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Oxidation states can be useful for balancing chemical equations for oxidation-reduction (or redox) reactions, because the changes in the oxidized atoms have to be balanced by the changes in the reduced atoms. For example, in the reaction of acetaldehyde with Tollens' reagent to form acetic acid (shown below), the carbonyl carbon atom changes its oxidation state from +1 to +3 (loses two electrons). This oxidation is balanced by reducing two cations to (gaining two electrons in total).
An inorganic example is the Bettendorf reaction using tin dichloride () to prove the presence of arsenite ions in a concentrated HCl extract. When arsenic(III) is present, a brown coloration appears forming a dark precipitate of arsenic, according to the following simplified reaction:
Here three tin atoms are oxidized from oxidation state +2 to +4, yielding six electrons that reduce two arsenic atoms from oxidation state +3 to 0. The simple one-line balancing goes as follows: the two redox couples are written down as they react;
One tin is oxidized from oxidation state +2 to +4, a two-electron step, hence 2 is written in front of the two arsenic partners. One arsenic is reduced from +3 to 0, a three-electron step, hence 3 goes in front of the two tin partners. An alternative three-line procedure is to write separately the half-reactions for oxidation and reduction, each balanced with electrons, and then to sum them up such that the electrons cross out. In general, these redox balances (the one-line balance or each half-reaction) need to be checked for the ionic and electron charge sums on both sides of the equation being indeed equal. If they are not equal, suitable ions are added to balance the charges and the non-redox elemental balance. | 0 | Theoretical and Fundamental Chemistry |
Pattern formation is when a solution containing NaOH, glucose, and dye is poured into a Petri dish that is open to the atmosphere. This will result in solution changing its structure over a period of time. Structures arise from molecular transport through diffusion and chemical kinetics. Patterns formed in the Petri dish can be described as a mosaic pattern; web-like, dynamic spiral, branching, and lines connecting to each others.
Changes in pattern formation are not homogeneous and can be affected by several factors. Different types of dye in solution will give the same pattern because of the bond's formation and the dynamics remain the same, this is because the solution has the same colour as the dye. Different amounts of dye can result in density change in the solution and this results in changing of convective motion. Different amounts of dye can bring in different amounts of convention cells which are also formed by different amounts of glucose and oxidized product. This can result in an interesting spatial phenomena. Time can also affect pattern formation. As the time passed, one pattern gradually faded away. Spirals and branches started to disappear and eventually disappeared fully. These facts indicate that oxygen affects the chemical reaction and this plays a fundamental role in the pattern formation. Pattern formation may also form from a chemically driven convective instability. This means that matter is exchanged across the air-reaction mixture interface, due to the fluctuations in the molecular nature of chemical systems. The temperature can affect the formation of pattern. Colder temperature formed a clearer pattern than hot temperature. The shape of the Petri dish also contributed to the pattern formation.
A group of researchers of the University of Glasgow named Pons, Batiste and Bees came up with a small conclusion about pattern formation in the methylene blue-glucose system. They came up with a conclusive statement that a similar pattern can be formed in a container with accessible oxygen. This resulting surface tension effect isnt required to produce the instability. Small holes were also found in the lid of container that oxygen cant access resulting in a thin, blue, and lower amount of oxygen. Pattern length and time scale had been explored in one of their experiments due to the variation in viscosity and fluid depth. The experiment reveals that the wavelength is formed as a pattern starts to form quickly. Then wavelength or pattern can be maintained or oscillate for a while. | 1 | Applied and Interdisciplinary Chemistry |
The data is weighted and integrated and a confidence score is calculated for all protein interactions. Results of the various computational predictions can be inspected from different designated views. There are two modes of STRING: Protein-mode and [https://www.ncbi.nlm.nih.gov/COG/ COG]-mode. Predicted interactions are propagated to proteins in other organisms for which interaction has been described by inference of orthology. A web interface is available to access the data and to give a fast overview of the proteins and their interactions. A plug-in for cytoscape to use STRING data is available.
Another possibility to access data STRING is to use the application programming interface (API) by constructing a URL that contain the request. | 1 | Applied and Interdisciplinary Chemistry |
In 1968, a mixture of dioxins and PCBs got into rice bran oil produced in northern Kyushu. Contaminated cooking oil sickened more than 1,860 people. The symptoms were called Yushō disease.
In Okinawa, high levels of PCB contamination in soil on Kadena Air Base were reported in 1987 at thousands of parts per million, some of the highest levels found in any pollution site in the world. | 1 | Applied and Interdisciplinary Chemistry |
Bromochlorodifluoromethane (BCF), also referred to by the code numbers Halon 1211 and Freon 12B1, is a haloalkane with the chemical formula CFClBr. It is used for fire suppression, especially for expensive equipment or items that could be damaged by the residue from other types of extinguishers. It is stored as a liquid under pressure and vaporizes when discharged to suppress fires.
The use of halons, including Halon 1211, has decreased over time due to their adverse impact on the ozone layer. Alternatives have been developed to mitigate environmental concerns while still providing effective fire suppression capabilities. | 1 | Applied and Interdisciplinary Chemistry |
Oxacillin, through its β-lactam ring, covalently binds to penicillin-binding proteins, which are enzymes involved in the synthesis of the bacterial cell wall. This binding interaction interferes with the transpeptidation reaction and inhibits the synthesis of peptidoglycan, a prominent component of the cell wall. By decreasing the integrity of the bacterial cell wall, it is thought that oxacillin and other penicillins kill actively growing bacteria through cell autolysis. | 0 | Theoretical and Fundamental Chemistry |
LDH is also regulated by the relative concentrations of its substrates. LDH becomes more active under periods of extreme muscular output due to an increase in substrates for the LDH reaction. When skeletal muscles are pushed to produce high levels of power, the demand for ATP in regards to aerobic ATP supply leads to an accumulation of free ADP, AMP, and Pi. The subsequent glycolytic flux, specifically production of pyruvate, exceeds the capacity for pyruvate dehydrogenase and other shuttle enzymes to metabolize pyruvate. The flux through LDH increases in response to increased levels of pyruvate and NADH to metabolize pyruvate into lactate. | 1 | Applied and Interdisciplinary Chemistry |
For the general case of any number of consecutive decays in a decay chain, i.e. , where is the number of decays and is a dummy index (), each nuclide population can be found in terms of the previous population. In this case , , ..., . Using the above result in a recursive form:
The general solution to the recursive problem is given by Bateman's equations: | 0 | Theoretical and Fundamental Chemistry |
Estimates of lake metabolism typically rely on the measurement of dissolved oxygen or carbon dioxide, or measurements of a carbon or oxygen tracer to estimate production and consumption of organic carbon. Oxygen is produced and carbon dioxide consumed through photosynthesis and oxygen is consumed and carbon dioxide produced through respiration. Here, organic matter is symbolized by glucose, though the chemical species produced and respired through these reactions vary widely.
Photosynthesis:
Respiration:
Photosynthesis and oxygen production only occurs in the presence of light, while the consumption of oxygen via respiration occurs in both the presence and absence of light. Lake metabolism terms include:
* GPP - gross primary production (e.g. total photosynthesis)
* R - total respiration
* - heterotrophic respiration
* - autotrophic respiration
* NEP - net ecosystem production = GPP - R
* NPP - net primary production = GPP - | 1 | Applied and Interdisciplinary Chemistry |
Lanthanum oxide is most useful as a precursor to other lanthanum compounds. Neither the oxide nor any of the derived materials enjoys substantial commercial value, unlike some of the other lanthanides. Many reports describe efforts toward practical applications of , as described below.
forms glasses of high density, refractive index, and hardness. Together with oxides of tungsten, tantalum, and thorium, improves the resistance of the glass to attack by alkali. is an ingredient in some piezoelectric and thermoelectric materials.
has been examined for the oxidative coupling of methane. | 0 | Theoretical and Fundamental Chemistry |
The output beam is collected by a detector and its intensity is calculated using
where is the visible frequency, is the IR frequency and is the SFG frequency. The constant of proportionality varies across literature, many of them including the product of the square of the output frequency, and the squared secant of the reflection angle, . Other factors include index of refractions for the three beams.
The second order susceptibility has two contributions
where is the non-resonating contribution and is the resonating contribution. The non-resonating contribution is assumed to be from electronic responses. Although this contribution has often been considered to be constant over the spectrum, because it is generated simultaneously with the resonant response, the two responses must compete for intensity. This competition shapes the nonresonant contribution in the presence of resonant features by resonant attenuation. Because it is not currently known how to adequately correct for nonresonant interferences, it is very important to experimentally isolate the resonant contributions from any nonresonant interference, often done using the technique of nonresonant suppression.
The resonating contribution is from the vibrational modes and shows changes in resonance. It can be expressed as a sum of a series of Lorentz oscillators
where is the strength or amplitude, is the resonant frequency, is the damping or linewidth coefficient (FWHM), and each indexes the normal (resonant vibrational) mode. The amplitude is a product of , the induced dipole moment, and , the polarizability. Together, this indicates that the transition must be both IR and Raman active.
The above equations can be combined to form
which is used to model the SFG output over a range of wavenumbers. When the SFG system scans over a vibrational mode of the surface molecule, the output intensity is resonantly enhanced. In a graphical analysis of the output intensity versus wavenumber, this is represented by Lorentzian peaks. Depending on the system, inhomogeneous broadening and interference between peaks may occur. The Lorentz profile can be convoluted with a Gaussian intensity distribution to better fit the intensity distribution. | 0 | Theoretical and Fundamental Chemistry |
Computational methods have played a large role in understanding the nature of bonding in both molecular and solid-state systems displaying inverted ligand fields. The Hoffman group has completed many calculations to probe occurrence of inverted ligand fields in varying systems. In a study of the absorption of CO on PtBi and PtBi2 surfaces, on an octahedral [Pt(BiH)] model with a Pt thought of having a formal 4+ oxidation state, the team found that the t metal orbitals were higher energy that the e orbitals. This inversion of the d orbital ordering was attributed to the bismuth based ligands being higher in energy than the metal d orbitals. In another study involving calculations on Ag(III) salt KAgF, other Ag(II), and Ag(III) compounds, the Ag d orbitals were found to be below those of the fluoride ligand orbitals, and was confirmed by Grochala and cowrokers by core and valence spectroscopies.
The Mealli group developed the program Computer Aided Composition of Atomic Orbitals (CACAO) to provide visualised molecular orbitals analyses based on perturbation theory principles. This program successfully displayed orbital energy inversion with organometallic complexes containing electronegative metals such as Ni or Cu bound to electropositive ligand atoms such as B, Si, or Sn. In these cases the bonding was described as a ligand to metal dative bond or sigma backdonation.
Alvarez and coworkers used computational methods to illustrate ligand field inversion in the band structures of solid state materials. The group found that, contrary to the classical bonding scheme, in calculated MoNiP band structures the e-type orbitals of the octahedral nickel atom were found to be the major component of an occupied band below the t set. Additionally, the band around the fermi level which included the Ni antibonding orbitals were found to be mostly of phosphorus character, a clear example if an inverted ligand field. Similar observations were made in other solid state materials like the skutterudite CoP structure. A consequence of the inverted ligand field in this case is that the conductivity in skutterudites is associated with the phosphorus rings rather than the metal atoms. | 0 | Theoretical and Fundamental Chemistry |
Natural iron ores are mixtures of iron and unwanted impurities, or gangue. In ancient times, these impurities were removed by slagging. Slag was removed by liquation, that is, solid gangue was converted into a liquid slag. The temperature of the process was high enough for the slag to exist in its liquid form.
