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The untranslated regions of mRNA became a subject of study as early as the late 1970s, after the first mRNA molecule was fully sequenced. In 1978, the 5 UTR of the human gamma-globin mRNA was fully sequenced. In 1980, a study was conducted on the 3 UTR of the duplicated human alpha-globin genes. | 1 | Biochemistry |
The Kastle–Meyer test is a presumptive blood test, first described in 1903, in which the chemical indicator phenolphthalein is used to detect the possible presence of hemoglobin. It relies on the peroxidase-like activity of hemoglobin in blood to catalyze the oxidation of phenolphthalin (the colorless reduced form of phenolphthalein) into phenolphthalein, which is visible as a bright pink color. The Kastle–Meyer test is a form of catalytic blood test, one of the two main classes of forensic tests commonly employed by crime labs in the chemical identification of blood. The other class of tests used for this purpose are microcrystal tests, such as the Teichmann crystal test and the Takayama crystal test.
The test was named after the American agricultural chemist, Joseph Hoeing Kastle (1864–1916), who in 1901, invented and tested the crude blood test, and the German physician and chemist, Erich Meyer (1874–1927), who modified the test in 1903. | 3 | Analytical Chemistry |
Depending on the arrangement of the three nitrogen atoms in triazol-5-ylidene, there are two possible isomers, namely 1,2,3-triazol-5-ylidenes and 1,2,4-triazol-5-ylidenes.
The triazol-5-ylidenes based on the 1,2,4-triazole ring are pictured below and were first prepared by Enders and coworkers by vacuum pyrolysis through loss of methanol from 2-methoxytriazoles. Only a limited range of these molecules have been reported, with the triphenyl substituted molecule being commercially available.
Triazole-based carbenes are thermodynamically stable and have diagnostic C NMR chemical shift values between 210 and 220 ppm for the carbenic carbon. The X-ray structure of the triphenyl substituted carbene above shows an N–C–N bond angle of around 101°. The 5-methoxytriazole precursor to this carbene was made by the treatment of a triazolium salt with sodium methoxide, which attacks as a nucleophile. This may indicate that these carbenes are less aromatic than imidazol-2-ylidenes, as the imidazolium precursors do not react with nucleophiles due to the resultant loss of aromaticity. | 0 | Organic Chemistry |
Bawendi was one of the most cited chemists of the decade from 2000 to 2010. He is a leading figure in the research and development of quantum dots. Quantum dots are tiny semiconducting crystals whose nanoscale size gives them unique optical and electronic properties.
A major challenge in quantum dot research was to find ways to create high quality quantum dots that are stable and uniform. Bawendi is recognized for his work in developing standardized methods for quantum dot synthesis. In 1993, Bawendi, and his PhD students David J. Norris and Christopher B. Murray, reported on a hot-injection synthesis method for producing reproducible quantum dots with well-defined size and with high optical quality.
This breakthrough in chemical production methods made it possible to “tune” quantum dots according to size, and achieve predictable properties as a result. It gave scientists much greater control over the material, and made it possible to achieve precise and reproducible results.
The method opened the door to the development of large-scale technological applications of quantum dots in a wide range of areas. Quantum dots are now used in light-emitting diodes (LEDs), photovoltaics (solar cells), photodetectors, photoconductors, lasers, biomedical imaging, biosensing and other applications. | 7 | Physical Chemistry |
The first evidence for phenomena related to the Aharonov–Bohm effect in CDWs was reported in a 1997 paper, which described experiments showing oscillations of period h/2e in CDW (not normal electron) conductance versus magnetic flux through columnar defects in NbSe. Later experiments, including some reported in 2012, show oscillations in CDW current versus magnetic flux, of dominant period h/2e, through TaS rings up to 85 μm in circumference above 77 K. This behavior is similar to that of the superconducting quantum interference device (see SQUID), lending credence to the idea that CDW electron transport is fundamentally quantum in nature (see quantum mechanics). | 7 | Physical Chemistry |
The extensive processing of eukaryotic pre-mRNA that leads to the mature mRNA is the RNA splicing, a mechanism by which introns or outrons (non-coding regions) are removed and exons (coding regions) are joined. | 1 | Biochemistry |
Also known as lidamycin, C-1027 is one of the most potent antitumor enediynes. C-1027 was first isolated from Streptomyces globisporus in a soil sample taken from the Qian-Jiang District of China. Unlike most enediynes, C-1027 does not undergo a triggering process to become an activated 1,4-benzenoid diradical. C-1027 has demonstrated potential efficacy against hypoxic tumors. | 0 | Organic Chemistry |
The electron transport chain carries both protons and electrons, passing electrons from donors to acceptors, and transporting protons across a membrane. These processes use both soluble and protein-bound transfer molecules. In mitochondria, electrons are transferred within the intermembrane space by the water-soluble electron transfer protein cytochrome c. This carries only electrons, and these are transferred by the reduction and oxidation of an iron atom that the protein holds within a heme group in its structure. Cytochrome c is also found in some bacteria, where it is located within the periplasmic space.
Within the inner mitochondrial membrane, the lipid-soluble electron carrier coenzyme Q10 (Q) carries both electrons and protons by a redox cycle. This small benzoquinone molecule is very hydrophobic, so it diffuses freely within the membrane. When Q accepts two electrons and two protons, it becomes reduced to the ubiquinol form (QH); when QH releases two electrons and two protons, it becomes oxidized back to the ubiquinone (Q) form. As a result, if two enzymes are arranged so that Q is reduced on one side of the membrane and QH oxidized on the other, ubiquinone will couple these reactions and shuttle protons across the membrane. Some bacterial electron transport chains use different quinones, such as menaquinone, in addition to ubiquinone.
Within proteins, electrons are transferred between flavin cofactors, iron–sulfur clusters and cytochromes. There are several types of iron–sulfur cluster. The simplest kind found in the electron transfer chain consists of two iron atoms joined by two atoms of inorganic sulfur; these are called [2Fe–2S] clusters. The second kind, called [4Fe–4S], contains a cube of four iron atoms and four sulfur atoms. Each iron atom in these clusters is coordinated by an additional amino acid, usually by the sulfur atom of cysteine. Metal ion cofactors undergo redox reactions without binding or releasing protons, so in the electron transport chain they serve solely to transport electrons through proteins. Electrons move quite long distances through proteins by hopping along chains of these cofactors. This occurs by quantum tunnelling, which is rapid over distances of less than 1.4 m. | 1 | Biochemistry |
Vertebrates were once thought to be unable to perform this cycle because there was no evidence of its two key enzymes, isocitrate lyase and malate synthase. However, some research suggests that this pathway may exist in some, if not all, vertebrates.
Specifically, some studies show evidence of components of the glyoxylate cycle existing in significant amounts in the liver tissue of chickens. Data such as these support the idea that the cycle could theoretically occur in even the most complex vertebrates. Other experiments have also provided evidence that the cycle is present among certain insect and marine invertebrate species, as well as strong evidence of the cycle's presence in nematode species. However, other experiments refute this claim. Some publications conflict on the presence of the cycle in mammals: for example, one paper has stated that the glyoxylate cycle is active in hibernating bears, but this report was disputed in a later paper. Evidence exists for malate synthase activity in humans due to a dual functional malate/B-methylmalate synthase of mitochondrial origin called CLYBL expressed in brown fat and kidney. Vitamin D may regulate this pathway in vertebrates. | 1 | Biochemistry |
Based on the Maxwellian behavior of the hydrogel and observations of erosion via surface plasmon resonance (SPR), the following data results for 3 common R-PEG types at their specified concentrations:
XKCY denotes X thousand daltons of molecular mass and Y carbon atoms.
These values can give us information on the degree of entanglement (or degree of cross linking, depending on what polymer is being considered). In general, higher degrees of entanglement leads to higher time required for the polymer to return to the undeformed state or relaxation times. | 7 | Physical Chemistry |
Novel self-cleaning mechanisms for solar panels are being developed. For instance, in 2019 via wet-chemically etched nanowires and a hydrophobic coating on the surface water droplets could remove 98% of dust particles, which may be especially relevant for applications in the desert.
In March 2022, MIT researchers announced the development of a waterless cleaning system for solar panels and mirrors to address the issue of dust accumulation, which can reduce solar output by up to 30 percent in one month. This system utilizes electrostatic repulsion to detach dust particles from the panel's surface, eliminating the need for water or brushes. An electrical charge imparted to the dust particles by passing a simple electrode over the panel causes them to be repelled by a charge applied to the panel itself. The system can be automated using a basic electric motor and guide rails. | 7 | Physical Chemistry |
Transcriptomics methods are highly parallel and require significant computation to produce meaningful data for both microarray and RNA-Seq experiments. Microarray data is recorded as high-resolution images, requiring feature detection and spectral analysis. Microarray raw image files are each about 750 MB in size, while the processed intensities are around 60 MB in size. Multiple short probes matching a single transcript can reveal details about the intron-exon structure, requiring statistical models to determine the authenticity of the resulting signal. RNA-Seq studies produce billions of short DNA sequences, which must be aligned to reference genomes composed of millions to billions of base pairs. De novo assembly of reads within a dataset requires the construction of highly complex sequence graphs. RNA-Seq operations are highly repetitious and benefit from parallelised computation but modern algorithms mean consumer computing hardware is sufficient for simple transcriptomics experiments that do not require de novo assembly of reads. A human transcriptome could be accurately captured using RNA-Seq with 30 million 100 bp sequences per sample. This example would require approximately 1.8 gigabytes of disk space per sample when stored in a compressed fastq format. Processed count data for each gene would be much smaller, equivalent to processed microarray intensities. Sequence data may be stored in public repositories, such as the Sequence Read Archive (SRA). RNA-Seq datasets can be uploaded via the Gene Expression Omnibus. | 1 | Biochemistry |
The upstream signaling pathway is triggered by the binding of a signaling molecule, a ligand, to a receiving molecule, a receptor. Receptors and ligands exist in many different forms, and only recognize/bond to particular molecules. Upstream extracellular signaling transduce a variety of intracellular cascades.
Receptors and ligands are common upstream signaling molecules that dictate the downstream elements of the signal pathway. A plethora of different factors affect which ligands bind to which receptors and the downstream cellular response that they initiate. | 1 | Biochemistry |
Elaidinization is any chemical reaction which convert a cis- olefin to a trans- olefin in unsaturated fatty acids. This is often performed on fats and oils to increase both the melting point and the shelf life without reducing the degree of unsaturation. The term originates from elaidic acid, the trans-isomer of oleic acid. | 0 | Organic Chemistry |
A primary metabolite is a kind of metabolite that is directly involved in normal growth, development, and reproduction. It usually performs a physiological function in the organism (i.e. an intrinsic function). A primary metabolite is typically present in many organisms or cells. It is also referred to as a central metabolite, which has an even more restricted meaning (present in any autonomously growing cell or organism). Some common examples of primary metabolites include: lactic acid, and certain amino acids. Note that primary metabolites do not show any pharmacological actions or effects.
