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* 2022 Alfred Bader Award
* 2020 Royal Society of Canada
* 2019 Montreal Medal
* 2019 American Chemical Society Arthur C. Cope Scholar Award
* 2018 Queens University prize for Excellence in Research'
* 2018 Chemical Institute of Canada Catalysis Award
* 2018 Precious Metal Institute Carol Tyler Award
* 2017 Canadian Society for Chemistry R.U. Lemieux Award | 0 | Organic Chemistry |
TALEN has been used to efficiently modify plant genomes, creating economically important food crops with favorable nutritional qualities. They have also been harnessed to develop tools for the production of biofuels. In addition, it has been used to engineer stably modified human embryonic stem cell and induced pluripotent stem cell (IPSCs) clones and human erythroid cell lines, to generate knockout C. elegans, knockout rats, knockout mice, and knockout zebrafish. Moreover, the method can be used to generate knockin organisms. Wu et al.obtained a Sp110 knockin cattle using Talen nickases to induce increased resistance of tuberculosis. This approach has also been used to generate knockin rats by TALEN mRNA microinjection in one-cell embryos.
TALEN has also been utilized experimentally to correct the genetic errors that underlie disease. For example, it has been used in vitro to correct the genetic defects that cause disorders such as sickle cell disease, xeroderma pigmentosum, and epidermolysis bullosa. Recently, it was shown that TALEN can be used as tools to harness the immune system to fight cancers; TALEN-mediated targeting can generate T cells that are resistant to chemotherapeutic drugs and show anti-tumor activity.
In theory, the genome-wide specificity of engineered TALEN fusions allows for correction of errors at individual genetic loci via homology-directed repair from a correct exogenous template. In reality, however, the in situ application of TALEN is currently limited by the lack of an efficient delivery mechanism, unknown immunogenic factors, and uncertainty in the specificity of TALEN binding.
Another emerging application of TALEN is its ability to combine with other genome engineering tools, such as meganucleases. The DNA binding region of a TAL effector can be combined with the cleavage domain of a meganuclease to create a hybrid architecture combining the ease of engineering and highly specific DNA binding activity of a TAL effector with the low site frequency and specificity of a meganuclease.
In comparison to other genome editing techniques, TALEN falls in the middle in terms of difficulty and cost. Unlike ZFNs, TALEN recognizes single nucleotides. It's far more straightforward to engineer interactions between TALEN DNA binding domains and their target nucleotides than it is to create interactions with ZFNs and their target nucleotide triplets. On the other hand, CRISPR relies on ribonucleotide complex formation instead of protein/DNA recognition. gRNAs have occasionally limitations regarding feasibility due to lack of PAM sites in the target sequence and even though they can be cheaply produced, the current development lead to a remarkable decrease of cost for TALENs, so that they are in a similar price and time range like CRISPR based genome editing. | 1 | Biochemistry |
So far only about two dozen sites have been identified where iron was made before the Roman invasion, mostly scattered across East Sussex and the Vale of Kent. A large site at Broadfield, Crawley is the westernmost place where smelting has been ascertained, although there is a possible site associated with an Iron Age enclosure at Piper's Copse near Northchapel in the western Weald. Continuity of pottery styles from the Iron Age into the early Roman period makes precise dating of many sites to before or after the Roman conquest difficult. Carbon dating has identified a site at Cullinghurst Wood, Hartfield to between 350 and 750 BC.
During his invasions of Britain in 55 and 54 BC Julius Caesar noted iron production near the coast, possibly at known sites at Sedlescombe and Crowhurst Park near Hastings. | 8 | Metallurgy |
Simple organochlorides slowly convert into phosgene when exposed to ultraviolet (UV) irradiation in the presence of oxygen. Before the discovery of the Ozone hole in the late 1970s large quantities of organochlorides were routinely used by industry, which inevitably led to them entering the atmosphere. In the 1970-80s phosgene levels in the troposphere were around 20-30 pptv (peak 60 pptv). However, these levels had not decreased significantly nearly 30 years later, despite organochloride production becoming restricted under the Montreal Protocol.
Phosgene in the troposphere can last up to about 70 days and is removed primarily by hydrolysis with ambient humidity or cloudwater. Less than 1% makes it to the stratosphere, where it is expected to have a lifetime of several years, since this layer is much drier and phosgene decomposes slowly through UV photolysis. Consequently, it does play a minor part in ozone depletion. | 0 | Organic Chemistry |
A biosignature must be able to dominate over all other processes that may produce similar physical, spectral, and chemical features. When investigating a potential biosignature, scientists must carefully consider all other possible origins of the biosignature in question. Many forms of life are known to mimic geochemical reactions. One of the theories on the origin of life involves molecules developing the ability to catalyse geochemical reactions to exploit the energy being released by them. These are some of the earliest known metabolisms (see methanogenesis). In such case, scientists might search for a disequilibrium in the geochemical cycle, which would point to a reaction happening more or less often than it should. A disequilibrium such as this could be interpreted as an indication of life. | 2 | Environmental Chemistry |
The plot of against has often been called a "Michaelis–Menten plot", even recently, but this is misleading, because Michaelis and Menten did not use such a plot. Instead, they plotted against , which has some advantages over the usual ways of plotting Michaelis–Menten data. It has as dependent variable, and thus does not distort the experimental errors in . Michaelis and Menten did not attempt to estimate directly from the limit approached at high , something difficult to do accurately with data obtained with modern techniques, and almost impossible with their data. Instead they took advantage of the fact that the curve is almost straight in the middle range and has a maximum slope of i.e. . With an accurate value of it was easy to determine from the point on the curve corresponding to .
This plot is virtually never used today for estimating and , but it remains of major interest because it has another valuable property: it allows the properties of isoenzymes catalysing the same reaction, but active in very different ranges of substrate concentration, to be compared on a single plot. For example, the four mammalian isoenzymes of hexokinase are half-saturated by glucose at concentrations ranging from about 0.02 mM for hexokinase A (brain hexokinase) to about 50 mM for hexokinase D ("glucokinase", liver hexokinase), more than a 2000-fold range. It would be impossible to show a kinetic comparison between the four isoenzymes on one of the usual plots, but it is easily done on a semi-logarithmic plot. | 7 | Physical Chemistry |
The genome is the total genetic material of an organism and includes both the genes and non-coding sequences. Eukaryotic genes can be annotated using FINDER. | 1 | Biochemistry |
Neopeltolide was originally isolated from sponges near the Jamaican coast and exhibits nanomolar cytoxic activity against several lines of cancer cells. The synthesis of the neopeltolide macrocyclic core displays a hydrogenation controlled by the ground state conformation of the macrocycle. | 0 | Organic Chemistry |
In 1953, Paul Flory first classified polymerization as "step-growth polymerization" and "chain-growth polymerization". IUPAC recommends to further simplify "chain-growth polymerization" to "chain polymerization". It is a kind of polymerization where an active center (free radical or ion) is formed, and a plurality of monomers can be polymerized together in a short period of time to form a macromolecule having a large molecular weight. In addition to the regenerated active sites of each monomer unit, polymer growth will only occur at one (or possibly more) endpoint.
Many common polymers can be obtained by chain polymerization such as polyethylene (PE), polypropylene (PP), polyvinyl chloride (PVC), poly(methyl methacrylate) (PMMA), polyacrylonitrile (PAN), polyvinyl acetate (PVA).
Typically, chain-growth polymerization can be understood with the chemical equation:
In this equation, P is the polymer while x represents degree of polymerization, * means active center of chain-growth polymerization, M is the monomer which will react with active center, and L may be a low-molar-mass by-product obtained during chain propagation. For most chain-growth polymerizations, there is no by-product L formed. However there are some exceptions, such as the polymerization of amino acid N-carboxyanhydrides to oxazolidine-2,5-diones.
This type of polymerization is described as "chain" or "chain-growth" because the reaction mechanism is a chemical chain reaction with an initiation step in which an active center is formed, followed by a rapid sequence of chain propagation steps in which the polymer molecule grows by addition of one monomer molecule to the active center in each step. The word "chain" here does not refer to the fact that polymer molecules form long chains. Some polymers are formed instead by a second type of mechanism known as step-growth polymerization without rapid chain propagation steps. | 7 | Physical Chemistry |
Near the end of mitosis, p130 and p107 are dephosphorylated from their hyperphosphorylated state by the phosphatase PP2a. Inhibition of PP2a activity reduced promoter binding of some of the proteins of the DREAM complex in the subsequent G1 phase and de-repression of gene expression.
Other components have been shown to be phosphorylated for DREAM complex assembly to occur. Of these, LIN52 phosphorylation on its S28 residue is the most well-understood. Substitution of this serine to alanine led to reduced binding of the MuvB core to p130 and impaired the ability of cells to enter quiescence. This indicates that LIN52 S28 phosphorylation is required for proper association and function of the DREAM complex via binding with p130.
One known regulator of phosphorylation of the S28 residue is the DYRK1A. The loss of this kinase leads to decreased phosphorylation of the S28 residue and association of p130 with MuvB. DYRK1A was also found to degrade cyclin D1, which would increase p21 levels – both of which contribute to cell cycle exit.
The DREAM complex was also shown to regulate cytokinesis through GAS2L3. | 1 | Biochemistry |
Plants respond to injury by signalling that damage has occurred, by secreting materials to seal off the damaged area, by producing antimicrobials to limit the spread of pathogens, and in some woody plants by regrowing over the wound. | 1 | Biochemistry |
Neuromodulators may alter the output of a physiological system by acting on the associated inputs (for instance, central pattern generators). However, modeling work suggests that this alone is insufficient, because the neuromuscular transformation from neural input to muscular output may be tuned for particular ranges of input. Stern et al. (2007) suggest that neuromodulators must act not only on the input system but must change the transformation itself to produce the proper contractions of muscles as output. | 1 | Biochemistry |
GLD-2, as a poly(A) polymerase (PAP) acts incorporating ATP at the 3' end of mRNAs in a template-independent manner. | 1 | Biochemistry |
In a narrow definition, harmful algal blooms are only those blooms that release toxins that affect other species. On the other hand, any algal bloom can cause dead zones due to low oxygen levels, and could therefore be called "harmful" in that sense. The usage of the term "harmful algal blooms" in the media and scientific literature is varied. In a broader definition, all "organisms and events are considered to be HABs if they negatively impact human health or socioeconomic interests or are detrimental to aquatic systems". A harmful algal bloom is "a societal concept rather than a scientific definition".
A similarly broad definition of HABs was adopted by the US Environmental Protection Agency in 2008 who stated that HABs include "potentially toxic (auxotrophic, heterotrophic) species and high-biomass producers that can cause hypoxia and anoxia and indiscriminate mortalities of marine life after reaching dense concentrations, whether or not toxins are produced". | 3 | Analytical Chemistry |
Novec 649 is a low-temperature heat-transfer fluid. It has been used as a full-immersion fluid in a proof of concept data center cooling system by Intel and SGI. As it boils off easily due to its boiling point, it is used in two-phase immersion cooling system with a condensing loop running cold water. Effects of evaporative cooling was utilized to remove additional heat. Novec 649 is also being considered to be used for cooling silicon photomultiplier (SiPM) sensors to in single-phase configuration as part of Large Hadron Collider’s high luminosity upgrade.
Traditional perfluorocarbon (PFC) based compounds used for cooling, such as Fluorinert, display high global warming potentials (GWPs), typically 5,000 to 10,000 times that of CO. Novec 649 was chosen as a good drop-in replacement due to it having similar thermo-physical properties to Fluorinert FC-72 (perfluorohexane, C6F14) while exhibiting a very low global warming potential of 1. | 2 | Environmental Chemistry |
Various factors enhance the likelihood of MPTP opening. In some mitochondria, such as those in the central nervous system, high levels of Ca within mitochondria can cause the MPT pore to open. This is possibly because Ca binds to and activates Ca binding sites on the matrix side of the MPTP.
