex start growing and become the nodule primordium where the rhizobia infect and differentiate into bacteroids and fix nitrogen. Activation of adjacent middle cortex cells leads to the formation of nodule meristem. | 1 | Biochemistry |
British endocrinologist Albert T. W. Simeons proposed HCG as an adjunct to an ultra-low-calorie weight-loss diet (fewer than 500 calories). Simeons, while studying pregnant women in India on a calorie-deficient diet, and fat boys with pituitary problems (Frölichs syndrome) treated with low-dose HCG, observed that both lost fat rather than lean (muscle) tissue. He reasoned that HCG must be programming the hypothalamus to do this in the former cases in order to protect the developing fetus by promoting mobilization and consumption of abnormal, excessive adipose deposits. Simeons in 1954 published a book entitled Pounds and Inches', designed to combat obesity. Simeons, practicing at Salvator Mundi International Hospital in Rome, Italy, recommended low-dose daily HCG injections (125 IU) in combination with a customized ultra-low-calorie (500 cal/day, high-protein, low-carbohydrate/fat) diet, which was supposed to result in a loss of adipose tissue without loss of lean tissue.
Other researchers did not find the same results when attempting experiments to confirm Simeons' conclusions, and in 1976 in response to complaints the FDA required Simeons and others to include the following disclaimer on all advertisements:
There was a resurgence of interest in the "HCG diet" following promotion by Kevin Trudeau, who was banned from making HCG diet weight-loss claims by the U.S. Federal Trade Commission in 2008, and eventually jailed over such claims.
A 1976 study in the American Journal of Clinical Nutrition concluded that HCG is not more effective as a weight-loss aid than dietary restriction alone.
A 1995 meta analysis found that studies supporting HCG for weight loss were of poor methodological quality and concluded that "there is no scientific evidence that HCG is effective in the treatment of obesity; it does not bring about weight-loss or fat-redistribution, nor does it reduce hunger or induce a feeling of well-being".
On November 15, 2016, the American Medical Association (AMA) passed policy that "The use of human chorionic gonadotropin (HCG) for weight loss is inappropriate."
According to the American Society of Bariatric Physicians, no new clinical trials have been published since the definitive 1995 meta-analysis.
The scientific consensus is that any weight loss reported by individuals on an "HCG diet" may be attributed entirely to the fact that such diets prescribe calorie intake of between 500 and 1,000 calories per day, substantially below recommended levels for an adult, to the point that this may risk health effects associated with malnutrition. | 1 | Biochemistry |
Pyrometallurgy involves high temperature processes where chemical reactions take place among gases, solids, and molten materials. Solids containing valuable metals are treated to form intermediate compounds for further processing or converted into their elemental or metallic state. Pyrometallurgical processes that involve gases and solids are typified by calcining and roasting operations. Processes that produce molten products are collectively referred to as smelting operations. The energy required to sustain the high temperature pyrometallurgical processes may derive from the exothermic nature of the chemical reactions taking place. Typically, these reactions are oxidation, e.g. of sulfide to sulfur dioxide . Often, however, energy must be added to the process by combustion of fuel or, in the case of some smelting processes, by the direct application of electrical energy.
Ellingham diagrams are a useful way of analysing the possible reactions, and so predicting their outcome. | 8 | Metallurgy |
Phase inversion or phase separation is a chemical phenomenon exploited in the fabrication of artificial membranes. It is performed by removing the solvent from a liquid-polymer solution, leaving a porous, solid membrane. | 7 | Physical Chemistry |
* geWorkbench is open-source software that can be downloaded and installed locally. A zip file of the released version Java source is also available.