Conversely, a secondary metabolite is not directly involved in those processes, but usually has an important ecological function (i.e. a relational function). A secondary metabolite is typically present in a taxonomically restricted set of organisms or cells (plants, fungi, bacteria, etc.). Some common examples of secondary metabolites include: ergot alkaloids, antibiotics, naphthalenes, nucleosides, phenazines, quinolines, terpenoids, peptides and growth factors.
Plant growth regulators may be classified as both primary and secondary metabolites due to their role in plant growth and development. Some of them are intermediates between primary and secondary metabolism. | 1 | Biochemistry |
There are several strategies for removal and/or negation of ion suppression. These approaches may require in-depth understanding of the ionisation mechanisms involved in different ionisation sources or may be completely independent of the physical factors involved. | 3 | Analytical Chemistry |
Lost-foam casting is a type of evaporative-pattern casting process that is similar to investment casting except foam is used for the pattern instead of wax. This process takes advantage of the low boiling point of foam to simplify the investment casting process by removing the need to melt the wax out of the mold. | 8 | Metallurgy |
As a consequence of the high shielding by the nearby ISS, the biological samples were predominantly exposed to galactic cosmic heavy ions, while electrons and a significant fraction of protons of the radiation belts and solar wind did not reach the samples. | 1 | Biochemistry |
The Sawmill is run by a D-3000 Cat diesel engine, Hawthorne Machinery in San Diego provided the cylinder liners. The Sawmill was re-assembled and improved following a donation from the Pederson Brothers who had operated it in the Big Bear area years ago. This is likely the only Sawmill that can be seen operating in San Diego County. | 8 | Metallurgy |
Heat is thermal energy associated with temperature-dependent motion of particles. The macroscopic energy equation for infinitesimal volume used in heat transfer analysis is
where is heat flux vector, is temporal change of internal energy ( is density, is specific heat capacity at constant pressure, is temperature and is time), and is the energy conversion to and from thermal energy ( and are for principal energy carriers). So, the terms represent energy transport, storage and transformation. Heat flux vector is composed of three macroscopic fundamental modes, which are conduction (, : thermal conductivity), convection (, : velocity), and radiation (, : angular frequency, : polar angle, : spectral, directional radiation intensity, : unit vector), i.e., .
Once states and kinetics of the energy conversion and thermophysical properties are known, the fate of heat transfer is described by the above equation. These atomic-level mechanisms and kinetics are addressed in heat transfer physics. The microscopic thermal energy is stored, transported, and transformed by the principal energy carriers: phonons (p), electrons (e), fluid particles (f), and photons (ph). | 7 | Physical Chemistry |
Multivariate optical computing, also known as molecular factor computing, is an approach to the development of compressed sensing spectroscopic instruments, particularly for industrial applications such as process analytical support. "Conventional" spectroscopic methods often employ multivariate and chemometric methods, such as multivariate calibration, pattern recognition, and classification, to extract analytical information (including concentration) from data collected at many different wavelengths. Multivariate optical computing uses an optical computer to analyze the data as it is collected. The goal of this approach is to produce instruments which are simple and rugged, yet retain the benefits of multivariate techniques for the accuracy and precision of the result.
An instrument which implements this approach may be described as a multivariate optical computer. Since it describes an approach, rather than any specific wavelength range, multivariate optical computers may be built using a variety of different instruments (including Fourier Transform Infrared (FTIR) and Raman).
The "software" in multivariate optical computing is encoded directly into an optical element spectral calculation engine such as an interference filter based multivariate optical element (MOE), holographic grating, liquid crystal tunable filter, spatial light modulator (SLM), or digital micromirror device (DMD) and is specific to the particular application. The optical pattern for the spectral calculation engine is designed for the specific purpose of measuring the magnitude of that multi-wavelength pattern in the spectrum of a sample, without actually measuring a spectrum.
Multivariate optical computing allows instruments to be made with the mathematics of pattern recognition designed directly into an optical computer, which extracts information from light without recording a spectrum. This makes it possible to achieve the speed, dependability, and ruggedness necessary for real time, in-line process control instruments.
Multivariate optical computing encodes an analog optical regression vector of a transmission function for an optical element. Light which emanates from a sample contains the spectral information of that sample, whether the spectrum is discovered or not. As light passes from a sample through the element, the normalized intensity, which is detected by a broad band detector, is proportional to the dot product of the regression vector with that spectrum, i.e. is proportional to the concentration of the analyte for which the regression vector was designed. The quality of the analysis is then equal to the quality of the regression vector which is encoded. If the resolution of the regression vector is encoded to the resolution of the laboratory instrument from which that regression vector was designed and the resolution of the detector is equivalent, then the measurement made by Multivariate Optical Computing will be equivalent to that laboratory instrument by conventional means. The technique is making headway in a niche market for harsh environment detection. Specifically the technique has been adopted for use in the oil industry for detection of hydrocarbon composition in oil wells and pipeline monitoring. In such situations, laboratory quality measurements are necessary, but in harsh environments. | 7 | Physical Chemistry |
1,4-Dioxane () is a heterocyclic organic compound, classified as an ether. It is a colorless liquid with a faint sweet odor similar to that of diethyl ether. The compound is often called simply dioxane because the other dioxane isomers (1,2- and 1,3-) are rarely encountered.
Dioxane is used as a solvent for a variety of practical applications as well as in the laboratory, and also as a stabilizer for the transport of chlorinated hydrocarbons in aluminium containers. | 6 | Supramolecular Chemistry |
Tribromoisocyanuric acid (CBrNO) is a chemical compound used as a reagent for bromination in organic synthesis. It is a white crystalline powder with a strong bromine odour. It is similar to trichloroisocyanuric acid. | 0 | Organic Chemistry |
Disiamylborane is prepared by hydroboration of trimethylethylene with diborane. The reaction stops at the secondary borane due to steric hindrance.
Disiamylborane is relatively selective for terminal alkynes and alkenes vs internal alkynes and alkenes. Like most hydroboration, the addition proceeds in an anti-Markovnikov manner. It can be used to convert terminal alkynes, into aldehydes.
The hydroboration process proceeds via an initial dissociation of the dimer. | 0 | Organic Chemistry |
The cell cycle is composed of a number of well-ordered, consecutive stages that result in cellular division. The fact that cells do not begin the next stage until the last one is finished, is a significant element of cell cycle regulation. Cell cycle checkpoints are characteristics that constitute an excellent monitoring strategy for accurate cell cycle and divisions. Cdks, associated cyclin counterparts, protein kinases, and phosphatases regulate cell growth and division from one stage to another. The cell cycle is controlled by the temporal activation of Cdks, which is governed by cyclin partner interaction, phosphorylation by particular protein kinases, and de-phosphorylation by Cdc25 family phosphatases. In response to DNA damage, a cell's DNA repair reaction is a cascade of signaling pathways that leads to checkpoint engagement, regulates, the repairing mechanism in DNA, cell cycle alterations, and apoptosis. Numerous biochemical structures, as well as processes that detect damage in DNA, are ATM and ATR, which induce the DNA repair checkpoints
The cell cycle is a sequence of activities in which cell organelles are duplicated and subsequently separated into daughter cells with precision. There are major events that happen during a cell cycle. The processes that happen in the cell cycle include cell development, replication and segregation of chromosomes. The cell cycle checkpoints are surveillance systems that keep track of the cell cycles integrity, accuracy, and chronology. Each checkpoint serves as an alternative cell cycle endpoint, wherein the cells parameters are examined and only when desirable characteristics are fulfilled does the cell cycle advance through the distinct steps. The cell cycles goal is to precisely copy each organisms DNA and afterwards equally split the cell and its components between the two new cells. Four main stages occur in the eukaryotes. In G1, the cell is usually active and continues to grow rapidly, while in G2, the cell growth continues while protein molecules become ready for separation. These are not dormant times; they are when cells gain mass, integrate growth factor receptors, establish a replicated genome, and prepare for chromosome segregation. DNA replication is restricted to a separate Synthesis in eukaryotes, which is also known as the S-phase. During mitosis, which is also known as the M-phase, the segregation of the chromosomes occur. DNA, like every other molecule, is capable of undergoing a wide range of chemical reactions. Modifications in DNAs sequence, on the other hand, have a considerably bigger impact than modifications in other cellular constituents like RNAs or proteins because DNA acts as a permanent copy of the cell genome. When erroneous nucleotides are incorporated during DNA replication, mutations can occur. The majority of DNA damage is fixed by removing the defective bases and then re-synthesizing the excised area. On the other hand, some DNA lesions can be mended by reversing the damage, which may be a more effective method of coping with common types of DNA damage. Only a few forms of DNA damage are mended in this fashion, including pyrimidine dimers caused by ultraviolet (UV) light changed by the insertion of methyl or ethyl groups at the purine rings O6 position. | 1 | Biochemistry |
Carboxypeptidase A (CPA) contains a zinc (Zn) metal center in a tetrahedral geometry with amino acid residues in close proximity around zinc to facilitate catalysis and binding. Out of the 307 amino acids bonded in a peptide chain, the following amino acid residues are important for catalysis and binding; Glu-270, Arg-71, Arg-127, Asn-144, Arg-145, and Tyr-248. Figure 1 illustrates the tetrahedral zinc complex active site with the important amino acid residues that surround the complex.
The zinc metal is a strong electrophilic Lewis acid catalyst which stabilizes a coordinated water molecule as well as stabilizes the negative intermediates that occur throughout the hydrolytic reaction. Stabilization of both the coordinated water molecule and negative intermediates are assisted by polar residues in the active site which are in close proximity to facilitate hydrogen bonding.
The active site can be characterized into two sub-sites denoted as S’ and S. The S’ sub-site is the hydrophobic pocket of the enzyme, and Tyr-248 acts to ‘cap’ the hydrophobic pocket after substrate or inhibitor is bound (SITE). The hydrogen bonding from the hydroxyl group in Tyr-248 facilitates this conformation due to interaction with the terminal carboxylates of substrates that bind. Substantial movement is required for this enzyme and induced fit model explains how this interaction occurs.
A triad of residues interact to the C-terminal carboxylate through hydrogen bonding:
* Salt linkage with positively charged Arg-145
* Hydrogen bond from Tyr-248
* Hydrogen bond from the nitrogen of the Asn-144 amide | 1 | Biochemistry |
Micromeritics is the science and technology of small particles pioneered by Joseph M. DallaValle. It is thus the study of the fundamental and derived properties of individual as well as a collection of particles. The knowledge and control of the size of particles has importance in pharmacy and materials science. The size, and hence the surface area of a particle, can be related to the physical, chemical and pharmacological properties of drugs. Clinically, the particle size of a drug can affect its release from dosage forms that are administered orally, parenterally, rectally and topically. The successful formulation of suspensions, emulsions and tablets; both physical stability and pharmacological response also depends on the particle size achieved in the product. | 7 | Physical Chemistry |
2D synchronous and asynchronous spectra are basically 3D-datasets and are generally represented by contour plots. X- and y-axes are identical to the x-axis of the original dataset, whereas the different contours represent the magnitude of correlation between the spectral intensities. The 2D synchronous spectrum is symmetric relative to the main diagonal. The main diagonal thus contains positive peaks. As the peaks at (x,y) in the 2D synchronous spectrum are a measure for the correlation between the intensity changes at x and y in the original data, these main diagonal peaks are also called autopeaks and the main diagonal signal is referred to as autocorrelation signal. The off-diagonal cross-peaks can be either positive or negative. On the other hand, the asynchronous spectrum is asymmetric and never has peaks on the main diagonal.