MPT induction is also due to the dissipation of the difference in voltage across the inner mitochondrial membrane (known as transmembrane potential, or Δψ).
In neurons and astrocytes, the contribution of membrane potential to MPT induction is complex, see.
The presence of free radicals, another result of excessive intracellular calcium concentrations, can also cause the MPT pore to open.
Other factors that increase the likelihood that the MPTP will be induced include the presence of certain fatty acids, and inorganic phosphate. However, these factors cannot open the pore without Ca, though at high enough concentrations, Ca alone can induce MPT.
Stress in the endoplasmic reticulum can be a factor in triggering MPT.
Conditions that cause the pore to close or remain closed include acidic conditions, high concentrations of ADP, high concentrations of ATP, and high concentrations of NADH. Divalent cations like Mg also inhibit MPT, because they can compete with Ca for the Ca binding sites on the matrix and/or cytoplasmic side of the MPTP. | 1 | Biochemistry |
The concept of residence time originated in models of chemical reactors. The first such model was an axial dispersion model by Irving Langmuir in 1908. This received little attention for 45 years; other models were developed such as the plug flow reactor model and the continuous stirred-tank reactor, and the concept of a washout function (representing the response to a sudden change in the input) was introduced. Then, in 1953, Peter Danckwerts resurrected the axial dispersion model and formulated the modern concept of residence time. | 9 | Geochemistry |
The nuclease hybridization assay, also called S1 nuclease cutting assay, is a nuclease protection assay-based hybridization ELISA. The assay is using S1 nuclease, which degrades single-stranded DNA and RNA into oligo- or mononucleotides, leaving intact double-stranded DNA and RNA.
In the nuclease hybridization assay, the oligonucleotide analyte is captured onto the solid support such as a 96-well plate via a fully complementary cutting probe. After enzymatic processing by S1 nuclease, the free cutting probe and the cutting probe hybridized to metabolites, i.e. shortmers of the analyte are degraded, allowing signal to be generated only from the full-length cutting probe-analyte duplex.
The assay is well tolerant to diverse chemistries, as exemplified by the development of a nuclease assay for morpholino oligonucleotides.
This assay set-up can lack robustness and is not suitable for validation following the FDA's guidelines for [https://www.fda.gov/files/drugs/published/Bioanalytical-Method-Validation-Guidance-for-Industry.pdf bioanalytical method validation]. This is demonstrated by an absence of published method that have been validated to the standards outlined by the FDA for bioanalytical methods. | 1 | Biochemistry |
* Bupropion
* DHβE
* Mecamylamine
* Memantine
* Methyllycaconitine
* PelA-5466, very selective, 300 fold more potent on α3β2 than α6/α3β2β3
* Tubocurarine | 1 | Biochemistry |
In the physical sciences, a phase is a region of material that is chemically uniform, physically distinct, and (often) mechanically separable. In a system consisting of ice and water in a glass jar, the ice cubes are one phase, the water is a second phase, and the humid air is a third phase over the ice and water. The glass of the jar is another separate phase. (See .)
More precisely, a phase is a region of space (a thermodynamic system), throughout which all physical properties of a material are essentially uniform. Examples of physical properties include density, index of refraction, magnetization and chemical composition.
The term phase is sometimes used as a synonym for state of matter, but there can be several immiscible phases of the same state of matter (as where oil and water separate into distinct phases, both in the liquid state). It is also sometimes used to refer to the equilibrium states shown on a phase diagram, described in terms of state variables such as pressure and temperature and demarcated by phase boundaries. (Phase boundaries relate to changes in the organization of matter, including for example a subtle change within the solid state from one crystal structure to another, as well as state-changes such as between solid and liquid.) These two usages are not commensurate with the formal definition given above and the intended meaning must be determined in part from the context in which the term is used. | 7 | Physical Chemistry |
There are several biological surfaces that have superhydrophobic properties far superior to any synthetic materials: lotus leaves, rice leaves, cicadia wings, and butterfly wings. | 7 | Physical Chemistry |
The surface tension of pure liquid water in contact with its vapor has been given by IAPWS as
where both and the critical temperature = 647.096 K are expressed in kelvins. The region of validity the entire vapor–liquid saturation curve, from the triple point (0.01 °C) to the critical point. It also provides reasonable results when extrapolated to metastable (supercooled) conditions, down to at least −25 °C. This formulation was originally adopted by IAPWS in 1976 and was adjusted in 1994 to conform to the International Temperature Scale of 1990.
The uncertainty of this formulation is given over the full range of temperature by IAPWS. For temperatures below 100 °C, the uncertainty is ±0.5%. | 6 | Supramolecular Chemistry |
In Orgel diagrams, the magnitude of the splitting energy exerted by the ligands on d orbitals, as a free ion approach a ligand field, is compared to the electron-repulsion energy, which are both sufficient at providing the placement of electrons. However, if the ligand field splitting energy, 10Dq, is greater than the electron-repulsion energy, then Orgel diagrams fail in determining electron placement. In this case, Orgel diagrams are restricted to only high spin complexes.
Tanabe–Sugano diagrams do not have this restriction, and can be applied to situations when 10Dq is significantly greater than electron repulsion. Thus, Tanabe–Sugano diagrams are utilized in determining electron placements for high spin and low spin metal complexes. However, they are limited in that they have only qualitative significance. Even so, Tanabe–Sugano diagrams are useful in interpreting UV-vis spectra and determining the value of 10Dq. | 7 | Physical Chemistry |
As a result of extensive cultivation of legumes (particularly soy, alfalfa, and clover), growing use of the Haber–Bosch process in the production of chemical fertilizers, and pollution emitted by vehicles and industrial plants, human beings have more than doubled the annual transfer of nitrogen into biologically available forms. In addition, humans have significantly contributed to the transfer of nitrogen trace gases from Earth to the atmosphere and from the land to aquatic systems. Human alterations to the global nitrogen cycle are most intense in developed countries and in Asia, where vehicle emissions and industrial agriculture are highest.
Generation of Nr, reactive nitrogen, has increased over 10 fold in the past century due to global industrialisation. This form of nitrogen follows a cascade through the biosphere via a variety of mechanisms, and is accumulating as the rate of its generation is greater than the rate of denitrification.
Nitrous oxide () has risen in the atmosphere as a result of agricultural fertilization, biomass burning, cattle and feedlots, and industrial sources. has deleterious effects in the stratosphere, where it breaks down and acts as a catalyst in the destruction of atmospheric ozone. Nitrous oxide is also a greenhouse gas and is currently the third largest contributor to global warming, after carbon dioxide and methane. While not as abundant in the atmosphere as carbon dioxide, it is, for an equivalent mass, nearly 300 times more potent in its ability to warm the planet.
Ammonia () in the atmosphere has tripled as the result of human activities. It is a reactant in the atmosphere, where it acts as an aerosol, decreasing air quality and clinging to water droplets, eventually resulting in nitric acid (HNO) that produces acid rain. Atmospheric ammonia and nitric acid also damage respiratory systems.
The very high temperature of lightning naturally produces small amounts of , , and , but high-temperature combustion has contributed to a 6- or 7-fold increase in the flux of to the atmosphere. Its production is a function of combustion temperature - the higher the temperature, the more is produced. Fossil fuel combustion is a primary contributor, but so are biofuels and even the burning of hydrogen. However, the rate that hydrogen is directly injected into the combustion chambers of internal combustion engines can be controlled to prevent the higher combustion temperatures that produce .
Ammonia and nitrous oxides actively alter atmospheric chemistry. They are precursors of tropospheric (lower atmosphere) ozone production, which contributes to smog and acid rain, damages plants and increases nitrogen inputs to ecosystems. Ecosystem processes can increase with nitrogen fertilization, but anthropogenic input can also result in nitrogen saturation, which weakens productivity and can damage the health of plants, animals, fish, and humans.
Decreases in biodiversity can also result if higher nitrogen availability increases nitrogen-demanding grasses, causing a degradation of nitrogen-poor, species-diverse heathlands. | 1 | Biochemistry |
Unlike conventional evolutionary and biochemical approaches to studying proteins, i.e. the so-called horizontal comparison of related protein homologues from different branch ends of the tree of life; ASR probes the statistically inferred ancestral proteins within the nodes of the tree – in a vertical manner (see diagram, right). This approach gives access to protein properties that may have transiently arisen over evolutionary time and has recently been used as a way to infer the potential selection pressures that resulted in present-day sequences. ASR has been used to probe the causative mutation that resulted in a proteins neofunctionalization after duplication by first determining that said mutation was located between ancestors 5 and 4 on the diagram (illustratively) using functional assays. In the field of protein biophysics, ASR has also been used to study the development of a proteins thermodynamic and kinetic landscapes over evolutionary time as well as protein folding pathways by combining many modern day analytical techniques such as HX/MS. These sort of insights are typically inferred from several ancestors reconstructed along a phylogeny – referring to the previous analogy, by studying nodes higher and higher (further and further back in evolutionary time) within the tree of life.
Most ASR studies are conducted in vitro, and have revealed ancestral protein properties that seem to be evolutionarily desirable traits – such as increased thermostability, catalytic activity and catalytic promiscuity. These data have been accredited to artifacts of the ASR algorithms, as well as indicative illustrations of ancient Earths environment – often, ASR research must be complemented with extensive controls (usually alternate ASR experiments) to mitigate algorithmic error. Not all studied ASR proteins exhibit this so-called ancestral superiority. The nascent field of evolutionary biochemistry has been bolstered by the recent increase in ASR studies using the ancestors as ways to probe organismal fitness within certain cellular contexts – effectively testing ancestral proteins in vivo. Due to inherent limitations in these sorts of studies – primarily being the lack of suitably ancient genomes to fit these ancestors in to, the small repertoire of well categorised laboratory model systems, and the inability to mimic ancient cellular environments; very few ASR studies in vivo have been conducted. Despite the above mentioned obstacles, preliminary insights into this avenue of research from a 2015 paper, have revealed that observed ancestral superiority in vitro were not recapitulated in vivo of a given protein. ASR presents one of a few mechanisms to study biochemistry of the Precambrian era of life (>541Ma) and is hence often used in paleogenetics; indeed Zuckerkandl and Pauling originally intended ASR to be the starting point of a field they termed Paleobiochemistry'. | 1 | Biochemistry |
The main goal of biochemical cascades in lymphocytes is the secretion of molecules that can suppress altered cells or eliminate pathogenic agents, through proliferation, differentiation and activation of these cells. Therefore, the antigenic receptors play a central role in signal transduction in lymphocytes, because when antigens interact with them lead to a cascade of signal events. These receptors, that recognize the antigen soluble (B cells) or linked to a molecule on Antigen Presenting Cells (T cells), do not have long cytoplasm tails, so they are anchored to signal proteins, which contain a long cytoplasmic tails with a motif that can be phosphorylated (ITAM – immunoreceptor tyrosine-based activation motif) and resulting in different signal pathways. The antigen receptor and signal protein form a stable complex, named BCR or TCR, in B or T cells, respectively. The family Src is essential for signal transduction in these cells, because it is responsible for phosphorylation of ITAMs. Therefore, Lyn and Lck, in lymphocytes B and T, respectively, phosphorylate immunoreceptor tyrosine-based activation motifs after the antigen recognition and the conformational change of the receptor, which leads to the binding of Syk/Zap-70 kinases to ITAM and its activation. Syk kinase is specific of lymphocytes B and Zap-70 is present in T cells. After activation of these enzymes, some adaptor proteins are phosphorylated, like BLNK (B cells) and LAT (T cells). These proteins after phosphorylation become activated and allow binding of others enzymes that continue the biochemical cascade. One example of a protein that binds to adaptor proteins and become activated is PLC that is very important in the lymphocyte signal pathways. PLC is responsible for PKC activation, via DAG and Ca, which leads to phosphorylation of CARMA1 molecule, and formation of CBM complex. This complex activates Iκκ kinase, which phosphorylates I-κB, and then allows the translocation of NF-κB to the nucleus and transcription of genes encoding cytokines, for example. Others transcriptional factors like NFAT and AP1 complex are also important for transcription of cytokines. The differentiation of B cells to plasma cells is also an example of a signal mechanism in lymphocytes, induced by a cytokine receptor. In this case, some interleukins bind to a specific receptor, which leads to activation of MAPK/ERK pathway. Consequently, the BLIMP1 protein is translated and inhibits PAX5, allowing immunoglobulin genes transcription and activation of XBP1 (important for the secretory apparatus formation and enhancing of protein synthesis). Also, the coreceptors (CD28/CD19) play an important role because they can improve the antigen/receptor binding and initiate parallel cascade events, like activation o PI3 Kinase. PIP3 then is responsible for activation of several proteins, like vav (leads to activation of JNK pathway, which consequently leads to activation of c-Jun) and btk (can also activate PLC). | 7 | Physical Chemistry |
The wide variety of electrophilic aminating reagents precludes generalization of reaction conditions. Electrophilic nitrogen sources are, however, either toxic or explosive in general. Great care should be taken while handling these reagents. Many electrophilic nitrogen sources do not provide amines immediately, but a number of methods exist to generate the corresponding amines.
