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AQC processes are of particular importance in laboratories analysing environmental samples where the concentration of chemical species present may be extremely low and close to the detection limit of the analytical method. In well managed laboratories, AQC processes are built into the routine operations of the laboratory often by the random introduction of known standards into the sample stream or by the use of spiked samples.
Quality control begins with sample collection and ends with the reporting of data. AQC is achieved through laboratory control of analytical performance. Initial control of the complete system can be achieved through specification of laboratory services, instrumentation, glassware, reagents, solvents, and gases. However, evaluation of daily performance must be documented to ensure continual production of valid data. A check should first be done to ensure that the data should be seen is precise and accurate. Next, systematic daily checks such as analysing blanks, calibration standards, quality control check samples, and references must be performed to establish the reproducibility of the data. The checks help certify that the methodology is measuring what is in the sample.
The quality of individual AQC efforts can be variable depending on the training, professional pride, and importance of a particular project to a particular analyst. The burden of an individual analyst originating AQC efforts can be lessened through the implementation of quality assurance programs. Through the implementation of established and routine quality assurance programs, two primary functions are fulfilled: the determination of quality, and the control of quality. By monitoring the accuracy and precision of results, the quality assurance program should increase confidence in the reliability of the reported analytical results, thereby achieving adequate AQC. | 2 | Environmental Chemistry |
Rewarming can be done with a number of methods including passive external rewarming, active external rewarming, and active internal rewarming. Passive external rewarming involves the use of a person's own ability to generate heat by providing properly insulated dry clothing and moving to a warm environment. Passive external rewarming is recommended for those with mild hypothermia.
Active external rewarming involves applying warming devices externally, such as a heating blanket. These may function by warmed forced air (Bair Hugger is a commonly used device), chemical reactions, or electricity. In wilderness environments, hypothermia may be helped by placing hot water bottles in both armpits and in the groin. Active external rewarming is recommended for moderate hypothermia. Active core rewarming involves the use of intravenous warmed fluids, irrigation of body cavities with warmed fluids (the chest or abdomen), use of warm humidified inhaled air, or use of extracorporeal rewarming such as via a heart lung machine or extracorporeal membrane oxygenation (ECMO). Extracorporeal rewarming is the fastest method for those with severe hypothermia. When severe hypothermia has led to cardiac arrest, effective extracorporeal warming results in survival with normal mental function about 50% of the time. Chest irrigation is recommended if bypass or ECMO is not possible.
Rewarming shock (or rewarming collapse) is a sudden drop in blood pressure in combination with a low cardiac output which may occur during active treatment of a severely hypothermic person. There was a theoretical concern that external rewarming rather than internal rewarming may increase the risk. These concerns were partly believed to be due to afterdrop, a situation detected during laboratory experiments where there is a continued decrease in core temperature after rewarming has been started. Recent studies have not supported these concerns, and problems are not found with active external rewarming. | 1 | Biochemistry |
The Dawson structure is a well-known structural motif for heteropoly acids. The Dawson structure can be viewed as the fusion of two defect Keggin structure, fragments with three missing octahedra. As in Keggin structures, the Dawson structure has an oxyanion at its core. Unlike Keggin structures, there are two such anions, one at each side of the ellipsoidal anion. An example is , which can also be described as .
Commonly, Dawson structures feature phosphate as the central oxyanions. When the Keggin anion is allowed to stand in aqueous solution, it converts to . | 7 | Physical Chemistry |
The Stokes Formulas can be used to calculate the ART fractions for any number of layers. Alternatively, they can be calculated by successive application of Benford's equation for "one more layer".
If , , and are known for the representative layer of a sample, and , and are known for a layer composed of representative layers, the ART fractions for a layer with thickness of are: | 7 | Physical Chemistry |
The isochore theory purported that the genome of "warm-blooded" vertebrates (mammals and birds) are mosaics of long isochoric regions of alternating GC-poor and GC-rich composition, as opposed to the genome of "cold-blooded" vertebrates (fishes and amphibians) that were supposed to lack GC-rich isochores.
These findings were explained by the thermodynamic stability hypothesis, attributing genomic structure to body temperature. GC-rich isochores were purported to be a form of adaptation to environmental pressures, as an increase in genomic GC-content could protect DNA, RNA, and proteins from degradation by heat.
Despite its attractive simplicity, the thermodynamic stability hypothesis has been repeatedly shown to be in error
Many authors showed the absence of a relationship between temperature and GC-content in vertebrates, while others showed the existence of GC-rich domains in "cold-blooded" vertebrates such as crocodiles, amphibians, and fish. | 1 | Biochemistry |
RiPPs consist of any peptides (i.e. molecular weight below 10 kDa) that are ribosomally-produced and undergo some degree of enzymatic post-translational modification. This combination of peptide translation and modification is referred to as "post-ribosomal peptide synthesis" (PRPS) in analogy with nonribosomal peptide synthesis (NRPS).
Historically, the current sub-classes of RiPPs were studied individually, and common practices in nomenclature varied accordingly in the literature. More recently, with the advent of broad genome sequencing, it has been realized that these natural products share a common biosynthetic origin. In 2013, a set of uniform nomenclature guidelines were agreed upon and published by a large group of researchers in the field. Prior to this report, RiPPs were referred to by a variety of designations, including post-ribosomal peptides, ribosomal natural products, and ribosomal peptides.
The acronym "RiPP" stands for "ribosomally synthesized and post-translationally modified peptide". | 1 | Biochemistry |
Two main ways of cultivating microalgae are raceway pond systems and photo-bioreactors. Raceway pond systems are constructed by a closed loop oval channel that has a paddle wheel to circulate water and prevent sedimentation. The channel is open to the air and its depth is in the range of . The pond needs to be kept shallow since self-shading and optical absorption can cause the limitation of light penetration through the solution of algae broth. PBRs's culture medium is constructed by closed transparent array of tubes. It has a central reservoir which circulated the microalgae broth. PBRs is an easier system to be controlled compare to the raceway pond system, yet it costs a larger overall production expenses.
The carbon emissions from microalgae biomass produced in raceway ponds could be compared to the emissions from conventional biodiesel by having inputs of energy and nutrients as carbon-intensive. The corresponding emissions from microalgae biomass produced in PBRs could also be compared and might even exceed the emissions from conventional fossil diesel. The inefficiency is due to the amount of electricity used to pump the algae broth around the system. Using co-product to generate electricity is one strategy that might improve the overall carbon balance. Another thing that needs to be acknowledged is that environmental impacts can also come from water management, carbon dioxide handling, and nutrient supply, several aspects that could constrain system design and implementation options. But, in general, Raceway Pond systems demonstrate a more attractive energy balance than PBR systems. | 0 | Organic Chemistry |
An example of a set of EPDs looks like the following chart. Each set of letters stands for a specific measurement with an accuracy reading and percent rank below it. Each EPD is compared to the breed average of a given year. The number given by the EPD is the amount above or below this given average. | 1 | Biochemistry |
In organic chemistry and biochemistry it is customary to use pK values for acid dissociation equilibria.
where log denotes a logarithm to base 10 or common logarithm, and K is a stepwise acid dissociation constant. For bases, the base association constant, pK is used. For any given acid or base the two constants are related by , so pK can always be used in calculations.
On the other hand, stability constants for metal complexes, and binding constants for host–guest complexes are generally expressed as association constants. When considering equilibria such as
:M + HL ML + H
it is customary to use association constants for both ML and HL. Also, in generalized computer programs dealing with equilibrium constants it is general practice to use cumulative constants rather than stepwise constants and to omit ionic charges from equilibrium expressions. For example, if NTA, nitrilotriacetic acid, N(CHCOH) is designated as HL and forms complexes ML and MHL with a metal ion M, the following expressions would apply for the dissociation constants.
The cumulative association constants can be expressed as
Note how the subscripts define the stoichiometry of the equilibrium product. | 7 | Physical Chemistry |
A superglass is a phase of matter which is characterized by superfluidity and a frozen amorphous structure at the same time.
J.C. Séamus Davis theorised that frozen helium-4 (at 0.2 K and 50 atm) may be a superglass. | 7 | Physical Chemistry |
The Lyman-alpha transition in hydrogen in the presence of the spin–orbit interaction involves the transitions
: and
In the presence of an external magnetic field, the weak-field Zeeman effect splits the 1S and 2P levels into 2 states each () and the 2P level into 4 states (). The Landé g-factors for the three levels are:
: for (j=1/2, l=0)
: for (j=1/2, l=1)
: for (j=3/2, l=1).
Note in particular that the size of the energy splitting is different for the different orbitals, because the g values are different. On the left, fine structure splitting is depicted. This splitting occurs even in the absence of a magnetic field, as it is due to spin–orbit coupling. Depicted on the right is the additional Zeeman splitting, which occurs in the presence of magnetic fields. | 7 | Physical Chemistry |
* J. Ipaktschi, M. R. Saidi: Metal-Mediated Cyclizations of Amines, Science of synthesis 2012, 40.1.1.5.5, p. 351–504. | 0 | Organic Chemistry |
Phytoglycogen is a type of glycogen extracted from plants. It is a highly branched, water-soluble polysaccharide derived from glucose.
Phytoglycogen is a highly branched polysaccharide used to store glucose in a similar way that glycogen is the glucose storage for animals. It is made up of branched, flexible chains on glucose molecules that grow similarly to synthetic dendrimers. The special structure of the phytoglycogen allows it to have low viscosity, high water retention, as well as high stability in water, and stabilize bioactive compounds and form films on surfaces. Thus, this monodisperse nanoparticle is able to be used in many different technologies. | 1 | Biochemistry |
The mucoadhesive process will differ greatly depending on the surface and properties of the adhesive. However, two general steps of the process have been identified: the contact stage and the consolidation stage. | 1 | Biochemistry |
RNA editing through the addition and deletion of uracil has been found in kinetoplasts from the mitochondria of Trypanosoma brucei.
Because this may involve a large fraction of the sites in a gene, it is sometimes called "pan-editing" to distinguish it from topical editing of one or a few sites.
Pan-editing starts with the base-pairing of the unedited primary transcript with a guide RNA (gRNA), which contains complementary sequences to the regions around the insertion/deletion points. The newly formed double-stranded region is then enveloped by an editosome, a large multi-protein complex that catalyzes the editing. The editosome opens the transcript at the first mismatched nucleotide and starts inserting uridines. The inserted uridines will base-pair with the guide RNA, and insertion will continue as long as A or G is present in the guide RNA and will stop when a C or U is encountered. The inserted nucleotides cause a frameshift, and result in a translated protein that differs from its gene.
The mechanism of the editosome involves an endonucleolytic cut at the mismatch point between the guide RNA and the unedited transcript. The next step is catalyzed by one of the enzymes in the complex, a terminal U-transferase, which adds Us from UTP at the 3 end of the mRNA. The opened ends are held in place by other proteins in the complex. Another enzyme, a U-specific exoribonuclease, removes the unpaired Us. After editing has made mRNA complementary to gRNA, an RNA ligase rejoins the ends of the edited mRNA transcript. As a consequence, the editosome can edit only in a 3 to 5' direction along the primary RNA transcript. The complex can act on only a single guide RNA at a time. Therefore, a RNA transcript requiring extensive editing will need more than one guide RNA and editosome complex. | 1 | Biochemistry |
Selenizza is a naturally occurring solid hydrocarbon bitumen found in native deposits in Selenice, in Albania, the only European asphalt mine still in use. The bitumen is found in the form of veins, filling cracks in a more or less horizontal direction. The bitumen content varies from 83% to 92% (soluble in carbon disulphide), with a penetration value near to zero and a softening point (ring and ball) around 120 °C. The insoluble matter, consisting mainly of silica ore, ranges from 8% to 17%.
Albanian bitumen extraction has a long history and was practiced in an organized way by the Romans. After centuries of silence, the first mentions of Albanian bitumen appeared only in 1868, when the Frenchman Coquand published the first geological description of the deposits of Albanian bitumen. In 1875, the exploitation rights were granted to the Ottoman government and in 1912, they were transferred to the Italian company Simsa. Since 1945, the mine was exploited by the Albanian government and from 2001 to date, the management passed to a French company, which organized the mining process for the manufacture of the natural bitumen on an industrial scale.