Generally contour plots of 2D spectra are oriented with rising axes from left to right and top to down. Other orientations are possible, but interpretation has to be adapted accordingly. | 7 | Physical Chemistry |
Thermomechanical processing is a metallurgical process that combines mechanical or plastic deformation process like compression or forging, rolling, etc. with thermal processes like heat-treatment, water quenching, heating and cooling at various rates into a single process. | 8 | Metallurgy |
Coinage metals, such as copper and silver, slowly corrode through use.
A patina of green-blue copper carbonate forms on the surface of copper with exposure to the water and carbon dioxide in the air. Silver coins or cutlery that are exposed to high sulfur foods such as eggs or the low levels of sulfur species in the air develop a layer of black silver sulfide.
Gold and platinum are extremely difficult to oxidize under normal circumstances, and require exposure to a powerful chemical oxidizing agent such as aqua regia.
Some common metals oxidize extremely rapidly in air. Titanium and aluminium oxidize instantaneously in contact with the oxygen in the air. These metals form an extremely thin layer of oxidized metal on the surface, which bonds with the underlying metal. This thin oxide layer protects the underlying bulk of the metal from the air preventing the entire metal from oxidizing. These metals are used in applications where corrosion resistance is important. Iron, in contrast, has an oxide that forms in air and water, called rust, that does not bond with the iron and therefore does not stop the further oxidation of the iron. Thus iron left exposed to air and water will continue to rust until all of the iron is oxidized. | 7 | Physical Chemistry |
To cope with high volume mass flows and for application, where a changing physical location of the sensor-based sorting process is of no benefit for the financial feasibility of the operation, stationary installations are applied. Another reason for applying stationary installations are multistage (Rougher, Scavenger, Cleaner) sensor-based ore sorting processes. Within stationary installations, sorters are usually located in parallel, which allows transport of the discharge fractions with one product and one waste belt respectively, which decreases plant footprint and amount of conveyors. | 3 | Analytical Chemistry |
Cellosaurus is an online knowledge base on cell lines, which attempts to document all cell lines used in biomedical research. It is provided by the Swiss Institute of Bioinformatics (SIB). It is an ELIXIR Core Data Resource as well as an IRDiRC's Recognized Resource. It is the contributing resource for cell lines on the Resource Identification Portal. As of December 2022, it contains information for more than 144,000 cell lines.
Its scope includes immortalised cell lines, naturally immortal cell lines (example: embryonic stem cells) and finite life cell lines when those are distributed and used widely. The Cellosaurus provides a wealth of manually curated information; for each cell line it lists a recommended name, synonyms and the species of origin. Other types of information include standardised disease terminology (for cancer or genetic disorder cell lines), the transformant used to immortalise a cell line, transfected or knocked-out genes, microsatellite instability, doubling time, gender and age of donor (patient or animal), important sequence variations, web links, publication references and cross-references to close to 100 different databases, ontologies, cell collections and other relevant resources.
Since many cell lines used in research have been misidentified or contaminated, the Cellosaurus keeps track of problematic cell lines, including all those listed in the International Cell Line Authentication Committee (ICLAC) tables. For human as well as some dog cell lines, it provides short tandem repeat (STR) profile information. Since July 2018, cell lines in the Cellosaurus are represented as items in Wikidata. In March 2020, the Cellosaurus created a page containing cell line information relevant to SARS-CoV-2 in response to the COVID-19 pandemic.
The Cellosaurus encyclopedia is widely recognized as an authoritative source for cell line information, providing unique identifiers and as source of curated information. | 1 | Biochemistry |
The Copper Age, also called the Eneolithic or the Chalcolithic Age, has been traditionally understood as a transitional period between the Neolithic and the Bronze Age, in which a gradual introduction of the metal (native copper) took place, while stone was still the main resource utilized. Recent archaeology has found that the metal was not introduced so gradually and that this entailed significant social changes, such as developments in the type of habitation (larger villages, launching of fortifications), long-distance trade, and copper metallurgy.
Some of the earliest Copper Age artifacts were found in the 5th and 6th millennia BCE archaeological sites of the Vinča culture such as Majdanpek, Jarmovac and Pločnik (including a copper axe from 5500 BCE). Somewhat later, in the 5th millennium BCE, metalwork is attested at Rudna Glava mine in Serbia, and at Ai Bunar mine in Bulgaria.
3rd millennium BCE copper metalwork is attested in places like Palmela (Portugal), Cortes (Navarre), and Stonehenge (England). However, as often happens with the prehistoric times, the limits of the age cannot be clearly defined and vary between different sources. | 8 | Metallurgy |
The asymmetric hydrogenation of furans and benzofurans is challenging.
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Asymmetric hydrogenation of thiophenes and benzothiophenes has been catalyzed by some ruthenium(II) complexes of N-heterocyclic carbenes (NHC). This system appears to possess superb selectivity (ee > 90%) and perfect diastereoselectivity (all cis) if the substrate has a fused (or directly bound) phenyl ring but yields only racemic product in all other tested cases.
<br /> | 0 | Organic Chemistry |
Sir Christopher Kelk Ingold (28 October 1893 – 8 December 1970) was a British chemist based in Leeds and London. His groundbreaking work in the 1920s and 1930s on reaction mechanisms and the electronic structure of organic compounds was responsible for the introduction into mainstream chemistry of concepts such as nucleophile, electrophile, inductive and resonance effects, and such descriptors as S1, S2, E1, and E2. He also was a co-author of the Cahn–Ingold–Prelog priority rules. Ingold is regarded as one of the chief pioneers of physical organic chemistry. | 4 | Stereochemistry |
Coulomb crystals of various ionic species have applications across much of physics, for example, in high precision spectroscopy, quantum information processing and cavity QED. | 7 | Physical Chemistry |
Self-complementarity refers to the fact that a sequence of DNA or RNA may fold back on itself, creating a double-strand like structure. Depending on how close together the parts of the sequence are that are self-complementary, the strand may form hairpin loops, junctions, bulges or internal loops. RNA is more likely to form these kinds of structures due to base pair binding not seen in DNA, such as guanine binding with uracil. | 1 | Biochemistry |
Ion balance is a key factor in plant development to produce yield. Too high salt concentration in soil lowers the water potential in root tissue which becomes toxic; stunting growth and inhibiting flowering by dehydrating the plant. Stomatal closure is also a response to high salinity, leading to lowered sugar production and transpiration rates. Plants respond to high salinity soils by accumulating sodium and chlorine, and reducing uptake of macronutrients and other ions. This accumulation results in inhibition of calcium signaling. In order to combat this type of stress, plants must have strategies and adaptations in place for survival, such as osmotic stress pathways. RNA sequencing and qRT-PCR analysis has made finding these gene expression pathways possible, such as the MAPK, allowing for the scrutiny of candidate genes responsible for greater tolerance to salinity. Candidate genes for this type of stress response have also been found in plant hormone signal transduction pathways. Different species of Cannabis carry unique variations of gene expression, with some having a greater ability to utilize salt tolerance by keeping potassium levels high enough as to deny sodium uptake.
Removing sodium from the cytoplasm by means of sodium or hydrogen anti-porters is another mechanism to resist desiccation from high salinity environments by using the salt overly sensitive (SOS) regulation pathway. The SOS pathway exchanges excess sodium for hydrogen, and it is set into action by calcium signal flux.
Modifying the cytoskeleton or utilizing an osmotic stress pathway are two other physiological defenses plants use to handle salinity. The ability to sense excess salinity is a valuable tool, where excess sodium can trigger an influx of calcium and reactive oxygen species (ROS). Without the ability to notice sodium, calcium wouldn't be triggered into a signaling cascade to flow into the cytosol. This flow notifies the system to block salt ions from entering into the roots by using any available defenses, such as modifying the cell wall. A plant without these sensing and signaling capabilities is considered salt-sensitive, known as a glycophyte. | 1 | Biochemistry |
The microbes or eukaryotic cells used for fermentation grow in (or on) specially designed growth medium which supplies the nutrients required by the organisms or cells. A variety of media exist, but invariably contain a carbon source, a nitrogen source, water, salts, and micronutrients. In the production of wine, the medium is grape must. In the production of bio-ethanol, the medium may consist mostly of whatever inexpensive carbon source is available.
Carbon sources are typically sugars or other carbohydrates, although in the case of substrate transformations (such as the production of vinegar) the carbon source may be an alcohol or something else altogether. For large scale fermentations, such as those used for the production of ethanol, inexpensive sources of carbohydrates, such as molasses, corn steep liquor, sugar cane juice, or sugar beet juice are used to minimize costs. More sensitive fermentations may instead use purified glucose, sucrose, glycerol or other sugars, which reduces variation and helps ensure the purity of the final product. Organisms meant to produce enzymes such as beta galactosidase, invertase or other amylases may be fed starch to select for organisms that express the enzymes in large quantity.
Fixed nitrogen sources are required for most organisms to synthesize proteins, nucleic acids and other cellular components. Depending on the enzyme capabilities of the organism, nitrogen may be provided as bulk protein, such as soy meal; as pre-digested polypeptides, such as peptone or tryptone; or as ammonia or nitrate salts. Cost is also an important factor in the choice of a nitrogen source. Phosphorus is needed for production of phospholipids in cellular membranes and for the production of nucleic acids. The amount of phosphate which must be added depends upon the composition of the broth and the needs of the organism, as well as the objective of the fermentation. For instance, some cultures will not produce secondary metabolites in the presence of phosphate.
Growth factors and trace nutrients are included in the fermentation broth for organisms incapable of producing all of the vitamins they require. Yeast extract is a common source of micronutrients and vitamins for fermentation media. Inorganic nutrients, including trace elements such as iron, zinc, copper, manganese, molybdenum, and cobalt are typically present in unrefined carbon and nitrogen sources, but may have to be added when purified carbon and nitrogen sources are used. Fermentations which produce large amounts of gas (or which require the addition of gas) will tend to form a layer of foam, since fermentation broth typically contains a variety of foam-reinforcing proteins, peptides or starches. To prevent this foam from occurring or accumulating, antifoaming agents may be added. Mineral buffering salts, such as carbonates and phosphates, may be used to stabilize pH near optimum. When metal ions are present in high concentrations, use of a chelating agent may be necessary.