* Tosylamines: tributyltin hydride
* Azo compounds: H/Pd
* Triazenes: sodium borohydride
* Azides: H/Pd, H/Pt, lithium aluminum hydride, triphenylphosphine
Conversion to other nitrogen-containing functionality, including enamines, imines, and amides, is also possible. | 0 | Organic Chemistry |
Photooxygenation reactions are easily confused with a number of processes baring similar names (i.e. photosensitized oxidation). Clear distinctions can be made based on three attributes: oxidation, the involvement of light, and the incorporation of molecular oxygen into the products: | 5 | Photochemistry |
The force measurements of the SFA are based primarily on Hooke's Law,
where F is the restoring force of a spring, k is the spring constant and x is the displacement of the spring.
Using a cantilevered spring, the lower surface is brought towards the top surface using a fine micrometer or piezotube. The force between the two surfaces is measured by
where is the change in displacement applied by the micrometer and is the change displacement measured by interferometry.
The spring constants can range anywhere from to . When measuring higher forces, a spring with a higher spring constant would be used. | 6 | Supramolecular Chemistry |
In electroplating, the item to be coated is placed into a container containing a solution of one or more tin salts. The item is connected to an electrical circuit, forming the cathode (negative) of the circuit while an electrode typically of the same metal to be plated forms the anode (positive). When an electric current is passed through the circuit, metal ions in the solution are attracted to the item. To produce a smooth, shiny surface, the electroplated sheet is then briefly heated above the melting point of tin. Most of the tin-plated steel made today is then further electroplated with a very thin layer of chromium to prevent dulling of the surface from oxidation of the tin. | 8 | Metallurgy |
In some cases, equations are unsolvable analytically, but can be solved using numerical methods if data values are given. There are two different ways to do this, by either using software programmes or mathematical methods such as the Euler method. Examples of software for chemical kinetics are i) Tenua, a Java app which simulates chemical reactions numerically and allows comparison of the simulation to real data, ii) Python coding for calculations and estimates and iii) the Kintecus software compiler to model, regress, fit and optimize reactions.
-Numerical integration: for a 1st order reaction A → B
The differential equation of the reactant A is:
It can also be expressed as
which is the same as
To solve the differential equations with Euler and Runge-Kutta methods we need to have the initial values. | 7 | Physical Chemistry |
Nucleic acid secondary structure is generally divided into helices (contiguous base pairs), and various kinds of loops (unpaired nucleotides surrounded by helices). Frequently these elements, or combinations of them, are further classified into additional categories including, for example, tetraloops, pseudoknots, and stem-loops. Topological approaches can be used to categorize and compare complex structures that arise from combining these elements in various arrangements. | 4 | Stereochemistry |
In organometallic chemistry, a transition metal indenyl complex is a coordination compound that contains one or more indenyl ligands. The indenyl ligand is formally the anion derived from deprotonation of indene. The η-indenyl ligand is related to the ηcyclopentadienyl anion (Cp), thus indenyl analogues of many cyclopentadienyl complexes are known. Indenyl ligands lack the 5-fold symmetry of Cp, so they exhibit more complicated geometries. Furthermore, some indenyl complexes also exist with only η-bonding mode. The η- and η-bonding modes sometimes interconvert. | 0 | Organic Chemistry |
The method was later transferred by Emil Fischer and Burckhardt Helferich to other chloro-substituted purines and produced thus for the first time synthetic nucleosides. It was later improved and modified by numerous chemists. | 0 | Organic Chemistry |
Malate dehydrogenases catalyzes the interconversion of malate to oxaloacetate. In the citric acid cycle, malate dehydrogenase is responsible for catalyzing the regeneration of oxaloacetate This reaction occurs through the oxidation of hydroxyl group on malate and reduction of NAD. The mechanism of the transfer of the hydride ion to NAD is carried out in a similar mechanism seen in lactate dehydrogenase and alcohol dehydrogenase. The ΔG'° of malate dehydrogenase is +29.7 kJ/mol and the ΔG (in the cell) is 0 kJ/mol. | 1 | Biochemistry |
Epileptic seizures occur when there is synchrony of electrical waves in the brain. Knowing the role that ephaptic coupling plays in maintaining synchrony in electrical signals, it makes sense to look for ephaptic mechanisms in this type of pathology. One study suggested that cortical cells represent an ideal place to observe ephaptic coupling due to the tight packing of axons, which allows for interactions between their electrical fields. They tested the effects of changing extracellular space (which affects local electrical fields) and found that one can block epileptic synchronization independent of chemical synapse manipulation simply by increasing the space between cells. Later, a model was created to predict this phenomenon and showed scenarios with greater extracellular spacing that effectively blocked epileptic synchronization in the brain. | 1 | Biochemistry |
In chemistry, a sultine is a cyclic ester of a sulfinic acid. This class of organosulfur compounds has few applications. These compounds are typically prepared by the dehydration of hydroxy-sulfinic acids or their equivalent. Illustrative of an alternative route, xylylene dibromide reacts with sodium sulfoxylate (source of SO) to give the sultine CH(CHS(O)OCH), which is a precursor to o-quinodimethane. | 0 | Organic Chemistry |
A single-molecule electrically operated motor made from a single molecule of n-butyl methyl sulfide (CHS) has been reported. The molecule is adsorbed onto a copper (111) single-crystal piece by chemisorption. | 6 | Supramolecular Chemistry |
George N. Phillips Jr. is a biochemist, researcher, and academic. He is the Ralph and Dorothy Looney Professor of Biochemistry and Cell Biology at Rice University, where he also serves as Associate Dean for Research at the Wiess School of Natural Sciences and as a professor of chemistry. Additionally, he holds the title of professor emeritus of biochemistry at the University of Wisconsin-Madison.
Phillips research is primarily centered on protein structure, protein dynamics, and computational biology, with a specific emphasis on understanding the correlation between the dynamics of proteins and their biological functions. He has authored book chapters, and is an editor for the Handbook of Proteins: Structure, Function and Methods Volume 2. He is the recipient of the Arnold O. Beckman Research Award, the American Heart Associations Established Investigator Award, and the Vilas Associate Award.
Phillips is an Elected Fellow of the Biophysical Society, the American Crystallographic Association, and the American Association for the Advancement of Science. He served as president and vice-president of the American Crystallographic Association from 2011 to 2013. He also holds the position of Editor-in-Chief for Structural Dynamics with the AIP Press and serves as an Associate Editor for Critical Reviews in Biochemistry and Molecular Biology. | 1 | Biochemistry |
"Redox" is a portmanteau of the words "reduction" and "oxidation". The term "redox" was first used in 1928.
The processes of oxidation and reduction occur simultaneously and cannot occur independently. In redox processes, the reductant transfers electrons to the oxidant. Thus, in the reaction, the reductant or reducing agent loses electrons and is oxidized, and the oxidant or oxidizing agent gains electrons and is reduced. The pair of an oxidizing and reducing agent that is involved in a particular reaction is called a redox pair. A redox couple is a reducing species and its corresponding oxidizing form, e.g., / .The oxidation alone and the reduction alone are each called a half-reaction because two half-reactions always occur together to form a whole reaction. | 9 | Geochemistry |
One problem with the SBSP concept is the cost of space launches and the amount of material that would need to be launched.
Much of the material launched need not be delivered to its eventual orbit immediately, which raises the possibility that high efficiency (but slower) engines could move SPS material from LEO to GEO at an acceptable cost. Examples include ion thrusters or nuclear propulsion.
To give an idea of the scale of the problem, assuming a solar panel mass of 20 kg per kilowatt (without considering the mass of the supporting structure, antenna, or any significant mass reduction of any focusing mirrors) a 4 GW power station would weigh about 80,000 metric tons, all of which would, in current circumstances, be launched from the Earth. This is, however, far from the state of the art for flown spacecraft, which as of 2015 was 150 W/kg (6.7 kg/kW), and improving rapidly. Very lightweight designs could likely achieve 1 kg/kW, meaning 4,000 metric tons for the solar panels for the same 4 GW capacity station. Beyond the mass of the panels, overhead (including boosting to the desired orbit and stationkeeping) must be added.
To these costs must be added the environmental impact of heavy space launch missions, if such costs are to be used in comparison to earth-based energy production. For comparison, the direct cost of a new coal or nuclear power plant ranges from $3 billion to $6 billion per GW (not including the full cost to the environment from emissions or storage of spent nuclear fuel, respectively). | 7 | Physical Chemistry |
A nanodomain is a nanometer-sized cluster of proteins found in a cell membrane. They are associated with the signal which occurs when a single calcium ion channel opens on a cell membrane, allowing an influx of calcium ions (Ca) which extend in a plume a few tens of nanometres from the channel pore. In a nanodomain, the coupling distance, that is, the distance between the calcium-binding proteins which sense the calcium, and the calcium channel, is very small, less than , which allows rapid signalling. The formation of a nanodomain signal is virtually instantaneous following the opening of the calcium channel, as calcium ions move rapidly into the cell along a steep concentration gradient. The nanodomain signal collapses just as quickly when the calcium channel closes, as the ions rapidly diffuse away from the pore. Formation of a nanodomain signal requires the influx of only approximately 1000 calcium ions.
Coupling distances greater than , mediated by a larger number of channels, are referred to as microdomains. nanodomain | 1 | Biochemistry |
The B form of the DNA helix twists 360° per 10.4-10.5 bp in the absence of torsional strain. But many molecular biological processes can induce torsional strain. A DNA segment with excess or insufficient helical twisting is referred to, respectively, as positively or negatively supercoiled. DNA in vivo is typically negatively supercoiled, which facilitates the unwinding (melting) of the double-helix required for RNA transcription.
Within the cell most DNA is topologically restricted. DNA is typically found in closed loops (such as plasmids in prokaryotes) which are topologically closed, or as very long molecules whose diffusion coefficients produce effectively topologically closed domains. Linear sections of DNA are also commonly bound to proteins or physical structures (such as membranes) to form closed topological loops.
Francis Crick was one of the first to propose the importance of linking numbers when considering DNA supercoils. In a paper published in 1976, Crick outlined the problem as follows:
Analysis of DNA topology uses three values:
* L = linking number - the number of times one DNA strand wraps around the other. It is an integer for a closed loop and constant for a closed topological domain.