Smelting was conducted in various types of furnaces. Examples are the bloomery furnace and the blast furnace. The condition in the furnace determines the morphology, chemical composition and the microstructure of the slag.
The bloomery furnace produced iron in a solid state. This is because the bloomery process was conducted at a temperature lower than the melting point of iron metal. Carbon monoxide from the incomplete combustion of charcoal slowly diffused through the hot iron oxide ore, converting it to iron metal and carbon dioxide.
Blast furnaces were used to produce liquid iron. The blast furnace was operated at higher temperatures and at a greater reducing condition than the bloomery furnace. A greater reducing environment was achieved by increasing the fuel to ore ratio. More carbon reacted with the ore and produced a cast iron rather than solid iron. Also, the slag produced was less rich in iron.
A different process was used to make "tapped" slag. Here, only charcoal was added to the furnace. It reacted with oxygen, and generated carbon monoxide, which reduced the iron ore to iron metal. The liquefied slag separated from the ore, and was removed through the tapping arch of the furnace wall.
In addition, the flux (purifying agent), the charcoal ash and the furnace lining contributed to the composition of the slag.
Slag may also form during smithing and refining. The product of the bloomery process is heterogeneous blooms of entrapped slag. Smithing is necessary to cut up and remove the trapped slag by reheating, softening the slag and then squeezing it out. On the other hand, refining is needed for the cast iron produced in the blast furnace. By re-melting the cast iron in an open hearth, the carbon is oxidized and removed from the iron. Liquid slag is formed and removed in this process. | 1 | Applied and Interdisciplinary Chemistry |
Summer training and project work in industries such as Ranbaxy, Glaxo, Lupin, Sarabhai Chemicals, Piramal Enterprises, IPCA, Dr. Reddy's Lab., Kirloskar Brothers, Cyno Pharma, Parke-Davis, Bridgestone and national institutes such as National Institute of Immunology, New Delhi, NCL, Pune, NIPER, Chandigarh, CDRI, Lucknow, IICT, Hyderabad, NEERI, Nagpur, RRL, Bhopal, National Research Centre for Soybean, Indore, Indian Institute of Petroleum, Dehradun, Central Food Technological Research Institute, Mysore, CAT, Indore, Inter University Consortium, Indore Centre, DMRL, Hyderabad, IISc, Bangalore. | 1 | Applied and Interdisciplinary Chemistry |
The cofactors 4-thiouridine and thiamine are produced by the action of persulfides. Cystathionase generates the persulfide of cysteine (sometimes called thiocysteine) from cystine.
Persulfides have been invoked as intermediates in the biodegradation of carbon disulfide and mercaptopyruvate. | 0 | Theoretical and Fundamental Chemistry |
When most materials are electrically polarized, the polarization induced, P, is almost exactly proportional to the applied external electric field E; so the polarization is a linear function. This is called linear dielectric polarization (see figure). Some materials, known as paraelectric materials, show a more enhanced nonlinear polarization (see figure). The electric permittivity, corresponding to the slope of the polarization curve, is not constant as in linear dielectrics but is a function of the external electric field.
In addition to being nonlinear, ferroelectric materials demonstrate a spontaneous nonzero polarization (after entrainment, see figure) even when the applied field E is zero. The distinguishing feature of ferroelectrics is that the spontaneous polarization can be reversed by a suitably strong applied electric field in the opposite direction; the polarization is therefore dependent not only on the current electric field but also on its history, yielding a hysteresis loop. They are called ferroelectrics by analogy to ferromagnetic materials, which have spontaneous magnetization and exhibit similar hysteresis loops.
Typically, materials demonstrate ferroelectricity only below a certain phase transition temperature, called the Curie temperature (T) and are paraelectric above this temperature: the spontaneous polarization vanishes, and the ferroelectric crystal transforms into the paraelectric state. Many ferroelectrics lose their pyroelectric properties above T completely, because their paraelectric phase has a centrosymmetric crystal structure. | 0 | Theoretical and Fundamental Chemistry |
Above is a picture showing 3D cell culturing through magnetic levitation with the Bio-Assembler cell culturing system. The figure's letters refer to the following:
(A) A magnetic iron oxide nanoparticle assembly known as the "Nanoshuttle" is added and dispersed over cells, and the mixture is incubated.
(B) After incubation with Nanoshuttle, cells are detached and transferred to a petri dish.
(C) A magnetic drive is then placed on top of a petri dish top.
(D) The magnetic field causes cells to rise to the air–medium interface.
(E) Human umbilical vein endothelial cells (HUVEC) levitated for 60 minutes (left images) and 4 hours (right images) (Scale bar, 50 μm).
The onset of cell-cell interaction takes place as soon as cells levitate, and 3D structures start to form. At 1 hour, the cells are still relatively dispersed, but they are already showing some signs of stretching. Formation of 3D structures is visible after 4 hours of levitation (arrows). | 0 | Theoretical and Fundamental Chemistry |
On December 1, 2015, the Chemical Heritage Foundation merged with the Life Sciences Foundation, also founded by Arnold Thackray. Recognizing that the joint organization's interests extended beyond the field of chemistry, the organization began a two-year renaming process, whose outcome required the agreement of its founding partners, the American Chemical Society and the American Institute of Chemical Engineers. On February 1, 2018, the organization was renamed the Science History Institute, to reflect its wider range of historical interests, extending from the chemical sciences and engineering to the life sciences and biotechnology. | 1 | Applied and Interdisciplinary Chemistry |
In fluid mechanics and hydraulics, open-channel flow is a type of liquid flow within a conduit with a free surface, known as a channel. The other type of flow within a conduit is pipe flow. These two types of flow are similar in many ways but differ in one important respect: open-channel flow has a free surface, whereas pipe flow does not, resulting in flow dominated by gravity but not hydraulic pressure. | 1 | Applied and Interdisciplinary Chemistry |
The word "benzene" derives from "gum benzoin" (benzoin resin), an aromatic resin known since ancient times in Southeast Asia, and later to European pharmacists and perfumers in the 16th century via trade routes. An acidic material was derived from benzoin by sublimation, and named "flowers of benzoin", or benzoic acid. The hydrocarbon derived from benzoic acid thus acquired the name benzin, benzol, or benzene. Michael Faraday first isolated and identified benzene in 1825 from the oily residue derived from the production of illuminating gas, giving it the name bicarburet of hydrogen. In 1833, Eilhard Mitscherlich produced it by distilling benzoic acid (from gum benzoin) and lime. He gave the compound the name benzin. In 1836, the French chemist Auguste Laurent named the substance "phène"; this word has become the root of the English word "phenol", which is hydroxylated benzene, and "phenyl", the radical formed by abstraction of a hydrogen atom from benzene.
In 1845, Charles Blachford Mansfield, working under August Wilhelm von Hofmann, isolated benzene from coal tar. Four years later, Mansfield began the first industrial-scale production of benzene, based on the coal-tar method. Gradually, the sense developed among chemists that a number of substances were chemically related to benzene, comprising a diverse chemical family. In 1855, Hofmann was the first to apply the word "aromatic" to designate this family relationship, after a characteristic property of many of its members. In 1997, benzene was detected in deep space. | 1 | Applied and Interdisciplinary Chemistry |
"Sequencing by synthesis" involves taking a single strand of the DNA to be sequenced and then synthesizing its complementary strand enzymatically. The pyrosequencing method is based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step. The template DNA is immobile, and solutions of A, C, G, and T nucleotides are sequentially added and removed from the reaction. Light is produced only when the nucleotide solution complements the first unpaired base of the template. The sequence of solutions which produce chemiluminescent signals allows the determination of the sequence of the template.
For the solution-based version of pyrosequencing, the single-strand DNA (ssDNA) template is hybridized to a sequencing primer and incubated with the enzymes DNA polymerase, ATP sulfurylase, luciferase and apyrase, and with the substrates adenosine 5´ phosphosulfate (APS) and luciferin.
# The addition of one of the four deoxynucleotide triphosphates (dNTPs) (dATPαS, which is not a substrate for a luciferase, is added instead of dATP to avoid noise) initiates the second step. DNA polymerase incorporates the correct, complementary dNTPs onto the template. This incorporation releases pyrophosphate (PPi).
# ATP sulfurylase converts PPi to ATP in the presence of adenosine 5´ phosphosulfate. This ATP acts as a substrate for the luciferase-mediated conversion of luciferin to oxyluciferin that generates visible light in amounts that are proportional to the amount. The light produced in the luciferase-catalyzed reaction is detected by a camera and analyzed in a program.
# Unincorporated nucleotides and ATP are degraded by the apyrase, and the reaction can restart with another nucleotide.
The process can be represented by the following equations:
* PPi + APS → ATP + Sulfate (catalyzed by ATP-sulfurylase);
* ATP + luciferin + O2 → AMP + PPi + oxyluciferin + + hv (catalyzed by luciferase);
where:
* PPi is pyrophosphate
* APS is adenosine 5-phosphosulfate;
* ATP is adenosine triphosphate;
* O2 is oxygen molecule;
* AMP is adenosine monophosphate;
* is carbon dioxide;
* hv is light. | 1 | Applied and Interdisciplinary Chemistry |
Plants can absorb nitrate or ammonium from the soil by their root hairs. If nitrate is absorbed, it is first reduced to nitrite ions and then ammonium ions for incorporation into amino acids, nucleic acids, and chlorophyll. In plants that have a symbiotic relationship with rhizobia, some nitrogen is assimilated in the form of ammonium ions directly from the nodules. It is now known that there is a more complex cycling of amino acids between Rhizobia bacteroids and plants. The plant provides amino acids to the bacteroids so ammonia assimilation is not required and the bacteroids pass amino acids (with the newly fixed nitrogen) back to the plant, thus forming an interdependent relationship. While many animals, fungi, and other heterotrophic organisms obtain nitrogen by ingestion of amino acids, nucleotides, and other small organic molecules, other heterotrophs (including many bacteria) are able to utilize inorganic compounds, such as ammonium as sole N sources. Utilization of various N sources is carefully regulated in all organisms. | 1 | Applied and Interdisciplinary Chemistry |
The 5' UTRs of mouse L1s contain a variable number of GC-rich tandemly repeated monomers of around 200 bp, followed by a short non-monomeric region. Human 5’ UTRs are ~900 bp in length and do not contain repeated motifs. All families of human L1s harbor in their most 5’ extremity a binding motif for the transcription factor YY1. Younger families also have two binding sites for SOX-family transcription factors, and both YY1 and SOX sites were shown to be required for human L1 transcription initiation and activation. Both mouse and human 5’ UTRs also contain a weak antisense promoter of unknown function. | 1 | Applied and Interdisciplinary Chemistry |
Like liquid crystals, plastic crystals can be considered a transitional stage between real solids and real liquids and can be considered soft matter. Another common denominator is the simultaneous presence of order and disorder. Both types of phases are usually observed between the true solid and liquid phases on the temperature scale:
The difference between liquid and plastic crystals is easily observed in X-ray diffraction. Plastic crystals possess strong long range order and therefore show sharp Bragg reflections. Liquid crystals show none or very broad Bragg peaks because the order is not long range. The molecules that give rise to liquid crystalline behavior often have a strongly elongated or disc like shape. Plastic crystals consist usually of almost spherical objects. In this respect one could see them as opposites.