* Prepackaged installer versions also exist for Windows, Macintosh, and Linux. | 1 | Biochemistry |
In waters of the U.S., Canada and other countries, water quality is monitored to protect the health of the general public. Bacteria contamination is one monitored pollutant. In the U.S., fecal coliform testing is one of the nine tests of water quality that form the overall water-quality rating in a process used by U.S. EPA. The fecal coliform assay should only be used to assess the presence of fecal matter in situations where fecal coliforms of non-fecal origin are not commonly encountered. EPA has approved a number of different methods to analyze samples for bacteria. | 3 | Analytical Chemistry |
A monochromator can use either the phenomenon of optical dispersion in a prism, or that of diffraction using a diffraction grating, to spatially separate the colors of light. It usually has a mechanism for directing the selected color to an exit slit. Usually the grating or the prism is used in a reflective mode. A reflective prism is made by making a right triangle prism (typically, half of an equilateral prism) with one side mirrored. The light enters through the hypotenuse face and is reflected back through it, being refracted twice at the same surface. The total refraction, and the total dispersion, is the same as would occur if an equilateral prism were used in transmission mode. | 7 | Physical Chemistry |
In the ecosystem, different substrates are attacked at different rates by consortia of organisms from different kingdoms. Aspergillus and other moulds play an important role in these consortia because they are adept at recycling starches, hemicelluloses, celluloses, pectins and other sugar polymers. Some aspergilli are capable of degrading more refractory compounds such as fats, oils, chitin, and keratin. Maximum decomposition occurs when there is sufficient nitrogen, phosphorus and other essential inorganic nutrients. Fungi also provide food for many soil organisms.
For Aspergillus the process of degradation is the means of obtaining nutrients. When these moulds degrade human-made substrates, the process usually is called biodeterioration. Both paper and textiles (cotton, jute, and linen) are particularly vulnerable to Aspergillus degradation. Our artistic heritage is also subject to Aspergillus assault. To give but one example, after Florence in Italy flooded in 1969, 74% of the isolates from a damaged Ghirlandaio fresco in the Ognissanti church were Aspergillus versicolor. | 2 | Environmental Chemistry |
Depletion gilding is a method for producing a layer of nearly pure gold on an object made of gold alloy by removing the other metals from its surface. It is sometimes referred to as a "surface enrichment" process. | 8 | Metallurgy |
The basic function of PDRCs is to be high in both solar reflectivity (in 0.4–2.5 µm) and in heat emissivity (in 8–13 µm), to maximize "net emission of longwave thermal radiation" and minimize "absorption of downward shortwave radiation." PDRCs use the infrared window (8–13 µm) for heat transfer with the coldness of outer space (~2.7 K) to radiate heat and subsequently lower ambient temperatures with zero energy input.
PDRCs mimic the natural process of radiative cooling, in which the Earth cools itself by releasing heat to outer space (Earth's energy budget), although during the daytime, lowering ambient temperatures under direct solar intensity. On a clear day, solar irradiance can reach 1000 W/m with a diffuse component between 50 and 100 W/m. The average PDRC has an estimated cooling power of ~100–150 W/m. The cooling power of PDRCs is proportional to the exposed surface area of the installation. | 7 | Physical Chemistry |
The geometry of a base, or base pair step can be characterized by 6 coordinates: shift, slide, rise, tilt, roll, and twist. These values precisely define the location and orientation in space of every base or base pair in a nucleic acid molecule relative to its predecessor along the axis of the helix. Together, they characterize the helical structure of the molecule. In regions of DNA or RNA where the normal structure is disrupted, the change in these values can be used to describe such disruption.
For each base pair, considered relative to its predecessor, there are the following base pair geometries to consider:
* Shear
* Stretch
* Stagger
* Buckle
* Propeller: rotation of one base with respect to the other in the same base pair.
* Opening
* Shift: displacement along an axis in the base-pair plane perpendicular to the first, directed from the minor to the major groove.
* Slide: displacement along an axis in the plane of the base pair directed from one strand to the other.
* Rise: displacement along the helix axis.
* Tilt: rotation around the shift axis.
* Roll: rotation around the slide axis.
* Twist: rotation around the rise axis.
* x-displacement
* y-displacement
* inclination
* tip
* pitch: the height per complete turn of the helix.
Rise and twist determine the handedness and pitch of the helix. The other coordinates, by contrast, can be zero. Slide and shift are typically small in B-DNA, but are substantial in A- and Z-DNA. Roll and tilt make successive base pairs less parallel, and are typically small.