* T = twist - total number of turns in the double stranded DNA helix. This will normally tend to approach the number of turns that a topologically open double stranded DNA helix makes free in solution: number of bases/10.5, assuming there are no intercalating agents (e.g., ethidium bromide) or other elements modifying the stiffness of the DNA.
* W = writhe - number of turns of the double stranded DNA helix around the superhelical axis
* L = T + W and ΔL = ΔT + ΔW
Any change of T in a closed topological domain must be balanced by a change in W, and vice versa. This results in higher order structure of DNA. A circular DNA molecule with a writhe of 0 will be circular. If the twist of this molecule is subsequently increased or decreased by supercoiling then the writhe will be appropriately altered, making the molecule undergo plectonemic or toroidal superhelical coiling.
When the ends of a piece of double stranded helical DNA are joined so that it forms a circle the strands are topologically knotted. This means the single strands cannot be separated any process that does not involve breaking a strand (such as heating). The task of un-knotting topologically linked strands of DNA falls to enzymes termed topoisomerases. These enzymes are dedicated to un-knotting circular DNA by cleaving one or both strands so that another double or single stranded segment can pass through. This un-knotting is required for the replication of circular DNA and various types of recombination in linear DNA which have similar topological constraints. | 4 | Stereochemistry |
Conjugated polymers offer the tantalizing possibility of organic molecules with a manipulable electronic band structure, but current methods for production have an uncontrolled topology. Sun, Lauher, and Goroff discovered that certain amides ensure a linear polymerization of poly(diiododiacetylene). The underlying mechanism is a self-organization of the amides via hydrogen bonds that then transfers to the diiododiacetylene monomers via halogen bonds. Although pure diiododiacetylene crystals do not polymerize spontaneously, the halogen-bond induced organization is sufficiently strong that the cocrystals do spontaneously polymerize. | 6 | Supramolecular Chemistry |
The atmospheres of low metallicity cool stars are composed primarily of hydrogen and helium. Collision-induced absorption by H-H and H-He transient complexes will be a more or less important opacity source of their atmospheres. For example, CIA in the H fundamental band, which falls on top of an opacity window between
HO/CH or HO/CO (depending on the temperature), plays an important role in shaping brown dwarf spectra. Higher gravity brown dwarf stars often show even stronger CIA, owing to the density squared dependence of CIA intensities, when other "ordinary" opacity sources are linearly dependent on density. CIA is also important in low-metallicity brown dwarfs, since "low metallicity" means reduced CNO (and other) elemental abundances compared to H and He, and thus stronger CIA compared to HO, CO, and CH absorption. CIA absorption of H-X collisional complexes is thus an important diagnostic of high-gravity and low-metallicity brown dwarfs. All of this is also true of the M dwarfs, but to a lesser extent. M dwarf atmospheres are hotter so that some increased
portion of the H molecules is in the dissociated state, which
weakens CIA by H--X complexes. The significance of CIA for cool
astronomical objects was long suspected or known to some degree. | 7 | Physical Chemistry |
Pitting corrosion is defined by localized attack, ranging from microns to millimeters in diameter, in an otherwise passive surface and only occurs for specific alloy and environmental combinations. Thus, this type of corrosion typically occurs in alloys that are protected by a tenacious (passivating) oxide film such as stainless steels, nickel alloys, aluminum alloys in environments that contain an aggressive species such as chlorides (Cl) or thiosulfates (SO). In contrast, alloy/environment combinations where the passive film is not very protective usually will not produce pitting corrosion. A good example of the importance of alloy/environment combinations is carbon steel. In environments where the pH value is lower than 10, carbon steel does not form a passivating oxide film and the addition of chloride results in uniform attack over the entire surface. However, at pH greater than 10 (alkaline) the oxide is protective and the addition of chloride results in pitting corrosion.
Besides chlorides, other anions implicated in pitting include thiosulfates (SO), fluorides and iodides. Stagnant water conditions with low concentrations of dissolved oxygen also favor pitting. Thiosulfates are particularly aggressive species and are formed by partial oxidation of pyrite (pyrite|, a ferrous disulfide), or partial sulfate reduction by microorganisms, a.o. by sulfate reducing bacteria (SRB). Thiosulfates are a concern for corrosion in many industries handling sulfur-derived compounds: sulfide ores processing, oil wells and pipelines transporting soured oils, kraft paper production plants, photographic industry, methionine and lysine factories. | 8 | Metallurgy |
The vast majority of refined bitumen is used in construction: primarily as a constituent of products used in paving and roofing applications. According to the requirements of the end use, bitumen is produced to specification. This is achieved either by refining or blending. It is estimated that the current world use of bitumen is approximately 102 million tonnes per year. Approximately 85% of all the bitumen produced is used as the binder in asphalt concrete for roads. It is also used in other paved areas such as airport runways, car parks and footways. Typically, the production of asphalt concrete involves mixing fine and coarse aggregates such as sand, gravel and crushed rock with asphalt, which acts as the binding agent. Other materials, such as recycled polymers (e.g., rubber tyres), may be added to the bitumen to modify its properties according to the application for which the bitumen is ultimately intended.
A further 10% of global bitumen production is used in roofing applications, where its waterproofing qualities are invaluable.
The remaining 5% of bitumen is used mainly for sealing and insulating purposes in a variety of building materials, such as pipe coatings, carpet tile backing and paint. Bitumen is applied in the construction and maintenance of many structures, systems, and components, such as:
* Highways
* Airport runways
* Footways and pedestrian ways
* Car parks
* Racetracks
* Tennis courts
* Roofing
* Damp proofing
* Dams
* Reservoir and pool linings
* Soundproofing
* Pipe coatings
* Cable coatings
* Paints
* Building water proofing
* Tile underlying waterproofing
* Newspaper ink production | 7 | Physical Chemistry |
An electric arc furnace (EAF) is a furnace that heats material by means of an electric arc.
Industrial arc furnaces range in size from small units of approximately one-tonne capacity (used in foundries for producing cast iron products) up to about 400-tonne units used for secondary steelmaking. Arc furnaces used in research laboratories and by dentists may have a capacity of only a few dozen grams. Industrial electric arc furnace temperatures can reach , while laboratory units can exceed .
In electric arc furnaces, the charged material (the material entered into the furnace for heating, not to be confused with electric charge) is directly exposed to an electric arc, and the current from the electrode terminals passes through the charged material.
Arc furnaces differ from induction furnaces, in which the charge is heated instead by eddy currents. | 8 | Metallurgy |
The nucleotide sequence of a gene's DNA specifies the amino acid sequence of a protein through the genetic code. Sets of three nucleotides, known as codons, each correspond to a specific amino acid. The principle that three sequential bases of DNA code for each amino acid was demonstrated in 1961 using frameshift mutations in the rIIB gene of bacteriophage T4 (see Crick, Brenner et al. experiment).
Additionally, a "start codon", and three "stop codons" indicate the beginning and end of the protein coding region. There are 64 possible codons (four possible nucleotides at each of three positions, hence 4 possible codons) and only 20 standard amino acids; hence the code is redundant and multiple codons can specify the same amino acid. The correspondence between codons and amino acids is nearly universal among all known living organisms. | 1 | Biochemistry |
A special numbering system is to be used for fluorinated alkanes, prefixed with Freon-, R-, CFC- and HCFC-, where the rightmost value indicates the number of fluorine atoms, the next value to the left is the number of hydrogen atoms plus 1, and the next value to the left is the number of carbon atoms less one (zeroes are not stated), and the remaining atoms are chlorine.
Freon-12, for example, indicates a methane derivative (only two numbers) containing two fluorine atoms (the second 2) and no hydrogen (1-1=0). It is therefore CClF.
Another equation that can be applied to get the correct molecular formula of the CFC/R/Freon class compounds is to take the numbering and add 90 to it. The resulting value will give the number of carbons as the first numeral, the second numeral gives the number of hydrogen atoms, and the third numeral gives the number of fluorine atoms. The rest of the unaccounted carbon bonds are occupied by chlorine atoms. The value of this equation is always a three figure number. An easy example is that of CFC-12, which gives: 90+12=102 -> 1 carbon, 0 hydrogens, 2 fluorine atoms, and hence 2 chlorine atoms resulting in CClF. The main advantage of this method of deducing the molecular composition in comparison with the method described in the paragraph above is that it gives the number of carbon atoms of the molecule.
Freons containing bromine are signified by four numbers. Isomers, which are common for ethane and propane derivatives, are indicated by letters following the numbers: | 2 | Environmental Chemistry |
(Note that COX1, COX2, and COX3 are mitochondrially encoded)
*COX4I1 001861
*COX5B NM_001862
*COX6B1 NM_001863
*COX6C NM_004374
*COX7A2 NM_001865 Homo sapiens cytochrome c oxidase subunit VIIa polypeptide 2 (liver) (COX7A2),
*COX7A2L NM_004718
*COX7C NM_001867
*COX8
*COX8A NM_004074 Homo sapiens cytochrome c oxidase subunit VIII (COX8), nuclear gene encoding
*COX11 NM_004375
*COX14 NM_032901
*COX15 NM_004376
*COX16 NM_016468
*COX19 NM_001031617
*COX20 NM_198076
*CYC1 Homo sapiens cytochrome c-1 (CYC1)
*UQCC NM_018244 Required for the assembly of the ubiquinol-cytochrome c reductase complex (mitochondrial respiratory chain complex III or cytochrome b-c1 complex)
*UQCR10 NM_013387
*UQCR11 NM_006830 Homo sapiens ubiquinol-cytochrome c reductase (6.4kD) subunit (UQCR), mRNA
*UQCRB NM_006294
*UQCRC1 NM_003365 Homo sapiens ubiquinol-cytochrome c reductase core protein I (UQCRC1), mRNA
*UQCRC2 NM_003366
*UQCRHL NM_001089591
*UQCRQ NM_014402 Homo sapiens low molecular mass ubiquinone-binding protein (9.5kD) (QP-C), mRNA | 1 | Biochemistry |
Many cyanobacteria are able to reduce nitrogen and carbon dioxide under aerobic conditions, a fact that may be responsible for their evolutionary and ecological success. The water-oxidizing photosynthesis is accomplished by coupling the activity of photosystem (PS) II and I (Z-scheme). In contrast to green sulfur bacteria which only use one photosystem, the use of water as an electron donor is energetically demanding, requiring two photosystems.
Attached to the thylakoid membrane, phycobilisomes act as light-harvesting antennae for the photosystems. The phycobilisome components (phycobiliproteins) are responsible for the blue-green pigmentation of most cyanobacteria. The variations on this theme are due mainly to carotenoids and phycoerythrins that give the cells their red-brownish coloration. In some cyanobacteria, the color of light influences the composition of the phycobilisomes. In green light, the cells accumulate more phycoerythrin, which absorbs green light, whereas in red light they produce more phycocyanin which absorbs red. Thus, these bacteria can change from brick-red to bright blue-green depending on whether they are exposed to green light or to red light. This process of "complementary chromatic adaptation" is a way for the cells to maximize the use of available light for photosynthesis.
A few genera lack phycobilisomes and have chlorophyll b instead (Prochloron, Prochlorococcus, Prochlorothrix). These were originally grouped together as the prochlorophytes or chloroxybacteria, but appear to have developed in several different lines of cyanobacteria. For this reason, they are now considered as part of the cyanobacterial group. | 5 | Photochemistry |
In general, the ideal buffer should have good conductivity, produce less heat and have a long life. There are a number of buffers used for agarose electrophoresis; common ones for nucleic acids include Tris/Acetate/EDTA (TAE) and Tris/Borate/EDTA (TBE). The buffers used contain EDTA to inactivate many nucleases which require divalent cation for their function. The borate in TBE buffer can be problematic as borate can polymerize, and/or interact with cis diols such as those found in RNA. TAE has the lowest buffering capacity, but it provides the best resolution for larger DNA. This means a lower voltage and more time, but a better product.