Certain liquid crystals go through plastic crystal phase before melting. In general, liquid crystals are closer to liquids while plastic crystals are closer to true crystals. | 0 | Theoretical and Fundamental Chemistry |
An example of facilitated diffusion is when glucose is absorbed into cells through Glucose transporter 2 (GLUT2) in the human body. There are many other types of glucose transport proteins, some that do require energy, and are therefore not examples of passive transport. Since glucose is a large molecule, it requires a specific channel to facilitate its entry across plasma membranes and into cells. When diffusing into a cell through GLUT2, the driving force that moves glucose into the cell is the concentration gradient. The main difference between simple diffusion and facilitated diffusion is that facilitated diffusion requires a transport protein to facilitate or assist the substance through the membrane. After a meal, the cell is signaled to move GLUT2 into membranes of the cells lining the intestines called enterocytes. With GLUT2 in place after a meal and the relative high concentration of glucose outside of these cells as compared to within them, the concentration gradient drives glucose across the cell membrane through GLUT2. | 1 | Applied and Interdisciplinary Chemistry |
The Long Harbour Nickel Processing Plant is a Canadian nickel concentrate processing facility located in Long Harbour, Newfoundland and Labrador.
Operated by Vale Limited, construction on the plant started in April 2009 and operations began in 2014. Construction costs were in excess of CAD $4.25 billion. Construction involved over 3,200 workers generating approximately 3,000 person-years of employment. Operation of the plant will require approximately 475 workers.
Production began in July 2014, reported in November 2014. Vales nickel processing plant in Long Harbour received its first major shipment from its Labrador mine in Voiseys Bay in May 2015. As of that date, a small proportion of the plants raw materials came from Voiseys Bay but the majority were imported from Indonesia. A spokesman for Vale said 100 per cent of the Long Harbour facilitys production materials will come from Voiseys Bay by early 2016.
Using the metal processing technology of hydrometallurgy, the plant is designed to produce per year of finished nickel product, together with associated cobalt and copper products. The hydrometallurgy technology was piloted at a demonstration plant that opened in Argentia, Newfoundland and Labrador in 2004. This demonstration plant operated until 2008 and was instrumental in helping Vale decide to use the hydrometallurgy process for the Long Harbour processing plant.
A processing plant on Newfoundland was one of the requirements established by the Government of Newfoundland and Labrador in order to exploit the nickel deposit at the Voiseys Bay Mine in Labrador. The bulk carrier MV Umiak I was one of several ice-strengthened bulk carriers built to transport nickel concentrate from Voiseys Bay to the Long Harbour Nickel Processing Plant.
The Long Harbour Nickel Processing Plant was built on a partially brownfield site near the port of Long Harbour. The facility consists of a wharf for offloading nickel ore concentrate from bulk carriers, crushing and grinding facilities, a main processing plant approximately south of the port, a pipeline to supply process water, an effluent discharge pipe and diffuser, and a residue pipeline to a nearby disposal area. The hydrometallurgical process in the plant will pressure-leach the nickel ore concentrate in acidic solutions to separate iron, sulfur and other impurities from nickel, copper and cobalt.
On June 11, 2018, Premier Dwight Ball announced Vale is moving forward with its underground mine at Voiseys Bay. Ball stated that the move will extend the mines operating life by at least 15 years. First ore is expected by April 2021 with processing to take place in Long Harbour. | 1 | Applied and Interdisciplinary Chemistry |
Recent experimental results
have demonstrated that gene expression is a stochastic process. Thus, many authors are now using the stochastic formalism, after the work by Arkin et al. Works on single gene expression and small synthetic genetic networks, such as the genetic toggle switch of Tim Gardner and Jim Collins, provided additional experimental data on the phenotypic variability and the stochastic nature of gene expression. The first versions of stochastic models of gene expression involved only instantaneous reactions and were driven by the Gillespie algorithm.
Since some processes, such as gene transcription, involve many reactions and could not be correctly modeled as an instantaneous reaction in a single step, it was proposed to model these reactions as single step multiple delayed reactions in order to account for the time it takes for the entire process to be complete.
From here, a set of reactions were proposed that allow generating GRNs. These are then simulated using a modified version of the Gillespie algorithm, that can simulate multiple time delayed reactions (chemical reactions where each of the products is provided a time delay that determines when will it be released in the system as a "finished product").
For example, basic transcription of a gene can be represented by the following single-step reaction (RNAP is the RNA polymerase, RBS is the RNA ribosome binding site, and Pro is the promoter region of gene i):
Furthermore, there seems to be a trade-off between the noise in gene expression, the speed with which genes can switch, and the metabolic cost associated their functioning. More specifically, for any given level of metabolic cost, there is an optimal trade-off between noise and processing speed and increasing the metabolic cost leads to better speed-noise trade-offs.
A recent work proposed a simulator (SGNSim, Stochastic Gene Networks Simulator), that can model GRNs where transcription and translation are modeled as multiple time delayed events and its dynamics is driven by a stochastic simulation algorithm (SSA) able to deal with multiple time delayed events.
The time delays can be drawn from several distributions and the reaction rates from complex
functions or from physical parameters. SGNSim can generate ensembles of GRNs within a set of user-defined parameters, such as topology. It can also be used to model specific GRNs and systems of chemical reactions. Genetic perturbations such as gene deletions, gene over-expression, insertions, frame shift mutations can also be modeled as well.
The GRN is created from a graph with the desired topology, imposing in-degree and out-degree distributions. Gene promoter activities are affected by other genes expression products that act as inputs, in the form of monomers or combined into multimers and set as direct or indirect. Next, each direct input is assigned to an operator site and different transcription factors can be allowed, or not, to compete for the same operator site, while indirect inputs are given a target. Finally, a function is assigned to each gene, defining the gene's response to a combination of transcription factors (promoter state). The transfer functions (that is, how genes respond to a combination of inputs) can be assigned to each combination of promoter states as desired.
In other recent work, multiscale models of gene regulatory networks have been developed that focus on synthetic biology applications. Simulations have been used that model all biomolecular interactions in transcription, translation, regulation, and induction of gene regulatory networks, guiding the design of synthetic systems. | 1 | Applied and Interdisciplinary Chemistry |
In this period, William Brownrigg (from 1742 a Fellow of the Royal Society) reported Wood's experiments on a metal, subsequently known as platinum. This had been found in the course of alluvial gold working in what is now Colombia, and had been smuggled from Cartagena to Jamaica. Wood reported this to Brownrigg in about 1741. Brownrigg reported it to the Royal Society in 1750. They found the metal did not react with acid and was unaffected by the usual process for extracting silver from lead. | 1 | Applied and Interdisciplinary Chemistry |
It is also possible to translate either by hand (for short sequences) or by computer (after first programming one appropriately, see section below); this allows biologists and chemists to draw out the chemical structure of the encoded protein on paper.
First, convert each template DNA base to its RNA complement (note that the complement of A is now U), as shown below. Note that the template strand of the DNA is the one the RNA is polymerized against; the other DNA strand would be the same as the RNA, but with thymine instead of uracil.
DNA -> RNA
A -> U
T -> A
C -> G
G -> C
A=T-> A=U
Then split the RNA into triplets (groups of three bases). Note that there are 3 translation "windows", or reading frames, depending on where you start reading the code.
Finally, use the table at Genetic code to translate the above into a structural formula as used in chemistry.
This will give the primary structure of the protein. However, proteins tend to fold, depending in part on hydrophilic and hydrophobic segments along the chain. Secondary structure can often still be guessed at, but the proper tertiary structure is often very hard to determine.
Whereas other aspects such as the 3D structure, called tertiary structure, of protein can only be predicted using sophisticated algorithms, the amino acid sequence, called primary structure, can be determined solely from the nucleic acid sequence with the aid of a translation table.
This approach may not give the correct amino acid composition of the protein, in particular if unconventional amino acids such as selenocysteine are incorporated into the protein, which is coded for by a conventional stop codon in combination with a downstream hairpin (SElenoCysteine Insertion Sequence, or SECIS).
There are many computer programs capable of translating a DNA/RNA sequence into a protein sequence. Normally this is performed using the Standard Genetic Code, however, few programs can handle all the "special" cases, such as the use of the alternative initiation codons which are biologically significant. For instance, the rare alternative start codon CTG codes for Methionine when used as a start codon, and for Leucine in all other positions.
Example: Condensed translation table for the Standard Genetic Code (from the NCBI Taxonomy webpage).
AAs = FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG
Starts = ---M---------------M---------------M----------------------------
Base1 = TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG
Base2 = TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG
Base3 = TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG
The "Starts" row indicate three start codons, UUG, CUG, and the very common AUG. It also indicates the first amino acid residue when interpreted as a start: in this case it is all methionine. | 1 | Applied and Interdisciplinary Chemistry |
Phytochromes (also known as phys) were initially discovered in green plants in 1945. The photoreversible pigment was later found in fungi, mosses, and other algae groups due to the development of whole-genome sequencing, as explained in Peter H. Quails 2010 journal article Phytochromes. As described in Hugo Scheers 1981 journal article Biliproteins, phytochromes function as a sensor of light intensity in ‘high-energy’ reactions, i.e. in higher plants (e.g. underground seedlings), during transformation of heterotrophic blanching growth to autotrophic photosynthetic growth. They carry out this function by monitoring the various parameters of light signals (such as presence/absence, colour, intensity and photoperiodicity). This information is then transduced via intracellular signaling pathways that trigger responses specific to the organism and its development state on both cellular and molecular levels, as explained by Quail. Phytochromes are also responsible for regulating many aspects of a plant's growth, development and reproduction throughout its lifecycle. | 1 | Applied and Interdisciplinary Chemistry |
As RNA integrity has long been known to be a problem in molecular biology studies, there are a few methods that have been used historically to determine the integrity of RNA. The most popular has long been agarose gel electrophoresis with ethidium bromide staining, allowing one to visualize the bands from the rRNA peaks. The height of the 28S and 18S bands can be compared to each other, with a 2:1 ratio indicating non-degraded RNA. While this method is very cheap and easy, there are several issues with this method, primarily its subjectivity, leading to inconsistent, non-standardized RNA quality assessments, and the large amounts of RNA that are needed to visualize it on an agarose gel, which can be problematic if there is not much RNA to work with. There are also a number of different problems that can arise from agarose gel electrophoresis, such as poor loading, uneven running, and uneven staining that lead to increased variability in the accuracy of using agarose gel electrophoresis to determine RNA integrity.
The RNA Integrity Number was developed by Agilent Technologies in 2005. The algorithm was generated by taking hundreds of samples and having specialists manually assign them all a value of 1 to 10 based on their integrity, with 10 being the highest. Adaptive learning tools using a Bayesian learning technique were used to generate an algorithm that could predict the RIN, predominantly by using the features listed below under "Computation". This allows for all Agilent software to produce the same RIN for a given RNA sample, standardizing the measurement and making it much less subjective than earlier methods. | 1 | Applied and Interdisciplinary Chemistry |
Pneumatic fracturing is a method that has become very popular in the last ten years used to remediate contaminated sites. The method consists of injecting gas into a contaminated subsurface at a pressure higher than that of the gases that are present. By doing this fractures "spider-web" throughout the subsurface so that pumps may be placed in the ground to suck out the contaminated water through these cracks. Substrates may also be injected into the soil through the cracks to further the remediation of the soil and ground water. The clean-up technique was developed and patented through the research of various professors at the New Jersey Institute of Technology in 1996 with hopes of cleaning up various United States Environmental Protection Agency (EPA) Superfund sites which are some of the most heavily contaminated sites in the country. The patent is held by John R. Schuring, PhD and PE, professor of civil and environmental engineering at the New Jersey Institute of Technology, developed in conjunction with Thomas M. Boland, Trevor C. King, Sean T. McGonigal, David S. Kosson, Conan D. Fitzgerald, and Sankar Venkatraman. This method has been adopted by environmental contractors all over the country since it has been patented. | 1 | Applied and Interdisciplinary Chemistry |
Acid–base homeostasis is the homeostatic regulation of the pH of the body's extracellular fluid (ECF). The proper balance between the acids and bases (i.e. the pH) in the ECF is crucial for the normal physiology of the body—and for cellular metabolism. The pH of the intracellular fluid and the extracellular fluid need to be maintained at a constant level.