Developing an optimal medium for fermentation is a key concept to efficient optimization. One-factor-at-a-time (OFAT) is the preferential choice that researchers use for designing a medium composition. This method involves changing only one factor at a time while keeping the other concentrations constant. This method can be separated into some sub groups. One is Removal Experiments. In this experiment all the components of the medium are removed one at a time and their effects on the medium are observed. Supplementation experiments involve evaluating the effects of nitrogen and carbon supplements on production. The final experiment is a replacement experiment. This involves replacing the nitrogen and carbon sources that show an enhancement effect on the intended production. Overall OFAT is a major advantage over other optimization methods because of its simplicity. | 1 | Biochemistry |
When an alien pathway is installed in a host (chassis) organism, and even when a native pathway is massively upregulated, reactive intermediates may accumulate to levels that negatively impact viability, growth, and flux through the pathway because a matching damage-control system is absent or has been overwhelmed. Engineering damage-control systems may thus be needed to support synthetic biology and metabolic engineering projects. | 1 | Biochemistry |
The use of alloys by humans started with the use of meteoric iron, a naturally occurring alloy of nickel and iron. It is the main constituent of iron meteorites. As no metallurgic processes were used to separate iron from nickel, the alloy was used as it was. Meteoric iron could be forged from a red heat to make objects such as tools, weapons, and nails. In many cultures it was shaped by cold hammering into knives and arrowheads. They were often used as anvils. Meteoric iron was very rare and valuable, and difficult for ancient people to work. | 8 | Metallurgy |
Like other Short interspersed nuclear elements (SINEs), MIR elements used the machinery of LINE elements for their propagation in the genome, which took place around 130 million years ago. They cannot retrotranspose anymore since the loss of activity of the required reverse transcriptase. | 1 | Biochemistry |
ATP2A2 also known as sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (SERCA2) is an ATPase associated with Darier's disease and Acrokeratosis verruciformis.
This gene encodes one of the SERCA Ca(2+)-ATPases, which are intracellular pumps located in the sarcoplasmic or endoplasmic reticula of muscle cells. This enzyme catalyzes the hydrolysis of ATP coupled with the translocation of calcium from the cytosol to the sarcoplasmic reticulum lumen, and is involved in calcium sequestration associated with muscular excitation and contraction. Alternative splicing results in multiple transcript variants encoding different isoforms. | 1 | Biochemistry |
The course of the action potential can be divided into five parts: the rising phase, the peak phase, the falling phase, the undershoot phase, and the refractory period. During the rising phase the membrane potential depolarizes (becomes more positive). The point at which depolarization stops is called the peak phase. At this stage, the membrane potential reaches a maximum. Subsequent to this, there is a falling phase. During this stage the membrane potential becomes more negative, returning towards resting potential. The undershoot, or afterhyperpolarization, phase is the period during which the membrane potential temporarily becomes more negatively charged than when at rest (hyperpolarized). Finally, the time during which a subsequent action potential is impossible or difficult to fire is called the refractory period, which may overlap with the other phases.
The course of the action potential is determined by two coupled effects. First, voltage-sensitive ion channels open and close in response to changes in the membrane voltage V. This changes the membranes permeability to those ions. Second, according to the Goldman equation, this change in permeability changes the equilibrium potential E, and, thus, the membrane voltage V. Thus, the membrane potential affects the permeability, which then further affects the membrane potential. This sets up the possibility for positive feedback, which is a key part of the rising phase of the action potential. A complicating factor is that a single ion channel may have multiple internal "gates" that respond to changes in V in opposite ways, or at different rates. For example, although raising V opens most gates in the voltage-sensitive sodium channel, it also closes the channels "inactivation gate", albeit more slowly. Hence, when V is raised suddenly, the sodium channels open initially, but then close due to the slower inactivation.
The voltages and currents of the action potential in all of its phases were modeled accurately by Alan Lloyd Hodgkin and Andrew Huxley in 1952, for which they were awarded the Nobel Prize in Physiology or Medicine in 1963. However, their model considers only two types of voltage-sensitive ion channels, and makes several assumptions about them, e.g., that their internal gates open and close independently of one another. In reality, there are many types of ion channels, and they do not always open and close independently. | 7 | Physical Chemistry |
The US Environmental Protection Agency (EPA) lists the following criteria for an organism to be an ideal indicator of fecal contamination:
# The organism should be present whenever enteric pathogens are present
# The organism should be useful for all types of water
# The organism should have a longer survival time than the hardiest enteric pathogen
# The organism should not grow in water
# The organism should be found in warm-blooded animals' intestines.
None of the types of indicator organisms that are currently in use fit all of these criteria perfectly, however, when cost is considered, use of indicators becomes necessary. | 3 | Analytical Chemistry |
In quantum mechanics, the energy levels of electrons in atoms depend on the reduced mass of the system of electron and nucleus. For the hydrogen atom, the role of reduced mass is most simply seen in the Bohr model of the atom, where the reduced mass appears in a simple calculation of the Rydberg constant and Rydberg equation, but the reduced mass also appears in the Schrödinger equation, and the Dirac equation for calculating atomic energy levels.
The reduced mass of the system in these equations is close to the mass of a single electron, but differs from it by a small amount about equal to the ratio of mass of the electron to the nucleus. For normal hydrogen, this amount is about , or 1.000545, and for deuterium it is even smaller: , or 1.0002725. The energies of electronic spectra lines for H and H therefore differ by the ratio of these two numbers, which is 1.000272. The wavelengths of all deuterium spectroscopic lines are shorter than the corresponding lines of light hydrogen, by 0.0272%. In astronomical observation, this corresponds to a blue Doppler shift of 0.0272% of the speed of light, or 81.6 km/s.
The differences are much more pronounced in vibrational spectroscopy such as infrared spectroscopy and Raman spectroscopy, and in rotational spectra such as microwave spectroscopy because the reduced mass of the deuterium is markedly higher than that of protium. In nuclear magnetic resonance spectroscopy, deuterium has a very different NMR frequency (e.g. 61 MHz when protium is at 400 MHz) and is much less sensitive. Deuterated solvents are usually used in protium NMR to prevent the solvent from overlapping with the signal, though deuterium NMR on its own right is also possible. | 9 | Geochemistry |
The Emeritus Group at MPI-Marburg is headed by renowned biochemist and Gottfried Wilhelm Leibniz Prize recipient, Rudolf K. Thauer, who was also the founding director of the institute when it was established in 1991. The scientific focus of the group is on the biochemistry of methanogenic archaea, methanotrophic archaea and saccharolytic clostridia. The following specific topics are being addressed:
* Hydrogen activation
* Methane formation and anaerobic methane oxidation
* Ferredoxin reduction | 9 | Geochemistry |
When people think of DNA analysis, they often think about television shows like NCIS or CSI, which portray DNA samples coming into a lab and being instantly analyzed, followed by the pulling up of a picture of the suspect within minutes. However, the reality is quite different, and perfect DNA samples are often not collected from the scene of a crime. Homicide victims are frequently left exposed to harsh conditions before they are found, and objects that are used to commit crimes have often been handled by more than one person. The two most prevalent issues that forensic scientists encounter when analyzing DNA samples are degraded samples and DNA mixtures. | 1 | Biochemistry |
Following the 2019 redefinition of the SI base units, the value of the triple point of water is no longer used as a defining point. However, its empirical value remains important: the unique combination of pressure and temperature at which liquid water, solid ice, and water vapor coexist in a stable equilibrium is approximately and a vapor pressure of .
Liquid water can only exist at pressures equal to or greater than the triple point. Below this, in the vacuum of outer space, solid ice sublimates, transitioning directly into water vapor when heated at a constant pressure. Conversely, above the triple point, solid ice first melts into liquid water upon heating at a constant pressure, then evaporates or boils to form vapor at a higher temperature.
For most substances, the gas–liquid–solid triple point is the minimum temperature where the liquid can exist. For water, this is not the case. The melting point of ordinary ice decreases with pressure, as shown by the phase diagram's dashed green line. Just below the triple point, compression at a constant temperature transforms water vapor first to solid and then to liquid.
Historically, during the Mariner 9 mission to Mars, the triple point pressure of water was used to define "sea level." Now, laser altimetry and gravitational measurements are preferred to define Martian elevation. | 7 | Physical Chemistry |
Van Gieson's stain is a mixture of picric acid and acid fuchsin. It is the simplest method of differential staining of collagen and other connective tissue. It was introduced to histology by American neuropsychiatrist and pathologist Ira Van Gieson.
HvG stain generally refers to the combination of hematoxylin and Van Giesons stain, but can possibly refer to a combination of hibiscus extract-iron solution and Van Giesons stain. | 1 | Biochemistry |
Limitations of evaporative cooling have restricted atomic BECs to "pulsed" operation, involving a highly inefficient duty cycle that discards more than 99% of atoms to reach BEC. Achieving continuous BEC has been a major open problem of experimental BEC research, driven by the same motivations as continuous optical laser development: high flux, high coherence matter waves produced continuously would enable new sensing applications.
Continuous BEC was achieved for the first time in 2022. | 7 | Physical Chemistry |
Arachidonoyl serotonin (N-arachidonoyl-serotonin, AA-5-HT) is an endogenous lipid signaling molecule. It was first described in 1998 as being an inhibitor of fatty acid amide hydrolase (FAAH). In 2007, it was shown to have analgesic properties and to act as an antagonist of the TRPV1 receptor. In 2011, it was shown to be present in the ileum and jejunum of the gastrointestinal tract and modulate glucagon-like peptide-1 (GLP-1) secretion. In addition to this, in 2016, AA-5-HT was also found to affect the signaling mechanisms responsible for anxiety, by inhibiting dopamine release from the Basolateral amygdala following fear behavior. In 2017, AA-5-HT was tested in its effects on the sleep wake cycle, where it was found to affect the sleep homeostasis when used in conjunction with molecules and chemicals that affect wake-related neurotransmitters. | 1 | Biochemistry |
After the sample has been processed for cryoprotection, the sperm is stored in small vials or straws holding between 0.4 and 1.0 ml of sperm and then cryogenically preserved in liquid nitrogen tanks. Two approaches for sperm cryoperservation include conventional freezing and vitrification. The conventional technique consists of a slow freezing process that is most commonly used for assisted reproduction technologies (ART). Whereas the vitrification method is a faster approach for sperm cryopreservation in converting liquid to solid state. The disadvantage of this latter process is increase in contamination from the liquid nitrogen and smaller sperm sample size to improve the speed for high cooling rate.
It has been proposed that there should be an upper limit on how long frozen sperm can be stored; however, a baby has been conceived in the United Kingdom using sperm frozen for 21 years and andrology experts believe sperm can be frozen indefinitely. The UK government places an upper limit for storage of 55 years.
Following the necessary quarantine period, which is usually six months, a sample will be thawed. To thaw a sperm sample, the vial or straw is left at room temperature for approximately 30 minutes, and then brought to body temperature by holding it in the hands of the person performing the insemination. Once a sperm sample is thawed, it cannot be frozen again, and should be used to artificially inseminate a recipient or used for another assisted reproduction technologies (ART) treatment immediately.
Freeze-drying is another promising alternative for storing semen for its accessibility with regular refrigerator. This method has been successfully replicated in animal species. However, DNA can be damaged in this process, therefore further research is warranted to determine factors that can effect the efficacy of this method. | 1 | Biochemistry |
Cyclic compounds can be partly or completely conjugated. Annulenes, completely conjugated monocyclic hydrocarbons, may be aromatic, nonaromatic or antiaromatic. | 7 | Physical Chemistry |
Soon after the first demonstration of hyper Rayleigh scattering optical activity in metal nanoparticles, the effect was replicated in organic molecules, specifically aromatic oligoamide foldamers. | 4 | Stereochemistry |
Although originally referred to as AT-AC introns, not all these introns are delimited by AT-AC dinucleotides. Some of them have GT-AG or AT-AG ends, at least. Thus, it is more correct to speak about the splicing machinery which is used to process them, differentiating between U2-type (canonical or major) and U12-type (non-canonical or minor). The main determinants for distinguishing U2- and U12-type introns are 5' splice site and branch site sequences.