Many other buffers have been proposed, e.g. lithium borate (LB), iso electric histidine, pK matched goods buffers, etc.; in most cases the purported rationale is lower current (less heat) and or matched ion mobilities, which leads to longer buffer life. Tris-phosphate buffer has high buffering capacity but cannot be used if DNA extracted is to be used in phosphate sensitive reaction. LB is relatively new and is ineffective in resolving fragments larger than 5 kbp; However, with its low conductivity, a much higher voltage could be used (up to 35 V/cm), which means a shorter analysis time for routine electrophoresis. As low as one base pair size difference could be resolved in 3% agarose gel with an extremely low conductivity medium (1 mM lithium borate).
Other buffering system may be used in specific applications, for example, barbituric acid-sodium barbiturate or Tris-barbiturate buffers may be used for in agarose gel electrophoresis of proteins, for example in the detection of abnormal distribution of proteins. | 1 | Biochemistry |
Arsenic exposure through groundwater is highly concerning throughout the perinatal period. Pregnant women are a high-risk population because not only are the mothers at risk for adverse outcomes, but in-utero exposure also poses health risks to the infant.
There is a dose-dependent relationship between maternal exposure to arsenic and infant mortality, meaning that infants born to women exposed to higher concentrations, or exposed for longer periods of time, have a higher mortality rate.
Studies have shown that ingesting arsenic through groundwater during pregnancy poses dangers to the mother including, but not limited to abdominal pain, vomiting, diarrhea, skin pigmentation changes, and cancer. Research has also demonstrated that arsenic exposure also causes low birth weight, low birth size, infant mortality, and a variety of other outcomes in infants. Some of these effects, like lower birth-rate and size may be due to the effects of arsenic on maternal weight gain during pregnancy. | 1 | Biochemistry |
The mountain banshee (Ikran in Navi) is an airborne predator which lives in mountainous territory on Pandora. Navi warriors attempt to bond with a banshee, a dangerous and required rite of passage. They are cousins to the great leonopteryx and they are scientifically known by xenobiologists as Pterodactylus giganteus. A banshee bonds to a Navi warrior for life. They are four-winged creatures that, like the leonopteryx and direhorse, have a biologically produced carbon fiber flexing on the skin. Neytiri had a banshee named Seze (translated from the language of the Navi roughly as "blue flower"). Page spent the most time designing the banshee for the film so it would be convincing when it flew or perched. The designer said, "The hardest thing of all was having a Navi on top of it and flying it. You had to backwards engineer it. It was like designing and engineering an aircraft." Barlowe, who contributed to the banshees design, was influenced by manta rays and skates as well as relatively little-known pterosaurs and plesiosaurs that had "many, unique aerodynamic and hydrodynamic" characteristics. Like the color scheme for the great leonopteryx, color schemes based on Earth animals were used for various banshees, though Page was inspired by Art Nouveau prints to warp the schemes so they would not look familiar to film audiences. | 1 | Biochemistry |
In organic chemistry, an acyl halide (also known as an acid halide) is a chemical compound derived from an oxoacid by replacing a hydroxyl group () with a halide group (, where X is a halogen).
If the acid is a carboxylic acid (), the compound contains a functional group, which consists of a carbonyl group () singly bonded to a halogen atom. The general formula for such an acyl halide can be written RCOX, where R may be, for example, an alkyl group, CO is the carbonyl group, and X represents the halide, such as chloride. Acyl chlorides are the most commonly encountered acyl halides, but acetyl iodide is the one produced (transiently) on the largest scale. Billions of kilograms are generated annually in the production of acetic acid. | 0 | Organic Chemistry |
Cloxacillin was discovered and developed by Beecham (now GlaxoSmithKline).
It is sold under a number of trade names, including Cloxapen, Cloxacap, Tegopen and Orbenin. | 4 | Stereochemistry |
As mentioned above, the deformed structure is often a 3-D cellular structure with walls consisting of dislocation tangles. As recovery proceeds these cell walls will undergo a transition towards a genuine subgrain structure. This occurs through a gradual elimination of extraneous dislocations and the rearrangement of the remaining dislocations into low-angle grain boundaries.
Sub-grain formation is followed by subgrain coarsening where the average size increases while the number of subgrains decreases. This reduces the total area of grain boundary and hence the stored energy in the material. Subgrain coarsen shares many features with grain growth.
If the sub-structure can be approximated to an array of spherical subgrains of radius R and boundary energy γ; the stored energy is uniform; and the force on the boundary is evenly distributed, the driving pressure P is given by:
Since γ is dependent on the boundary misorientation of the surrounding subgrains, the driving pressure generally does not remain constant throughout coarsening. | 8 | Metallurgy |
* The copper cycle is not entirely well described. It is suggested that the presence of a base results in the formation of a π-alkyne complex E. This increases the acidity of the terminal proton and leads to the formation of copper acetylide, complex F, upon deprotonation.
* Acetylide F is then involved in the transmetallation reaction with palladium intermediate B. | 0 | Organic Chemistry |
Inhibitors and inducers of the cytochrome P450 enzyme CYP3A4 may influence the levels and efficacy of drospirenone. Treatment for 10 days with 200 mg twice daily ketoconazole, a strong CYP3A4 inhibitor among other actions, has been found to result in a moderate 2.0- to 2.7-fold increase in exposure to drospirenone. Drospirenone does not appear to influence the metabolism of omeprazole (metabolized via CYP2C19), simvastatin (metabolized via CYP3A4), or midazolam (metabolized via CYP3A4), and likely does not influence the metabolism of other medications that are metabolized via these pathways. Drospirenone may interact with potassium-sparing medications such as ACE inhibitors, angiotensin II receptor antagonists, potassium-sparing diuretics, potassium supplements, heparin, antimineralocorticoids, and nonsteroidal anti-inflammatory drugs to further increase potassium levels. This may increase the risk of hyperkalemia (high potassium levels). | 4 | Stereochemistry |
In order for proteins to adsorb, they must first come into contact with the surface through one or more of these major transport mechanisms: diffusion, thermal convection, bulk flow, or a combination thereof. When considering the transport of proteins, it is clear how concentration gradients, temperature, protein size and flow velocity will influence the arrival of proteins to a solid surface. Under conditions of low flow and minimal temperature gradients, the adsorption rate can be modeled after the diffusion rate equation. | 1 | Biochemistry |
Digestion of some fats can begin in the mouth where lingual lipase breaks down some short chain lipids into diglycerides. However fats are mainly digested in the small intestine. The presence of fat in the small intestine produces hormones that stimulate the release of pancreatic lipase from the pancreas and bile from the liver which helps in the emulsification of fats for absorption of fatty acids. Complete digestion of one molecule of fat (a triglyceride) results a mixture of fatty acids, mono- and di-glycerides, but no glycerol. | 1 | Biochemistry |
In 1986, convincing evidence was provided that selenocysteine (Sec) was incorporated co-translationally. Moreover, the codon partially directing its incorporation in the polypeptide chain was identified as UGA also known as the opal termination codon. Different mechanisms for overriding the termination function of this codon have been identified in prokaryotes and in eukaryotes. A particular difference between these kingdoms is that cis elements seem restricted to the neighborhood of the UAG codon in prokaryotes while in eukaryotes this restriction is not present. Instead such locations seem disfavored albeit not prohibited.
In 2003, a landmark paper described the identification of all known selenoproteins in humans: 25 in total. Similar analyses have been run for other organisms.
The UAG codon can translate into pyrrolysine (Pyl) in a similar manner. | 1 | Biochemistry |
Glycinamide is a organic compound with the molecular formula HNCHC(O)NH. It is the amide derivative of the amino acid glycine. It is a water-soluble, white solid. Amino acid amides, such as glycinamide are prepared by treating the amino acid ester with ammonia.
It is a ligand for transition metals.
The hydrochloride salt of glycinamide, glycinamide hydrochloride, is one of Good's buffers with a pH in the physiological range. Glycinamide hydrochloride has a pKa near the physiological pH (8.20 at 20°C), making it useful in cell culture work. Its ΔpKa/°C is -0.029 and it has a solubility in water at 0 °C of 6.4 M.
Glycinamide is a reagent used in the synthesis of glycineamide ribonucleotide (an intermediate in de novo purine biosynthesis). | 1 | Biochemistry |
The same reaction can be described with the GEBIK and GEBIF equations under the BFEI and QSS approximations as
where has been substituted with because the rate
constants in the third reaction have been assumed to equal those
of the second reaction. | 7 | Physical Chemistry |
*Obligate aerobes need oxygen to grow. In a process known as cellular respiration, these organisms use oxygen to oxidize substrates (for example sugars and fats) and generate energy.
*Facultative anaerobes use oxygen if it is available, but also have anaerobic methods of energy production.
*Microaerophiles require oxygen for energy production, but are harmed by atmospheric concentrations of oxygen (21% O).
*Aerotolerant anaerobes do not use oxygen but are not harmed by it.
When an organism is able to survive in both oxygen and anaerobic environments, the use of the Pasteur effect can distinguish between facultative anaerobes and aerotolerant organisms. If the organism is using fermentation in an anaerobic environment, the addition of oxygen will cause facultative anaerobes to suspend fermentation and begin using oxygen for respiration. Aerotolerant organisms must continue fermentation in the presence of oxygen.
Facultative organisms grow in both oxygen rich media and oxygen free media. | 1 | Biochemistry |
Ethers like diethyl ether and tetrahydrofuran (THF) can form highly explosive organic peroxides upon exposure to oxygen and light. THF is normally more likely to form such peroxides than diethyl ether. One of the most susceptible solvents is diisopropyl ether, but all ethers are considered to be potential peroxide sources.
The heteroatom (oxygen) stabilizes the formation of a free radical which is formed by the abstraction of a hydrogen atom by another free radical. The carbon-centered free radical thus formed is able to react with an oxygen molecule to form a peroxide compound. The process of peroxide formation is greatly accelerated by exposure to even low levels of light, but can proceed slowly even in dark conditions.
Unless a desiccant is used which can destroy the peroxides, they will concentrate during distillation, due to their higher boiling point. When sufficient peroxides have formed, they can form a crystalline, shock-sensitive solid precipitate at the mouth of a container or bottle. Minor mechanical disturbances, such as scraping the inside of a vessel or the dislodging of a deposit, merely twisting the cap may provide sufficient energy for the peroxide to explode or detonate. Peroxide formation is not a significant problem when fresh solvents are used up quickly; they are more of a problem in laboratories which may take years to finish a single bottle. Low-volume users should acquire only small amounts of peroxide-prone solvents, and dispose of old solvents on a regular periodic schedule.
To avoid explosive peroxide formation, ethers should be stored in an airtight container, away from light, because both light and air can encourage peroxide formation.
A number of tests can be used to detect the presence of a peroxide in an ether; one is to use a combination of iron(II) sulfate and potassium thiocyanate. The peroxide is able to oxidize the Fe ion to an Fe ion, which then forms a deep-red coordination complex with the thiocyanate.