Today the mine is predominantly exploited in an open pit quarry but several of the many underground mines (deep and extending over several km) still remain viable. Selenizza is produced primarily in granular form, after melting the bitumen pieces selected in the mine.
Selenizza is mainly used as an additive in the road construction sector. It is mixed with traditional bitumen to improve both the viscoelastic properties and the resistance to ageing. It may be blended with the hot bitumen in tanks, but its granular form allows it to be fed in the mixer or in the recycling ring of normal asphalt plants. Other typical applications include the production of mastic asphalts for sidewalks, bridges, car-parks and urban roads as well as drilling fluid additives for the oil and gas industry. Selenizza is available in powder or in granular material of various particle sizes and is packaged in sacks or in thermal fusible polyethylene bags.
A life-cycle assessment study of the natural selenizza compared with petroleum bitumen has shown that the environmental impact of the selenizza is about half the impact of the road asphalt produced in oil refineries in terms of carbon dioxide emission. | 7 | Physical Chemistry |
Glycerol 2-phosphate is the conjugate base of phosphoric ester of glycerol. It is commonly known as β-glycerophosphate or BGP. Unlike glycerol 1-phosphate and glycerol 3-phosphate, this isomer is not chiral. It is also less common. | 1 | Biochemistry |
BASys (Bacterial Annotation System) is a freely available web server that can be used to perform automated, comprehensive annotation of bacterial genomes. With the advent of next generation DNA sequencing it is now possible to sequence the complete genome of a bacterium (typically ~4 million bases) within a single day. This has led to an explosion in the number of fully sequenced microbes. In fact, as of 2013, there were more than 2700 fully sequenced bacterial genomes deposited with GenBank. However, a continuing challenge with microbial genomics is finding the resources or tools for annotating the large number of newly sequenced genomes. BASys was developed in 2005 in anticipation of these needs. In fact, BASys was the world’s first publicly accessible microbial genome annotation web server. Because of its widespread popularity, the BASys server was updated in 2011 through the addition of multiple server nodes to handle the large number of queries it was receiving.
The BASys server is designed to accept either assembled genome data (raw DNA sequence data) or complete proteome assignments as input. If raw DNA sequence is provided, BASys employs Glimmer (version 2.1.3) to identify the genes. The output from BASys is a comprehensive genome-wide annotation (with ~60 annotation subfields for each gene) and a zoomable, hyperlinked genome map of the query genome. BASys uses nearly 30 different programs to determine and annotate gene/protein names, GO functions, COG functions, possible paralogues and orthologues, molecular weight, isoelectric point, operon structure, subcellular localization, signal peptides, transmembrane regions, secondary structure, 3D structure, reactions and pathways. The full list of programs used by BASys is given below:
In addition to its extensive annotation for each gene/protein in the query genome, BASys also generates colorful, clickable and fully zoomable circular maps of each input chromosome. These bacterial genome maps are generated used a program called CGView (Circular Genome Viewer) which was developed in 2004. The genome maps are designed to allow rapid navigation and detailed visualization of all the BASys-generated gene annotations. A complete BASys run takes approximately 16 h for an average bacterial chromosome (approximately 4 Megabases). BASys annotations may be viewed and downloaded anonymously or through a password protected access system. BASys will store its bacterial genome annotations on the server for a maximum of 180 days. BASys handles approximately 1000 submissions a year. BASys is accessible at https://www.basys.ca/ | 1 | Biochemistry |
Mechanisms for C-H activations by metal centers can be classified into three general categories:
*(i) Oxidative addition, in which a low-valent metal center inserts into a carbon-hydrogen bond, which cleaves the bond and oxidizes the metal:
:LM + RH → LMR(H)
*(ii) Electrophilic activation in which an electrophilic metal attacks the hydrocarbon, displacing a proton:
:LM + RH → LMR + H
*(iii) Sigma-bond metathesis, which proceeds through a "four-centered" transition state in which bonds break and form in a single step:
:LMX + RH → LMR + XH | 0 | Organic Chemistry |
The LaMer model for the kinetics of the formation of hydrosols is widely applicable for production of monodisperse systems, and it was originally hypothesized that the Stöber process followed this monomer addition model. This model includes a rapid burst of nucleation forming all of the particle growth sites, then proceeds with hydrolysis as the rate-limiting step for condensation of triethylsilanol monomers to the nucleation sites. The production of monodisperse particle sizes is attributed to monomer addition happening at a slower rate on larger particles as a consequence of diffusion-limited mass transfer of TEOS. However, experimental evidence demonstrates that the concentration of hydrolyzed TEOS stays above that required for nucleation until late into the reaction, and the introduction of seeded growth nuclei does not match the kinetics of a monomer addition process. Consequently, the LaMer model has been rejected in favour of a kinetic model based around growth via particle aggregation.
Under an aggregation-based model, nucleation sites are continually being generated and absorbed where the merging leads to particle growth. The generation of the nucleation sites and the interaction energy between merging particles dictates the overall kinetics of the reaction. The generation of the nucleation sites follows the equation below:
Where J is the nucleation rate, k and k are rate constants based on the concentrations of HO and NH and g is the normalization factor based on the amount of silica precursor. Adjusting the concentration ratios of these compounds directly influences the rate at which nucleation sites are produced.
Merging of nucleation sites between particles is influenced by their interaction energies. The total interaction energy is dependent on three forces: electrostatic repulsion of like charges, vanderWaals attraction between particles, and the effects of solvation. These interaction energies (equations below) describe the particle aggregation process and demonstrate why the Stöber process produces particles that are uniform in size.
The van der Waals attraction forces are governed by the following equation:
Where A is the Hamaker constant, R is the distance between the centers of the two particles and a, a are the radii of the two particles. For electrostatic repulsion force the equation is as follows:
: where
Where ε is the dielectric constant of the medium, k is Boltzmanns constant, e is the elementary charge, T is the absolute temperature, κ is the inverse Debye length for a 1:1 electrolyte, x is the (variable) distance between the particles, and φ' is the surface potential. The final component of the total interaction energy is the solvation repulsion which is as follows:
Where A is the pre-exponential factor (1.5 × 10 J m) and L is the decay length (1 × 10 m).
This model for controlled growth aggregation fits with experimental observations from small-angle X-ray scattering techniques and accurately predicts particle sizing based on initial conditions. In addition, experimental data from techniques including microgravity analysis and variable pH analysis agree with predictions from the aggregate growth model. | 7 | Physical Chemistry |
Neuropeptides are small proteins used for communication in the nervous system. Neuropeptides represent the most diverse class of signaling molecules. There are 90 known genes that encode human neuropeptide precursors. In invertebrates, there are ~50 known genes encoding neuropeptide precursors. Most neuropeptides bind to G-protein coupled receptors, however some neuropeptides directly gate ion channels or act through kinase receptors.
* Opioid peptides – a large family of endogenous neuropeptides that are widely distributed throughout the central and peripheral nervous system. Opiate drugs such as heroin and morphine act at the receptors of these neurotransmitters.
# Endorphins
# Enkephalins
# Dynorphins
* Vasopressin
* Oxytocin
* Gastrin
* Cholecystokinins
* Somatostatin
* Cortistatins
* RF-amides
* Neuropeptide FF
* Neuropeptide Y -
* Pancreatic Polypeptide
* Peptide YY
* Prolactin-releasing peptide
* Calcitonin
* Adrenomedullin
* Natriuretic
* Bombesin-like peptides
* Endothelin
* Glucagon
* Secretin
* Vasoactive Intestinal Peptide
* Growth Hormone Releasing Hormone
* Gastric Inhibitory Peptide
* Corticotropin Releasing Hormone
* Urocortin
* Urotensin
* Substance P
* Neuromedins
* Tensin
* Kinin
* Granin
* Nerve Growth Factor
* Motilin
* Ghrelin
* Galanin
* Neuropeptide B/W
* Neurexophilin
* Insulin
* Relaxin
* Agouti-related protein homolog gene
* Prolactin
* Apelin
* Metastasis-suppressor
* Diazepam-binding inhibitor
* Cerebellins
* Leptin
* Adiponectin
* Visfatin
* Resistin
* Nucleibindin
* Ubiquitin | 1 | Biochemistry |
Teeth (singular tooth) are small whitish structures found in the jaws (or mouths) of many vertebrates that are used to tear, scrape, milk and chew food. Teeth are not made of bone, but rather of tissues of varying density and hardness, such as enamel, dentine and cementum. Human teeth have a blood and nerve supply which enables proprioception. This is the ability of sensation when chewing, for example if we were to bite into something too hard for our teeth, such as a chipped plate mixed in food, our teeth send a message to our brain and we realise that it cannot be chewed, so we stop trying.
The shapes, sizes and numbers of types of animals' teeth are related to their diets. For example, herbivores have a number of molars which are used to grind plant matter, which is difficult to digest. Carnivores have canine teeth which are used to kill and tear meat. | 1 | Biochemistry |
YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48000 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references. It also includes the description of about 300 specific DNA binding sites for more than a hundred characterized TFs. Further information about each Yeast gene has been extracted from the Saccharomyces Genome Database (SGD). For each gene the associated Gene Ontology (GO) terms and their hierarchy in GO was obtained from the GO consortium. Currently, YEASTRACT maintains more than 7100 terms from GO. The nucleotide sequences of the promoter and coding regions for Yeast genes were obtained from Regulatory Sequence Analysis Tools (RSAT). All the information in YEASTRACT is updated regularly to match the latest data from SGD, GO consortium, RSA Tools and recent literature on yeast regulatory networks.
YEASTRACT includes DISCOVERER, a set of tools that can be used to identify complex motifs found to be over-represented in the promoter regions of co-regulated genes. DISCOVERER is based on the MUSA algorithm. These algorithms take as input a list of genes and identify over-represented motifs, which can then be compared with transcription factor binding sites described in the YEASTRACT database.
Facilities are also provided to enable the exploitation of the gathered data when solving a number of biological questions, as exemplified in the Tutorial. YEASTRACT allows the identification of documented or potential transcription regulators of a given gene and of documented or potential regulons for each transcription factor. It also renders possible the comparison between DNA motifs and the transcription factor binding sites described in the literature. The system also provides a useful mechanism for grouping a list of genes (for instance a set of genes with similar expression profiles as revealed by microarray analysis) based on their regulatory associations with known transcription factors.
YEASTRACT provides a set of queries to search and retrieve important biological information from the gathered data and to predict transcription regulation networks in yeast from data emerging from gene-by-gene analysis or global approaches. | 1 | Biochemistry |
Radical clocks are used in reduction of alkyl halides with sodium naphthalenide, reaction of enones, the Wittig rearrangement, reductive elimination reactions of dialkylmercury compounds, dioxirane dihydroxylations, and electrophilic fluorinations. | 7 | Physical Chemistry |
In chemical kinetics, the entropy of activation of a reaction is one of the two parameters (along with the enthalpy of activation) which are typically obtained from the temperature dependence of a reaction rate constant, when these data are analyzed using the Eyring equation of the transition state theory. The standard entropy of activation is symbolized and equals the change in entropy when the reactants change from their initial state to the activated complex or transition state ( = change, = entropy, = activation). | 7 | Physical Chemistry |
Gaia scientists see the participation of living organisms in the carbon cycle as one of the complex processes that maintain conditions suitable for life. The only significant natural source of atmospheric carbon dioxide (CO) is volcanic activity, while the only significant removal is through the precipitation of carbonate rocks. Carbon precipitation, solution and fixation are influenced by the bacteria and plant roots in soils, where they improve gaseous circulation, or in coral reefs, where calcium carbonate is deposited as a solid on the sea floor. Calcium carbonate is used by living organisms to manufacture carbonaceous tests and shells. Once dead, the living organisms' shells fall. Some arrive at the bottom of shallow seas where the heat and pressure of burial, and/or the forces of plate tectonics, eventually convert them to deposits of chalk and limestone. Much of the falling dead shells, however, redissolve into the ocean below the carbon compensation depth.