The minor spliceosome consists of U11, U12, U4atac, and U6atac, together with U5 and an unknown number of non-snRNP proteins. The U11, U12 and U4atac/U6atac snRNPs are functional analogs of the U1, U2 and U4/U6 snRNPs in the major spliceosome. Although the minor U4atac and U6atac snRNAs are functional analogs of U4 and U6, respectively, they share only limited sequence homology (c. 40%). Furthermore, the sequence of U11 in comparison with U1, as well as U12 compared with U2, are completely unrelated. Despite this fact, the minor U11, U12, U4atac and U6atac snRNAs can be folded into structures similar to U1, U2, U4 and U6, respectively. | 1 | Biochemistry |
Loam molding was formerly used for making cast iron or bronze cannon and is still used for casting large bells.
Loam (pronounced low-m) is a mixture of sand and clay with water, sometimes with horse dung (valuable for its straw content), animal hair or coke. The object of including dung or hair was to make the mould permeable and allow gas (such as steam) to escape during casting.
The mold for a cylindrically symmetrical object, such as a cannon, is built up in stages around a spindle, to which is fixed a strickle board with the shape of the eventual casting. The mold also has provision for the casting of a gunhead, beyond the muzzle of the cannon, into which slag can float during casting. If the object is to be hollow, a straw rope is wound around the spindle and covered in a friable material to the dimensions of the exterior of the cannon, the strickle board being turned on the spindle to ensure it is cylindrical. Decorative elements and models of the trunnions are then attached. This is then covered in a thick layer of loam. The mold is then fired. After this the straw rope is then pulled out with the rest of the material used to form the shape of the cannon.
The mould is then mounted vertically in a casting put in front of the furnace. If the cannon is to be cast hollow, a core is mounted in the mould. The furnace was then tapped and metal run into the mold. The mold is then broken off the casting. The gunhead is cut off, and the bore of the cannon reamed out using a boring mill.
The process for the cylinder for a steam engine would be similar. The process for casting a bell is of the same nature, but the procedure is necessarily different. | 8 | Metallurgy |
Supramolecular catalysis is not a well-defined field but it generally refers to an application of supramolecular chemistry, especially molecular recognition and guest binding, toward catalysis. This field was originally inspired by enzymatic system which, unlike classical organic chemistry reactions, utilizes non-covalent interactions such as hydrogen bonding, cation-pi interaction, and hydrophobic forces to dramatically accelerate rate of reaction and/or allow highly selective reactions to occur. Because enzymes are structurally complex and difficult to modify, supramolecular catalysts offer a simpler model for studying factors involved in catalytic efficiency of the enzyme. Another goal that motivates this field is the development of efficient and practical catalysts that may or may not have an enzyme equivalent in nature.
A closely related field of study is asymmetric catalysis which requires molecular recognition to differentiate two chiral starting material or chiral transition states and thus it could be categorized as an area of supramolecular catalysis, but supramolecular catalysis however does not necessarily have to involve asymmetric reaction. As there is another Wikipedia article already written about small molecule asymmetric catalysts, this article focuses primarily on large catalytic host molecules. Non-discrete and structurally poorly defined system such as micelle and dendrimers are not included. | 6 | Supramolecular Chemistry |
The A ring synthesis (Scheme 3) started with a Diels-Alder reaction of diene 3.1 with the commercially available dienophile 2-chloroacrylonitrile 3.2 to give cyclohexene 3.3 with complete regioselectivity. Hydrolysis of the cyanochloro group and simultaneous cleavage of the acetate group led to hydroxyketone 3.4. The hydroxyl group was protected as a tert-butyldimethylsilyl ether (3.5). In preparation for a Shapiro reaction, this ketone was converted to hydrazone 3.6. | 0 | Organic Chemistry |
The term phosphorescence comes from the ancient Greek word φῶς (phos), meaning "light", and the Greek suffix -φόρος (-phoros), meaning "to bear", combined with the Latin suffix -escentem, meaning "becoming of", "having a tendency towards", or "with the essence of". Thus, phosphorescence literally means "having a tendency to bear light". It was first recorded in 1766.
The term phosphor had been used since the Middle Ages to describe minerals that glowed in the dark. One of the most famous, but not the first, was Bolognian phosphor. Around 1604, Vincenzo Casciarolo discovered a "lapis solaris" near Bologna, Italy. Once heated in an oxygen-rich furnace, it thereafter absorbed sunlight and glowed in the dark. In 1677, Hennig Brand isolated a new element that glowed due to a chemiluminescent reaction when exposed to air, and named it "phosphorus".
In contrast, the term luminescence (from the Latin lumen for "light"), was coined by Eilhardt Wiedemann in 1888 as a term to refer to "light without heat", while "fluorescence" by Sir George Stokes in 1852, when he noticed that, when exposing a solution of quinine sulfate to light refracted through a prism, the solution glowed when exposed to the mysterious invisible-light (now known to be UV light) beyond the violet end of the spectrum. Stokes formed the term from a combination of fluorspar and opalescence (preferring to use a mineral instead of a solution), albeit it was later discovered that fluorspar glows due to phosphorescence.
There was much confusion between the meanings of these terms throughout the late nineteenth to mid-twentieth centuries. Whereas the term "fluorescence" tended to refer to luminescence that ceased immediately (by human-eye standards) when removed from excitation, "phosphorescence" referred to virtually any substance that glowed for appreciable periods in darkness, sometimes to include even chemiluminescence (which occasionally produced substantial amounts of heat). Only after the 1950s and 1960s did advances in quantum electronics, spectroscopy, and lasers provide a measure to distinguish between the various processes that emit the light, although in common speech the distinctions are still often rather vague. | 7 | Physical Chemistry |
A meta-analysis of four RCTs concluded that there is no support for selenium supplementation for prevention of type 2 diabetes mellitus in Caucasians. | 1 | Biochemistry |
The kilocalorie per mole is a unit to measure an amount of energy per number of molecules, atoms, or other similar particles. It is defined as one kilocalorie of energy (1000 thermochemical gram calories) per one mole of substance. The unit symbol is written kcal/mol or kcal⋅mol. As typically measured, one kcal/mol represents a temperature increase of one degree Celsius in one liter of water (with a mass of 1 kg) resulting from the reaction of one mole of reagents.
In SI units, one kilocalorie per mole is equal to 4.184 kilojoules per mole (kJ/mol), which comes to approximately joules per molecule, or about 0.043 eV per molecule. At room temperature (25 °C, 77 °F, or 298.15 K), one kilocalorie per mole is approximately equal to 1.688 units in the kT term of Boltzmann's equation.
Even though it is not an SI unit, the kilocalorie per mole is still widely used in chemistry and biology for thermodynamical quantities such as thermodynamic free energy, heat of vaporization, heat of fusion and ionization energy. This is due to a variety of factors, including the ease with which it can be calculated based on the units of measure typically employed in quantifying a chemical reaction, especially in aqueous solution. In addition, for many important biological processes, thermodynamic changes are on a convenient order of magnitude when expressed in kcal/mol. For example, for the reaction of glucose with ATP to form glucose-6-phosphate and ADP, the free energy of reaction is −4.0 kcal/mol using the pH = 7 standard state. | 7 | Physical Chemistry |
An alternative approach to the identification and quantification of patient samples is through the use of mass spectrometry. This approach offers excellent precision and sensitivity in the identification, characterization and quantification of metabolites in multiple patient sample types, such as blood and urine. The mass spectrometry (MS) approach is typically coupled to gas chromatography (GC), in GC-MS or liquid chromatography (LC), in LC-MS, which aid in initially separating out the metabolite components within complex sample mixtures, and can allow for the isolation of particular metabolite subsets for analysis. GC-MS can provide relatively precise quantification of metabolites, as well as chemical structural information that can be compared to pre-existing chemical libraries. GC-MS can be conducted in a relatively high-throughput manner (greater than 100 samples per day) with greater detection sensitivity than NMR analysis. A limitation of GC-MS for this application, however, is that processed metabolite components must be readily volatilized for sample processing.
LC-MS initially separates out the components of a sample mixture based on properties such as hydrophobicity, before processing them for identification and quantification by mass spectrometry (MS). Overall, LC-MS is an extremely flexible method for processing most compound types in a somewhat high-throughput manner (20-100 samples a day), also with greater sensitivity than NMR analysis. For both GC-MS and LC-MS there are limitations in the reproducibility of metabolite quantification. Furthermore, sample processing for downstream mass spectrometry (MS) analysis is much more intensive than in NMR application, and results in the destruction of the original sample (via trypsin digestion).
Following identification and quantification of metabolites in individual patient samples, NMR and mass spectrometry (MS) output is compiled into a dataset. These datasets include information on the identity and levels of individual metabolites detected within processed samples, as well as characteristics of each metabolite during the detection process (e.g. mass-to-charge ratios for mass spectrometry (MS)-based analysis). Multiple datasets can be created and compiled into large databases for individual patients in order to monitor varying metabolic profiles over a treatment course (i.e. pre- and post-treatment profiles). Each database is then processed through a type of informatics platform with software designed to characterize and analyze the data to generate an overall metabolic profile for the patient. To generate this overall profile, computational programs are designed to:
* identify metabolic disease signatures
* assess treatment class (pre- or post-treatment)
* identify compounds present in a patient sample that may alter drug response, or be caused by a therapy
* identify metabolite variables and interactions among these variables
* map identified variables to known metabolic and biochemical pathways | 1 | Biochemistry |
The electro-absorption is a type of Stark effect in the neutral polymer, it is predominant at the electrode edge since there is a strong voltage drop. Electro-absorption can be observed from the second harmonic charge modulation spectroscopy spectra. | 7 | Physical Chemistry |
Recently, encapsulin nanocompartments have begun to receive considerable interest from bioengineers because of their potential to allow the targeted delivery of drugs, proteins, and mRNAs to specific cells of interest. | 1 | Biochemistry |
The exergy of the system is the maximal amount of useful work that the system can generate, during a process which brings it to equilibrium with its environment, or the amount of energy available. During an irreversible process, such as heat exchanges with reservoirs, exergy is destroyed. Generally, the theorem states thatwhere is the rate at which exergy is destroyed, and is the rate at which entropy is generated. As above, time derivatives are denoted by dots.
Unlike the lost work formulation, this version of the theorem holds for both the system (the control volume) and for its surroundings (the environment and the thermal reservoirs) separately:andwhere the index "sys" denotes quantities produced within or by the system itself, and "surr" within or by the surroundings. Therefore, summing these two forms, the theorem also holds for the thermodynamic universe as a whole:where the index "tot" denotes the total quantities of the entire universe.
Thus, the exergy formulation of the theorem is less limited, as it can be applied on different regions separately. Nevertheless, the work form is used more often.