Peroxides may be removed by washing with acidic iron(II) sulfate, filtering through alumina, or distilling from sodium/benzophenone. Alumina degrades the peroxides but some could remain intact in it, therefore it must be disposed of properly. The advantage of using sodium/benzophenone is that moisture and oxygen are removed as well. | 2 | Environmental Chemistry |
Until recent decades, the mechanism of methyl isocyanate toxicity in humans was largely unknown or unclear. Methyl isocyanate and other isocyanates are electrophiles and are currently thought to cause toxicity by the alkylation of biomolecules. The mechanism of methyl isocyanate was previously suspected to be the carbamylation of hemoglobin, thus interfering with its oxygen-binding capability and causing hypoxia. However, experiments showed that when rats and guinea pigs were exposed to methyl isocyanate at concentrations above the median lethal concentration (LC, the concentration sufficient to kill 50% of the tested population), only 2% of hemoglobin molecules were carbamylated, suggesting that this is probably not the mechanism of toxicity. | 9 | Geochemistry |
Low-energy ion scattering spectroscopy (LEIS), sometimes referred to simply as ion scattering spectroscopy (ISS), is a surface-sensitive analytical technique used to characterize the chemical and structural makeup of materials. LEIS involves directing a stream of charged particles known as ions at a surface and making observations of the positions, velocities, and energies of the ions that have interacted with the surface. Data that is thus collected can be used to deduce information about the material such as the relative positions of atoms in a surface lattice and the elemental identity of those atoms. LEIS is closely related to both medium-energy ion scattering (MEIS) and high-energy ion scattering (HEIS, known in practice as Rutherford backscattering spectroscopy, or RBS), differing primarily in the energy range of the ion beam used to probe the surface. While much of the information collected using LEIS can be obtained using other surface science techniques, LEIS is unique in its sensitivity to both structure and composition of surfaces. Additionally, LEIS is one of a very few surface-sensitive techniques capable of directly observing hydrogen atoms, an aspect that may make it an increasingly more important technique as the hydrogen economy is being explored. | 7 | Physical Chemistry |
By 1900 the US was the largest producer and also the lowest cost producer, and demand for steel seemed inexhaustible. Output had tripled since 1890, but customers, not producers, mostly benefitted. Productivity-enhancing technology encouraged faster and faster rates of investment in new plants. However, during recessions, demand fell sharply taking down output, prices, and profits. Charles M. Schwab of Carnegie Steel proposed a solution: consolidation. Financier J. P. Morgan arranged the buyout of Carnegie and most other major firms, and put Elbert Gary in charge. The massive Gary Works steel mill on Lake Michigan was for many years the largest steel producing facility in the world.
US Steel combined finishing firms (American Tin Plate (controlled by William Henry "Judge" Moore), American Steel and Wire, and National Tube) with two major integrated companies, Carnegie Steel and Federal Steel. It was capitalized at $1.466 billion, and included 213 manufacturing mills, one thousand miles of railroad, and 41 mines. In 1901, it accounted for 66% of Americas steel output, and almost 30% of the worlds. During World War I, its annual production exceeded the combined output of all German and Austrian firms.
The Steel Strike of 1919 disrupted the entire industry for months, but the union lost and its membership sharply declined. Rapid growth of cities made the 1920s boom years. President Harding and social reformers forced it to end the 12-hour day in 1923.
Earnings were recorded at $2.650 billion for 2016. | 8 | Metallurgy |
In organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R″ represent any group, typically organyl groups or hydrogen atoms. The amide group is called a peptide bond when it is part of the main chain of a protein, and an isopeptide bond when it occurs in a side chain, as in asparagine and glutamine. It can be viewed as a derivative of a carboxylic acid () with the hydroxyl group () replaced by an amine group (); or, equivalently, an acyl (alkanoyl) group () joined to an amine group.
Common of amides are formamide (), acetamide (), benzamide (), and dimethylformamide (). Some uncommon examples of amides are N-chloroacetamide () and chloroformamide ().
Amides are qualified as primary, secondary, and tertiary according to whether the amine subgroup has the form , , or , where R and R' are groups other than hydrogen. | 0 | Organic Chemistry |
The term plasmid was introduced in 1952 by the American molecular biologist Joshua Lederberg to refer to "any extrachromosomal hereditary determinant." The term's early usage included any bacterial genetic material that exists extrachromosomally for at least part of its replication cycle, but because that description includes bacterial viruses, the notion of plasmid was refined over time to comprise genetic elements that reproduce autonomously.
Later in 1968, it was decided that the term plasmid should be adopted as the term for extrachromosomal genetic element, and to distinguish it from viruses, the definition was narrowed to genetic elements that exist exclusively or predominantly outside of the chromosome and can replicate autonomously. | 1 | Biochemistry |
Hattori was the first female undergraduate student in the Geology Department at the University of Tokyo, which was established in 1877. She completed her master's and PhD in isotope geochemistry there. | 9 | Geochemistry |
If it is the liver that cannot effectively transfer the indirect bilirubin into bilirubin glucuronide and further into bilirubin di-glucuronide, the consequence will be hyperbilirubinemia or intrahepatic (or hepatocellular) jaundice.
Moreover, the unconjugated hyperbilirubinemia arises in case the components of liver transfer the indirect bilirubin into bilirubin glucuronide in the rate slower than they should be. This condition is associated with either decreased uptake of bilirubin into hepatocytes (Rotor syndrome) or defective intracellular protein binding.
In similar fashion, the conjugated hyperbilirubinemia emerges in case the components of the liver have difficulty turning bilirubin glucuronide into bilirubin di-glucuronide. Note that biliary duct blockage can also lead to conjugated hyperbilirubinemia but the pathophysiology is that backflow of bilirubin di-glucuronide with little indirect bilirubin and bilirubin glucuronide from bile duct through liver into blood plasma. These conditions are associated with either defective intracellular protein binding (for the second time) or disturbed secretion into the bile canaliculi (Dubin–Johnson syndrome).
Liver failure and hepatitis are the most etiological in liver-genesis hyperbilirubinemia. In case of hyperbilirubinemia due to intrahepatic or extrahepatic bile ducts blockage, e.g. gallstone, the name is given as Post-hepatic (or obstructive) jaundice.
Bilirubin concentration is not a sensitive early indicator of liver diseases as the liver may have reserved its capacity in removal of bilirubin to save energy and unreserved the previously reserved capacity when encountering a sudden rise of unconjugated bilirubin. In short, there is still a chance for an ill liver to get rid of excessive unconjugated bilirubin in the blood plasma, displaying a total bilirubin level that is within normal reference range. | 1 | Biochemistry |
Ethylene signaling pathway is a signal transduction in plant cells to regulate important growth and developmental processes. Acting as a plant hormone, the gas ethylene is responsible for promoting the germination of seeds, ripening of fruits, the opening of flowers, the abscission (or shedding) of leaves and stress responses. It is the simplest alkene gas and the first gaseous molecule discovered to function as a hormone.
Most of the understanding on ethylene signal transduction come from studies on Arabidopsis thaliana. Ethylene can bind to at least five different membrane receptors. Although structurally diverse, the ethylene receptors all exhibit similarity (homology) to two-component regulatory system in bacteria, indicating their common ancestry from bacterial ancestor. Ethylene binds to the receptors on the cell membrane of the endoplasmic reticulum. Although homodimers of the receptors are required for functional state, only one ethylene molecule binds to each dimer.
Unlike in other signal transductions, ethylene is the suppressor of its receptor activity. Ethylene receptors are active without ethylene due to binding with other enzymatically active co-receptors such as constitutive triple response 1 (CTR1) and ethylene insensitive 2 (EIN2). Ethylene binding causes EIN2 to split in two, of which the C-terminal portion of the protein can activate different transcription factors to bring about the effects of ethylene. There is also non-canonical pathway in which ethylene activates cytokinin receptor, and thereby regulate seed development (stomatal aperture) and growth of root (the apical meristem). | 1 | Biochemistry |
Lipids (oleaginous) are chiefly fatty acid esters, and are the basic building blocks of biological membranes. Another biological role is energy storage (e.g., triglycerides). Most lipids consist of a polar or hydrophilic head (typically glycerol) and one to three non polar or hydrophobic fatty acid tails, and therefore they are amphiphilic. Fatty acids consist of unbranched chains of carbon atoms that are connected by single bonds alone (saturated fatty acids) or by both single and double bonds (unsaturated fatty acids). The chains are usually 14-24 carbon groups long, but it is always an even number.
For lipids present in biological membranes, the hydrophilic head is from one of three classes:
* Glycolipids, whose heads contain an oligosaccharide with 1-15 saccharide residues.
* Phospholipids, whose heads contain a positively charged group that is linked to the tail by a negatively charged phosphate group.
* Sterols, whose heads contain a planar steroid ring, for example, cholesterol.
Other lipids include prostaglandins and leukotrienes which are both 20-carbon fatty acyl units synthesized from arachidonic acid.
They are also known as fatty acids | 0 | Organic Chemistry |
The Kalium Database is a manually curated biomedical database on K channel ligands found in the venom of scorpions, spiders, sea anemones, cone snails, snakes, centipedes, bees, and more. The first release of the Kalium Database was dedicated to scorpion toxins only, while its second release (Kalium 2.0) included toxins from other living organisms. The most recent update (Kalium 3.0) added information on their artificial derivatives. The Kalium Database is meant to assist structural biologists, toxinologists, pharmacologists, medicinal chemists, and other researchers in their pursuit to develop new drugs for cardiovascular and neurological diseases. | 1 | Biochemistry |
Because it has just one valence state (Zn), zinc is a redox-inert element. The electronic configurations of Zn and Zn are shown below: | 9 | Geochemistry |
Gating also includes activation and inactivation by second messengers from the inside of the cell membrane – rather than from outside the cell, as in the case for ligands.
*Some potassium channels:
**Inward-rectifier potassium channels: These channels allow potassium ions to flow into the cell in an "inwardly rectifying" manner: potassium flows more efficiently into than out of the cell. This family is composed of 15 official and 1 unofficial member and is further subdivided into 7 subfamilies based on homology. These channels are affected by intracellular ATP, PIP, and G-protein βγ subunits. They are involved in important physiological processes such as pacemaker activity in the heart, insulin release, and potassium uptake in glial cells. They contain only two transmembrane segments, corresponding to the core pore-forming segments of the K and K channels. Their α subunits form tetramers.
**Calcium-activated potassium channels: This family of channels is activated by intracellular Ca and contains 8 members.
**Tandem pore domain potassium channel: This family of 15 members form what are known as leak channels, and they display Goldman-Hodgkin-Katz (open) rectification. Contrary to their common name of Two-pore-domain potassium channels, these channels have only one pore but two pore domains per subunit.
*Two-pore channels include ligand-gated and voltage-gated cation channels, so-named because they contain two pore-forming subunits. As their name suggests, they have two pores.
*Light-gated channels like channelrhodopsin are directly opened by photons.
*Mechanosensitive ion channels open under the influence of stretch, pressure, shear, and displacement.
*Cyclic nucleotide-gated channels: This superfamily of channels contains two families: the cyclic nucleotide-gated (CNG) channels and the hyperpolarization-activated, cyclic nucleotide-gated (HCN) channels. This grouping is functional rather than evolutionary.
**Cyclic nucleotide-gated channels: This family of channels is characterized by activation by either intracellular cAMP or cGMP. These channels are primarily permeable to monovalent cations such as K and Na. They are also permeable to Ca, though it acts to close them. There are 6 members of this family, which is divided into 2 subfamilies.
**Hyperpolarization-activated cyclic nucleotide-gated channels
*Temperature-gated channels: Members of the transient receptor potential ion channel superfamily, such as TRPV1 or TRPM8, are opened either by hot or cold temperatures. | 1 | Biochemistry |
Due to herbicide resistance – a major concern in agriculture – a number of products combine herbicides with different means of action. Integrated pest management may use herbicides alongside other pest control methods.
Integrated weed management (IWM) approach utilizes several tactics to combat weeds and forestall resistance. This approach relies less on herbicides and so selection pressure should be reduced. By relying on diverse weed control methods, including non-herbicide methods of weed control, the selection pressure on weeds to evolve resistance can be lowered. Researchers warn that if herbicide resistance is combatted only with more herbicides, "evolution will most likely win." In 2017, the USEPA issued a revised Pesticide Registration Notice (PRN 2017-1), which provides guidance to pesticide registrants on required pesticide resistance management labeling. This requirement applies to all conventional pesticides and is meant to provide end-users with guidance on managing pesticide resistance. An example of a fully executed label compliant with the USEPA resistance management labeling guidance can be seen on the specimen label for the herbicide, cloransulam-methyl, updated in 2022.