The three dimensional structures of many extracellular proteins, such as the plasma proteins and membrane proteins of the body's cells, are very sensitive to the extracellular pH. Stringent mechanisms therefore exist to maintain the pH within very narrow limits. Outside the acceptable range of pH, proteins are denatured (i.e. their 3D structure is disrupted), causing enzymes and ion channels (among others) to malfunction.
An acid–base imbalance is known as acidemia when the pH is acidic, or alkalemia when the pH is alkaline. | 0 | Theoretical and Fundamental Chemistry |
Synaptic transmission can be changed by previous activity. These changes are called synaptic plasticity and may result in either a decrease in the efficacy of the synapse, called depression, or an increase in efficacy, called potentiation. These changes can either be long-term or short-term. Forms of short-term plasticity include synaptic fatigue or depression and synaptic augmentation. Forms of long-term plasticity include long-term depression and long-term potentiation. Synaptic plasticity can be either homosynaptic (occurring at a single synapse) or heterosynaptic (occurring at multiple synapses). | 1 | Applied and Interdisciplinary Chemistry |
In ancient history, Hippocrates discussed bile pigments in two of the four humours in the context of a relationship between yellow and black biles. Hippocrates visited Democritus in Abdera who was regarded as the expert in melancholy "black bile".
Relevant documentation emerged in 1827 when M. Louis Jacques Thénard examined the biliary tract of an elephant that had died at a Paris zoo. He observed dilated bile ducts were full of yellow magma, which he isolated and found to be insoluble in water. Treating the yellow pigment with hydrochloric acid produced a strong green color. Thenard suspected the green pigment was caused by impurities derived from mucus of bile.
Leopold Gmelin experimented with nitric acid in 1826 to establish the redox behavior in change from bilirubin to biliverdin, although the nomenclature did not exist at the time. The term biliverdin was coined by Jöns Jacob Berzelius in 1840, although he preferred "bilifulvin" (yellow/red) over "bilirubin" (red). The term "bilirubin" was thought to have become mainstream based on the works of Staedeler in 1864 who crystallized bilirubin from cattle gallstones.
Rudolf Virchow in 1847 recognized hematoidin to be identical to bilirubin. It is not always distinguished from hematoidin, which one modern dictionary defines as synonymous with it but another defines as "apparently chemically identical with bilirubin but with a different site of origin, formed locally in the tissues from hemoglobin, particularly under conditions of reduced oxygen tension." The synonymous identity of bilirubin and hematoidin was confirmed in 1923 by Fischer and Steinmetz using analytical crystallography.
In the 1930s, significant advances in bilirubin isolation and synthesis were described by Hans Fischer, Plieninger, and others, and pioneering work pertaining to endogenous formation of bilirubin from heme was likewise conducted in the same decade. The suffix IXα is partially based on a system developed Fischer, which means the bilin's parent compound was protoporphyrin IX cleaved at the alpha-methine bridge (see protoporphyrin IX nomenclature).
Origins pertaining to the physiological activity of bilirubin were described by Ernst Stadelmann in 1891, who may have observed the biotransformation of infused hemoglobin into bilirubin possibly inspired by Ivan Tarkhanov's 1874 works. Georg Barkan suggested the source of endogenous bilirubin to be from hemoglobin in 1932. Plieninger and Fischer demonstrated an enzymatic oxidative loss of the alpha-methine bridge of heme resulting in a bis-lactam structure in 1942. It is widely accepted that Irving London was the first to demonstrate endogenous formation of bilirubin from hemoglobin in 1950, and Sjostrand demonstrated hemoglobin catabolism produces carbon monoxide between 1949 and 1952. 14C labeled protoporphyrin biotransformation to bilirubin evidence emerged in 1966 by Cecil Watson. Rudi Schmid and Tenhunen discovered heme oxygenase, the enzyme responsible, in 1968. Earlier in 1963, Nakajima described a soluble "heme alpha-methnyl oxygeanse" which what later determined to be a non-enzymatic pathway, such as formation of a 1,2-Dioxetane intermediate at the methine bridge resulting in carbon monoxide release and biliverdin formation. | 1 | Applied and Interdisciplinary Chemistry |
Highly connected nodes (proteins) are called hubs. Han et al. have coined the term "party hub" for hubs whose expression is correlated with its interaction partners. Party hubs also connect proteins within functional modules such as protein complexes. In contrast, "date hubs" do not exhibit such a correlation and appear to connect different functional modules. Party hubs are found predominantly in AP/MS data sets, whereas date hubs are found predominantly in binary interactome network maps. Note that the validity of the date hub/party hub distinction was disputed. Party hubs generally consist of multi-interface proteins whereas date hubs are more frequently single-interaction interface proteins. Consistent with a role for date-hubs in connecting different processes, in yeast the number of binary interactions of a given protein is correlated to the number of phenotypes observed for the corresponding mutant gene in different physiological conditions. | 1 | Applied and Interdisciplinary Chemistry |
Southern Ocean sediments are a major sink for biogenic silica (50-75% of the oceanic total of 4.5 × 10 g SiO yr; DeMaster, 1981), but only a minor sink for organic carbon ( g of organic C yr). These relatively high rates of biogenic silica accumulation in the Southern Ocean sediments (predominantly beneath the Polar Front) relative to organic carbon (60:1 on a weight basis) results from the preferential preservation of biogenic silica in the Antarctic water column.
In contrast to what was previously thought, these high rates of biogenic silica accumulation are not the result from high rates of primary production. Biological production in the Southern Ocean is strongly limited due to the low levels of irradiance coupled with deep mixed layers and/or by limited amounts of micronutrients, such as iron.
This preferential preservation of biogenic silica relative to organic carbon is evident in the steadily increasing ratio of silica/organic C as function of depth in the water column. About thirty-five percent of the biogenic silica produced in the euphotic zone survives dissolution within the surface layer; whereas only 4% of the organic carbon escapes microbial degradation in these near-surface waters.
Consequently, considerable decoupling of organic C and silica occurs during settling through the water column. The accumulation of biogenic silica in the seabed represents 12% of the surface production, whereas the seabed organic-carbon accumulation rate accounts for solely <0.5% of the surface production. As a result, polar sediments account for most of the ocean's biogenic silica accumulation, but only a small amount of the sedimentary organic-carbon flux. | 1 | Applied and Interdisciplinary 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. | 0 | Theoretical and Fundamental Chemistry |
Sieverts' law can be readily rationalized by considering the reaction of dissolution of the gas in the metal, which involves dissociation of the molecule of the gas. For example, for nitrogen:
: N (molecular gas) 2 N (dissolved atoms)
For the above reaction, the equilibrium constant is
where:
: c is the concentration of the dissolved atoms into the metal (in the case above, atomic nitrogen N),
: p is the partial pressure of the gas at the interface with the metal (in the case above, the molecular nitrogen N).
Therefore, | 1 | Applied and Interdisciplinary Chemistry |
In molecular clouds, simple carbon molecules are formed, including carbon monoxide and dicarbon. Reactions with the trihydrogen cation of the simple carbon molecules yield carbon containing ions that readily react to form larger organic molecules. Carbon compounds that exist as ions, or isolated gas molecules in the interstellar medium, can condense onto dust grains. Carbonaceous dust grains consist mostly of carbon. Grains can stick together to form larger aggregates. | 0 | Theoretical and Fundamental Chemistry |
An EMF meter is a scientific instrument for measuring electromagnetic fields (abbreviated as EMF). Most meters measure the electromagnetic radiation flux density (DC fields) or the change in an electromagnetic field over time (AC fields), essentially the same as a radio antenna, but with quite different detection characteristics.
The two largest categories are single axis and tri-axis. Single axis meters are cheaper than tri-axis meters, but take longer to complete a survey because the meter only measures one dimension of the field. Single axis instruments have to be tilted and turned on all three axes to obtain a full measurement. A tri-axis meter measures all three axes simultaneously, but these models tend to be more expensive.
Electromagnetic fields can be generated by AC current or DC currents. An EMF meter can measure AC electromagnetic fields, which are usually emitted from man-made sources such as electrical wiring, while gaussmeters or magnetometers measure DC fields, which occur naturally in Earth's geomagnetic field and are emitted from other sources where direct current is present. | 1 | Applied and Interdisciplinary Chemistry |
Determining the point group is a useful way to predict polarity of a molecule. In general, a molecule will not possess dipole moment if the individual bond dipole moments of the molecule cancel each other out. This is because dipole moments are euclidean vector quantities with magnitude and direction, and a two equal vectors that oppose each other will cancel out.
Any molecule with a centre of inversion ("i") or a horizontal mirror plane ("σ") will not possess dipole moments.
Likewise, a molecule with more than one C axis of rotation will not possess a dipole moment because dipole moments cannot lie in more than one dimension. As a consequence of that constraint, all molecules with dihedral symmetry (D) will not have a dipole moment because, by definition, D point groups have two or multiple C axes.
Since C, C,C C and C point groups do not have a centre of inversion, horizontal mirror planes or multiple C axis, molecules in one of those point groups will have dipole moment. | 0 | Theoretical and Fundamental Chemistry |
Bilirubin is degraded by light. Blood collection tubes containing blood or (especially) serum to be used in bilirubin assays should be protected from illumination. For adults, blood is typically collected by needle from a vein in the arm. In newborns, blood is often collected from a heel stick, a technique that uses a small, sharp blade to cut the skin on the infant's heel and collect a few drops of blood into a small tube. Non-invasive technology is available in some health care facilities that will measure bilirubin by using an bilirubinometer which shines light onto the skin and calculates the amount of bilirubin by analysing how the light is absorbed or reflects. This device is also known as a transcutaneous bilirubin meter.
Bilirubin (in blood) is found in two forms:
Note: Conjugated bilirubin is often incorrectly called "direct bilirubin" and unconjugated bilirubin is incorrectly called "indirect bilirubin". Direct and indirect refer solely to how compounds are measured or detected in solution. Direct bilirubin is any form of bilirubin which is water-soluble and is available in solution to react with assay reagents; direct bilirubin is often made up largely of conjugated bilirubin, but some unconjugated bilirubin (up to 25%) can still be part of the "direct" bilirubin fraction. Likewise, not all conjugated bilirubin is readily available in solution for reaction or detection (for example, if it is hydrogen bonding with itself) and therefore would not be included in the direct bilirubin fraction.
Total bilirubin (TBIL) measures both BU and BC. Total bilirubin assays work by using surfactants and accelerators (like caffeine) to bring all of the different bilirubin forms into solution where they can react with assay reagents. Total and direct bilirubin levels can be measured from the blood, but indirect bilirubin is calculated from the total and direct bilirubin.