The proof of the theorem, in both forms, uses the first law of thermodynamics, writing out the terms , , and in the relevant regions, and comparing them. | 7 | Physical Chemistry |
Cannabinoid CP55,940 and △-tetrahydrocannabinol (△-THC) can induce the release of dynorphin B, which in return acts as an agonist of κ-opioid receptors, resulting in the production of antinociception. Similarly, Tyr-D-Arg-Phe-Sar (TAPS) is capable of promoting a release of dynorphin B through the simulation of μ-opioid receptors, causing a production of antinociception. The antinociceptive effect produced by dynorphin B allows for spinal analgesia. | 1 | Biochemistry |
The inventory of carbon-14 in Earth's biosphere is about 300 megacuries (11 EBq), of which most is in the oceans.
The following inventory of carbon-14 has been given:
* Global inventory: ~8500 PBq (about 50 t)
** Atmosphere: 140 PBq (840 kg)
** Terrestrial materials: the balance
* From nuclear testing (until 1990): 220 PBq (1.3 t) | 9 | Geochemistry |
The requirement for a good leaving group is relaxed in conjugate base elimination reactions. These reactions include loss of a leaving group in the β position of an enolate as well as the regeneration of a carbonyl group from the tetrahedral intermediate in nucleophilic acyl substitution. Under forcing conditions, even amides can be made to undergo basic hydrolysis, a process that involves the expulsion of an extremely poor leaving group, RN. Even more dramatic, decarboxylation of benzoate anions can occur by heating with copper or CuO, involving the loss of an aryl anion. This reaction is facilitated by the fact that the leaving group is most likely an arylcopper compound rather than the much more basic alkali metal salt.
This dramatic departure from normal leaving group requirements occurs mostly in the realm of C=O double bond formation where formation of the very strong C=O double bond can drive otherwise unfavorable reactions forward. The requirement for a good leaving group is still relaxed in the case of C=C bond formation via E1cB mechanisms, but because of the relative weakness of the C=C double bond, the reaction still exhibits some leaving group sensitivity. Notably, changing the leaving groups identity (and willingness to leave) can change the nature of the mechanism in elimination reactions. With poor leaving groups, the E1cB mechanism is favored, but as the leaving groups ability changes, the reaction shifts from having a rate determining loss of leaving group from carbanionic intermediate B via TS BC through having a rate determining deprotonation step via TS AB (not pictured) to a concerted E2 elimination. In the latter situation, the leaving group X has become good enough that the former transition state connecting intermediates B and C has become lower in energy than B, which is no longer a stationary point on the potential energy surface for the reaction. Because only one transition state connects starting material A and product C, the reaction is now concerted (albeit very asynchronous in the pictured case) due to the increase in leaving group ability of X. | 0 | Organic Chemistry |
Methanesulfonyl chloride (mesyl chloride) is an organosulfur compound with the formula . Using the organic pseudoelement symbol Ms for the methanesulfonyl (or mesyl) group –, it is frequently abbreviated MsCl in reaction schemes or equations. It is a colourless liquid that dissolves in polar organic solvents but is reactive toward water, alcohols, and many amines. The simplest organic sulfonyl chloride, it is used to make methanesulfonates and to generate the elusive molecule sulfene (methylenedioxosulfur(VI)). | 0 | Organic Chemistry |
In the Newman-Kwart rearrangement O-thiocarbamates can isomerise to S-thiocarbamates. This reaction, which generally requires high temperatures, is an important method for the synthesis of thiophenols. | 0 | Organic Chemistry |
The importance of tin to the success of Bronze Age cultures and the scarcity of the resource offers a glimpse into that time periods trade and cultural interactions, and has therefore been the focus of intense archaeological studies. However, a number of problems have plagued the study of ancient tin such as the limited archaeological remains of placer mining, the destruction of ancient mines by modern mining operations, and the poor preservation of pure tin objects due to tin disease or tin pest'. These problems are compounded by the difficulty in provenancing tin objects and ores to their geological deposits using isotopic or trace element analyses. Current archaeological debate is concerned with the origins of tin in the earliest Bronze Age cultures of the Near East. | 8 | Metallurgy |
A variety or organosulfur compounds occur in nature. Most abundant are the amino acids methionine, cysteine, and cystine. The vitamins biotin and thiamine, as well as lipoic acid contain sulfur heterocycles. Glutathione is the primary intracellular antioxidant. Penicillin and cephalosporin are life-saving antibiotics, derived from fungi. Gliotoxin is a sulfur-containing mycotoxin produced by several species of fungi under investigation as an antiviral agent. | 9 | Geochemistry |
Viruses that infect plant and animal cells have also been manipulated to introduce foreign genes into plant and animal cells. The natural ability of viruses to adsorb to cells, introduce their DNA and replicate have made them ideal vehicles to transfer foreign DNA into eukaryotic cells in culture. A vector based on Simian virus 40 (SV40) was used in first cloning experiment involving mammalian cells. A number of vectors based on other type of viruses like Adenoviruses and Papilloma virus have been used to clone genes in mammals. At present, retroviral vectors are popular for cloning genes in mammalian cells. In case of plants like Cauliflower mosaic virus, Tobacco mosaic virus and Gemini viruses have been used with limited success. | 1 | Biochemistry |
Digital polymerase chain reaction (digital PCR, DigitalPCR, dPCR, or dePCR) is a biotechnological refinement of conventional polymerase chain reaction methods that can be used to directly quantify and clonally amplify nucleic acids strands including DNA, cDNA, or RNA. The key difference between dPCR and traditional PCR lies in the method of measuring nucleic acids amounts, with the former being a more precise method than PCR, though also more prone to error in the hands of inexperienced users. A "digital" measurement quantitatively and discretely measures a certain variable, whereas an “analog” measurement extrapolates certain measurements based on measured patterns. PCR carries out one reaction per single sample. dPCR also carries out a single reaction within a sample, however the sample is separated into a large number of partitions and the reaction is carried out in each partition individually. This separation allows a more reliable collection and sensitive measurement of nucleic acid amounts. The method has been demonstrated as useful for studying variations in gene sequences — such as copy number variants and point mutations — and it is routinely used for clonal amplification of samples for next-generation sequencing. | 1 | Biochemistry |
Many evaluation criteria apply globally to an entire experimental structure, most notably the resolution, the anisotropy or incompleteness of the data, and the residual or R-factor that measures overall model-to-data match (see below). Those help a user choose the most accurate among related Protein Data Bank entries to answer their questions. Other criteria apply to individual residues or local regions in the 3D structure, such as fit to the local electron density map or steric clashes between atoms. Those are especially valuable to the structural biologist for making improvements to the model, and to the user for evaluating the reliability of that model right around the place they care about - such as a site of enzyme activity or drug binding. Both types of measures are very useful, but although global criteria are easier to state or publish, local criteria make the greatest contribution to scientific accuracy and biological relevance. As expressed in the Rupp textbook, "Only local validation, including assessment of both geometry and electron density, can give an accurate picture of the reliability of the structure model or any hypothesis based on local features of the model." | 1 | Biochemistry |
where S is a singlet and T a triplet whose subscripts denote states (0 is the ground state, and 1 the excited state). Transitions can also occur to higher energy levels, but the first excited state is denoted for simplicity. | 7 | Physical Chemistry |
One of the most common base analogs is 5-bromouracil (5BU), the abnormal base found in the mutagenic nucleotide analog BrdU. When a nucleotide containing 5-bromouracil is incorporated into the DNA, it is most likely to pair with adenine; however, it can spontaneously shift into another isomer which pairs with a different nucleobase, guanine. If this happens during DNA replication, a guanine will be inserted as the opposite base analog, and in the next DNA replication, that guanine will pair with a cytosine. This results in a change in one base pair of DNA, specifically a transition mutation.
Additionally, nitrous acid (HNO2) is a potent mutagen that acts on replicating and non-replicating DNA. It can cause deamination of the amino groups of adenine, guanine and cytosine. Adenine is deaminated to hypoxanthine, which base pairs to cytosine instead of thymine. Cytosine is deaminated to uracil, which base pairs with adenine instead of guanine. Deamination of guanine is not mutagenic. Nitrous acid-induced mutations also are induced to mutate back to wild-type. | 1 | Biochemistry |
COX exists in three conformational states: fully oxidized (pulsed), partially reduced, and fully reduced. Each inhibitor has a high affinity to a different state. In the pulsed state, both the heme a and the Cu nuclear centers are oxidized; this is the conformation of the enzyme that has the highest activity. A two-electron reduction initiates a conformational change that allows oxygen to bind at the active site to the partially-reduced enzyme. Four electrons bind to COX to fully reduce the enzyme. Its fully reduced state, which consists of a reduced Fe at the cytochrome a heme group and a reduced Cu binuclear center, is considered the inactive or resting state of the enzyme.
Cyanide, azide, and carbon monoxide all bind to cytochrome c oxidase, inhibiting the protein from functioning and leading to the chemical asphyxiation of cells. Higher concentrations of molecular oxygen are needed to compensate for increasing inhibitor concentrations, leading to an overall decrease in metabolic activity in the cell in the presence of an inhibitor. Other ligands, such as nitric oxide and hydrogen sulfide, can also inhibit COX by binding to regulatory sites on the enzyme, reducing the rate of cellular respiration.
Cyanide is a non-competitive inhibitor for COX, binding with high affinity to the partially-reduced state of the enzyme and hindering further reduction of the enzyme. In the pulsed state, cyanide binds slowly, but with high affinity. The ligand is posited to electrostatically stabilize both metals at once by positioning itself between them. A high nitric oxide concentration, such as one added exogenously to the enzyme, reverses cyanide inhibition of COX.
Nitric oxide can reversibly bind to either metal ion in the binuclear center to be oxidized to nitrite. NO and CN will compete with oxygen to bind at the site, reducing the rate of cellular respiration. Endogenous NO, however, which is produced at lower levels, augments CN inhibition. Higher levels of NO, which correlate with the existence of more enzyme in the reduced state, lead to a greater inhibition of cyanide. At these basal concentrations, NO inhibition of Complex IV is known to have beneficial effects, such as increasing oxygen levels in blood vessel tissues. The inability of the enzyme to reduce oxygen to water results in a buildup of oxygen, which can diffuse deeper into surrounding tissues. NO inhibition of Complex IV has a larger effect at lower oxygen concentrations, increasing its utility as a vasodilator in tissues of need.
Hydrogen sulfide will bind COX in a noncompetitive fashion at a regulatory site on the enzyme, similar to carbon monoxide. Sulfide has the highest affinity to either the pulsed or partially reduced states of the enzyme, and is capable of partially reducing the enzyme at the heme a center. It is unclear whether endogenous HS levels are sufficient to inhibit the enzyme. There is no interaction between hydrogen sulfide and the fully reduced conformation of COX.
Methanol in methylated spirits is converted into formic acid, which also inhibits the same oxidase system. High levels of ATP can allosterically inhibit cytochrome c oxidase, binding from within the mitochondrial matrix. | 1 | Biochemistry |
* Alzate O. "Neuroproteomics." Frontiers in Neuroscience Series (October 2010) C.R.C. Press.