"Tilt" has often been used differently in the scientific literature, referring to the deviation of the first, inter-strand base-pair axis from perpendicularity to the helix axis. This corresponds to slide between a succession of base pairs, and in helix-based coordinates is properly termed "inclination". | 4 | Stereochemistry |
Root systems in plants with an expressed BIK1 gene and in plants with a loss-of-function mutant show that without an expressed BIK1 gene, roots grow more laterally, in greater numbers, and with shorter primary roots. With a functional BIK1 gene, roots grew downward into the soil and had less root hairs. Additionally, without a functional BIK1 gene, leaves showed serrated edges and considerable wrinkles whereas leaves with a functional BIK1 gene showed stronger, smoother leaves. Flowering plants that lack a functional BIK1 gene flower an average of six days before those with a functional BIK1 gene and show weaker stem strengths, reduced fertility, and smaller siliques. The BIK1 protein contributes to overall stronger stems, broader leaves, and a healthy flowering timeline. Plants lacking a BIK1 protein or that have a BIK1 protein whose functions are being inhibited may exhibit a shorter flowering period and a smaller stature for the plant overall. This suggests that BIK1 plays a significant role in a plant's ability to grow properly as well as its ability to maintain an adequate rigidity and stem strength that contribute to overall plant health. | 1 | Biochemistry |
The total synthesis of the complex biomolecule vitamin B was accomplished in two different approaches by the collaborating research groups of Robert Burns Woodward at Harvard and Albert Eschenmoser at ETH in 1972. The accomplishment required the effort of no less than 91 postdoctoral researchers (Harvard: 77, ETH: 14), and 12 Ph.D. students (at ETH) from 19 different nations over a period of almost 12 years. The synthesis project induced and involved a major change of paradigm in the field of natural product synthesis. | 0 | Organic Chemistry |
In biology, depolarization or hypopolarization is a change within a cell, during which the cell undergoes a shift in electric charge distribution, resulting in less negative charge inside the cell compared to the outside. Depolarization is essential to the function of many cells, communication between cells, and the overall physiology of an organism.
Most cells in higher organisms maintain an internal environment that is negatively charged relative to the cells exterior. This difference in charge is called the cells membrane potential. In the process of depolarization, the negative internal charge of the cell temporarily becomes more positive (less negative). This shift from a negative to a more positive membrane potential occurs during several processes, including an action potential. During an action potential, the depolarization is so large that the potential difference across the cell membrane briefly reverses polarity, with the inside of the cell becoming positively charged.
The change in charge typically occurs due to an influx of sodium ions into a cell, although it can be mediated by an influx of any kind of cation or efflux of any kind of anion. The opposite of a depolarization is called a hyperpolarization.
Usage of the term "depolarization" in biology differs from its use in physics, where it refers to situations in which any form of polarity (i.e. the presence of any electrical charge, whether positive or negative) changes to a value of zero.
Depolarization is sometimes referred to as "hypopolarization" (as opposed to hyperpolarization). | 7 | Physical Chemistry |
Mefloquine, sold under the brand name Lariam among others, is a medication used to prevent or treat malaria. When used for prevention it is typically started before potential exposure and continued for several weeks after potential exposure. It can be used to treat mild or moderate malaria but is not recommended for severe malaria. It is taken by mouth.
Common side effects include vomiting, diarrhea, headaches, sleep disorders, and a rash. Serious side effects include potentially long-term mental health problems such as depression, hallucinations, and anxiety and neurological side effects such as poor balance, seizures, and ringing in the ears. It is therefore not recommended in people with a history of mental health problems or epilepsy. It appears to be safe during pregnancy and breastfeeding.
Mefloquine was developed by the United States Army in the 1970s and came into use in the mid-1980s. It is on the World Health Organization's List of Essential Medicines. It is available as a generic medication. | 4 | Stereochemistry |
A type III secretion system means that a molecular syringe is used through which a bacterium (e.g. certain types of Salmonella, Shigella, Yersinia) can inject nutrients into protist cells. One such mechanism was first discovered in Y. pestis and showed that toxins could be injected directly from the bacterial cytoplasm into the cytoplasm of its host's cells rather than be secreted into the extracellular medium. | 1 | Biochemistry |
1-Chloro-1,1-difluoroethane (HCFC-142b) is a haloalkane with the chemical formula CHCClF. It belongs to the hydrochlorofluorocarbon (HCFC) family of man-made compounds that contribute significantly to both ozone depletion and global warming when released into the environment. It is primarily used as a refrigerant where it is also known as R-142b and by trade names including Freon-142b. | 2 | Environmental Chemistry |
Micro RNAs are involved in regulating the expression of many proteins. Med1 is targeted by miR-1, which is important in gene regulation in cancers. The tumor suppressor miR-137 also regulates MED1. | 1 | Biochemistry |
Arginylation is a post-translational modification in which proteins are modified by the addition of arginine (Arg) at the N-terminal amino group or side chains of reactive amino acids by the enzyme, arginyltransferase (ATE1). Recent studies have also revealed that hundreds of proteins in vivo are arginylated, proteins which are essential for many biological pathways. While still poorly understood in a biological setting, the ATE1 enzyme is highly conserved which suggests that arginylation is an important biological post-translational modification.