Indirect bilirubin is fat-soluble and direct bilirubin is water-soluble. | 1 | Applied and Interdisciplinary Chemistry |
In medicine it is often referred to as the Law of Laplace, used in the context of cardiovascular physiology, and also respiratory physiology, though the latter use is often erroneous. | 1 | Applied and Interdisciplinary Chemistry |
Dispersion forces are usually dominant over the three van der Waals forces (orientation, induction, dispersion) between atoms and molecules, with the exception of molecules that are small and highly polar, such as water. The following contribution of the dispersion to the total intermolecular interaction energy has been given: | 0 | Theoretical and Fundamental Chemistry |
Protein catabolism produces amino acids that are used to form other proteins or oxidized to meet the energy needs of the cell. The amino acids that are produced by protein catabolism can then be further catabolized in amino acid catabolism. Among the several degradative processes for amino acids are Deamination (removal of an amino group), transamination (transfer of amino group), decarboxylation (removal of carboxyl group), and dehydrogenation (removal of hydrogen). Degradation of amino acids can function as part of a salvage pathway, whereby parts of degraded amino acids are used to create new amino acids, or as part of a metabolic pathway whereby the amino acid is broken down to release or recapture chemical energy. For example, the chemical energy that is released by oxidization in a dehydrogenation reaction can be used to reduce NAD to NADH, which can then be fed directly into the Krebs/Citric Acid (TCA) Cycle. | 1 | Applied and Interdisciplinary Chemistry |
In the mid-19th century, a German pathologist named Rudolf Virchow discovered that cholesterol was to be found in the artery walls of people that died from occlusive vascular diseases, like myocardial infarction. The cholesterol was found to be responsible for the thickening of the arterial walls and thus decreasing the radius in the arteries which leads in most cases to hypertension and increased risk of occlusive vascular diseases.
In the 1950s the Framingham heart study led by Dawber revealed the correlation between high blood cholesterol levels and coronary heart diseases. Following up from that study the researchers explored a novel way to lower blood cholesterol levels without modifying the diet and lifestyle of subjects suffering with elevated blood cholesterol levels. The primary goal was to inhibit the cholesterol biosynthesis in the body. Hence HMG-CoA reductase (HMGR) became a natural target. HMGR was found to be the rate-limiting enzyme in the cholesterol biosynthetic pathway. There is no build-up of potentially toxic precursors when HMGR is inhibited, because hydroxymethylglutarate is water-soluble and there are alternative metabolic pathways for its breakdown.
In the 1970s the Japanese microbiologist Akira Endo first discovered natural products with a powerful inhibitory effect on HMGR in a fermentation broth of Penicillium citrinum, during his search for antimicrobial agents. The first product was named compactin (ML236B or mevastatin). Animal trials showed very good inhibitory effect as in clinical trials, however in a long term toxicity study in dogs it resulted in toxic effects at higher doses and as a result was believed to be too toxic to be given to humans. In 1978, Alfred Alberts and colleagues at Merck Research Laboratories discovered a new natural product in a fermentation broth of Aspergillus terreus, their product showed good HMGR inhibition and they named the product mevinolin, which later became known as lovastatin.
The cholesterol controversy began in the early promotion of statins. | 1 | Applied and Interdisciplinary Chemistry |
Magnesium oxalate is an organic compound comprising a magnesium cation with a 2+ charge bonded to an oxalate anion. It has the chemical formula MgCO. Magnesium oxalate is a white solid that comes in two forms: an anhydrous form and a dihydrate form where two water molecules are complexed with the structure. Both forms are practically insoluble in water and are insoluble in organic solutions. | 0 | Theoretical and Fundamental Chemistry |
In 1983 Pearson together with Robert Parr extended the qualitative HSAB theory with a quantitative definition of the chemical hardness (η) as being proportional to the second derivative of the total energy of a chemical system with respect to changes in the number of electrons at a fixed nuclear environment:
The factor of one-half is arbitrary and often dropped as Pearson has noted.
An operational definition for the chemical hardness is obtained by applying a three-point finite difference approximation to the second derivative:
where I is the ionization potential and A the electron affinity. This expression implies that the chemical hardness is proportional to the band gap of a chemical system, when a gap exists.
The first derivative of the energy with respect to the number of electrons is equal to the chemical potential, μ, of the system,
from which an operational definition for the chemical potential is obtained from a finite difference approximation to the first order derivative as
which is equal to the negative of the electronegativity (χ) definition on the Mulliken scale: μ = −χ.
The hardness and Mulliken electronegativity are related as
and in this sense hardness is a measure for resistance to deformation or change. Likewise a value of zero denotes maximum softness, where softness is defined as the reciprocal of hardness.
In a compilation of hardness values only that of the hydride anion deviates. Another discrepancy noted in the original 1983 article are the apparent higher hardness of Tl compared to Tl. | 0 | Theoretical and Fundamental Chemistry |
An organoberyllium carbene consists of a carbene attached to beryllium. The types of carbene includes a N-heterocyclic carbenes (NHC) and cyclic alkyl amino carbenes (CAAC). | 0 | Theoretical and Fundamental Chemistry |
The product of layer thickness (d) and elevation height (h) is constant (d·h = constant), the two quantities are inversely proportional. The surface of the liquid between the planes is hyperbola. | 0 | Theoretical and Fundamental Chemistry |
In combination with its use as an insecticide, boric acid also prevents and destroys existing wet and dry rot in timbers. It can be used in combination with an ethylene glycol carrier to treat external wood against fungal and insect attack. It is possible to buy borate-impregnated rods for insertion into wood via drill holes where dampness and moisture is known to collect and sit. It is available in a gel form and injectable paste form for treating rot affected wood without the need to replace the timber. Concentrates of borate-based treatments can be used to prevent slime, mycelium, and algae growth, even in marine environments.
Boric acid is added to salt in the curing of cattle hides, calfskins, and sheepskins. This helps to control bacterial development, and helps to control insects. | 0 | Theoretical and Fundamental Chemistry |
Calorie restriction, vitamin E, and increased glutathione appear to reduce or halt the production of lipofuscin.
The nootropic drug piracetam appears to significantly reduce accumulation of lipofuscin in the brain tissue of rats.
Other possible treatments:
*Centrophenoxine
*Acetyl-L-carnitine
*Ginkgo biloba
*Dimethylethanolamine
*Curcumin
Wet macular degeneration can be treated using selective photothermolysis where a pulsed unfocused laser predominantly heats and kills lipofuscin-rich cells, leaving untouched healthy cells to multiply and fill in the gaps. The technique is also used as a skin treatment to remove tattoos, liverspots, and in general make skin appear younger. This ability to selectively target lipofuscin has opened up research opportunities in the field of anti-aging medicine.
Soraprazan (remofuscin) has been found to remove lipofuscin from retinal pigment epithelial cells in animals. This opens up a new therapy option for the treatment of dry age-related macular degeneration and Stargardt disease, for which there is currently no treatment. The drug has now been granted orphan drug designation for the treatment of Stargardt disease by the European Medicines Agency. | 1 | Applied and Interdisciplinary Chemistry |
Contact between a contaminant and an organism can occur through any route. The possible routes of exposure are: inhalation, if the contaminant is present in the air; ingestion, through food, drinking or hand-to-mouth behavior; and dermal absorption, if the contaminant can be absorbed through the skin.
Exposure to a contaminant can and does occur through multiple routes, simultaneously or at different times. In many cases the main route of exposure is not obvious and needs to be investigated carefully. For example, exposure to byproducts of water chlorination can obviously occur by drinking, but also through the skin, while swimming or washing, and even through inhalation from droplets aerosolized during a shower. The relative proportion of exposure from these different routes cannot be determined a priori. Therefore, the equation in the previous section is correct in a strict mathematical sense, but it is a gross oversimplification of actual exposures, which are the sum of the integrals of all activities in all microenvironments. For example, the equation would have to be calculated with the specific concentration of a compound in the air in the room during the time interval. Similarly, the concentration in the ambient air would apply to the time that the person spends outdoors, whereas the concentration in the food that the person ingests would be added. The concentration integrals via all routes would be added for the exposure duration, e.g. hourly, daily or annually as
where is the initial time and the ending time of last in the series of time periods spent in each microenvironment over the exposure duration. | 1 | Applied and Interdisciplinary Chemistry |
The TET enzymes are a family of ten-eleven translocation (TET) methylcytosine dioxygenases. They are instrumental in DNA demethylation. 5-Methylcytosine (see first Figure) is a methylated form of the DNA base cytosine (C) that often regulates gene transcription and has several other functions in the genome.
Demethylation by TET enzymes (see second Figure), can alter the regulation of transcription. The TET enzymes catalyze the hydroxylation of DNA 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), and can further catalyse oxidation of 5hmC to 5-formylcytosine (5fC) and then to 5-carboxycytosine (5caC). 5fC and 5caC can be removed from the DNA base sequence by base excision repair and replaced by cytosine in the base sequence.
TET enzymes have central roles in DNA demethylation required during embryogenesis, gametogenesis, memory, learning, addiction and pain perception. | 1 | Applied and Interdisciplinary Chemistry |
A "wet" standpipe is filled with water and is pressurized at all times. In contrast to dry standpipes, which can be used only by firefighters, wet standpipes can be used by building occupants. Wet standpipes generally already come with hoses so that building occupants may fight fires quickly. This type of standpipe may also be installed horizontally on bridges. | 1 | Applied and Interdisciplinary Chemistry |
The first widescale use of VCIs can be traced to Shell's patent for dicyclohexylammonium nitrite (DICHAN), which was eventually commercialized as VPI 260. DICHAN was used extensively by the US military to protect a wide variety of metallic components from corrosion via various delivery systems, VCI powder, VCI paper, VCI solution, VCI slushing compound, etc.
Safety and health concerns as well as inherent limitations has led to the abandonment of DICHAN as a VCI. At present, commercial VCI compounds are typically salts of moderately strong bases and weak volatile acids. The typical bases are amines and the acids are carbonic, nitrous and carboxylic. | 1 | Applied and Interdisciplinary Chemistry |
First, a probe is constructed. The probe must be large enough to hybridize specifically with its target but not so large as to impede the hybridization process. The probe is tagged directly with fluorophores, with targets for antibodies or with biotin. Tagging can be done in various ways, such as nick translation, or polymerase chain reaction using tagged nucleotides.
Then, an interphase or metaphase chromosome preparation is produced. The chromosomes are firmly attached to a substrate, usually glass. Repetitive DNA sequences must be blocked by adding short fragments of DNA to the sample. The probe is then applied to the chromosome DNA and incubated for approximately 12 hours while hybridizing. Several wash steps remove all unhybridized or partially hybridized probes. The results are then visualized and quantified using a microscope that is capable of exciting the dye and recording images.
If the fluorescent signal is weak, amplification of the signal may be necessary in order to exceed the detection threshold of the microscope. Fluorescent signal strength depends on many factors such as probe labeling efficiency, the type of probe, and the type of dye. Fluorescently tagged antibodies or streptavidin are bound to the dye molecule. These secondary components are selected so that they have a strong signal. | 1 | Applied and Interdisciplinary Chemistry |
The process of equilibration can be described using the H-theorem or the relaxation theorem, see also entropy production. | 0 | Theoretical and Fundamental Chemistry |
The durability assessment has been implemented in European design codes at the beginning of the 90s. It is required for designers to include the effects of long-term corrosion of steel rebar during the design stage, in order to avoid unacceptable damages during the service life of the structure. Different approaches are then available for the durability design. | 1 | Applied and Interdisciplinary Chemistry |
With increasing temperature, the reaction rate increases, but hydrogen production becomes less favorable thermodynamically since the water gas shift reaction is moderately exothermic; this shift in chemical equilibrium can be explained according to Le Chatelier's principle. Over the temperature range of 600–2000 K, the equilibrium constant for the WGSR has the following relationship:
</div> | 0 | Theoretical and Fundamental Chemistry |
Sodium hydroxide is a popular strong base used in industry. Sodium hydroxide is used in the manufacture of sodium salts and detergents, pH regulation, and organic synthesis. In bulk, it is most often handled as an aqueous solution, since solutions are cheaper and easier to handle.
