1.
Pembrey Airport
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Pembrey West Wales International Airport is located 6 NM west northwest of Llanelli in Pembrey, Carmarthenshire, in Wales. Pembrey has one Hard Runway designated as 22LH/C and 04RH/C, Pembrey airport is situated inside the Royal Air Force danger area D118 known as Pembrey Sands Air Weapons Range. The Airport has an NDB on site designated as the PMB, construction of the airfield for RAF Flying Training Command started in 1937 and by September 1939, the RAFs No.2 Air Armament School was the first unit to be stationed at the airfield. By May 1940, the three runways had been completed. Between 1946 and 1949 RAF Fighter Command was in control of the airfield, from 1949 to 195221 Wing RAF Regiment were based at Pembrey. With Runway 04/22 extended to nearly 6000 feet,233 OCU moved in on 1 September 1952, initially with D. H Vampire aircraft, the unit stayed until 13 July 1957. The airfield closed in September 1957, post 1958 part of former RAF Pembrey airfield was turned over to agriculture and part was used as a motor racing circuit. On Thursday 22 August 1997 Pembrey was officially opened as a civil airfield, on 18 December 2009, Isles of Scilly Skybus operated the first charter flight into the airport. The flight originated from Newquay using a 16-seater aircraft, there were plans to lengthen the runway and lighting arrays to allow larger commercial aircraft to land. Pembrey Airport is also the hub for South Western Airways. Other airlines that have operated at Pembrey, Air Wales Air Independence Air Winton RAF Pembrey Court Farm, Pembrey Official website
2.
Pfam
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Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 31.0, was released in March 2017, the general purpose of the Pfam database is to provide a complete and accurate classification of protein families and domains. Originally, the rationale behind creating the database was to have a method of curating information on known protein families to improve the efficiency of annotating genomes. The Pfam classification of families has been widely adopted by biologists because of its wide coverage of proteins. Early genome projects, such as human and fly used Pfam extensively for functional annotation of genomic data, the Pfam website allows users to submit protein or DNA sequences to search for matches to families in the database. If DNA is submitted, a translation is performed, then each frame is searched. Family is the class, which simply indicates that members are related. Domains are defined as a structural unit or reusable sequence unit that can be found in multiple protein contexts. Repeats are not usually stable in isolation, but rather are required to form tandem repeats in order to form a domain or extended structure. Motifs are usually shorter sequence units found outside of globular domains, the descriptions of Pfam families are managed by the general public using Wikipedia. As of release 29.0,76. 1% of protein sequences in UniprotKB matched to at least one Pfam domain, new families come from a range of sources, primarily the PDB and analysis of complete proteomes to find genes with no Pfam hit. For each family, a subset of sequences are aligned into a high-quality seed alignment. Sequences for the alignment are taken primarily from pfamseq with some supplementation from UniprotKB. This seed alignment is used to build a profile hidden Markov model using HMMER. This HMM is then searched against sequence databases, and all hits that reach a curated gathering threshold are classified as members of the protein family, the resulting collection of members is then aligned to the profile HMM to generate a full alignment. For each family, a curated gathering threshold is assigned that maximises the number of true matches to the family while excluding any false positive matches. False positives are estimated by observing overlaps between Pfam family hits that are not from the same clan and this threshold is used to assess whether a match to a family HMM should be included in the protein family. Upon each update of Pfam, gathering thresholds are reassessed to prevent overlaps between new and existing families, domains of Unknown Function represent a growing fraction of the Pfam database
3.
InterPro
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The contents of InterPro consist of diagnostic signatures and the proteins that they significantly match. The signatures consist of models which describe protein families, domains or sites, models are built from the amino acid sequences of known families or domains and they are subsequently used to search unknown sequences in order to classify them. Each of the databases of InterPro contribute towards a different niche, from very high-level. InterPros intention is to provide a one-stop-shop for protein classification, where all the signatures produced by the different member databases are placed into entries within the InterPro database. Signatures which represent equivalent domains, sites or families are put into the same entry, additional information such as a description, consistent names and Gene Ontology terms are associated with each entry, where possible. InterPro contains three main entities, proteins, signatures and entries, the proteins in UniProtKB are also the central protein entities in InterPro. Information regarding which signatures significantly match these proteins are calculated as the sequences are released by UniProtKB, only signatures deemed to be of sufficient quality are integrated into InterPro. InterPro also includes data for splice variants and the contained in the UniParc. The signatures from InterPro come from 11 member databases, which are listed below, cATH-Gene3D describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity, mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains. Functional annotation is provided to proteins from multiple resources, functional prediction and analysis of domain architectures is available from the Gene3D website. HAMAP stands for High-quality Automated and Manual Annotation of microbial Proteomes, HAMAP profiles are manually created by expert curators they identify proteins that are part of well-conserved bacterial, archaeal and plastid-encoded proteins families or subfamilies. PANTHER is a collection of protein families that have been subdivided into functionally related subfamilies. Hidden Markov models are built for each family and subfamily for classifying additional protein sequences, Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. The primary PIRSF classification unit is the family, whose members are both homologous and homeomorphic. PRINTS is a compendium of protein fingerprints, a fingerprint is a group of conserved motifs used to characterise a protein family, its diagnostic power is refined by iterative scanning of UniProt. Usually the motifs do not overlap, but are separated along a sequence, ProDom domain database consists of an automatic compilation of homologous domains. Current versions of ProDom are built using a procedure based on recursive PSI-BLAST searches
4.