Examples of ATE1 targets which have been identified include ornithine decarboxylase., thyroglobulin, insulin, and neurotensin. | 1 | Biochemistry |
Although kinetic isotope effect measurements at natural abundance are a powerful tool for understanding reaction mechanisms, the amounts of material required for analysis can make this technique inaccessible for reactions that employ expensive reagents or unstable starting materials. In order to mitigate these limitations, Jacobsen and coworkers developed H to C polarization transfer as a means to reduce the time and material required for kinetic isotope effect measurements at natural abundance. The distortionless enhancement by polarization transfer (DEPT) takes advantage of the larger gyromagnetic ratio of H over C to theoretically improve measurement sensitivity by a factor of 4 or decrease experiment time by a factor of 16. This method for natural abundance kinetic isotope measurement is favorable for analysis for reactions containing unstable starting materials, and catalysts or products that are relatively costly.
Jacobsen and coworkers identified the thiourea-catalyzed glycosylation of galactose as a reaction that met both of the aforementioned criteria (expensive materials and unstable substrates) and was a reaction with a poorly understood mechanism. Glycosylation is a special case of nucleophilic substitution that lacks clear definition between S1 and S2 mechanistic character. The presence of the oxygen adjacent to the site of displacement (i.e., C1) can stabilize positive charge. This charge stabilization can cause any potential concerted pathway to become asynchronous and approaches intermediates with oxocarbenium character of the S1 mechanism for glycosylation.
Jacobsen and coworkers observed small normal KIE's at C1, C2, and C5 which suggests significant oxocarbenium character in the transition state and an asynchronous reaction mechanism with a large degree of charge separation. | 7 | Physical Chemistry |
The alkA gene product is a glycosylase that can repair a variety of lesions, removing a base from the sugar-phosphate backbone, producing an abasic site. | 1 | Biochemistry |
Climate scientists Michael Mann of Penn State and Stefan Rahmstorf from the Potsdam Institute for Climate Impact Research suggested that the observed cold pattern during years of temperature records is a sign that the Atlantic Oceans Meridional overturning circulation (AMOC) may be weakening. They published their findings, and concluded that the AMOC circulation shows exceptional slowdown in the last century, and that Greenland melt is a possible contributor. Tom Delworth of NOAA suggested that natural variability, which includes different modes, here namely the North Atlantic Oscillation and the Atlantic Multidecadal Oscillation through wind driven ocean temperatures are also a factor. A 2014 study by Jon Robson et al. from the University of Reading concluded about the anomaly, "...suggest that a substantial change in the AMOC is unfolding now.'" Another study by Didier Swingedouw concluded that the slowdown of AMOC in the 1970s may have been unprecedented over the last millennium. | 9 | Geochemistry |
For example, hydrogen fluoride—which has three lone pairs on the F atom but only one H atom—can form only two bonds; (ammonia has the opposite problem: three hydrogen atoms but only one lone pair). | 6 | Supramolecular Chemistry |
ChimerDB in computational biology is a database of fusion sequences.
ChimerDB currently consists of three searchable datasets.
*[http://203.255.191.229:8080/chimerdbv31/mchimerkb.cdb ChimerKB] is a curated knowledge base of 1,066 fusion genes sourced from publicly available scientific literature.
*[http://203.255.191.229:8080/chimerdbv31/mchimerpub.cdb ChimerPub] provides continuously updated descriptions on fusion genes text mined from publications.
*[http://203.255.191.229:8080/chimerdbv31/mchimerseq.cdb ChimerSeq] is a database of RNA-seq data of fusion sequences downloaded from the [https://tcga-data.nci.nih.gov/docs/publications/tcga/? TCGA data portal]. | 1 | Biochemistry |
Subsets and Splits