Sodium hydroxide is used in many scenarios where it is desirable to increase the alkalinity of a mixture, or to neutralize acids. For example, in the petroleum industry, sodium hydroxide is used as an additive in drilling mud to increase alkalinity in bentonite mud systems, to increase the mud viscosity, and to neutralize any acid gas (such as hydrogen sulfide and carbon dioxide) which may be encountered in the geological formation as drilling progresses. Another use is in salt spray testing where pH needs to be regulated. Sodium hydroxide is used with hydrochloric acid to balance pH. The resultant salt, NaCl, is the corrosive agent used in the standard neutral pH salt spray test.
Poor quality crude oil can be treated with sodium hydroxide to remove sulfurous impurities in a process known as caustic washing. Sodium hydroxide reacts with weak acids such as hydrogen sulfide and mercaptans to yield non-volatile sodium salts, which can be removed. The waste which is formed is toxic and difficult to deal with, and the process is banned in many countries because of this. In 2006, Trafigura used the process and then dumped the waste in Ivory Coast.
Other common uses of sodium hydroxide include:
* for making soaps and detergents. Sodium hydroxide is used for hard bar soap, while potassium hydroxide is used for liquid soaps. Sodium hydroxide is used more often than potassium hydroxide because it is cheaper and a smaller quantity is needed.
* as drain cleaners that convert pipe-clogging fats and grease into soap, which dissolves in water
* for making artificial textile fibres such as rayon
* in the manufacture of paper. Around 56% of sodium hydroxide produced is used by industry, 25% of which is used in the paper industry.
* in purifying bauxite ore from which aluminium metal is extracted. This is known as the Bayer process.
* de-greasing metals
* oil refining
* making dyes and bleaches
* in water treatment plants for pH regulation
* to treat bagels and pretzel dough, giving the distinctive shiny finish | 0 | Theoretical and Fundamental Chemistry |
In recent years, thermal physics has applied the definition of chemical potential to systems in particle physics and its associated processes. For example, in a quark–gluon plasma or other QCD matter, at every point in space there is a chemical potential for photons, a chemical potential for electrons, a chemical potential for baryon number, electric charge, and so forth.
In the case of photons, photons are bosons and can very easily and rapidly appear or disappear. Therefore, at thermodynamic equilibrium, the chemical potential of photons is in most physical situations always and everywhere zero. The reason is, if the chemical potential somewhere was higher than zero, photons would spontaneously disappear from that area until the chemical potential went back to zero; likewise, if the chemical potential somewhere was less than zero, photons would spontaneously appear until the chemical potential went back to zero. Since this process occurs extremely rapidly - at least, it occurs rapidly in the presence of dense charged matter or also in the walls of the textbook example for a photon gas of blackbody radiation - it is safe to assume that the photon chemical potential here is never different from zero. A physical situation where the chemical potential for photons can differ from zero are material-filled optical microcavities, with spacings between cavity mirrors in the wavelength regime. In such two-dimensional cases, photon gases with tuneable chemical potential, much reminiscent to gases of material particles, can be observed.
Electric charge is different because it is intrinsically conserved, i.e. it can be neither created nor destroyed. It can, however, diffuse. The "chemical potential of electric charge" controls this diffusion: Electric charge, like anything else, will tend to diffuse from areas of higher chemical potential to areas of lower chemical potential. Other conserved quantities like baryon number are the same. In fact, each conserved quantity is associated with a chemical potential and a corresponding tendency to diffuse to equalize it out.
In the case of electrons, the behaviour depends on temperature and context. At low temperatures, with no positrons present, electrons cannot be created or destroyed. Therefore, there is an electron chemical potential that might vary in space, causing diffusion. At very high temperatures, however, electrons and positrons can spontaneously appear out of the vacuum (pair production), so the chemical potential of electrons by themselves becomes a less useful quantity than the chemical potential of the conserved quantities like (electrons minus positrons).
The chemical potentials of bosons and fermions is related to the number of particles and the temperature by Bose–Einstein statistics and Fermi–Dirac statistics respectively. | 0 | Theoretical and Fundamental Chemistry |
Glyceraldehyde 3-phosphate occurs as a byproduct in the biosynthesis pathway of tryptophan, an essential amino acid that cannot be produced by the human body. | 0 | Theoretical and Fundamental Chemistry |
Dexrazoxane has been used to protect the heart against the cardiotoxic side effects of chemotherapeutic drugs such as anthracyclines, such as daunorubicin or doxorubicin or other chemotherapeutic agents. However, in July 2011 the European Medicines Agency (EMA) released a statement restricting use only in adult patients with cancer who have received > 300 mg/m doxorubicin or > 540 mg/m epirubicin and general approval for use for cardioprotection. That showed a possibly higher rate of secondary malignancies and acute myelogenous leukemia in pediatric patients treated for different cancers with both dexrazoxane and other chemotherapeutic agents that are associated with secondary malignancies. On July 19, 2017, based on evaluation of the currently available data the European Commission issued an EU-wide legally binding decision to implement the recommendations of the Committee for Medicinal Products for Human Use (CHMP) on dexrazoxane and lifted its 2011-contraindication for primary prevention of anthracycline-induced cardiotoxicity with dexrazoxane in children and adolescents where high doses (≥ 300 mg/m) of anthracyclines are anticipated.
Dexrazoxane was designated by the US FDA as an orphan drug for "prevention of cardiomyopathy for children and adults 0 through 16 years of age treated with anthracyclines". This decision allows virtually all children to receive dexrazoxane starting with the first dose of anthracycline at the discretion of the treating provider. The label change by the agency announcing dexrazoxane as an approved cardio-oncology protectant has been followed by a review by the agency. Currently, the only FDA and EMA approved cardioprotective treatment for anthracycline cardioprotection is dexrazoxane, which provides effective primary cardioprotection against anthracycline-induced cardiotoxicity without reducing anthracycline activity and without enhancing secondary malignancies.
The United States Food and Drug Administration has also approved a dexrazoxane for use as a treatment of extravasation resulting from IV anthracycline chemotherapy. Extravasation is an adverse event in which chemotherapies containing anthracylines leak out of the blood vessel and necrotize the surrounding tissue. | 0 | Theoretical and Fundamental Chemistry |
The following energies are called the thermodynamic potentials,
and the corresponding fundamental thermodynamic relations or "master equations" are: | 0 | Theoretical and Fundamental Chemistry |
Being strong acids, sulfonic acids are also used as catalysts. The simplest examples are methanesulfonic acid, CHSOOH and p-toluenesulfonic acid, which are regularly used in organic chemistry as acids that are lipophilic (soluble in organic solvents). Polymeric sulfonic acids are also useful. Dowex resin are sulfonic acid derivatives of polystyrene and is used as catalysts and for ion exchange (water softening). Nafion, a fluorinated polymeric sulfonic acid is a component of proton exchange membranes in fuel cells. | 0 | Theoretical and Fundamental Chemistry |
Maintenance respiration (or maintenance energy) refers to metabolism occurring in an organism that is needed to maintain that organism in a healthy, living state. Maintenance respiration contrasts with growth respiration, which is responsible for the synthesis of new structures in growth, nutrient uptake, nitrogen (N) reduction and phloem loading, whereas maintenance respiration is associated with protein and membrane turnover and maintenance of ion concentrations and gradients. | 1 | Applied and Interdisciplinary Chemistry |
NeuroD, also called Beta2, is a basic helix-loop-helix transcription factor expressed in certain parts of brain, beta pancreatic cells and enteroendocrine cells. It is involved in the differentiation of nervous system and development of pancreas. It heterodimerizes with the products of E2A gene and controls the transcription of a variety of genes by identifying and binding E boxes in their promoter region. In rodents NeuroD is involved in the development of the retina.
In mammals there are two types of this factor:
*NeuroD1
*NeuroD2
*NeuroD4
*NeuroD6 | 1 | Applied and Interdisciplinary Chemistry |
Magnetic surveys can suffer from noise coming from a range of sources. Different magnetometer technologies suffer different kinds of noise problems.
Heading errors are one group of noise. They can come from three sources:
*Sensor
*Console
*Operator
Some total field sensors give different readings depending on their orientation. Magnetic materials in the sensor itself are the primary cause of this error. In some magnetometers, such as the vapor magnetometers (caesium, potassium, etc.), there are sources of heading error in the physics that contribute small amounts to the total heading error.
Console noise comes from magnetic components on or within the console. These include ferrite in cores in inductors and transformers, steel frames around LCDs, legs on IC chips and steel cases in disposable batteries. Some popular MIL spec connectors also have steel springs.
Operators must take care to be magnetically clean and should check the magnetic hygiene of all apparel and items carried during a survey. Akubra hats are very popular in Australia, but their steel rims must be removed before use on magnetic surveys. Steel rings on notepads, steel capped boots and steel springs in overall eyelets can all cause unnecessary noise in surveys. Pens, mobile phones and stainless steel implants can also be problematic.
The magnetic response (noise) from ferrous object on the operator and console can change with heading direction because of induction and remanence. Aeromagnetic survey aircraft and quad bike systems can use special compensators to correct for heading error noise.
Heading errors look like herringbone patterns in survey images. Alternate lines can also be corrugated. | 0 | Theoretical and Fundamental Chemistry |
DSIF plays the same role for HIV-1 gene expression as it would normally in transcription. This is because P-TEFb phosphorylates DSIF the same regardless of whether or not P-TEFb goes through normal cellular regulation or bypasses it due to Tat. | 1 | Applied and Interdisciplinary Chemistry |
Holmes was elected Fellow of the Royal Society (FRS) in 2000, and Fellow of the Australian Academy of Science in 2006. In 2003, he received the Descartes Prize and in 2012 the Royal Medal of the Royal Society. His formal titles include Chemistry alumnus, Laureate Professor of Chemistry, University of Melbourne; CSIRO Fellow, CSIRO Division of Materials Science and Engineering; Emeritus Professor and Distinguished Research Fellow, Imperial College London; Fellow of the Royal Society; Fellow of the Australian Academy of Science; Fellow of the Australian Academy of Technological Sciences and Engineering; and Foreign Secretary and (as of 2014) President of the Australian Academy of Science. In 2011, he received the Royal Society of Chemistry's John B Goodenough Award.
In 2004 he was appointed a Member of the Order of Australia "for service to science through research and development, particularly in the fields of organic synthesis and polymer chemistry"; and in 2017 was appointed Companion of the Order of Australia for eminent service to science through developments in the field of organic and polymer chemistry as a researcher, editor and academic, and through the governance of nationally recognised, leading scientific organisations. He was awarded the 2021 Matthew Flinders Medal and Lecture. | 0 | Theoretical and Fundamental Chemistry |
The operational proof for the flux connectivity theorem relies on making perturbations to enzyme levels such that the pathway flux is unchanged but a single metabolite level is changed. This can be illustrated with the following pathway:
Let us make a change to the rate through by increasing the concentration of enzyme . Assume is increased by an amount, . This will result in a change to the steady-state of the pathway. The concentrations of , and the flux, through the pathway will increase, and the concentration of will decrease because it is upstream of the disturbance.
Impose a second change to the pathway such that the flux, is restored to what it was before the original change. Since the flux increased when was changed, the flux can be decreased by decreasing one of the other enzyme levels. If the concentration of is decreased, this will reduce the flux. Decreasing will also cause the concentration of to further increase. However, and will change in the opposite direction compared to when was increased.
When is sufficiently changed so that the flux is restored to its original value, the concentrations of and will also be restored to their original values. It is only that will differ. This is true because the flux through is now the same as it was originally (since we’ve restored the flux), and has not been manipulated in anyway. This means that the concentration of and all
species upstream of must be the same as they were before the modulations occurred. The same arguments apply to and all species downstream of .