One of these organisms is Emiliania huxleyi, an abundant coccolithophore algae which may have a role in the formation of clouds. CO excess is compensated by an increase of coccolithophorid life, increasing the amount of CO locked in the ocean floor. Coccolithophorids, if the CLAW Hypothesis turns out to be supported (see "Regulation of Global Surface Temperature" above), could help increase the cloud cover, hence control the surface temperature, help cool the whole planet and favor precipitation necessary for terrestrial plants. Lately the atmospheric CO concentration has increased and there is some evidence that concentrations of ocean algal blooms are also increasing.
Lichen and other organisms accelerate the weathering of rocks in the surface, while the decomposition of rocks also happens faster in the soil, thanks to the activity of roots, fungi, bacteria and subterranean animals. The flow of carbon dioxide from the atmosphere to the soil is therefore regulated with the help of living organisms. When CO levels rise in the atmosphere the temperature increases and plants grow. This growth brings higher consumption of CO by the plants, who process it into the soil, removing it from the atmosphere. | 9 | Geochemistry |
The Pandoran biosphere is a fictional habitat introduced in James Camerons 2009 science fiction film Avatar. The ecology of the lush exomoon Pandora, which teems with a biodiversity of bioluminescent species ranging from hexapodal animals to other types of exotic fauna and flora, forms a vast neural network spanning the entire lunar surface into which the Navi and other creatures can connect. The strength of this collective consciousness is illustrated when the human invaders are defeated in battle by the Pandoran ecology, after the Na'vi are nearly defeated. Cameron utilized a team of expert advisors to make the various examples of fauna and flora as scientifically feasible as possible. | 1 | Biochemistry |
In the gas phase at ultralow pressures, single-molecule experiments have been around for decades, but in the condensed phase only since 1989 with the work by W. E. Moerner and Lothar Kador. One year later, Michel Orrit and Jacky Bernard were able to show also the detection of the absorption of single molecules by their fluorescence.
Many techniques have the ability to observe one molecule at a time, most notably mass spectrometry, where single ions are detected. In addition, one of the earliest means of detecting single molecules, came about in the field of ion channels with the development of the patch clamp technique by Erwin Neher and Bert Sakmann (who later went on to win the Nobel prize for their seminal contributions). However, the idea of measuring conductance to look at single molecules placed a serious limitation on the kind of systems which could be observed.
Fluorescence is a convenient means of observing one molecule at a time, mostly due to the sensitivity of commercial optical detectors, capable of counting single photons. However, spectroscopically, the observation of one molecule requires that the molecule is in an isolated environment and that it emits photons upon excitation, which owing to the technology to detect single photons by use of photomultiplier tubes (PMT) or avalanche photodiodes (APD), enables one to record photon emission events with great sensitivity and time resolution.
More recently, single-molecule fluorescence is the subject of intense interest for biological imaging, through the labeling of biomolecules such as proteins and nucleotides to study enzymatic function which cannot easily be studied on the bulk scale, due to subtle time-dependent movements in catalysis and structural reorganization. The most studied protein has been the class of myosin/actin enzymes found in muscle tissues. Through single-molecule techniques the step mechanism has been observed and characterized in many of these proteins.
In 1997, single-molecule detection was demonstrated with surface-enhanced Raman spectroscopy (SERS) by Katrin Kneipp, H. Kneipp, Y. Wang, L.T. Perelman and others at MIT and independently by S. Nie and S. R. Emory at Indiana University. The MIT team used non-resonance Raman excitation and surface enhancement with silver nanoclusters to detect single cresyl violet molecules, while the team at Indiana University used resonance Raman excitation and surface enhancement with silver nanoparticles to detect single rhodamine 6G molecules.
Nanomanipulators such as the atomic force microscope are also suited to single-molecule experiments of biological significance, since they work on the same length scale of most biological polymers. Besides, atomic force microscopy (AFM) is appropriate for the studies of synthetic polymer molecules. AFM provides a unique possibility of 3D visualization of polymer chains. For instance, AFM tapping mode is gentle enough for the recording of adsorbed polyelectrolyte molecules (for example, 0.4 nm thick chains of poly(2-vinylpyridine)) under liquid medium. The location of two-chain-superposition correspond in these experiments to twice the thickness of single chain (0.8 nm in the case of the mentioned example). At the application of proper scanning parameters, conformation of such molecules remain unchanged for hours that allows the performance of experiments under liquid media having various properties. Furthermore, by controlling the force between the tip and the sample high resolution images can be obtained. Optical tweezers have also been used to study and quantify DNA-protein interactions. | 7 | Physical Chemistry |
Cation-exchange capacity (CEC) is a measure of how many cations can be retained on soil particle surfaces. Negative charges on the surfaces of soil particles bind positively-charged atoms or molecules (cations), but allow these to exchange with other positively charged particles in the surrounding soil water. This is one of the ways that solid materials in soil alter the chemistry of the soil. CEC affects many aspects of soil chemistry, and is used as a measure of soil fertility, as it indicates the capacity of the soil to retain several nutrients (e.g. K, NH, Ca) in plant-available form. It also indicates the capacity to retain pollutant cations (e.g. Pb). | 9 | Geochemistry |
F-gases are ozone-friendly, enable energy efficiency, and are relatively safe for use by the public due to their low levels of toxicity and flammability. However, most F-gases have a high global warming potential (GWP), and some are nearly inert to removal by chemical processes. If released, HFCs stay in the atmosphere for decades and both PFCs and SF can stay in the atmosphere for millennia.
The total atmospheric concentration of F-gases, CFCs, and HCFCs has grown rapidly since the mid-twentieth century; a time which marks the start of their production and use at industrial scale. As a group in year 2019, these unnatural man-made gases are responsible for about one-tenth of the direct radiative forcing from all long-lived anthropogenic greenhouse gases.
F-gases are used in a number of applications intended for climate change mitigation, that can generate further positive feedback for atmospheric heating. For example, refrigeration and air conditioning systems are increasingly utilized by humans within a warming environment. Likewise, expansions of electrical infrastructure, as driven by the alternatives to fossil fuels, has led to rising demand for SF. If recent trends of aggressive (5% and greater CAGR) annual growth for such types of F-gas production were to continue into the future without complimentary reductions in GWP and/or atmospheric leakage, their warming influence could soon rival those of CO and CH which are trending at less than about 2% annual growth. | 2 | Environmental Chemistry |
There is one assay office at Aradippou.
The Law governing the marking of precious metal articles has been ratified by the House of Representatives in 1991, creating a new semi-Governmental Organisation, the Cyprus Organisation for the Hallmarking of precious metals. The Cyprus Assay Office (CAO) is under the jurisdiction of the Ministry of Commerce, Industry and Tourism.
The Cyprus Hallmark consists of three compulsory symbols: 1. The manufacturers mark - Consists of the initials of the manufacturer of the article surrounded by a small shield; 2. The fineness mark - The purity of the metal, in parts per thousand; 3. The official mark - the Head of Aphrodite until December 2001 and a ship as from January 2002 denotes that the article is made of gold, and the fish that the article is made of silver. The manufacturers mark must be struck on the articles by the manufacturer before it is submitted to the Assay Office for hallmarking. The manufacturer may make arrangements for the manufacture's mark to be struck by the Assay Office upon submission of the article to be struck with the approved hallmarks.
The manufacturer's mark which is registered under the relevant section of the law shall include the initial letters of the name or names of the manufacturer and shall be of such design as may be approved by the Assay Office. The standards of fineness of gold and silver articles that are hallmarked are for gold: 375, 585, 750 and 916 parts per thousand; for silver: 800, 830 and 925 parts per thousand; no negative tolerance is permitted on the above standards of fineness. | 3 | Analytical Chemistry |
Because T-RFLP relies on DNA extraction methods and PCR, the biases inherent to both will affect the results of the analysis. Also, the fact that only the terminal fragments are being read means that any two distinct sequences which share a terminal restriction site will result in one peak only on the electropherogram and will be indistinguishable. Indeed, when T-RFLP is applied on a complex microbial community the result is often a compression of the total diversity to normally 20-50 distinct peaks only representing each an unknown number of distinct sequences. Although this phenomenon makes the T-RFLP results easier to handle, it naturally introduces biases and oversimplification of the real diversity. Attempts to minimize (but not overcome) this problem are often done by applying several restriction enzymes and/ or labeling both primers with a different fluorescent dye. The inability to retrieve sequences from T-RFLP often leads to the need to construct and analyze one or more clone libraries in parallel to the T-RFLP analysis which adds to the effort and complicates analysis. The possible appearance of false (pseudo) T-RFs, as discussed above, is yet another drawback. To handle this researchers often only consider peaks which can be affiliated to sequences in a clone library. | 1 | Biochemistry |
* Fluorescence microscopy of tissues, cells or subcellular structures is accomplished by labeling an antibody with a fluorophore and allowing the antibody to find its target antigen within the sample. Labeling multiple antibodies with different fluorophores allows visualization of multiple targets within a single image.
* Automated sequencing of DNA by the chain termination method; each of four different chain terminating bases has its own specific fluorescent tag. As the labeled DNA molecules are separated, the fluorescent label is excited by a UV source, and the identity of the base terminating the molecule is identified by the wavelength of the emitted light.
* DNA detection: the compound ethidium bromide, when free to change its conformation in solution, has very little fluorescence. Ethidium bromide's fluorescence is greatly enhanced when it binds to DNA, so this compound is very useful in visualising the location of DNA fragments in agarose gel electrophoresis. Ethidium bromide can be toxic – a purportedly safer alternative is the dye SYBR Green.
* The DNA microarray.
* Immunology: An antibody has a fluorescent chemical group attached, and the sites (e.g., on a microscopic specimen) where the antibody has bound can be seen, and even quantified, by the fluorescence.
* FACS (fluorescent-activated cell sorting).
* Microscale Thermophoresis (MST) uses fluorescence as readout to quantify the directed movement of biomolecules in microscopic temperature gradients.
* Fluorescence has been used to study the structure and conformations of DNA and proteins with techniques such as Fluorescence resonance energy transfer, which measures distance at the angstrom level. This is especially important in complexes of multiple biomolecules.
* Fluorescence can be applied to study colocalization of various proteins of interest. It then can be analyzed using a specialized software, like CoLocalizer Pro.
Also, many biological molecules have an intrinsic fluorescence that can sometimes be used without the need to attach a chemical tag. Sometimes this intrinsic fluorescence changes when the molecule is in a specific environment, so the distribution or binding of the molecule can be measured. Bilirubin, for instance, is highly fluorescent when bound to a specific site on serum albumin. Zinc protoporphyrin, formed in developing red blood cells instead of hemoglobin when iron is unavailable or lead is present, has a bright fluorescence and can be used to detect these problems.
The number of fluorescence applications in the biomedical, biological and related sciences continuously expands. Methods of analysis in these fields are also growing, often with nomenclature in the form of acronyms such as: FLIM, FLI, FLIP, CALI, FLIE, FRET, FRAP, FCS, PFRAP, smFRET, FIONA, FRIPS, SHREK, SHRIMP or TIRF. Most of these techniques rely on fluorescence microscopes, which use high intensity light sources, usually mercury or xenon lamps, LEDs, or lasers, to excite fluorescence in the samples under observation. Optical filters then separate excitation light from emitted fluorescence to be detected by eye or with a (CCD) camera or other light detector (e.g., photomultiplier tubes, spectrographs). Considerable research is underway to improve the capabilities of such microscopes, the fluorescent probes used, and the applications they are applied to. Of particular note are confocal microscopes, which use a pinhole to achieve optical sectioning, which affords a quantitative, 3D view of the sample. | 1 | Biochemistry |
The Felkin model (1968) named after Hugh Felkin also predicts the stereochemistry of nucleophilic addition reactions to carbonyl groups. Felkin argued that the Cram model suffered a major drawback: an eclipsed conformation in the transition state between the carbonyl substituent (the hydrogen atom in aldehydes) and the largest α-carbonyl substituent. He demonstrated that by increasing the steric bulk of the carbonyl substituent from methyl to ethyl to isopropyl to isobutyl, the stereoselectivity also increased, which is not predicted by Cram's rule:
The Felkin rules are:
* The transition states are reactant-like.