* Abul-Husn, Noura S., Lakshmi A. Devi. "Neuroproteomics of the Synapse and Drug Addiction." The Journal of Pharmacology and Experimental Therapeutics 138 (2006): 461-468.
* Becker, Michael, Jens Schindler, Hans G. Nothwang. "Neuroproteomics - the Tasks Lying Ahead." Electrophoresis 27 (2006): 2819-2829.
* Butcher, James. "Neuroproteomics Comes of Age." The Lancet Neurology 6 (2007): 851-852.
* Kim, Sandra I., Hans Voshol, Jan van Oostrum, Terri G. Hastings, Michael Casico, Marc J. Glucksmann. “Neuroproteomics: Expression Profiling of the Brain’s Proteomes in Health and Disease.” Neurochemical Research 29 (2004): 1317-1331
* Kobeissy, Firas H., Andrew K. Ottens, Zhiqun Zhang, Ming Cheng Liu, Nancy D. Denslow, Jitendra R. Dave, Frank C. Tortella, Ronald L. Hayes, Kevin K. Wang. "Novel Differential Neuroproteomics Analysis of Traumatic Brain Injury in Rats." Molecular & Cellular Proteomics 5 (2006): 1887-1898.
* Liu, Tong, Veera D'mello, Longwen Deng, Jun Hu, Michael Ricardo, Sanqiang Pan, Xiaodong Lu, Scott Wadsworth, John Siekierka, Raymond Birge, Hong Li. "A Multiplexed Proteomics Approach to Differentiate Neurite Outgrowth Patterns." Journal of Neuroscience Methods 158 (2006): 22-29.
* Ottens, Andrew K., Firas H. Kobeissy, Erin C. Golden, Zhiqun Zhang, William E. Haskins, Su-Shing Chen, Ronald L. Hayes, Kevin K. Wang, Nancy D. Denslow. "Neuroproteomics in Neurotrauma." Mass Spectrometry Reviews 25 (2006): 380-406.
* Ottens, Andrew K. "The methodology of neuroproteomics." Methods Mol Biol. (2009) 566:1-21.
* Southey, Bruce R., Andinet Amare, Tyler A. Zimmerman, Sandra L. Rodriguez, Jonathan V. Sweedler. "NeuroPred: a Tool to Predict Cleavage Sites in Neuropeptide Precursors and Provide the Masses of the Resulting Peptides." Nucleic Acids Research 34 (2006): 267-272.
* Tribl, F, K Marcus, G Bringmann, H.E. Meyer, M Gerlach, P Riederer. "Proteomics of the Human Brain: Sub-Proteomes Might Hold the Key to Handle Brain Complexity." Journal of Neural Transmission 113 (2006): 1041-1054.
* Williams, Kenneth, Terence Wu, Christopher Colangelo, Angus C. Nairn. "Recent Advances in Neuroproteomics and Potential Application to Studies of Drug Addiction." Neuropharmacology 47 (2004): 148-166.
* Kobeissy, Firas H., Sadasivan S, Liu J, Mark S Gold, Kevin K. Wang. "Psychiatric research: psychoproteomics, degradomics and systems biology." Expert Rev Proteomics 5 (2008): 293-314. | 1 | Biochemistry |
When surfactants are present above the critical micelle concentration (CMC), they can act as emulsifiers that will allow a compound that is normally insoluble (in the solvent being used) to dissolve. This occurs because the insoluble species can be incorporated into the micelle core, which is itself solubilized in the bulk solvent by virtue of the head groups' favorable interactions with solvent species. The most common example of this phenomenon is detergents, which clean poorly soluble lipophilic material (such as oils and waxes) that cannot be removed by water alone. Detergents clean also by lowering the surface tension of water, making it easier to remove material from a surface. The emulsifying property of surfactants is also the basis for emulsion polymerization.
Micelles may also have important roles in chemical reactions. Micellar chemistry uses the interior of micelles to harbor chemical reactions, which in some cases can make multi-step chemical synthesis more feasible. Doing so can increase reaction yield, create conditions more favorable to specific reaction products (e.g. hydrophobic molecules), and reduce required solvents, side products, and required conditions (e.g. extreme pH). Because of these benefits, Micellular chemistry is thus considered a form of green chemistry. However, micelle formation may also inhibit chemical reactions, such as when reacting molecules form micelles that shield a molecular component vulnerable to oxidation.
The use of cationic micelles of cetrimonium chloride, benzethonium chloride, and cetylpyridinium chloride can accelerate chemical reactions between negatively charged compounds (such as DNA or Coenzyme A) in an aqueous environment up to 5 million times. Unlike conventional micellar catalysis, the reactions occur solely on the charged micelles' surface.
Micelle formation is essential for the absorption of fat-soluble vitamins and complicated lipids within the human body. Bile salts formed in the liver and secreted by the gall bladder allow micelles of fatty acids to form. This allows the absorption of complicated lipids (e.g., lecithin) and lipid-soluble vitamins (A, D, E, and K) within the micelle by the small intestine.
During the process of milk-clotting, proteases act on the soluble portion of caseins, κ-casein, thus originating an unstable micellar state that results in clot formation.
Micelles can also be used for targeted drug delivery as gold nanoparticles. | 6 | Supramolecular Chemistry |
Planktonic prokaryotes are further defined into two categories, free-living or particle associated. The two are separated by filtration. Particle-associated bacteria are often difficult to study because marine snow aggregates are often ranging in sizes from 0.2 to 200 μm, often rendering sampling efforts difficult. These aggregates are hotspots for microbial activity. Marine bacteria are the most abundant organisms in aggregates followed by cyanobacteria and then nanoflagellates. Aggregates can be enriched about one thousand times more than the surrounding seawater. Seasonal variability can also have an effect on microbial communities of marine snow aggregates with concentrations being the highest during the summer.
As illustrated in the diagram, phytoplankton fix carbon dioxide in the euphotic zone using solar energy and produce particulate organic carbon. The particulate organic carbon formed in the euphotic zone is processed by marine microorganisms (microbes), zooplankton and their consumers into organic aggregates (marine snow), which is then exported to the mesopelagic (200–1000 m depth) and bathypelagic zones by sinking and vertical migration by zooplankton and fish.
Export flux is defined as the sedimentation out of the surface layer (at approximately 100 m depth) and sequestration flux is the sedimentation out of the mesopelagic zone (at approximately 1000 m depth). A portion of the particulate organic carbon is respired back to CO in the oceanic water column at depth, mostly by heterotrophic microbes and zooplankton, thus maintaining a vertical gradient in concentration of dissolved inorganic carbon (DIC). This deep-ocean DIC returns to the atmosphere on millennial timescales through thermohaline circulation. Between 1% and 40% of the primary production is exported out of the euphotic zone, which attenuates exponentially towards the base of the mesopelagic zone and only about 1% of the surface production reaches the sea floor.
The largest component of biomass are marine protists (eukaryotic microorganisms). Marine snow aggregates collected from the bathypelagic zone were found to consist largely of fungi and labyrinthulomycetes. Smaller aggregates do not harbor as many eukaryotic organisms which is similar to what is found in the deep ocean. The bathypelagic aggregates mostly resembled those found in the surface ocean. It implies higher rates of remineralization in the bathypelagic zone.
Numerically, the largest component of marine snow are the prokaryotes that colonize the aggregates. Bacteria are largely responsible for the remineralisation and fragmentation of aggregates. Remineralization occurs typically below 200 m depth.
Microbial communities that form on the aggregates vary from the communities in the water column. The concentration of attached microbes are typically orders of magnitude larger than free-living microbes. Isolated bacterial cultures have up to 20 times more enzymatic activity within 2 hours of aggregate attachment. The dark ocean harbors around 65% of all pelagic Bacteria and Archaea.(Whitman et al., 1998)
It was previously thought that due to fragmentation, bacterial communities would shift as they travel down the water column. As seen in experiments, it now appears that the communities that form during aggregation remain associated with the aggregate and any community changes are due to grazing or fragmentation rather than new bacterial colony formation. | 9 | Geochemistry |
Fructo-oligosaccharides (FOS), which are found in many vegetables, are short chains of fructose molecules. They differ from fructans such as inulin, which as polysaccharides have a much higher degree of polymerization than FOS and other oligosaccharides, but like inulin and other fructans, they are considered soluble dietary fibre. Using fructo-oligosaccharides (FOS) as fiber supplementations is shown to have an effect on glucose homeostasis quite similar to insulin. These (FOS) supplementations can be considered prebiotics which produce short-chain fructo-oligosaccharides (scFOS). Galacto-oligosaccharides (GOS) in particular are used to create a prebiotic effect for infants that are not being breastfed.
Galactooligosaccharides (GOS), which also occur naturally, consist of short chains of galactose molecules. Human milk is an example of this and contains oligosaccharides, known as human milk oligosaccharides (HMOs), which are derived from lactose. These oligosaccharides have biological function in the development of the gut flora of infants. Examples include lacto-N-tetraose, lacto-N-neotetraose, and lacto-N-fucopentaose. These compounds cannot be digested in the human small intestine, and instead pass through to the large intestine, where they promote the growth of Bifidobacteria, which are beneficial to gut health.
HMOs can also protect infants by acting as decoy receptors against viral infection. HMOs accomplish this by mimicking viral receptors which draws the virus particles away from host cells. Experimentation has been done to determine how glycan-binding occurs between HMOs and many viruses such as influenza, rotavirus, human immunodeficiency virus (HIV), and respiratory syncytial virus (RSV). The strategy HMOs employ could be used to create new antiviral drugs.
Mannan oligosaccharides (MOS) are widely used in animal feed to improve gastrointestinal health. They are normally obtained from the yeast cell walls of Saccharomyces cerevisiae. Mannan oligosaccharides differ from other oligosaccharides in that they are not fermentable and their primary mode of action includes agglutination of type-1 fimbria pathogens and immunomodulation. | 0 | Organic Chemistry |
Kurt Martin Mislow (June 5, 1923 – October 5, 2017) was a German-born American organic chemist who specialized in stereochemistry.
Born in Berlin on June 5, 1923, Mislow had moved to London by 1938, after some time in Milan. With the help of his uncle Alfred Eisenstaedt, Mislows family left London for New York City in 1940. Mislow earned a bachelors degree in chemistry from Tulane University in 1944, and received a doctorate from the California Institute of Technology, where he was supervised by Linus Pauling. Mislow first taught at New York University, then moved to Princeton University in 1964. While at Princeton, Mislow served as Hugh Stott Taylor Professor of Chemistry and led the chemistry department from 1968 to 1974. He became a professor emeritus in 1988.
Over the course of his career, Mislow was named a Guggenheim fellow twice, in 1956 and 1974. Between 1959 and 1963, Mislow was granted the Sloan Research Fellowship. He became a member of the National Academy of Sciences in 1972, followed by fellowships in the American Academy of Arts and Sciences, granted in 1974, and the American Association for the Advancement of Science, bestowed in 1980. In 1999, Mislow was named a foreign member of the Accademia dei Lincei. The American Chemical Society honored Mislow with several awards, among them the James Flack Norris Award in Physical Organic Chemistry (1975), the William H. Nichols Medal Award (1987), and the Arthur C. Cope Scholar Award (1995). | 4 | Stereochemistry |
Particular chemoreceptors, called ASICs, detect the levels of carbon dioxide in the blood. To do this, they monitor the concentration of hydrogen ions in the blood, which decrease the pH of the blood. This can be a direct consequence of an increase in carbon dioxide concentration, because aqueous carbon dioxide in the presence of carbonic anhydrase reacts to form a proton and a bicarbonate ion.