Optimising herbicide input to the economic threshold level should avoid the unnecessary use of herbicides and reduce selection pressure. Herbicides should be used to their greatest potential by ensuring that the timing, dose, application method, soil and climatic conditions are optimal for good activity. In the UK, partially resistant grass weeds such as Alopecurus myosuroides (blackgrass) and Avena genus (wild oat) can often be controlled adequately when herbicides are applied at the 2-3 leaf stage, whereas later applications at the 2-3 tiller stage can fail badly. Patch spraying, or applying herbicide to only the badly infested areas of fields, is another means of reducing total herbicide use. | 2 | Environmental Chemistry |
The term tephrochronology appears to have been used by Sigurdur Thórarinsson as early as 1944. A key point in the establishment of this scientific field of study with what evolved to be a unique geoscientific method was in 1961 after a proposal supported by him led by Japanese researchers including Professor Kunio Kobayashi resulted in the establishment of an international scientific group. Much work had preceded this, but was limited by the techniques available at the time in geology. This had resulted in tephra formations not being linked and inaccurate timings that could not be related to events say with worldwide traces.
What would now be known as cryptotephra studies occurred in sea floor samples in the 1940s but Christer Persson in Scandinavia, was the first to publish articles in this field in the 1960s. Andrew Dugmore in 1989 was the first to use modern systematic methodology. Since then researchers have targeted stratigraphic archives of peat, lake sediment, ice cores, marine sediments, loess, floors of caves and rock shelters or stalagmites as well as contemporary eruption deposits.
Early tephra horizons were identified with the Saksunarvatn tephra (Icelandic origin, cal. ka BP), forming a horizon in the late Pre-Boreal of Northern Europe, the Vedde ash (also Icelandic in origin, c. 12.0 cal. ka BP) and the Laacher See tephra (in the Eifel volcanic field, c. 12.9 cal. ka BP). Major volcanoes which have been used in tephrochronological studies include Vesuvius, Hekla and Santorini. Minor volcanic events may also leave their fingerprint in the geological record: Hayes Volcano is responsible for a series of six major tephra layers in the Cook Inlet region of Alaska. Tephra horizons provide a synchronous check against which to correlate the palaeoclimatic reconstructions that are obtained from terrestrial records, like fossil pollen studies (palynology), from varves in lake sediments or from marine deposits and ice-core records, and to extend the limits of carbon-14 dating.
A pioneer in the use of tephra layers as marker horizons to establish chronology was Sigurdur Thorarinsson, who began by studying the layers he found in his native Iceland. Since the late 1990s, techniques developed by Chris S. M. Turney (QUB, Belfast; now University of Exeter) and others for extracting tephra horizons invisible to the naked eye ("cryptotephra") have revolutionised the application of tephrochronology. This technique relies upon the difference between the specific gravity of the microtephra shards and the host sediment matrix. It has led to the first discovery of the Vedde ash on the mainland of Britain, in Sweden, in the Netherlands, in the Swiss Lake Soppensee and in two sites on the Karelian Isthmus of Baltic Russia.
It has also revealed previously undetected ash layers, such as the Borrobol Tephra first discovered in northern Scotland, dated to c. 14.4 cal. ka BP, the microtephra horizons of equivalent geochemistry from southern Sweden, dated at 13,900 Cariaco varve yrs BP and from northwest Scotland, dated at 13.6 cal. ka BP.
Since 2010 Bayesian age modelling built around ever-improving 14C-calibration curves and other age-related data,such as zircon double dating continues to better define tephrochronology. | 9 | Geochemistry |
Also known as the two-site Langmuir equation. This equation describes the adsorption of one adsorbate to two or more distinct types of adsorption sites. Each binding site can be described with its own Langmuir expression, as long as the adsorption at each binding site type is independent from the rest.
where
: – total amount adsorbed at a given adsorbate concentration,
: – maximum capacity of site type 1,
: – maximum capacity of site type 2,
: – equilibrium (affinity) constant of site type 1,
: – equilibrium (affinity) constant of site type 2,
: – adsorbate activity in solution at equilibrium
This equation works well for adsorption of some drug molecules to activated carbon in which some adsorbate molecules interact with hydrogen bonding while others interact with a different part of the surface by hydrophobic interactions (hydrophobic effect). The equation was modified to account for the hydrophobic effect (also known as entropy-driven adsorption):
The hydrophobic effect is independent of concentration, since Therefore, the capacity of the adsorbent for hydrophobic interactions can obtained from fitting to experimental data. The entropy-driven adsorption originates from the restriction of translational motion of bulk water molecules by the adsorbate, which is alleviated upon adsorption. | 7 | Physical Chemistry |
A spiropyran is a 2H-pyran isomer that has the hydrogen atom at position two replaced by a second ring system linked to the carbon atom at position two of the pyran molecule in a spiro way. So there is a carbon atom which is common on both rings, the pyran ring and the replaced ring. The second ring, the replaced one, is usually heterocyclic but there are exceptions.
When the spiropyran is in a solution with polar solvents or when it receives heating (thermochromism) or radiation (photochromism) it becomes coloured because its structure has changed and it has been transformed into the merocyanine form.
The structural differences between spiropyran and merocyanine form is that, while in the first one the ring is in the closed form, in the other one the ring is opened. The photochromism is due to electrocyclic cleavage of the C-spiro-O bond with photoexcitation. | 5 | Photochemistry |
*[https://photoiupac2022.amsterdam IUPAC SYmposium on Photochemistry] (biennial)
*[https://icp2023.jp International Conference on Photochemitry] (biennial)
The organization of these conferences is facilitated by the International Foundation for Photochemistry. | 5 | Photochemistry |
Wnt signaling and β-catenin dependent gene expression plays a critical role during the formation of different body regions in the early embryo. Experimentally modified embryos that do not express this protein will fail to develop mesoderm and initiate gastrulation.
Early embryos endomesoderm specification also involves the activation of the β-catenin dependent transcripional activity by the first morphogenetic movements of embryogenesis, though mechanotransduction processes. This feature being shared by vertebrate and arthropod bilateria, and by cnidaria, it was proposed to have been evolutionary inherited from its possible involvement in the endomesoderm specification of first metazoa.
During the blastula and gastrula stages, Wnt as well as BMP and FGF pathways will induce the antero-posterior axis formation, regulate the precise placement of the primitive streak (gastrulation and mesoderm formation) as well as the process of neurulation (central nervous system development).
In Xenopus oocytes, β-catenin is initially equally localized to all regions of the egg, but it is targeted for ubiquitination and degradation by the β-catenin destruction complex. Fertilization of the egg causes a rotation of the outer cortical layers, moving clusters of the Frizzled and Dsh proteins closer to the equatorial region. β-catenin will be enriched locally under the influence of Wnt signaling pathway in the cells that inherit this portion of the cytoplasm. It will eventually translocate to the nucleus to bind TCF3 in order to activate several genes that induce dorsal cell characteristics. This signaling results in a region of cells known as the grey crescent, which is a classical organizer of embryonic development. If this region is surgically removed from the embryo, gastrulation does not occur at all. β-Catenin also plays a crucial role in the induction of the blastopore lip, which in turn initiates gastrulation. Inhibition of GSK-3 translation by injection of antisense mRNA may cause a second blastopore and a superfluous body axis to form. A similar effect can result from the overexpression of β-catenin. | 1 | Biochemistry |
Methyl isocyanate reacts readily with many substances that contain N-H or O-H groups. With water, it forms 1,3-dimethylurea and carbon dioxide with the evolution of heat (1358.5 joules, or 325 calories, per gram of MIC): It is relatively slow to react at below 68 °F, but will increase its rate with elevated temperatures or in the presence of acid or base.
At 25 °C, in excess water, half of the MIC is consumed in 9 min.; if the heat is not efficiently removed from the reacting mixture, the rate of the reaction will increase and rapidly cause the MIC to boil. Such a reaction triggered the Bhopal disaster after a large amount of water was introduced to a MIC storage tank. The consequence of the out of control exothermic process was a runaway reaction and the direct release of 42 tons of MIC to the atmosphere.
If MIC is in excess, 1,3,5-trimethylbiuret is formed along with carbon dioxide. Alcohols and phenols, which contain an O-H group, react slowly with MIC, but the reaction can be catalyzed by trialkylamines or dialkyltin dicarboxylate. Oximes, hydroxylamines, and enols also react with MIC to form methylcarbamates. These reactions produce the products described below (Uses).
Ammonia, primary, and secondary amines rapidly react with MIC to form substituted ureas. Other N-H compounds, such as amides and ureas, react much more slowly with MIC.
It also reacts with itself to form a trimer or higher-molecular-weight polymers. In the presence of catalysts, MIC reacts with itself to form a solid trimer, trimethyl isocyanurate, or a higher-molecular-weight polymer:
Sodium methoxide, triethyl phosphine, ferric chloride and certain other metal compounds catalyze the formation of the MIC-trimer, while the high-molecular-weight polymer formation is catalyzed by certain trialkylamines. Since the formation of the MIC trimer is exothermic (1246 joules, or 298 calories, per gram of MIC), the reaction can lead to violent boiling of the MIC. The high-molecular-weight polymer hydrolyzes in hot water to form the trimethyl isocyanurate. Since catalytic metal salts can be formed from impurities in commercial grade MIC and steel, this product must not be stored in steel drums or tanks. | 9 | Geochemistry |
For an ideal gas the equation of state can be written as
where is the ideal gas constant. The differential change of the chemical potential between two states of slightly different pressures but equal temperature (i.e., ) is given by
where ln p is the natural logarithm of p.
For real gases the equation of state will depart from the simpler one, and the result above derived for an ideal gas will only be a good approximation provided that (a) the typical size of the molecule is negligible compared to the average distance between the individual molecules, and (b)
the short range behavior of the inter-molecular potential can be neglected, i.e., when the molecules can be considered to rebound elastically off each other during molecular collisions. In other words, real gases behave like ideal gases at low pressures and high temperatures. At moderately high pressures, attractive interactions between molecules reduce the pressure compared to the ideal gas law; and at very high pressures, the sizes of the molecules are no longer negligible and repulsive forces between molecules increases the pressure. At low temperatures, molecules are more likely to stick together instead of rebounding elastically.
The ideal gas law can still be used to describe the behavior of a real gas if the pressure is replaced by a fugacity , defined so that
and
That is, at low pressures is the same as the pressure, so it has the same units as pressure. The ratio
is called the fugacity coefficient.
If a reference state is denoted by a zero superscript, then integrating the equation for the chemical potential gives
Note this can also be expressed with , a dimensionless quantity, called the activity.
Numerical example: Nitrogen gas (N) at 0 °C and a pressure of atmospheres (atm) has a fugacity of atm. This means that the molar Gibbs energy of real nitrogen at a pressure of 100 atm is equal to the molar Gibbs energy of nitrogen as an ideal gas at . The fugacity coefficient is .