* Torsional strain (Pitzer strain) involving partial bonds (in transition states) represents a substantial fraction of the strain between fully formed bonds, even when the degree of bonding is quite low. The conformation in the TS is staggered and not eclipsed with the substituent R skew with respect to two adjacent groups one of them the smallest in TS A.
: For comparison TS B is the Cram transition state.
* The main steric interactions involve those around R and the nucleophile but not the carbonyl oxygen atom.
* Attack of the nucleophile occurs according to the Dunitz angle (107 degrees), eclipsing the hydrogen, rather than perpendicular to the carbonyl.
* A polar effect or electronic effect stabilizes a transition state with maximum separation between the nucleophile and an electron-withdrawing group. For instance haloketones do not obey Cram's rule, and, in the example above, replacing the electron-withdrawing phenyl group by a cyclohexyl group reduces stereoselectivity considerably. | 4 | Stereochemistry |
It is extremely difficult to generalize at what pressures or temperatures the deviation from the ideal gas becomes important. As a rule of thumb, the ideal gas law is reasonably accurate up to a pressure of about 2 atm, and even higher for small non-associating molecules. For example, methyl chloride, a highly polar molecule and therefore with significant intermolecular forces, the experimental value for the compressibility factor is at a pressure of 10 atm and temperature of 100 °C. For air (small non-polar molecules) at approximately the same conditions, the compressibility factor is only (see table below for 10 bars, 400 K). | 7 | Physical Chemistry |
Nuclei also have distinct energy states that are widely separated and lead to gamma ray spectra. Distinct nuclear spin states can have their energy separated by a magnetic field, and this allows for nuclear magnetic resonance spectroscopy. | 7 | Physical Chemistry |
MAP4 was previously not thought to exist in neuronal tissue however the MAP-SP has been found in certain mammalian brain tissue. MAP4 is not confined to just nerve cells, but rather can be found in nearly all types of cells. | 1 | Biochemistry |
Free Ocean CO Enrichment (FOCE) is a technology facilitating studies of the consequences of ocean acidification for marine organisms and communities by enabling the precise control of CO enrichment within in situ, partially open, experimental enclosures. Current FOCE systems control experimental CO perturbations by real-time monitoring of differences in seawater pH between treatment (i.e. high-CO) and control (i.e. ambient) seawater within experimental enclosures. | 9 | Geochemistry |
Members of the enediyne family all share a unique enediyne core that is the cause of their potent cytotoxicity. The enediyne cores are derived from linear, probably polyketide, precursors that consist of seven or eight head-to-tail coupled acetate units. Enediyne assembly involves a highly conserved, iterative type I polyketide synthase (PKS) pathway Sequencing of enediyne gene clusters has confirmed the polyketide origin of the enediyne core, and elucidated the biosynthetic pathways and mechanisms of enediynes.
Differences in the biosynthetic pathways of enediynes are due to the different origins of the -yne carbons as well as differences in isotope incorporation patterns. More differentiation comes from the attachment of various functional groups at different positions to the enediyne warheads during their maturation stage. These moieties can be either aromatic or sugars and define sequence specificity of DNA binding as well as the physical properties of the enediyne chromophores.
Due to the cytotoxicity of the enediyne chromophores, their biosynthesis is tightly regulated, although the regulatory mechanisms are still largely unclear. Organisms that produce enediynes have been shown to protect themselves with a self-resistance mechanism that uses a self-sacrificing protein. Notably, some microbes use CalC to sequester calicheamicin so that the reactive diradical abstracts hydrogens from a glycine inside of the protein instead of from DNA. | 0 | Organic Chemistry |
The Chesapeake Bay is a main feature for tourists who visit Maryland and Virginia each year. Fishing, crabbing, swimming, boating, kayaking, and sailing are extremely popular activities enjoyed on the waters of the Chesapeake Bay. As a result, tourism has a notable impact on Marylands economy. One report suggested that Annapolis was an appealing spot for families, water sports and boating. Commentator Terry Smith spoke about the Bays beauty:
One account suggested how the Chesapeake attracts people:
The Chesapeake Bay plays an important role in Maryland, Virginia, and Pennsylvania's economies, in addition to the ecosystem. The nature-based recreation of wildlife, boating, and ecotourism are dependent on enforcement of the Clean Water Act (CWA), which regulates pollutant discharges and supports related pollution control programs. In 2006, "roughly eight million wildlife watchers spent $636 million, $960 million, and $1.4 billion in Maryland, Virginia, and Pennsylvania" according to the Chesapeake Bay Foundation. | 2 | Environmental Chemistry |
Oxidative addition and reductive elimination are two important and related classes of reactions in organometallic chemistry. Oxidative addition is a process that increases both the oxidation state and coordination number of a metal centre. Oxidative addition is often a step in catalytic cycles, in conjunction with its reverse reaction, reductive elimination. | 0 | Organic Chemistry |
is mainly produced as its sulfuric acid salt, hydroxylammonium hydrogen sulfate (), by the hydrogenation of nitric oxide over platinum catalysts in the presence of sulfuric acid. | 0 | Organic Chemistry |
This was first called the liquid ordered phase by Ipsen et al. (1987). However, it has also been called the LG subgel phase by Huang et al. (1993) and the β phase by Vist and Davis (1990). | 1 | Biochemistry |
Both hypoxic conditions and serum deprivation induced increased expression of SFRP1 in leiomyoma cells. However, the smooth muscle cells cultured from the myometrium showed no significant correlation between SFRP1 expression and oxygen concentration. This suggests that SFRP1 may protect the cells from the damage caused by these stresses. | 1 | Biochemistry |
Potentiometric pH meters measure the voltage between two electrodes and display the result converted into the corresponding pH value. They comprise a simple electronic amplifier and a pair of electrodes, or alternatively a combination electrode, and some form of display calibrated in pH units. It usually has a glass electrode and a reference electrode, or a combination electrode. The electrodes, or probes, are inserted into the solution to be tested. pH meters may also be based on the antimony electrode (typically used for rough conditions) or the quinhydrone electrode.
In order to accurately measure the potential difference between the two sides of the glass membrane reference electrode, typically a silver chloride electrode or calomel electrode are required on each side of the membrane. Their purpose is to measure changes in the potential on their respective side. One is built into the glass electrode. The other, which makes contact with the test solution through a porous plug, may be a separate reference electrode or may be built into a combination electrode. The resulting voltage will be the potential difference between the two sides of the glass membrane possibly offset by some difference between the two reference electrodes, that can be compensated for. The article on the glass electrode has a good description and figure.
The design of the electrodes is the key part: These are rod-like structures usually made of glass, with a bulb containing the sensor at the bottom. The glass electrode for measuring the pH has a glass bulb specifically designed to be selective to hydrogen-ion concentration. On immersion in the solution to be tested, hydrogen ions in the test solution exchange for other positively charged ions on the glass bulb, creating an electrochemical potential across the bulb. The electronic amplifier detects the difference in electrical potential between the two electrodes generated in the measurement and converts the potential difference to pH units. The magnitude of the electrochemical potential across the glass bulb is linearly related to the pH according to the Nernst equation.
The reference electrode is insensitive to the pH of the solution, being composed of a metallic conductor, which connects to the display. This conductor is immersed in an electrolyte solution, typically potassium chloride, which comes into contact with the test solution through a porous ceramic membrane. The display consists of a voltmeter, which displays voltage in units of pH.
On immersion of the glass electrode and the reference electrode in the test solution, an electrical circuit is completed, in which there is a potential difference created and detected by the voltmeter. The circuit can be thought of as going from the conductive element of the reference electrode to the surrounding potassium-chloride solution, through the ceramic membrane to the test solution, the hydrogen-ion-selective glass of the glass electrode, to the solution inside the glass electrode, to the silver of the glass electrode, and finally the voltmeter of the display device. The voltage varies from test solution to test solution depending on the potential difference created by the difference in hydrogen-ion concentrations on each side of the glass membrane between the test solution and the solution inside the glass electrode. All other potential differences in the circuit do not vary with pH and are corrected for by means of the calibration.
For simplicity, many pH meters use a combination probe, constructed with the glass electrode and the reference electrode contained within a single probe. A detailed description of combination electrodes is given in the article on glass electrodes.
The pH meter is calibrated with solutions of known pH, typically before each use, to ensure accuracy of measurement. To measure the pH of a solution, the electrodes are used as probes, which are dipped into the test solutions and held there sufficiently long for the hydrogen ions in the test solution to equilibrate with the ions on the surface of the bulb on the glass electrode. This equilibration provides a stable pH measurement. | 7 | Physical Chemistry |
Schuster was recruited to New York University by Kurt Mislow, who was also interested in photochemistry, and joined the faculty there in late 1961 in what was at the time the University Heights, Bronx campus. He remained at NYU for his entire academic career. Schuster received tenure in 1968 and spent the 1968–69 academic year on sabbatical in London in the laboratory of George Porter. In 1974 NYU closed its Bronx campus, requiring Schuster to move his laboratory to the Manhattan campus near Washington Square Park. Among Schuster's influential advisees are structural biologist Dinshaw Patel and synthetic organic chemist Phil Baran, who worked in the laboratory as an NYU undergraduate. Schuster closed his laboratory and retired, assuming professor emeritus status, in 2010.
Schuster was elected a fellow of the American Association for the Advancement of Science in 1992 and received the Arthur C. Cope Scholar Award, given by the American Chemical Society, in 2012. | 5 | Photochemistry |
The Landsupport consortium consists of the following partners:
*University of Naples, Italy
*ARIESPACE, Italy
*Barcelona Supercomputing Center, Spain
*University of Natural Resources and Life Sciences, Vienna, Austria
*Consiglio Nazionale delle Ricerche, Italy
*Crops for the Future, Malaysia
*ICARDA, Tunisia
*Institute of Advanced Studies, Hungary
*Institute for Environmental Protection and Research, Italy
*Rasdaman GmbH, Germany
*Joint Research Center, European Commission
*Regione Campania, Italy
*University of Milan, Italy
*Zala County, Hungary
*CMAST / Modis, Belgium
*Acteon, France
*Federal Environment Agency, Austria
*Slovenian Forestry Institute, Slovenia | 1 | Biochemistry |
IHC staining for FH is used to detect lack of this protein in patients with papillary renal cell carcinoma type 2. The lack of FH in renal carcinoma cells induces pro-survival metabolic adaptations where several cascades are affected. | 1 | Biochemistry |
Measuring contact angles for pendant drops is much more complicated than for sessile drops due to the inherent unstable nature of inverted drops. This complexity is further amplified when one attempts to incline the surface. Experimental apparatus to measure pendant drop contact angles on inclined substrates has been developed recently. This method allows for the deposition of multiple microdrops on the underside of a textured substrate, which can be imaged using a high resolution CCD camera. An automated system allows for tilting the substrate and analysing the images for the calculation of advancing and receding contact angles. | 7 | Physical Chemistry |
MetPetDB is a relational database and repository for global geochemical data on and images collected from metamorphic rocks from the Earth's crust. MetPetDB is designed and built by a global community of metamorphic petrologists in collaboration with computer scientists at Rensselaer Polytechnic Institute as part of the National Cyberinfrastructure Initiative and supported by the National Science Foundation. MetPetDB is unique in that it incorporates image data collected by a variety of techniques, e.g. photomicrographs, backscattered electron images (SEM), and X-ray maps collected by wavelength dispersive spectroscopy or energy dispersive spectroscopy. | 9 | Geochemistry |
In order to enhance DNA-RNA affinity, enzyme processivity, and thermostability, five amino acid substitutions were incorporated into the M-MLV reverse transcriptase. The mutant M-MLV RT was then incorporated into PE1 to give rise to (Cas9 (H840A)-M-MLV RT(D200N/L603W/T330P/T306K/W313F)). Efficiency improvement was observed over PE1. | 1 | Biochemistry |
Caused by different structural modifications in the genome, fusion genes have gained attention because of their relationship with cancer. The ability of RNA-Seq to analyze a sample's whole transcriptome in an unbiased fashion makes it an attractive tool to find these kinds of common events in cancer.