The response is that the respiratory centre (in the medulla), sends nervous impulses to the external intercostal muscles and the diaphragm, via the intercostal nerve and the phrenic nerve, respectively, to increase breathing rate and the volume of the lungs during inhalation.
Chemoreceptors that regulate the depth and rhythm of breathing are broken down into two categories.
* central chemoreceptors are located on the ventrolateral surface of medulla oblongata and detect changes in pH of cerebrospinal fluid. They have also been shown experimentally to respond to hypercapnic hypoxia (elevated , decreased O2), and eventually desensitize, partly due to redistribution of bicarbonate out of the cerebrospinal fluid (CSF) and increased renal excretion of bicarbonate. These are sensitive to pH and .
* peripheral chemoreceptors: consists of aortic and carotid bodies. Aortic body detects changes in blood oxygen and carbon dioxide, but not pH, while carotid body detects all three. They do not desensitize. Their effect on breathing rate is less than that of the central chemoreceptors. | 3 | Analytical Chemistry |
The basis of ferroics is to understand the large changes in physical characteristics that occur over a very narrow temperature range. The changes in physical characteristics occur when phase transitions take place around some critical temperature value, normally denoted by . Above this critical temperature, the crystal is in a nonferroic state and does not exhibit the physical characteristic of interest. Upon cooling the material down below it undergoes a spontaneous phase transition. Such a phase transition typically results in only a small deviation from the nonferroic crystal structure, but in altering the shape of the unit cell the point symmetry of the material is reduced. This breaking of symmetry is physically what allows the formation of the ferroic phase.
In ferroelectrics, upon lowering the temperature below , a spontaneous dipole moment is induced along an axis of the unit cell. Although individual dipole moments can sometimes be small, the effect of unit cells gives rise to an electric field that over the bulk substance that is not insignificant. An important point about ferroelectrics is that they cannot exist in a centrosymmetric crystal. A centrosymmetric crystal is one where a lattice point can be mapped onto a lattice point .
Ferromagnets is a term that most people are familiar with, and, as with ferroelastics, the spontaneous magnetization of a ferromagnet can be attributed to a breaking of point symmetry in switching from the paramagnetic to the ferromagnetic phase. In this case, is normally known as the Curie Temperature.
In ferroelastic crystals, in going from the nonferroic (or prototypic phase) to the ferroic phase, a spontaneous strain is induced. An example of a ferroelastic phase transition is when the crystal structure spontaneously changes from a tetragonal structure (a square prism shape) to a monoclinic structure (a general parallelepiped). Here the shapes of the unit cell before and after the phase transition are different, and hence a strain is induced within the bulk.
In recent years, multiferroics have been attracting increased interest. These materials exhibit more than one ferroic property simultaneously in a single phase. A fourth ferroic order termed ferrotoroidic order has also been proposed. | 7 | Physical Chemistry |
Lake Chichoj is located near the city of San Cristóbal Verapaz, in the department of Alta Verapaz, in Guatemala. It is long, wide, with an area of , an average water volume of [], and a maximum depth of . | 2 | Environmental Chemistry |
Where it is impossible to find the primitive or primary magma composition, it is often useful to attempt to identify a parental melt. A parental melt is a magma composition from which the observed range of magma chemistries has been derived by the processes of igneous differentiation. It need not be a primitive melt.
For instance, a series of basalt lava flows is assumed to be related to one another. A composition from which they could reasonably be produced by fractional crystallization is termed a parental melt. To prove this, fractional crystallization models would be produced to test the hypothesis that they share a common parental melt. | 9 | Geochemistry |
The effect of solvent on elimination and nucleophillic substitution reactions was originally studied by British chemists Edward D. Hughes and Christopher Kelk Ingold. Using a simple solvation model that considered only pure electrostatic interactions between ions or dipolar molecules and solvents in initial and transition states, all nucleophilic and elimination reactions were organized into different charge types (neutral, positively charged, or negatively charged).
Hughes and Ingold then made certain assumptions about the extent of solvation to be expected in these situations:
* increasing magnitude of charge will increase solvation
* increasing delocalization will decrease solvation
* loss of charge will decrease solvation more than the dispersal of charge
The applicable effect of these general assumptions are shown in the following examples:
* An increase in solvent polarity accelerates the rates of reactions where a charge is developed in the activated complex from neutral or slightly charged reactant
* An increase in solvent polarity decreases the rates of reactions where there is less charge in the activated complex in comparison to the starting materials
* A change in solvent polarity will have little or no effect on the rates of reaction when there is little or no difference in charge between the reactants and the activated complex. | 7 | Physical Chemistry |
In addition to causing secondary emission, positive ions can strike the cathode with sufficient force to eject particles of the material from which the cathode is made. This process is called sputtering and it gradually ablates the cathode. Sputtering is useful when using spectroscopy to analyze the composition of the cathode, as is done in Glow-discharge optical emission spectroscopy.
However, sputtering is not desirable when glow discharge is used for lighting, because it shortens the life of the lamp. For example, neon signs have hollow cathodes designed to minimize sputtering, and contain charcoal to continuously remove undesired ions and atoms. | 3 | Analytical Chemistry |
Rosenthal's reagent can be prepared by reduction of titanocene or zirconocene dichloride with magnesium in the presence of bis(trimethylsilyl)acetylene in THF. The illustrated product for a titanocene complex can be represented by the resonance structures A and B. If zirconium is used as central atom, additional ligands (e.g. pyridine) are necessary for stabilization. | 0 | Organic Chemistry |
According to the VSEPR theory of molecular bonding, the preferred geometry of a molecule is that in which both bonding and non-bonding electrons are as far apart as possible. In molecules, it is quite common for these angles to be somewhat compressed or expanded compared to their optimal value. This strain is referred to as angle strain, or Baeyer strain. The simplest examples of angle strain are small cycloalkanes such as cyclopropane and cyclobutane, which are discussed below. Furthermore, there is often eclipsing or Pitzer strain in cyclic systems. These and possible transannular interactions were summarized early by H.C. Brown as internal strain, or I-Strain. Molecular mechanics or force field approaches allow to calculate such strain contributions, which then can be correlated e.g. with reaction rates or equilibria. Many reactions of alicyclic compounds, including equilibria, redox and solvolysis reactions, which all are characterized by transition between sp2 and sp3 state at the reaction center, correlate with corresponding strain energy differences SI (sp2 -sp3). The data reflect mainly the unfavourable vicinal angles in medium rings, as illustrated by the severe increase of ketone reduction rates with increasing SI (Figure 1). Another example is the solvolysis of bridgehead tosylates with steric energy differences between corresponding bromide derivatives (sp3) and the carbenium ion as sp2- model for the transition state. (Figure 2)
In principle, angle strain can occur in acyclic compounds, but the phenomenon is rare. | 4 | Stereochemistry |
The Venus Express orbiter collected Venus science data from April 2006 until December 2014. In 2008, Piccioni, et al. reported measurements of night-side airglow emission in the atmosphere of Venus made with the Visible and Infrared Thermal Imaging Spectrometer (VIRTIS) on Venus Express. They attributed emission bands in wavelength ranges of 1.40 - 1.49 micrometers and 2.6 - 3.14 micrometers to vibrational transitions of OH. This was the first evidence for OH in the atmosphere of any planet other than Earth's. | 0 | Organic Chemistry |
A wide variety of phenols undergo O-methylation to give anisole derivatives. This process, catalyzed by such enzymes as caffeoyl-CoA O-methyltransferase, is a key reaction in the biosynthesis of lignols, percursors to lignin, a major structural component of plants.
Plants produce flavonoids and isoflavones with methylations on hydroxyl groups, i.e. methoxy bonds. This 5-O-methylation affects the flavonoid's water solubility. Examples are 5-O-methylgenistein, 5-O-methylmyricetin, and 5-O-methylquercetin (azaleatin). | 0 | Organic Chemistry |
2-Methoxyethoxymethyl chloride is an organic compound with formula . A colorless liquid, it is classified as a chloroalkyl ether. It is used as an alkylating agent. In organic synthesis, it is used for introducing the methoxyethoxy ether (MEM) protecting group. MEM protecting groups are generally preferred to methoxymethyl (MOM) protecting groups, both in terms of formation and removal.
Typically, the alcohol to be protected is deprotonated with a non-nucleophilic base such as N,N-diisopropylethylamine (DIPEA) in dichloromethane followed by addition of 2-methoxyethoxymethyl chloride.
The MEM protecting group can be cleaved (deprotection) with a range of Lewis and Bronsted acids. | 0 | Organic Chemistry |
), functioning as a hexadentate [[ligand]] -->
18-Crown-6 has a high affinity for the hydronium ion HO, as it can fit inside the crown ether. Thus, reaction of 18-crown-6 with strong acids gives the cation . For example, interaction of 18-crown-6 with HCl gas in toluene with a little moisture gives an ionic liquid layer with the composition , from which the solid can be isolated on standing. Reaction of the ionic liquid layer with two molar equivalents of water gives the crystalline product . | 6 | Supramolecular Chemistry |
Cryptic binding sites are the binding sites that are transiently formed in an apo form or that are induced by ligand binding. Considering the cryptic binding sites increases the size of the potentially “druggable” human proteome from ~40% to ~78% of disease-associated proteins. The binding sites have been investigated by: support vector machine applied to "CryptoSite" data set, Extension of "CryptoSite" data set, long timescale molecular dynamics simulation with Markov state model and with biophysical experiments, and cryptic-site index that is based on relative accessible surface area. | 1 | Biochemistry |
The plant sorghum is well established model organism and can adapt in hot and dry environments. For this reason, it is used as a model to study calmodulins role in plants. Sorghum contains seedlings that express a glycine-rich RNA-binding protein, SbGRBP. This particular protein can be modulated by using heat as a stressor. Its unique location in the cell nucleus and cytosol demonstrates interaction with calmodulin that requires the use of Ca. By exposing the plant to versatile stress conditions, it can cause different proteins that enable the plant cells to tolerate environmental changes to become repressed. These modulated stress proteins are shown to interact with CaM. The CaMBP' genes expressed in the sorghum are depicted as a “model crop” for researching the tolerance to heat and drought stress. | 1 | Biochemistry |
The pachysolen tannophilus nuclear code (translation table 26) is a genetic code found in the ascomycete fungus Pachysolen tannophilus. | 1 | Biochemistry |
Bryostatins are a group of macrolide lactones from (bacterial symbionts of) the marine organism Bugula neritina that were first collected and provided to JL Hartwell’s anticancer drug discovery group at the National Cancer Institute (NCI) by Jack Rudloe. Bryostatins are potent modulators of protein kinase C. They have been studied in clinical trials as anti-cancer agents, as anti-AIDS/HIV agents and in people with Alzheimer's disease. | 0 | Organic Chemistry |
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