The contribution of nonideality to the molar Gibbs energy of a real gas is equal to . For nitrogen at 100 atm, , which is less than the ideal value because of intermolecular attractive forces. Finally, the activity is just without units. | 7 | Physical Chemistry |
Radical reactions must be carried out under inert atmosphere as dioxygen is a triplet radical which will intercept radical intermediates. Because the relative rates of a number of processes are important to the reaction, concentrations must be carefully adjusted to optimize reaction conditions. Reactions are generally carried out in solvents whose bonds have high bond dissociation energies (BDEs), including benzene, methanol or benzotrifluoride. Even aqueous conditions are tolerated, since water has a strong O-H bond with a BDE of 494 kJ/mol. This is in contrast to many polar processes, where hydroxylic solvents (or polar X-H bonds in the substrate itself) may not be tolerated due to the nucleophilicity or acidity of the functional group. | 0 | Organic Chemistry |
Generally, there are two types of protein carbohydrate binding important in biological processes: Lectin and antibody. | 0 | Organic Chemistry |
In plasma physics, the degree of ionization refers to the proportion of neutral particles that are ionized:
where is the ion density and the neutral density (in particles per cubic meter). It is a dimensionless number, sometimes expressed as a percentage.
The terms fractional ionization and ionization fraction are also used to describe either the proportion of neutral particles that are ionized or the proportion of free electrons.
When referred to an atom, "fully ionized" means that there are no bound electrons left, resulting in a bare nucleus.
A particular case of fully ionized gases are very hot thermonuclear plasmas, such as plasmas artificially produced in nuclear explosions or naturally formed in the Sun and all stars in the universe. Regular stars largely contain hydrogen and helium that are fully ionized into protons (H) and alpha-particles (He). | 7 | Physical Chemistry |
Degradation can be detected before serious cracks are seen in a product by using infrared spectroscopy, which is able to detect chemical species formed by photo-oxidation. In particular, peroxy-species and carbonyl groups have distinct absorption bands.
In the example shown at left, carbonyl groups were easily detected by IR spectroscopy from a cast thin film. The product was a road cone made by rotational moulding in LDPE, which had cracked prematurely in service. Many similar cones also failed because an anti-UV additive had not been used during processing. Other plastic products which failed included polypropylene mancabs used at roadworks which cracked after service of only a few months.
The effects of degradation can also be characterized through scanning electron microscopy (SEM). For example, through SEM, defects like cracks and pits can be directly visualized, as shown at right. These samples were exposed to 840 hours of exposure to UV light and moisture using a test chamber. Crack formation is often associated with degradation, such that materials that do not display significant cracking behavior, such as HDPE in the right example, are more likely to be stable against photooxidation compared to other materials like LDPE and PP. However, some plastics that have undergone photooxidation may also appear smoother in an SEM image, with some defects like grooves having disappeared afterwards. This is seen in polystyrene in the right example. | 5 | Photochemistry |
N mers form the polymer, whose total unfolded length is:
where N is the number of mers.
In this very simple approach where no interactions between mers are considered, the energy of the polymer is taken to be independent of its shape, which means that at thermodynamic equilibrium, all of its shape configurations are equally likely to occur as the polymer fluctuates in time, according to the Maxwell–Boltzmann distribution.
Let us call the total end to end vector of an ideal chain and the vectors corresponding to individual mers. Those random vectors have components in the three directions of space. Most of the expressions given in this article assume that the number of mers N is large, so that the central limit theorem applies. The figure below shows a sketch of a (short) ideal chain.
The two ends of the chain are not coincident, but they fluctuate around each other, so that of course:
Throughout the article the brackets will be used to denote the mean (of values taken over time) of a random variable or a random vector, as above.
Since are independent, it follows from the Central limit theorem that is distributed according to a normal distribution (or gaussian distribution): precisely, in 3D, and are distributed according to a normal distribution of mean 0 and of variance:
So that . The end to end vector of the chain is distributed according to the following probability density function:
The average end-to-end distance of the polymer is:
A quantity frequently used in polymer physics is the radius of gyration:
It is worth noting that the above average end-to-end distance, which in the case of this simple model is also the typical amplitude of the system's fluctuations, becomes negligible compared to the total unfolded length of the polymer at the thermodynamic limit. This result is a general property of statistical systems.
Mathematical remark: the rigorous demonstration of the expression of the density of probability is not as direct as it appears above: from the application of the usual (1D) central limit theorem one can deduce that , and are distributed according to a centered normal distribution of variance . Then, the expression given above for is not the only one that is compatible with such distribution for , and . However, since the components of the vectors are uncorrelated for the random walk we are considering, it follows that , and are also uncorrelated. This additional condition can only be fulfilled if is distributed according to . Alternatively, this result can also be demonstrated by applying a multidimensional generalization of the central limit theorem, or through symmetry arguments. | 7 | Physical Chemistry |
The Nicolaou Taxol total synthesis, published by K. C. Nicolaou and his group in 1994 concerns the total synthesis of taxol. Taxol is an important drug in the treatment of cancer but also expensive because the compound is harvested from a scarce resource, namely the pacific yew.
This synthetic route to taxol is one of several; other groups have presented their own solutions, notably the group of Holton with a linear synthesis starting from borneol, the Samuel Danishefsky group starting from the Wieland-Miescher ketone and the Wender group from pinene.
The Nicolaou synthesis is an example of convergent synthesis because the molecule is assembled from three pre-assembled synthons. Two major parts are cyclohexene rings A and C that are connected by two short bridges creating an 8 membered ring in the middle (ring B). The third pre-assembled part is an amide tail. Ring
D is an oxetane ring fused to ring C. Two key chemical transformations are the Shapiro reaction and the pinacol coupling reaction.
The overall synthesis was published in 1995 in a series of four papers. | 0 | Organic Chemistry |
The coffee-ring pattern originates from the capillary flow induced by the evaporation of the drop: liquid evaporating from the edge is replenished by liquid from the interior. The resulting current can carry nearly all the dispersed material to the edge. As a function of time, this process exhibits a "rush-hour" effect, that is, a rapid acceleration of the flow towards the edge at the final stage of the drying process.
Evaporation induces a Marangoni flow inside a droplet. The flow, if strong, redistributes particles back to the center of the droplet. Thus, for particles to accumulate at the edges, the liquid must have a weak Marangoni flow, or something must occur to disrupt the flow. For example, surfactants can be added to reduce the liquid's surface tension gradient, disrupting the induced flow. Water has a weak Marangoni flow to begin with, which is then reduced significantly by natural surfactants.
Interaction of the particles suspended in a droplet with the free surface of the droplet is important in creating a coffee ring. "When the drop evaporates, the free surface collapses and traps the suspended particles ... eventually all the particles are captured by the free surface and stay there for the rest of their trip towards the edge of the drop." This result means that surfactants can be used to manipulate the motion of the solute particles by changing the surface tension of the drop, rather than trying to control the bulk flow inside the drop. A number of interesting morphologies of the deposited particles can result. For example, an enantiopure poly (isocyanate) derivative has been shown to form ordered arrays of squashed donut structures. | 7 | Physical Chemistry |
* Acid value
* Bromine number
* Amine value
* Epoxy value
* Iodine value
* Peroxide value
* Saponification value | 3 | Analytical Chemistry |
Under normal conditions, small disk-shape platelets circulate in the blood freely and without interaction with one another. ADP is stored in dense bodies inside blood platelets and is released upon platelet activation. ADP interacts with a family of ADP receptors found on platelets (P2Y1, P2Y12, and P2X1), which leads to platelet activation.
* P2Y1 receptors initiate platelet aggregation and shape change as a result of interactions with ADP.
* P2Y12 receptors further amplify the response to ADP and draw forth the completion of aggregation.
ADP in the blood is converted to adenosine by the action of ecto-ADPases, inhibiting further platelet activation via adenosine receptors. | 1 | Biochemistry |
The operation of a detonation gun is a very loud process due to the multiple explosions occurring in the chamber per second. This could cause damage to operators hearing if in close proximity to the D-gun. As a result, detonation spraying should be performed within a sound proof room and no one should be present in the room during operation. Also operators should wear ear protection (such as ear muffs and/or ear plugs) while working with a D-gun. | 8 | Metallurgy |
Miyata's distance is based on 2 physicochemical properties: volume and polarity.
Distance between amino acids a and a is calculated as where is value of polarity difference between replaced amino acids and and is difference for volume; and are standard deviations for and | 1 | Biochemistry |
Sulfur concrete, sometimes named thioconcrete or sulfurcrete, is a composite construction material, composed mainly of sulfur and aggregate (generally a coarse aggregate made of gravel or crushed rocks and a fine aggregate such as sand). Cement and water, important compounds in normal concrete, are not part of sulfur concrete. The concrete is heated above the melting point of elemental sulfur () at ca. in a ratio of between 12% and 25% sulfur, the rest being aggregate.
Low-volatility (i.e., with a high boiling point) organic admixtures (sulfur modifiers), such as dicyclopentadiene (DCPD), styrene, turpentine, or furfural, are also added to the molten sulfur to inhibit its crystallization and to stabilize its polymeric structure after solidification.
In the absence of modifying agents, elemental sulfur crystallizes in its most stable allotropic (polymorphic) crystal phase at room temperature. With the addition of some modifying agents, elemental sulfur forms a copolymer (linear chains with styrene, cross-linking structure with DCPD) and remains plastic.
Sulfur concrete then achieves high mechanical strength within of cooling. It does not require a prolonged curing period like conventional cement concrete, which after setting (a few hours) must still harden to reach its expected nominal strength at 28 days. The rate of hardening of sulfur concrete depends on its cooling rate and also on the nature and concentration of modifying agents (cross-linking process). Its hardening is governed by the fairly rapid liquid/solid state change and associated phase transition processes (the added modifiers maintaining the plastic state while avoiding its recrystallization). It is a thermoplastic material whose physical state depends on temperature. It can be recycled and reshaped in a reversible way, simply by remelting it at high temperature.
A sulfur concrete patent was already registered in 1900 by McKay. Sulfur concrete was studied in the 1920s and 1930s and received renewed interest in the 1970s because of the accumulation of large quantities of sulfur as a by-product of the hydrodesulfurization process of oil and gas production and its low cost. | 8 | Metallurgy |
The full ecological consequences of the changes in calcification due to ocean acidification are complex but it appears likely that many calcifying species will be adversely affected by ocean acidification. Increasing ocean acidification makes it more difficult for shell-accreting organisms to access carbonate ions, essential for the production of their hard exoskeletal shell. Oceanic calcifying organism span the food chain from autotrophs to heterotrophs and include organisms such as coccolithophores, corals, foraminifera, echinoderms, crustaceans and molluscs.
Overall, all marine ecosystems on Earth will be exposed to changes in acidification and several other ocean biogeochemical changes. Ocean acidification may force some organisms to reallocate resources away from productive endpoints in order to maintain calcification. For example, the oyster Magallana gigas is recognized to experience metabolic changes alongside altered calcification rates due to energetic tradeoffs resulting from pH imbalances.
Under normal conditions, calcite and aragonite are stable in surface waters since the carbonate ions are supersaturated with respect to seawater. However, as ocean pH falls, the concentration of carbonate ions also decreases. Calcium carbonate thus becomes undersaturated, and structures made of calcium carbonate are vulnerable to calcification stress and dissolution. In particular, studies show that corals, coccolithophores, coralline algae, foraminifera, shellfish and pteropods experience reduced calcification or enhanced dissolution when exposed to elevated . Even with active marine conservation practices it may be impossible to bring back many previous shellfish populations.
Some studies have found different responses to ocean acidification, with coccolithophore calcification and photosynthesis both increasing under elevated atmospheric p, and an equal decline in primary production and calcification in response to elevated , or the direction of the response varying between species.
Similarly, the sea star, Pisaster ochraceus, shows enhanced growth in waters with increased acidity.
Reduced calcification from ocean acidification may affect the ocean's biologically driven sequestration of carbon from the atmosphere to the ocean interior and seafloor sediment, weakening the so-called biological pump. Seawater acidification could also reduce the size of Antarctic phytoplankton, making them less effective at storing carbon. Such changes are being increasingly studied and synthesized through the use of physiological frameworks, including the Adverse Outcome Pathway (AOP) framework. | 9 | Geochemistry |
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