The idea follows from the process of aligning the short transcriptomic reads to a reference genome. Most of the short reads will fall within one complete exon, and a smaller but still large set would be expected to map to known exon-exon junctions. The remaining unmapped short reads would then be further analyzed to determine whether they match an exon-exon junction where the exons come from different genes. This would be evidence of a possible fusion event, however, because of the length of the reads, this could prove to be very noisy. An alternative approach is to use paired-end reads, when a potentially large number of paired reads would map each end to a different exon, giving better coverage of these events (see figure). Nonetheless, the end result consists of multiple and potentially novel combinations of genes providing an ideal starting point for further validation. | 1 | Biochemistry |
The Pidgeon process is a practical method for smelting magnesium. The most common method involves the raw material, dolomite being fed into an externally heated reduction tank and then thermally reduced to metallic magnesium using 75% ferrosilicon as a reducing agent in a vacuum. Overall the processes in magnesium smelting via the Pidgeon process involve dolomite calcination, grinding and pelleting, and vacuum thermal reduction. Besides the Pidgeon process, electrolysis of magnesium chloride for commercial production of magnesium is also used, at one point in time accounting for 75% of the world's magnesium production. | 8 | Metallurgy |
The phagemid used to transform E. coli cells may be "rescued" from the selected cells by infecting them with VCS-M13 helper phage. The resulting phage particles that are produced contain the single-stranded phagemids and are used to infect XL-1 Blue cells. The double-stranded phagemids are subsequently collected from these XL-1 Blue cells, essentially reversing the process used to produce the original library phage. Finally, the DNA sequences are determined through dideoxy sequencing. | 1 | Biochemistry |
* Fellow of The World Academy of Sciences (TWAS)
* Fellow of Islamic World Academy of Sciences
* Foreign Fellow of Korean Academy of Sciences
* Fellow of Pakistan Academy of Sciences
* Fellow of the Royal Society, London (July 2006)
* Honorary Life Fellow King's College, Cambridge, UK (2007)
* Fellow of Chinese Chemical Society (1997)
* Foreign Academician of the Chinese Academy of Sciences (2015) | 0 | Organic Chemistry |
If one assumes infinite shunt resistance, the characteristic equation can be solved for V:
Thus, an increase in I produces a reduction in V proportional to the inverse of the logarithm of the increase. This explains mathematically the reason for the reduction in V that accompanies increases in temperature described above. The effect of reverse saturation current on the I-V curve of a crystalline silicon solar cell are shown in the figure to the right. Physically, reverse saturation current is a measure of the "leakage" of carriers across the p-n junction in reverse bias. This leakage is a result of carrier recombination in the neutral regions on either side of the junction. | 7 | Physical Chemistry |
Pearlite is a two-phased, lamellar (or layered) structure composed of alternating layers of ferrite (87.5 wt%) and cementite (12.5 wt%) that occurs in some steels and cast irons. During slow cooling of an iron-carbon alloy, pearlite forms by a eutectoid reaction as austenite cools below (the eutectoid temperature). Pearlite is a microstructure occurring in many common grades of steels. | 8 | Metallurgy |
Adenylyl cyclase is regulated by G proteins, which can be found in the monomeric form or the heterotrimeric form, consisting of three subunits. Adenylyl cyclase activity is controlled by heterotrimeric G proteins. The inactive or inhibitory form exists when the complex consists of alpha, beta, and gamma subunits, with GDP bound to the alpha subunit. In order to become active, a ligand must bind to the receptor and cause a conformational change. This conformational change causes the alpha subunit to dissociate from the complex and become bound to GTP. This G-alpha-GTP complex then binds to adenylyl cyclase and causes activation and the release of cAMP. Since a good signal requires the help of enzymes, which turn on and off signals quickly, there must also be a mechanism in which adenylyl cyclase deactivates and inhibits cAMP. The deactivation of the active G-alpha-GTP complex is accomplished rapidly by GTP hydrolysis due to the reaction being catalyzed by the intrinsic enzymatic activity of GTPase located in the alpha subunit. It is also regulated by forskolin, as well as other isoform-specific effectors:
* Isoforms I, III, and VIII are also stimulated by Ca/calmodulin.
* Isoforms V and VI are inhibited by Ca in a calmodulin-independent manner.
* Isoforms II, IV and IX are stimulated by alpha subunit of the G protein.
* Isoforms I, V and VI are most clearly inhibited by Gi, while other isoforms show less dual regulation by the inhibitory G protein.
* Soluble AC (sAC) is not a transmembrane form and is not regulated by G proteins or forskolin, instead acts as a bicarbonate/pH sensor. It is anchored at various locations within the cell and, with phosphodiesterases, forms local cAMP signalling domains.
In neurons, calcium-sensitive adenylyl cyclases are located next to calcium ion channels for faster reaction to Ca influx; they are suspected of playing an important role in learning processes. This is supported by the fact that adenylyl cyclases are coincidence detectors, meaning that they are activated only by several different signals occurring together. In peripheral cells and tissues adenylyl cyclases appear to form molecular complexes with specific receptors and other signaling proteins in an isoform-specific manner. | 1 | Biochemistry |
Like ammonia, amines are bases. Compared to alkali metal hydroxides, amines are weaker.
The basicity of amines depends on:
# The electronic properties of the substituents (alkyl groups enhance the basicity, aryl groups diminish it).
# The degree of solvation of the protonated amine, which includes steric hindrance by the groups on nitrogen. | 0 | Organic Chemistry |
Starch is a glucose polymer in which glucopyranose units are bonded by alpha-linkages. It is made up of a mixture of amylose (15–20%) and amylopectin (80–85%). Amylose consists of a linear chain of several hundred glucose molecules, and Amylopectin is a branched molecule made of several thousand glucose units (every chain of 24–30 glucose units is one unit of Amylopectin). Starches are insoluble in water. They can be digested by breaking the alpha-linkages (glycosidic bonds). Both humans and other animals have amylases so that they can digest starches. Potato, rice, wheat, and maize are major sources of starch in the human diet. The formations of starches are the ways that plants store glucose. | 0 | Organic Chemistry |
Actinic light was first commonly used in early photography to distinguish light that would expose the monochrome films from light that would not. A non-actinic safe-light (e.g., red or amber) could be used in a darkroom without risk of exposing (fogging) light-sensitive films, plates or papers.
Early "non colour-sensitive" (NCS) films, plates and papers were only sensitive to the high-energy end of the visible spectrum from green to UV (shorter-wavelength light). This would render a print of the red areas as a very dark tone because the red light was not actinic. Typically, light from xenon flash lamps is highly actinic, as is daylight as both contain significant green-to-UV light.
In the first half of the 20th century, developments in film technology produced films sensitive to red and yellow light, known as orthochromatic and panchromatic, and extended that through to near infra-red light. These gave a truer reproduction of human perception of lightness across the color spectrum. In photography, therefore, actinic light must now be referenced to the photographic material in question. | 7 | Physical Chemistry |
The Arc system is a two-component system found in some bacteria that regulates gene expression in faculatative anaerobes such as Escheria coli. Two-component system means that it has a sensor molecule and a response regulator. Arc is an abbreviation for Anoxic Redox Control system. Arc systems are instrumental in maintaining energy metabolism during transcription of bacteria. The ArcA response regulator looks at growth conditions and expresses genes to best suit the bacteria. The Arc B sensor kinase, which is a tripartite protein, is membrane bound and can autophosphorylate.
The Arc System was first reported in E. coli strains and subsequently many followed. ArcA/ArcB were first identified as playing an important role in regulation of aerobic and anaerobic pathways by Shiro Iuchi and E. C. Lin. These two scientists designed a genetic screen using the sdh-lacZ operon in a Δlac strain of E. coli. It was shown that mutations in arcA and arcB resulted in elevated levels of enzymes involved in anaerobic fermentation pathways. These two scientists are responsible for the name arc, which originally stood for aerobic respiration control. | 1 | Biochemistry |
Convergent synthesis of a dendrimer begins with what will eventually become the surface of the dendrimer and proceeds inward. The convergent synthetic approach makes use of orthogonal protecting groups (two protecting groups whose deprotection conditions will not remove one another); this is an additional consideration not present when using a divergent approach. The figure below depicts a general scheme for a convergent synthetic approach.
Convergent synthesis as shown above begins with the dendritic subunit composed of reactive "focal group" and branched group B (B can be multiply branched in the most generalized scenario, but PAMAMs only split once at each branching point). First, is orthogonally protected and set aside for further reactions. B is also orthogonally protected, leaving the unprotected on this molecule to couple with each of the unprotected B groups from the initial compound. This results in a new higher-generation species that is protected on both and B. Selective deprotection of yields a new molecule which can again be coupled onto the original monomer, thus forming another new generation. This process can then be repeated to form more and more layers.
* Note that the black protecting groups for group B represent what will become the outermost layer of the final molecule, and remain attached throughout the synthetic process; their purpose is to guarantee that propagation of dendrimer growth can take place in a controlled fashion by preventing unwanted side reactions.
* In forming each new layer, the number of B couplings is restricted to two, in sharp contrast to the divergent synthetic approach, which involves exponentially more couplings per layer.
* Incomplete reaction products (single addition adduct, unreacted starting materials) will have a markedly different molecular weight from the desired product, especially for higher-generation compounds, making purification more straightforward.
* The reactive focal group must be terminated onto a final acceptor at some point during the synthetic process; until then, each compound can only be considered a dendron and not a full dendrimer (see page for disambiguation).
* An advantage to synthesizing dendrons with focal group as a chemical handle is the ability to attach multiple equivalents of the dendron to a polyfunctional core molecule; changing the core element does not require rebuilding the entire dendrimer. In the case of PAMAM, the focal points of convergently synthesized fragments have been used to create unsymmetrical dendrimers as well as dendrimers with various core functionalization.
* Since each successive generation of dendron becomes bulkier, with final attachment to the dendrimer core being the most prohibitive step of all, steric constraints can severely impact yield. | 6 | Supramolecular Chemistry |
One estimate (2006) suggested that 1 million tonnes of PCBs had been produced. 40% of this material was thought to remain in use. Another estimate put the total global production of PCBs on the order of 1.5 million tonnes. The United States was the single largest producer with over 600,000 tonnes produced between 1930 and 1977. The European region follows with nearly 450,000 tonnes through 1984. It is unlikely that a full inventory of global PCB production will ever be accurately tallied, as there were factories in Poland, East Germany, and Austria that produced unknown amounts of PCBs. There are still 21,500 tons of PCBs stored in the easternmost regions of Slovakia.
Although deliberate production of PCBs is banned by international treaty, significant amounts of PCBs are still being "inadvertently" produced. Research suggests that 45,000 tons of by-product PCBs are legally produced per year in the US as part of certain chemical and product formulations. | 2 | Environmental Chemistry |
Owing to the decreased electron density in the aromatic system, electrophilic substitutions are suppressed in pyridine and its derivatives. Friedel–Crafts alkylation or acylation, usually fail for pyridine because they lead only to the addition at the nitrogen atom. Substitutions usually occur at the 3-position, which is the most electron-rich carbon atom in the ring and is, therefore, more susceptible to an electrophilic addition.
Direct nitration of pyridine is sluggish. Pyridine derivatives wherein the nitrogen atom is screened sterically and/or electronically can be obtained by nitration with nitronium tetrafluoroborate (NOBF). In this way, 3-nitropyridine can be obtained via the synthesis of 2,6-dibromopyridine followed by nitration and debromination.
Sulfonation of pyridine is even more difficult than nitration. However, pyridine-3-sulfonic acid can be obtained. Reaction with the SO group also facilitates addition of sulfur to the nitrogen atom, especially in the presence of a mercury(II) sulfate catalyst.
In contrast to the sluggish nitrations and sulfonations, the bromination and chlorination of pyridine proceed well. | 0 | Organic Chemistry |
Huang joined the Shanghai Institute of Organic Chemistry (SIOC), Chinese Academy of Sciences in 1955. In 1958, he responded to the demand of Chinese defense industry, stopped his established organic natural product research work and pursued research in the field of organofluorine chemistry. Under his leadership, the major base for organofluorine chemistry in China was established at the SIOC.