The net result is that has been increased by resuling a change in flux of . The concentration of was decreased such that the flux was restored to it original value, . In the process, changed by but neither or . In fact no other species in the entire system has changed other than .
This thought experiment can be expressed mathematically as follows. The system equations in terms of the flux control coefficients can be written as:
There are only two terms because only and were changed.
The local change at each step can be written for and in terms of elasticities:
Note that won't necessarily equal and by construction both rates, and showed no change. Also by construction only changed.
The local equation can be rearranged as:
The right-hand sides can be inserted into the system equation the change in flux:
Therefore:
However, by construction of the perturbations, does not equal zero, hence we arrive at the connectivity theorem:
The operational method can also be used for systems where a given metabolite can influence multiple steps. This would apply to cases such as branched systems or systems with negative feedback loops.
The same approach can be used to derive the concentration connectivity theorems except one can consider either the case that focuses on a single species or a second case where the system equation is written to consider the effect on a distance species. | 1 | Applied and Interdisciplinary Chemistry |
In orthopedics, methods with minimum invasion are desired and improving injectable systems is a leading aim. Bone cavities can be filled by polymerizing materials when injected and adaptation to the shape of the cavity can be provided. Shorter surgical operation time, minimum large muscle retraction harm, smaller scar size, less pain after operation and consequently faster recovery can be obtained by using such systems. In a study to evaluate if injectable fibrin scaffold is helpful for transplantation of bone marrow stromal cell (BMSC) when central nervous system (CNS) tissue is damaged, Yasuda et al. found that BMSC has extended survival, migration and differentiation after transplantation to rat cortical lesion although there is complete degradation of fibrin matrix after four weeks. Another study to assess if fibrin glue enriched with platelet is better than just platelet rich plasma (PRP) on bone formation was conducted. Each combined with bone marrow mesenchymal stem cells and bone morphogenetic protein 2 (BMP-2) are injected into the subcutaneous space. Results shows that fibrin glue enriched with platelet has better osteogenic properties when compared to PRP. To initiate and speed up tissue repair and regeneration, platelet-rich fibrin gels are ideal since they have a high concentration of platelet releasing growth factors and bioactive proteins. Addition of fibrin glue to calcium phosphate granules has promising results leading to faster bone repair by inducing mineralization and possible effects of fibrin on angiogenesis, cell attachment and proliferation. | 1 | Applied and Interdisciplinary Chemistry |
: Genes (Quantitative trait loci (abbreviated as QTL) or quantitative trait genes or minor genes or major genes) involved in controlling trait of interest are identified. The process is known as mapping. Mapping of such genes can be done using molecular markers. QTL mapping can involve single large family, unrelated individuals or multiple families (see: Family based QTL mapping). The basic idea is to identify genes or markers associated with genes that correlate to a phenotypic measurement and that can be used in marker assisted breeding / selection. | 1 | Applied and Interdisciplinary Chemistry |
Post-treatment disinfection provides secondary protection against compromised membranes and downstream problems. Disinfection by means of ultraviolet (UV) lamps (sometimes called germicidal or bactericidal) may be employed to sterilize pathogens that evade the RO process. Chlorination or chloramination (chlorine and ammonia) protects against pathogens that may have lodged in the distribution system downstream. | 0 | Theoretical and Fundamental Chemistry |
Nitrogen containing bisphosphonates are the current most used drugs in the class because of their potency. Studies have showed that nitrogen on bisphosphonates forms hydrogen bond with threonine (Thr201) and the carbonyl part of Lysine (Lys200) on target enzyme, therefore enhancing the binding of the complex. Altering the position of nitrogen can significantly change the ability for the nitrogen hydrogen bond to occur. | 1 | Applied and Interdisciplinary Chemistry |
The targeted DamID (TaDa) approach uses the phenomenon of ribosome reinitiation to express Dam-fusion proteins at appropriately low levels for DamID (i.e. Dam is non-saturating, thus avoiding toxicity). This construct can be combined with cell-type specific promoters resulting in tissue-specific methylation. This approach can be used to assay transcription factor binding in a cell type of interest or alternatively, dam can be fused to Pol II subunits to determine binding of RNA polymerase and thus infer cell-specific gene expression. Targeted DamID has been demonstrated in Drosophila and mouse cells. | 1 | Applied and Interdisciplinary Chemistry |
The tetrazole-alkene "photoclick" reaction is another dipolar addition that Huisgen first introduced in the late 1960s ChemBioChem 2007, 8, 1504. (68) Clovis, J. S.; Eckell, A.; Huisgen, R.; Sustmann, R. Chem. Ber. 1967, 100, 60.) Tetrazoles with amino or styryl groups that can be activated by UV light at 365 nm (365 does not damage cells) react quickly (so that the UV light does not have to be on for a long time, usually around 1–4 minutes) to make fluorogenic pyrazoline products. This reaction scheme is well suited for the purpose of labeling in live cells, because UV light at 365 nm damages cells minimally. Moreover, the reaction proceeds quickly, so that the UV light can be administered for short durations. Quantum yields for short wavelength UV light can be higher than 0.5. This allows tetrazoles to be used wavelength selectively in combination with another photoligation reaction, where at the short wavelength the tetrazole ligation reaction proceeds nearly exclusively and at longer wavelength another reaction (ligation via o-quinodimethanes) proceeds exclusively. Finally, the non-fluorogenic reactants give rise to a fluorogenic product, equipping the reaction with a built-in spectrometry handle.
Both tetrazoles and the alkene groups have been incorporated as protein handles as unnatural amino acids, but this benefit is not unique. Instead, the photoinducibility of the reaction makes it a prime candidate for spatiotemporal specificity in living systems. Challenges include the presence of endogenous alkenes, though usually cis (as in fatty acids) they can still react with the activated tetrazole. | 0 | Theoretical and Fundamental Chemistry |
While aerobic organisms during respiration use oxygen as a terminal electron acceptor, anaerobic organisms use other electron acceptors. These inorganic compounds release less energy in cellular respiration, which leads to slower growth rates than aerobes. Many facultative anaerobes can use either oxygen or alternative terminal electron acceptors for respiration depending on the environmental conditions.
Most respiring anaerobes are heterotrophs, although some do live autotrophically. All of the processes described below are dissimilative, meaning that they are used during energy production and not to provide nutrients for the cell (assimilative). Assimilative pathways for many forms of anaerobic respiration are also known. | 1 | Applied and Interdisciplinary Chemistry |
As at 2017, the company operated the following stations:
*Alexandria Station, Northern Territory
* Boomarra Station, Queensland
* Coolullah Station, Queensland
*Coorabulka Station, Queensland
* Cungelella Station, Queensland
*Glenormiston Station, Queensland
* Goldsborough Station, Queensland
*Kynuna Station (includes Dagworth Station), Queensland
* Landsborough Station, Queensland
*Marion Downs Station, Queensland
*Mittiebah Station, Northern Territory
*Monkira Station, Queensland
*Portland Downs Station, Queensland
* Wainui Feedlot and Farm, Queensland
Other properties that the company has owned include:
*Gordon Downs, Queensland | 1 | Applied and Interdisciplinary Chemistry |
Anisotropic terahertz microspectroscopy (ATM) is a spectroscopic technique in which molecular vibrations in an anisotropic material are probed with short pulses of terahertz radiation whose electric field is linearly polarized parallel to the surface of the material. The technique has been demonstrated in studies involving single crystal sucrose, fructose, oxalic acid, and molecular protein crystals in which the spatial orientation of molecular vibrations are of interest. | 0 | Theoretical and Fundamental Chemistry |
Hügelkultur (), literally mound bed or mound culture, is a horticultural technique where a mound constructed from decaying wood debris and other compostable biomass plant materials is later (or immediately) planted as a raised bed. Considered a permaculture practice, advocates claim that the technique helps to improve soil fertility, water retention, and soil warming, thus benefitting plants grown on or near such mounds. | 1 | Applied and Interdisciplinary Chemistry |
Since much of the challenge in solving the Boltzmann equation originates with the complex collision term, attempts have been made to "model" and simplify the collision term. The best known model equation is due to Bhatnagar, Gross and Krook. The assumption in the BGK approximation is that the effect of molecular collisions is to force a non-equilibrium distribution function at a point in physical space back to a Maxwellian equilibrium distribution function and that the rate at which this occurs is proportional to the molecular collision frequency. The Boltzmann equation is therefore modified to the BGK form:
where is the molecular collision frequency, and is the local Maxwellian distribution function given the gas temperature at this point in space. This is also called "relaxation time approximation". | 1 | Applied and Interdisciplinary Chemistry |
In the gram-negative bacterium Escherichia coli (E. coli), cell division may be partially regulated by AI-2-mediated quorum sensing. This species uses AI-2, which is produced and processed by the lsr operon. Part of it encodes an ABC transporter, which imports AI-2 into the cells during the early stationary (latent) phase of growth. AI-2 is then phosphorylated by the LsrK kinase, and the newly produced phospho-AI-2 can be either internalized or used to suppress LsrR, a repressor of the lsr operon (thereby activating the operon). Transcription of the lsr operon is also thought to be inhibited by dihydroxyacetone phosphate (DHAP) through its competitive binding to LsrR. Glyceraldehyde 3-phosphate has also been shown to inhibit the lsr operon through cAMP-CAPK-mediated inhibition. This explains why, when grown with glucose, E. coli will lose the ability to internalize AI-2 (because of catabolite repression). When grown normally, AI-2 presence is transient.
E. coli and Salmonella enterica do not produce AHL signals commonly found in other gram-negative bacteria. However, they have a receptor that detects AHLs from other bacteria and change their gene expression in accordance with the presence of other "quorate" populations of gram-negative bacteria. AHL quorum sensing regulates a wide range of genes through cell density. Other species of bacteria produce AHLs that Eschericia and Salmonella can detect. E.coli and Salmonella produce a receptor like protein (SdiA) allowing the amino acid sequence that is similar to AHL show AHLs can be found in the bovine rumen and E. Coli responds to AHLs taken out of the bovine rumen. Most animals do not have AHL in their gastrointestinal tracts. | 1 | Applied and Interdisciplinary Chemistry |
Phosphorus tribromide is a colourless liquid with the formula PBr. The liquid fumes in moist air due to hydrolysis and has a penetrating odour. It is used in the laboratory for the conversion of alcohols to alkyl bromides. | 0 | Theoretical and Fundamental Chemistry |
A photosynthetic reaction center is a complex of several proteins, pigments, and other co-factors that together execute the primary energy conversion reactions of photosynthesis. Molecular excitations, either originating directly from sunlight or transferred as excitation energy via light-harvesting antenna systems, give rise to electron transfer reactions along the path of a series of protein-bound co-factors. These co-factors are light-absorbing molecules (also named chromophores or pigments) such as chlorophyll and pheophytin, as well as quinones. The energy of the photon is used to excite an electron of a pigment. The free energy created is then used, via a chain of nearby electron acceptors, for a transfer of hydrogen atoms (as protons and electrons) from HO or hydrogen sulfide towards carbon dioxide, eventually producing glucose. These electron transfer steps ultimately result in the conversion of the energy of photons to chemical energy. | 0 | Theoretical and Fundamental Chemistry |
A common motif features a four iron ions and four sulfide ions placed at the vertices of a cubane-type cluster. The Fe centers are typically further coordinated by cysteinyl ligands. The [FeS] electron-transfer proteins ([FeS] ferredoxins) may be further subdivided into low-potential (bacterial-type) and high-potential (HiPIP) ferredoxins. Low- and high-potential ferredoxins are related by the following redox scheme:
In HiPIP, the cluster shuttles between [2Fe, 2Fe] (FeS) and [3Fe, Fe] (FeS). The potentials for this redox couple range from 0.4 to 0.1 V. In the bacterial ferredoxins, the pair of oxidation states are [Fe, 3Fe] (FeS) and [2Fe, 2Fe] (FeS). The potentials for this redox couple range from −0.3 to −0.7 V. The two families of 4Fe–4S clusters share the FeS oxidation state. The difference in the redox couples is attributed to the degree of hydrogen bonding, which strongly modifies the basicity of the cysteinyl thiolate ligands. A further redox couple, which is still more reducing than the bacterial ferredoxins is implicated in the nitrogenase.