Huang discovered the sulfinatodehalogenation reaction in 1981, which converts perfluoroalkyl halides to the corresponding perfluoroalkanesulfinates with sulfinatodehalogenation reagents such as sodium dithionite. He and his students identified this reaction as a single electron transfer reaction. This reaction opens a new and practical way for perfluoroalkylation of unsaturated substrates such as alkenes alkynes and aromatics compounds with sulfinatodehalogenation reagents. This reaction is well documented internationally and he won the Second-class Award of National Natural Science in 1986.
Huang has published more than 200 research papers and has mentored twenty Ph.D. candidates, including the first Ph.D. in Organic Chemistry in Mainland China. He was the first one in China (1958) to introduce NMR and IR applications in organic chemistry.
He was elected as an academician of the Chinese Academy of Sciences in 1980. Huang was deputy director of SIOC (1978-1984) and director from 1984-1987. SIOC is the major Chinese chemistry research center and the place edits and publishes several major Chinese academic journals of chemistry.
Huang was the founder and chief editor of the Chinese Journal of Chemistry. He was elected as President of the Chinese Chemical Society (1986-1990).
Huang was in the first delegation from the Chinese chemist community to visit USA in 1977 and he made great efforts to establish the good relationship in exchange of scholars and visiting between Chinese and American chemists.
Huang received broad recognition from international chemistry community. He was elected as bureau member of IUPAC (1985-1993). He was awarded the Moissan Medal in 1986 at the conference "Centenary of the Discovery of Fluorine" in Paris. He was the co-chairman of 17th international symposium of fluorine chemistry in 2003. | 0 | Organic Chemistry |
The bulk electronic band structure of transition metal oxides consists of overlapping 2p orbitals from oxygen atoms, forming the lower energy, highly populated valence band, while the sparsely populated, higher energy conduction band consists of overlapping d orbitals of the transition metal cation. In contrast to metals, having a continuous band of electronic states, semiconductors have a band gap that prevents the recombination of electron/hole pairs that have been separated into the conduction band/ valence band. The nanosecond scale life times of these electron/hole separations allows for charge transfer to occur with an adsorbed species on the semiconductor surface. The Potential of an acceptor must be more positive than the conduction band potential of the semiconductor in order for reduction of the species to commence. Conversely, the potential of the donor species must be more negative than that of the valence band of the semiconductor for oxidation of the species to occur.
Near the surface of a semi-conducting metal oxide the valence and conduction bands are of higher energy, causing the upward bending of the band energy as shown in the band energy diagram, such that promotion of an electron from the valence band to the conduction band by light of energy greater than the band gap results in migration of the electron towards the bulk of the solid or to a counter electrode, while the hole left in the valence band moves towards the surface. The increased concentration of holes near the surface facilitates electron transfer to the solid, such as the example shown in the figure of the oxidation of redox couple D-/D. In the absence of any mechanism to remove electrons from the bulk of the solid irradiation continues to excite electrons to the conduction band producing holes in the valence band. This leads to the reduction of the upward bending of the band energies near the surface, and the subsequent increase in excited electron availability for reduction reactions.
The following equations are useful in describing the populations of valence and conduction bands in terms of holes and electrons for the bulk metal. is the density of electrons in the bulk metal conduction band, and is the density of holes in the bulk metal valence band. E is the lowest energy of the conduction band, E is the Fermi energy (electrochemical energy of the electrons), E is the highest energy of the valence band, N is the effective mass and mobility of an electron in the conduction band (constant), and N is the effective mass and mobility of a valence band hole (constant).
where k is Boltzmanns constant and T is the absolute temperature in kelvins.
The use of quantum mechanics perturbation theory can aid in calculating the probability of an electronic transition taking place. The probability is proportional to the square of the amplitude of the radiation field, E, and the square of the transition dipole moment |μ|.
The quantum yield for an ideal system undergoing photocatalytic events is measured as the number of events occurring per photon absorbed. The typical assumption in determining the quantum yield is that all photons are absorbed on the semiconductor surface, and the quantum yield is referred to as the apparent quantum yield. This assumption is necessary due to the difficulty in measuring the actual photons absorbed by the solid surface. The relation between the quantum yield, the rate of charge transfer, k, and the electron/hole recombination rate, k, is given by the following equation.
Photoinduced molecular transformations at transition metal oxide surfaces can be organized in two general classes. Photoexcitation of the adsorbate which then reacts with the catalyst substrate is classified as a catalyzed photoreaction. Photoexcitation of the catalyst followed by interaction of the catalyst with a ground state reactant is classified as a sensitized photoreaction. | 7 | Physical Chemistry |
The canonical umpolung reagent is the cyanide ion. The cyanide ion is unusual in that a carbon triply bonded to a nitrogen would be expected to have a (+) polarity due to the higher electronegativity of the nitrogen atom. Yet, the negative charge of the cyanide ion is localized on the carbon, giving it a (-) formal charge. This chemical ambivalence results in umpolung in many reactions where cyanide is involved.
For example, cyanide is a key catalyst in the benzoin condensation, a classical example of polarity inversion.
The net result of the benzoin reaction is that a bond has been formed between two carbons that are normally electrophiles. | 0 | Organic Chemistry |
Parker and Williams constructed a NAND logic gate based on turning on strong emission from a terbium complex of phenanthridine. When acid and oxygen (the two inputs) are absent (input “0”), the fluorescence from the terbium center is turned on (output “1”). Hence, the system acts as a molecular NAND gate. | 6 | Supramolecular Chemistry |
This is also known as the P test. It uses a 1–5% ethanolic solution of para-phenylenediamine (PD), made by placing a drop of ethanol (70–95%) over a few crystals of the chemical; this yields an unstable, light sensitive solution that lasts for about a day. An alternative form of this solution, called Steiners solution, is much longer lasting although it produces less intense colour reactions. It is typically prepared by dissolving 1 gram of PD, 10 grams of sodium sulfite, and 0.5 millilitres of detergent in 100 millilitres of water; initially pink in colour, the solution becomes purple with age. Steiners solution will last for months. The phenylenediamine reacts with aldehydes to yield Schiff bases according to the following reaction:
Products of this reaction are yellow to red in colour. Most β-orcinol depsidones and some β-orcinol depsides will react positively. The PD test, known for its high specificity towards substances that yield K+ yellow or red reactions, has largely replaced the simpler yet less conclusive K test. PD is poisonous both as a powder and a solution, and surfaces that come in contact with it (including skin) will discolour.
Some common and widely distributed lichens that have lichen products with a positive reaction to P include Parmelia subrudecta, which is PD+ (yellow) because of the didepside atranorin, and Hypogymnia physodes, which is PD+ (orange) because of the depsidone physodalic acid. | 3 | Analytical Chemistry |
While all deactivating groups are inductively withdrawing (–I), most of them are also withdrawing through resonance (–M) as well. Halogen substituents are an exception: they are resonance donors (+M). With the exception of the halides, they are meta directing groups.
Halides are ortho, para directing groups but unlike most ortho, para directors, halides mildly deactivate the arene. This unusual behavior can be explained by two properties:
# Since the halogens are very electronegative they cause inductive withdrawal (withdrawal of electrons from the carbon atom of benzene).
# Since the halogens have non-bonding electrons they can donate electron density through pi bonding (resonance donation).
The inductive and resonance properties compete with each other but the resonance effect dominates for purposes of directing the sites of reactivity. For nitration, for example, fluorine directs strongly to the para position because the ortho position is inductively deactivated (86% para, 13% ortho, 0.6% meta). On the other hand, iodine directs to ortho and para positions comparably (54% para and 45% ortho, 1.3% meta). | 0 | Organic Chemistry |
Atropisomers are stereoisomers resulting from hindered rotation about single bonds where the steric strain barrier to rotation is high enough to allow for the isolation of the conformers. | 4 | Stereochemistry |
Photoprotection is the biochemical process that helps organisms cope with molecular damage caused by sunlight. Plants and other oxygenic phototrophs have developed a suite of photoprotective mechanisms to prevent photoinhibition and oxidative stress caused by excess or fluctuating light conditions. Humans and other animals have also developed photoprotective mechanisms to avoid UV photodamage to the skin, prevent DNA damage, and minimize the downstream effects of oxidative stress. | 5 | Photochemistry |
Stacking of the nucleotides in a double helix is a major determinant of the helixs stability. With the added surface area and hydrogen available for bonding, stacking potential for the nucleobases increases with the addition of a benzene spacer. By increasing the separation between the nitrogenous bases and either sugar-phosphate backbone, the helixs stacking energy is less variable and therefore more stable. The energies for natural nucleobase pairs vary from 18 to 52 kJ/mol. This variance is only 14–40 kJ/mol for xDNA.
Due to an increased overlap between and expanded strand of DNA and its neighbouring strand, there are greater interstrand interactions in expanded and mixed helices, resulting in a significant increase in the helixs stability. xDNA has enhanced stacking abilities resultant from changes in inter- and intrastrand hydrogen bonding that arise from the addition of a benzene spacer, but expanding the bases does not alter hydrogens contribution to the stability of the duplex. These stacking abilities are exploited by helices consisting of both xDNA and B-DNA in order to optimize the strength of the helix. Increased stacking is seen most prominently in strands consisting only of A and xA and T and xT, as T-xA has stronger stacking interactions than T-A.
The energy resultant from pyrimidines ranges from 30 to 49 kJ/mol. The range for purines is between 40-58kJ/mol. By replacing one nucleotide in a double-helix with an expanded nucleotide, the strength of the stacking interactions increases by 50%. Expanding both nucleotides results in a 90% increase in stacking strength. While xG has an overall negative effect on the binding strength of the helix, the other three expanded bases outweigh this with their positive effects. The change in energy caused by expanding the bases is mostly dependent on the rotation of the bond about the nucleobases' centers of mass, and center of mass stacking interactions improve the stacking potential of the helix. Because the size-expanded bases widen the helix, it is more thermally stable with a higher melting temperature. | 1 | Biochemistry |
Lilleby closed on the same day Norway was attacked by Nazi Germany, but it did not remain closed for long. The Norwegian aluminium industry was of great strategic importance for the German government, which requested that Lilleby resume operation right away. Birger Solberg was placed in charge, because professor Pedersen had left with his family to Sweden. Solberg was dismissed the day that Pederson returned, undoubtedly related to his views on the occupation, which differed from Professor Pedersen's views: Pedersen was a supporter of Nazi Germany and wanted to collaborate with the occupation.
During the war, the plant was geared mostly towards aluminium, which was more important for the German war effort; however, many employees sabotaged the work in order to keep productivity low. | 8 | Metallurgy |
Polytetrafluoroethylene (PTFE) is a synthetic fluoropolymer used in various applications including non-stick coatings. Teflon is a brand of PTFE, often used as a generic term for PTFE. The metallic substrate is roughened by abrasive blasting, then sometimes electric-arc sprayed with stainless steel. The irregular surface promotes adhesion of the PTFE and also resists abrasion of the PTFE. Then one to seven layers of PTFE are sprayed or rolled on, with a larger number of layers and spraying being better. The number and thickness of the layers and quality of the material determine the quality of the non-stick coating. Better-quality coatings are more durable, and less likely to peel and flake, and keep their non-stick properties for longer. Any PTFE-based coating will rapidly lose its non-stick properties if overheated; all manufacturers recommend that temperatures be kept below, typically, .
Utensils used with PTFE-coated pans can scratch the coating if the utensils are harder than the coating; this can be prevented by using non-metallic (usually plastic or wood) cooking tools. | 7 | Physical Chemistry |
The first application of the pump–probe technique in biology was in vitro imaging of stimulated emission of a dye-labelled cell. Pump–probe imaging is now widely used for melanin imaging to differentiate between the two main forms of melanin eumelanin (brown/black) and pheomelanin (red/yellow). In melanoma, eumelanin is substantially increased. Therefore, imaging the distribution of eumelanin and pheomelanin can help to distinguish benign lesions and melanoma with high sensitivity | 7 | Physical Chemistry |
In physics, a photon gas is a gas-like collection of photons, which has many of the same properties of a conventional gas like hydrogen or neon – including pressure, temperature, and entropy. The most common example of a photon gas in equilibrium is the black-body radiation.