Some 4Fe–4S clusters bind substrates and are thus classified as enzyme cofactors. In aconitase, the Fe–S cluster binds aconitate at the one Fe centre that lacks a thiolate ligand. The cluster does not undergo redox, but serves as a Lewis acid catalyst to convert citrate to isocitrate. In radical SAM enzymes, the cluster binds and reduces S-adenosylmethionine to generate a radical, which is involved in many biosyntheses.
The second cubane shown here with mixed valence pairs (2 Fe3+ and 2 Fe2+), has a greater stability from covalent communication and strong covalent delocalization of the “extra” electron from the reduced Fe2+ that results in full ferromagnetic coupling. | 0 | Theoretical and Fundamental Chemistry |
In chain terminator sequencing (Sanger sequencing), extension is initiated at a specific site on the template DNA by using a short oligonucleotide primer complementary to the template at that region. The oligonucleotide primer is extended using a DNA polymerase, an enzyme that replicates DNA. Included with the primer and DNA polymerase are the four deoxynucleotide bases (DNA building blocks), along with a low concentration of a chain terminating nucleotide (most commonly a di-deoxynucleotide). The deoxynucleotides lack in the OH group both at the 2 and at the 3 position of the ribose molecule, therefore once they are inserted within a DNA molecule they prevent it from being further elongated. In this sequencer four different vessels are employed, each containing only of the four dideoxyribonucleotides; the incorporation of the chain terminating nucleotides by the DNA polymerase in a random position results in a series of related DNA fragments, of different sizes, that terminate with a given dideoxiribonucleotide. The fragments are then size-separated by electrophoresis in a slab polyacrylamide gel, or more commonly now, in a narrow glass tube (capillary) filled with a viscous polymer.
An alternative to the labelling of the primer is to label the terminators instead, commonly called dye terminator sequencing. The major advantage of this approach is the complete sequencing set can be performed in a single reaction, rather than the four needed with the labeled-primer approach. This is accomplished by labelling each of the dideoxynucleotide chain-terminators with a separate fluorescent dye, which fluoresces at a different wavelength. This method is easier and quicker than the dye primer approach, but may produce more uneven data peaks (different heights), due to a template dependent difference in the incorporation of the large dye chain-terminators. This problem has been significantly reduced with the introduction of new enzymes and dyes that minimize incorporation variability.
This method is now used for the vast majority of sequencing reactions as it is both simpler and cheaper. The major reason for this is that the primers do not have to be separately labelled (which can be a significant expense for a single-use custom primer), although this is less of a concern with frequently used universal primers. This is changing rapidly due to the increasing cost-effectiveness of second- and third-generation systems from Illumina, 454, ABI, Helicos, and Dover. | 1 | Applied and Interdisciplinary Chemistry |
β-Oxidation of unsaturated fatty acids poses a problem since the location of a cis-bond can prevent the formation of a trans-Δ bond which is essential for continuation of β-Oxidation as this conformation is ideal for enzyme catalysis. This is handled by additional two enzymes, Enoyl CoA isomerase and 2,4 Dienoyl CoA reductase.
β-oxidation occurs normally until the acyl CoA (because of the presence of a double bond) is not an appropriate substrate for acyl CoA dehydrogenase, or enoyl CoA hydratase:
* If the acyl CoA contains a cis-Δ bond, then cis-Δ-Enoyl CoA isomerase will convert the bond to a trans-Δ bond, which is a regular substrate.
* If the acyl CoA contains a cis-Δ double bond, then its dehydrogenation yields a 2,4-dienoyl intermediate, which is not a substrate for enoyl CoA hydratase. However, the enzyme 2,4 Dienoyl CoA reductase reduces the intermediate, using NADPH, into trans-Δ-enoyl CoA. This compound is converted into a suitable intermediate by 3,2-Enoyl CoA isomerase and β-Oxidation continues. | 1 | Applied and Interdisciplinary Chemistry |
Directional transmittance of a surface, denoted T, is defined as
where
*L is the radiance transmitted by that surface;
*L is the radiance received by that surface. | 0 | Theoretical and Fundamental Chemistry |
Cancer biomarkers have an extremely high upside for therapeutic interventions in cancer patients. Most cancer biomarkers consist of proteins or altered segments of DNA, and are expressed in all cells, just at higher rates in cancer cells. There has not yet been one, universal tumor biomarker, but there is a biomarker for every type of cancer. These tumor biomarkers are used to track the health of tumors, but cannot serve as the sole diagnostic for specific cancers. Examples of tumoral markers used to follow up cancer treatment are the Carcinoembryonic Antigen (CEA) for colorectal cancer and the Prostate Specific Antigen (PSA) for prostate cancer. In 2014, Cancer research identified Circulating Tumor Cells (CTCs) and Circulating Tumor DNA (ctDNA) as metastasizing tumor biomarkers with special cellular differentiation and prognostic skills. Innovative technology needs to be harnessed to determine the full capabilities of CTCs and ctDNA, but insight into their roles has potential for new understanding of cancer evolution, invasion and metastasis. | 1 | Applied and Interdisciplinary Chemistry |
Alkylating agents are a type of chemotherapeutic drug which keeps the cell from undergoing mitosis by damaging its DNA. They work in all phases of the cell cycle. The use of alkylating agents may result in leukemia due to them being able to target the cells of the bone marrow. | 1 | Applied and Interdisciplinary Chemistry |
As is standard for resonance diagrams, a double-headed arrow is used to indicate that the two structures are not distinct entities, but merely hypothetical possibilities. Neither is an accurate representation of the actual compound, which is best represented by a hybrid (average) of these structures, which can be seen at right. A C=C bond is shorter than a C−C bond, but benzene is perfectly hexagonal—all six carbon-carbon bonds have the same length, intermediate between that of a single and that of a double bond.
A better representation is that of the circular π bond (Armstrongs inner cycle'), in which the electron density is evenly distributed through a π-bond above and below the ring. This model more correctly represents the location of electron density within the aromatic ring.
The single bonds are formed with electrons in line between the carbon nuclei — these are called σ-bonds. Double bonds consist of a σ-bond and a π-bond. The π-bonds are formed from overlap of atomic p-orbitals above and below the plane of the ring. The following diagram shows the positions of these p-orbitals:
Since they are out of the plane of the atoms, these orbitals can interact with each other freely, and become delocalized. This means that, instead of being tied to one atom of carbon, each electron is shared by all six in the ring. Thus, there are not enough electrons to form double bonds on all the carbon atoms, but the "extra" electrons strengthen all of the bonds on the ring equally. The resulting molecular orbital has π symmetry. | 0 | Theoretical and Fundamental Chemistry |
There are two types of VMATs expressed in humans: VMAT1 and VMAT2. VMAT1 is expressed mainly in large dense-core vesicles (LDCVs) of the peripheral nervous system. VMAT1 may be found in neuroendocrine cells, particularly chromaffin and enterochromaffin granules, which are primarily found in the medulla of the adrenal glands.
VMAT2 favors expression in a variety of monoaminergic cells of the central nervous system, such as the brain, sympathetic nervous system, mast cells, It is prevalent in β-cells, expressed in blood platelets, and co-expressed in chromaffin cells. Expression of the two transporters in internal organs seems to differ between species: only VMAT1 is expressed in rat adrenal medulla cells, whereas VMAT2 is the major transporter in bovine adrenal medulla cells. | 1 | Applied and Interdisciplinary Chemistry |
Copper-catalyzed allylic substitutions are characterized by their unique regioselectivity compared to other transition-metal-catalyzed allylic substitutions, the most well-known being the palladium-catalyzed Tsuji-Trost reaction. The distinct mechanism of copper-catalyzed allylic substitutions has been known to provide high regioselectivity of the γ substituted product, compared to the α substituted isomer. The copper catalyst used can be symmetrical with two identical R groups, or with two different ligands. These reactions typically utilize “hard” carbon nucleophiles such as Grignard, diorganozinc, organolithium, and trialkyl aluminum reagents. This contrasts palladium-catalyzed allylic substitutions which involve “soft” nucleophiles.. | 0 | Theoretical and Fundamental Chemistry |
* Handling of small quantities is not always simple.
* Higher accuracy of weighing is necessary (e.g. use of accurate balance).
* Sample surface preparation can have a major impact on measurement results. | 0 | Theoretical and Fundamental Chemistry |
Located in the cell nucleus, the microprocessor complex cleaves primary miRNA (pri-miRNA) into precursor miRNA (pre-miRNA). Its two subunits have been determined as necessary and sufficient for the mediation of the development of miRNAs from the pri-miRNAs. These molecules of around 70 nucleotides contain a stem-loop or hairpin structure. Pri-miRNA substrates can be derived either from non-coding RNA genes or from introns. In the latter case, there is evidence that the microprocessor complex interacts with the spliceosome and that the pri-miRNA processing occurs prior to splicing.
Microprocessor cleavage of pri-miRNAs typically occurs co-transcriptionally and leaves a characteristic RNase III single-stranded overhang of 2-3 nucleotides, which serves as a recognition element for the transport protein exportin-5. Pre-miRNAs are exported from the nucleus to the cytoplasm in a RanGTP-dependent manner and are further processed, typically by the endoribonuclease enzyme Dicer.
Hemin allows for the increased processing of pri-miRNAs through an induced conformational change of the DGCR8 subunit, and also enhances DGCR8's binding specificity for RNA. DGCR8 recognizes the junctions between hairpin structures and single-stranded RNA and serves to orient Drosha to cleave around 11 nucleotides away from the junctions, and remains in contact with the pri-miRNAs following cleavage and dissociation of Drosha.
Although the large majority of miRNAs undergo processing by microprocessor, a small number of exceptions called mirtrons have been described; these are very small introns which, after splicing, have the appropriate size and stem-loop structure to serve as a pre-miRNA. The processing pathways for microRNA and for exogenously derived small interfering RNA converge at the point of Dicer processing and are largely identical downstream. Broadly defined, both pathways constitute RNAi. Microprocessor is also found to be involved in ribosomal biogenesis specifically in the removal of R-loops and activating transcription of ribosomal protein encoding genes. | 1 | Applied and Interdisciplinary Chemistry |
Soft chemistry (also known as chimie douce) is a type of chemistry that uses reactions at ambient temperature in open reaction vessels with reactions similar to those occurring in biological systems. | 1 | Applied and Interdisciplinary Chemistry |
This type of categorisation of drugs is from a biological perspective and categorises them by the anatomical or functional change they induce. Drug classes that are defined by common modes of action (i.e. the functional or anatomical change they induce) include:
* Antifungals
* Antimicrobials
* Antithrombotics
* Bronchodilator
* Chronotrope (positive or negative)
* Decongestant
* Diuretic or Antidiuretic
* Inotrope (positive or negative) | 1 | Applied and Interdisciplinary Chemistry |
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