Photons are part of a family of particles known as bosons, particles that follow Bose–Einstein statistics and with integer spin. A gas of bosons with only one type of particle is uniquely described by three state functions such as the temperature, volume, and the number of particles. However, for a black body, the energy distribution is established by the interaction of the photons with matter, usually the walls of the container, and the number of photons is not conserved. As a result, the chemical potential of the black-body photon gas is zero at thermodynamic equilibrium. The number of state variables needed to describe a black-body state is thus reduced from three to two (e.g. temperature and volume). | 7 | Physical Chemistry |
Iron metallurgy in Africa developed within Africa; though initially assumed to be of external origin, this assumption has been rendered untenable; archaeological evidence has increasingly supported an indigenous origin. Some recent studies date the inception of iron metallurgy in Africa between 3000 BCE and 2500 BCE. Archaeometallurgical scientific knowledge and technological development originated in numerous centers of Africa; the centers of origin were located in West Africa, Central Africa, and East Africa; consequently, as these origin centers are located within inner Africa, these archaeometallurgical developments are thus native African technologies.
Iron metallurgical development occurred 2631 BCE – 2458 BCE at Lejja, in Nigeria, 2136 BCE – 1921 BCE at Obui, in Central Africa Republic, 1895 BCE – 1370 BCE at Tchire Ouma 147, in Niger, and 1297 BCE – 1051 BCE at Dekpassanware, in Togo. Evidence exists for early iron metallurgy in parts of Nigeria, Cameroon, and Central Africa, possibly from as early as around 2,000 BCE. Iron metallurgy may have been independently developed in the Nok culture between the 9th century BCE and 550 BCE. The nearby Djenné-Djenno culture of the Niger Valley in Mali shows evidence of iron production from 250 BCE. The Bantu expansion spread the technology to Eastern and Southern Africa between 500 BCE and 400 CE, as shown in the Urewe culture. | 8 | Metallurgy |
Chain polymerization products are widely used in many aspects of life, including electronic devices, food packaging, catalyst carriers, medical materials, etc. At present, the world's highest yielding polymers such as polyethylene (PE), polyvinyl chloride (PVC), polypropylene (PP), etc. can be obtained by chain polymerization.
In addition, some carbon nanotube polymer is used for electronical devices. Controlled living chain-growth conjugated polymerization will also enable the synthesis of well-defined advanced structures, including block copolymers. Their industrial applications extend to water purification, biomedical devices and sensors. | 7 | Physical Chemistry |
Kacser and Burns introduced an additional coefficient that described how a biochemical pathway would respond the external environment. They termed this coefficient the response coefficient and designated it using the symbol R. The response coefficient is an important metric because it can be used to assess how much a nutrient or perhaps more important, how a drug can influence a pathway. This coefficient is therefore highly relevant to the pharmaceutical industry.
The response coefficient is related to the core of metabolic control analysis via the response coefficient theorem, which is stated as follows:
where is a chosen observable such as a flux or metabolite concentration, is the step that the external factor targets, is the control coefficient of the target steps, and is the elasticity of the target step with respect to the external factor .
The key observation of this theorem is that an external factor such as a therapeutic drug, acts on the organism's phenotype via two influences: 1) How well the drug can affect the target itself through effective binding of the drug to the target protein and its effect on the protein activity. This effectiveness is described by the elasticity and 2) How well do modifications of the target influence the phenotype by transmission of the perturbation to the rest of the network. This is indicated by the control coefficient .
A drug action, or any external factor, is most effective when both these factors are strong. For example, a drug might be very effective at changing the activity of its target protein, however if that perturbation in protein activity is unable to be transmitted to the final phenotype then the effectiveness of the drug is greatly diminished.
If a drug or external factor, , targets multiple sites of action, for example sites, then the overall response in a phenotypic factor , is the sum of the individual responses: | 1 | Biochemistry |
Buffer solutions resist pH change because of a chemical equilibrium between the weak acid HA and its conjugate base A:
When some strong acid is added to an equilibrium mixture of the weak acid and its conjugate base, hydrogen ions (H) are added, and the equilibrium is shifted to the left, in accordance with Le Chatelier's principle. Because of this, the hydrogen ion concentration increases by less than the amount expected for the quantity of strong acid added.
Similarly, if strong alkali is added to the mixture, the hydrogen ion concentration decreases by less than the amount expected for the quantity of alkali added. In Figure 1, the effect is illustrated by the simulated titration of a weak acid with pK = 4.7. The relative concentration of undissociated acid is shown in blue, and of its conjugate base in red. The pH changes relatively slowly in the buffer region, pH = pK ± 1, centered at pH = 4.7, where [HA] = [A]. The hydrogen ion concentration decreases by less than the amount expected because most of the added hydroxide ion is consumed in the reaction
and only a little is consumed in the neutralization reaction (which is the reaction that results in an increase in pH)
Once the acid is more than 95% deprotonated, the pH rises rapidly because most of the added alkali is consumed in the neutralization reaction. | 7 | Physical Chemistry |
Bio-available nitrogen occurs in the ocean in several forms, including simple ionic forms such as nitrate (NO), nitrite (NO) and ammonium (NH), and more complex organic forms such as urea ((NH2)CO). These forms are utilised by autotrophic phytoplankton to synthesise organic molecules such as amino acids (the building blocks of proteins). Grazing of phytoplankton by zooplankton and larger organisms transfers this organic nitrogen up the food chain and throughout the marine food-web.
When nitrogenous organic molecules are ultimately metabolised by organisms, they are returned to the water column as ammonium (or more complex molecules that are then metabolised to ammonium). This is known as regeneration, since the ammonium can be used by phytoplankton, and again enter the food-web. Primary production fuelled by ammonium in this way is thus referred to as regenerated production.
However, ammonium can also be oxidised to nitrate (via nitrite), by the process of nitrification. This is performed by different bacteria in two stages :
NH + O → NO + 3H + 2e
NO + HO → NO + 2H + 2e
Crucially, this process is believed to only occur in the absence of light (or as some other function of depth). In the ocean, this leads to a vertical separation of nitrification from primary production, and confines it to the aphotic zone. This leads to the situation whereby any nitrate in the water column must be from the aphotic zone, and must have originated from organic material transported there by sinking. Primary production fuelled by nitrate is, therefore, making use of a "fresh" nutrient source rather than a regenerated one. Production by nitrate is thus referred to as new production.
To sum up, production based on nitrate is using nutrient molecules newly arrived from outside the productive layer, it is termed new production. The rate of nitrate utilization remains a good measure of the new production. While if the organic matter is then eaten, respired and the nitrogen excreted as ammonia, its subsequent uptake and re-incorporation in organic matter by phytoplankton is termed recycled (or regenerated) production. The rate of ammonia utilization is, in the same sense, a measure of recycled production.
The use of N-compounds makes it possible to measure the fractions of new nitrogen and regenerated nitrogen associated with the primary production in the sea. | 9 | Geochemistry |
Soil biota (soil microflora, soil animals) are sensitive to soil pH, either directly upon contact or after soil ingestion or indirectly through the various soil properties to which pH contributes (e.g. nutrient status, metal toxicity, humus form). According to the various physiological and behavioural adaptations of soil biota, the species composition of soil microbial and animal communities varies with soil pH. Along altitudinal gradients, changes in the species distribution of soil animal and microbial communities can be at least partly ascribed to variation in soil pH. The shift from toxic to non-toxic forms of aluminium around pH5 marks the passage from acid-tolerance to acid-intolerance, with few changes in the species composition of soil communities above this threshold, even in calcareous soils. Soil animals exhibit distinct pH preferences when allowed to exert a choice along a range of pH values, explaining that various field distributions of soil organisms, motile microbes included, could at least partly result from active movement along pH gradients. Like for plants, competition between acido-tolerant and acido-intolerant soil-dwelling organisms was suspected to play a role in the shifts in species composition observed along pH ranges.
The opposition between acido-tolerance and acido-intolerance is commonly observed at species level within a genus or at genus level within a family, but it also occurs at much higher taxonomic rank, like between soil fungi and bacteria, here too with a strong involvement of competition.
It has been suggested that soil organisms more tolerant of soil acidity, and thus living mainly in soils at pH less than 5, were more primitive than those intolerant of soil acidity. A cladistic analysis on the collembolan genus Willemia showed that tolerance to soil acidity was correlated with tolerance of other stress factors and that stress tolerance was an ancestral character in this genus. However the generality of these findings remains to be established.
At low pH, the oxidative stress induced by aluminium (Al) affects soil animals the body of which is not protected by a thick chitinous exoskeleton like in arthropods, and thus are in more direct contact with the soil solution, e.g. protists, nematodes, rotifers (microfauna), enchytraeids (mesofauna) and earthworms (macrofauna).
Effects of pH on soil biota can be mediated by the various functional interactions of soil foodwebs. It has been shown experimentally that the collembolan Heteromurus nitidus, commonly living in soils at pH higher than 5, could be cultured in more acid soils provided that predators were absent. Its attraction to earthworm excreta (mucus, urine, faeces), mediated by ammonia emission, provides food and shelter within earthworm burrows in mull humus forms associated with less acid soils. | 9 | Geochemistry |
Recognition of stop codons in bacteria have been associated with the so-called tripeptide anticodon, a highly conserved amino acid motif in RF1 (PxT) and RF2 (SPF). Even though this is supported by structural studies, it was shown that the tripeptide anticodon hypothesis is an oversimplification. | 1 | Biochemistry |
Two of the main functions of carbohydrates are energy storage and providing structure. One of the common sugars known as glucose is a carbohydrate, but not all carbohydrates are sugars. There are more carbohydrates on Earth than any other known type of biomolecule; they are used to store energy and genetic information, as well as play important roles in cell to cell interactions and communications.
The simplest type of carbohydrate is a monosaccharide, which among other properties contains carbon, hydrogen, and oxygen, mostly in a ratio of 1:2:1 (generalized formula CHO, where n is at least 3). Glucose (CHO) is one of the most important carbohydrates; others include fructose (CHO), the sugar commonly associated with the sweet taste of fruits, and deoxyribose (CHO), a component of DNA. A monosaccharide can switch between acyclic (open-chain) form and a cyclic form. The open-chain form can be turned into a ring of carbon atoms bridged by an oxygen atom created from the carbonyl group of one end and the hydroxyl group of another. The cyclic molecule has a hemiacetal or hemiketal group, depending on whether the linear form was an aldose or a ketose.
In these cyclic forms, the ring usually has 5 or 6 atoms. These forms are called furanoses and pyranoses, respectively—by analogy with furan and pyran, the simplest compounds with the same carbon-oxygen ring (although they lack the carbon-carbon double bonds of these two molecules). For example, the aldohexose glucose may form a hemiacetal linkage between the hydroxyl on carbon 1 and the oxygen on carbon 4, yielding a molecule with a 5-membered ring, called glucofuranose. The same reaction can take place between carbons 1 and 5 to form a molecule with a 6-membered ring, called glucopyranose. Cyclic forms with a 7-atom ring called heptoses are rare.
Two monosaccharides can be joined by a glycosidic or ester bond into a disaccharide through a dehydration reaction during which a molecule of water is released. The reverse reaction in which the glycosidic bond of a disaccharide is broken into two monosaccharides is termed hydrolysis. The best-known disaccharide is sucrose or ordinary sugar, which consists of a glucose molecule and a fructose molecule joined. Another important disaccharide is lactose found in milk, consisting of a glucose molecule and a galactose molecule. Lactose may be hydrolysed by lactase, and deficiency in this enzyme results in lactose intolerance.
When a few (around three to six) monosaccharides are joined, it is called an oligosaccharide (oligo- meaning "few"). These molecules tend to be used as markers and signals, as well as having some other uses. Many monosaccharides joined form a polysaccharide. They can be joined in one long linear chain, or they may be branched. Two of the most common polysaccharides are cellulose and glycogen, both consisting of repeating glucose monomers. Cellulose is an important structural component of plants cell walls and glycogen' is used as a form of energy storage in animals.
Sugar can be characterized by having reducing or non-reducing ends. A reducing end of a carbohydrate is a carbon atom that can be in equilibrium with the open-chain aldehyde (aldose) or keto form (ketose). If the joining of monomers takes place at such a carbon atom, the free hydroxy group of the pyranose or furanose form is exchanged with an OH-side-chain of another sugar, yielding a full acetal. This prevents opening of the chain to the aldehyde or keto form and renders the modified residue non-reducing. Lactose contains a reducing end at its glucose moiety, whereas the galactose moiety forms a full acetal with the C4-OH group of glucose. Saccharose does not have a reducing end because of full acetal formation between the aldehyde carbon of glucose (C1) and the keto carbon of fructose (C2). | 1 | Biochemistry |
The pillar was installed as a trophy in building the Quwwat-ul-Islam mosque and the Qutb complex by Sultan Iltutmish in the 13th century. Its original location, whether on the site itself or from elsewhere, is debated.
According to the inscription of king Chandra, the pillar was erected at Vishnupadagiri (Vishnupada). J. F. Fleet (1898) identified this place with Mathura, because of its proximity to Delhi (the find spot of the inscription) and the citys reputation as a Vaishnavite pilgrimage centre. However, archaeological evidence indicates that during the Gupta period, Mathura was a major centre of Buddhism, although Vaishnavism may have existed there. Moreover, Mathura lies in plains, and only contains some small hillocks and mounds: there is no true giri' (hill) in Mathura.
Based on paleographic similarity to the dated inscriptions from Udayagiri, the Gupta-era iconography, analysis of metallurgy and other evidence, Meera Dass and R. Balasubramaniam (2004) theorized that the iron pillar was originally erected at Udayagiri. According to them, the pillar, with a wheel or discus at the top, was originally located at the Udayagiri Caves. This conclusion was partly based on the fact that the inscription mentions Vishnupada-giri (IAST: Viṣṇupadagiri, meaning "hill with footprint of Viṣṇu"). This conclusion was endorsed and elaborated by Michael D. Willis in his The Archaeology of Hindu Ritual, published in 2009.
The key point in favour of placing the iron pillar at Udayagiri is that this site was closely associated with Chandragupta and the worship of Vishnu in the Gupta period. In addition, there are well-established traditions of mining and working iron in central India, documented particularly by the iron pillar at Dhar and local place names like Lohapura and Lohangī Pīr (see Vidisha). The king of Delhi, Iltutmish, is known to have attacked and sacked Vidisha in the thirteenth century and this would have given him an opportunity to remove the pillar as a trophy to Delhi, just as the Tughluq rulers brought Asokan pillars to Delhi in the 1300s. | 8 | Metallurgy |
For buffers in acid regions, the pH may be adjusted to a desired value by adding a strong acid such as hydrochloric acid to the particular buffering agent. For alkaline buffers, a strong base such as sodium hydroxide may be added. Alternatively, a buffer mixture can be made from a mixture of an acid and its conjugate base. For example, an acetate buffer can be made from a mixture of acetic acid and sodium acetate. Similarly, an alkaline buffer can be made from a mixture of the base and its conjugate acid. | 7 | Physical Chemistry |
A later paper by Edwards and Pearson, following research done by Jencks and Carriuolo in 1960 led to the discovery of an additional factor in nucleophilic reactivity, which Edwards and Pearson called the alpha effect, where nucleophiles with a lone pair of electrons on an atom adjacent to the nucleophilic center have enhanced reactivity. The alpha effect, basicity, and polarizability are still accepted as the main factors in determining nucleophilic reactivity. As such, the Edwards equation is applied in a qualitative sense much more frequently than in a quantitative one.
In studying nucleophilic reactions, Edwards and Pearson noticed that for certain classes of nucleophiles most of the contribution of nucleophilic character originated from their basicity, resulting in large β values. For other nucleophiles, most of the nucleophilic character came from their high polarizability, with little contribution from basicity, resulting in large α values. This observation led Pearson to develop his hard-soft acid-base theory, which is arguably the most important contribution that the Edwards equation has made to current understanding of organic and inorganic chemistry. Nucleophiles, or bases, that were polarizable, with large α values, were categorized as “soft”, and nucleophiles that were non-polarizable, with large β and small α values, were categorized as “hard”.
The Edwards equation parameters have since been used to help categorize acids and bases as hard or soft, due to the approach's simplicity. | 7 | Physical Chemistry |
The skeletal formula, line-angle formula, or shorthand formula of an organic compound is a type of molecular structural formula that serves as a shorthand representation of a molecule's bonding and some details of its molecular geometry. A skeletal formula shows the skeletal structure or skeleton of a molecule, which is composed of the skeletal atoms that make up the molecule. It is represented in two dimensions, as on a piece of paper. It employs certain conventions to represent carbon and hydrogen atoms, which are the most common in organic chemistry.
An early form of this representation was first developed by organic chemist August Kekulé, while the modern form is closely related to and influenced by the Lewis structure of molecules and their valence electrons. Hence they are sometimes termed Kekulé structures or Lewis–Kekulé structures. Skeletal formulae have become ubiquitous in organic chemistry, partly because they are relatively quick and simple to draw, and also because the curved arrow notation used for discussions of reaction mechanisms and electron delocalization can be readily superimposed.
Several other ways of depicting chemical structures are also commonly used in organic chemistry (though less frequently than skeletal formulae). For example, conformational structures look similar to skeletal formulae and are used to depict the approximate positions of atoms in 3D space, as a perspective drawing. Other types of representation, such as Newman projection, Haworth projection or Fischer projection, also look somewhat similar to skeletal formulae. However, there are slight differences in the conventions used, and the reader needs to be aware of them in order to understand the structural details encoded in the depiction. While skeletal and conformational structures are also used in organometallic and inorganic chemistry, the conventions employed also differ somewhat. | 0 | Organic Chemistry |
Colored dissolved organic matter (CDOM) is estimated to range 20-70% of carbon content of the oceans, being higher near river outlets and lower in the open ocean.
Marine life is largely similar in biochemistry to terrestrial organisms, except that they inhabit a saline environment. One consequence of their adaptation is that marine organisms are the most prolific source of halogenated organic compounds. | 9 | Geochemistry |
Gold working in the Bronze Age British Isles refers to the use of gold to produce ornaments and other prestige items in the British Isles during the Bronze Age, between and in Britain, and up to about 550 BCE in Ireland. In this period, communities in Britain and Ireland first learned how to work metal, leading to the widespread creation of not only gold but also copper and bronze items as well. Gold artefacts in particular were prestige items used to designate the high status of those individuals who wore, or were buried with them.
Around 1,500 gold objects dating to the Bronze Age survive in collections, around 1000 of them from Ireland and the other 500 from Britain; this is a much smaller number than would have been originally crafted, leading archaeologists to believe that "many thousands of gold objects were made and used" in the Bronze Age British Isles.
Records indicate that Bronze Age gold artefacts had begun to be discovered by the 18th century at the least, although at the time many were melted down or lost. Only with the rise of the antiquarian and then archaeological movements were the antiquity of these items recognised, after which they were more usually preserved in collections.
The archaeologist George Eogan noted that investigation of Bronze Age gold artefacts revealed not only "the work of craftsmen and technicians" from that period but also aided our understanding of "broader aspects of society such as social stratification, trade, commerce and ritual." | 8 | Metallurgy |
The R symbol was introduced by 19th-century French chemist Charles Frédéric Gerhardt, who advocated its adoption on the grounds that it would be widely recognizable and intelligible given its correspondence in multiple European languages to the initial letter of "root" or "residue": French ("root") and ("residue"), these terms respective English translations along with radical (itself derived from Latin below), Latin ("root") and ("residue"), and German ' ("remnant" and, in the context of chemistry, both "residue" and "radical"). | 0 | Organic Chemistry |
The Surface Force Apparatus (SFA) is a scientific instrument which measures the interaction force of two surfaces as they are brought together and retracted using multiple beam interferometry to monitor surface separation and directly measure contact area and observe any surface deformations occurring in the contact zone. One surface is held by a cantilevered spring, and the deflection of the spring is used to calculate the force being exerted. The technique was pioneered by David Tabor and R.H.S. Winterton in the late 1960s at Cambridge University. By the mid-1970s, J.N. Israelachvili had adapted the original design to operate in liquids, notably aqueous solutions, while at the Australian National University, and further advanced the technique to support friction and electro-chemical surface studies while at the University of California Santa Barbara. | 6 | Supramolecular Chemistry |
Ideality of solutions is analogous to ideality for gases, with the important difference that intermolecular interactions in liquids are strong and cannot simply be neglected as they can for ideal gases. Instead we assume that the mean strength of the interactions are the same between all the molecules of the solution.
More formally, for a mix of molecules of A and B, then the interactions between unlike neighbors (U) and like neighbors U and U must be of the same average strength, i.e., 2 U = U + U and the longer-range interactions must be nil (or at least indistinguishable). If the molecular forces are the same between AA, AB and BB, i.e., U = U = U, then the solution is automatically ideal.
If the molecules are almost identical chemically, e.g., 1-butanol and 2-butanol, then the solution will be almost ideal. Since the interaction energies between A and B are almost equal, it follows that there is only a very small overall energy (enthalpy) change when the substances are mixed. The more dissimilar the nature of A and B, the more strongly the solution is expected to deviate from ideality. | 7 | Physical Chemistry |
The process of nitrification begins with the first stage of ammonia oxidation, where ammonia (NH) or ammonium (NH) get converted into nitrite (NO). This first stage is sometimes known as nitritation. It is performed by two groups of organisms, ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). | 1 | Biochemistry |
Thermal laser epitaxy (TLE) is a physical vapor deposition technique that utilizes irradiation from continuous-wave lasers to heat sources locally for growing films on a substrate. This technique can be performed under ultra-high vacuum pressure or in the presence of a background atmosphere, such as ozone, to deposit oxide films.
TLE operates at power densities between 10 – 10 W/cm, which results in evaporation or sublimation of the source material, with no plasma or high-energy particle species being produced. Despite operating at comparatively low power densities, TLE is capable of depositing many materials with low vapor pressures, including refractory metals, a process that is challenging to perform with molecular beam epitaxy. | 3 | Analytical Chemistry |
The chemistry of the Mg ion, as applied to enzymes, uses the full range of this ions unusual reaction chemistry to fulfill a range of functions. Mg interacts with substrates, enzymes, and occasionally both (Mg may form part of the active site). In general, Mg interacts with substrates through inner sphere coordination, stabilising anions or reactive intermediates, also including binding to ATP and activating the molecule to nucleophilic attack. When interacting with enzymes and other proteins, Mg may bind using inner or outer sphere coordination, to either alter the conformation of the enzyme or take part in the chemistry of the catalytic reaction. In either case, because Mg is only rarely fully dehydrated during ligand binding, it may be a water molecule associated with the Mg that is important rather than the ion itself. The Lewis acidity of Mg (pK' 11.4) is used to allow both hydrolysis and condensation reactions (most common ones being phosphate ester hydrolysis and phosphoryl transfer) that would otherwise require pH values greatly removed from physiological values. | 1 | Biochemistry |
Physical Chemistry Chemical Physics is a weekly peer-reviewed scientific journal publishing research and review articles on any aspect of physical chemistry, chemical physics, and biophysical chemistry. It is published by the Royal Society of Chemistry on behalf of eighteen participating societies. The editor-in-chief is Anouk Rijs, (Vrije Universiteit Amsterdam).
The journal was established in 1999 as the results of a merger between Faraday Transactions and a number of other physical chemistry journals published by different societies. | 7 | Physical Chemistry |
The position of Whitley Professor of Biochemistry at the University of Oxford is one of the permanent chairs of the university, and the first in the field of biochemistry at the university. It is associated with a fellowship at Trinity College, Oxford, and was established with an endowment of £10,000 by Edward Whitley of Trinity College. Benjamin Moore was nominated by Whitley, a former student of Moore, as the first professor. Since its creation, the position has been held by:
* Benjamin Moore 1920–22
* Sir Rudolph Peters 1923–54
* Sir Hans Adolf Krebs 1954–67
* Rodney Robert Porter 1967–85
* Sir Edwin Southern 1985–2005
* Kim Nasmyth 2006-2022
* Dame Amanda Fisher 2023 onwards | 1 | Biochemistry |
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