Protein Data Bank
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The Protein Data Bank is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is overseen by a called the Worldwide Protein Data Bank. The PDB is a key resource in areas of structural biology, most major scientific journals, and some funding agencies, now require scientists to submit their structure data to the PDB. Many other databases use protein structures deposited in the PDB, for example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. By 1971, one of Meyers programs, SEARCH, enabled researchers to access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the beginning of the PDB. Upon Hamiltons death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years, in January 1994, Joel Sussman of Israels Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics, the new director was Helen M. Berman of Rutgers University. In 2003, with the formation of the wwPDB, the PDB became an international organization, the founding members are PDBe, RCSB, and PDBj. Each of the four members of wwPDB can act as deposition, data processing, the data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are automatically checked for plausibility. The PDB database is updated weekly, likewise, the PDB holdings list is also updated weekly. As of 14 March 2017, the breakdown of current holdings is as follows,103,514 structures in the PDB have a structure factor file,9,057 structures have an NMR restraint file. 2,826 structures in the PDB have a chemical shifts file, therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy, the significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the electron density server, however, since 2007, the rate of accumulation of new protein structures appears to have plateaued. The file format used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line, around 1996, the macromolecular Crystallographic Information file format, mmCIF, which is an extension of the CIF format started to be phased in
5.
Protein
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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
6.
Amino acid
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Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an acid are carbon, hydrogen, oxygen. About 500 amino acids are known and can be classified in many ways, in the form of proteins, amino acids comprise the second-largest component of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in such as neurotransmitter transport. In biochemistry, amino acids having both the amine and the acid groups attached to the first carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids and they include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins. These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as standard amino acids. The other two are selenocysteine, and pyrrolysine, pyrrolysine and selenocysteine are encoded via variant codons, for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine is generally considered as a form of methionine rather than as a separate proteinogenic amino acid, codon–tRNA combinations not found in nature can also be used to expand the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids also play critical roles within the body. Nine proteinogenic amino acids are called essential for humans because they cannot be created from other compounds by the human body, others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, cystine was discovered in 1810, although its monomer, cysteine, remained undiscovered until 1884. Glycine and leucine were discovered in 1820, usage of the term amino acid in the English language is from 1898. Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis, in the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as amino acids
7.
Atomic mass unit
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The unified atomic mass unit or dalton is a standard unit of mass that quantifies mass on an atomic or molecular scale. One unified atomic mass unit is approximately the mass of one nucleon and is equivalent to 1 g/mol. The CIPM has categorised it as a non-SI unit accepted for use with the SI, the amu without the unified prefix is technically an obsolete unit based on oxygen, which was replaced in 1961. However, many still use the term amu but now define it in the same way as u. In this sense, most uses of the atomic mass units. For standardization a specific atomic nucleus had to be chosen because the mass of a nucleon depends on the count of the nucleons in the atomic nucleus due to mass defect. This is also why the mass of a proton or neutron by itself is more than 1 u, the atomic mass unit is not the unit of mass in the atomic units system, which is rather the electron rest mass. The relative atomic mass scale has traditionally been a relative value and this evaluation was made prior to the discovery of the existence of elemental isotopes, which occurred in 1912. The divergence of these values could result in errors in computations, the chemistry amu, based on the relative atomic mass of natural oxygen, was about 1.000282 as massive as the physics amu, based on pure isotopic 16O. For these and other reasons, the standard for both physics and chemistry was changed to carbon-12 in 1961. The choice of carbon-12 was made to minimise further divergence with prior literature. The new and current unit was referred to as the atomic mass unit u. and given a new symbol, u. The Dalton is another name for the atomic mass unit. 1 u = m u =112 m Despite this change, modern sources often use the old term amu but define it as u. Therefore, in general, amu likely does not refer to the old oxygen standard unit, the unified atomic mass unit and the dalton are different names for the same unit of measure. As with other names such as watt and newton, dalton is not capitalized in English. In 2003 the Consultative Committee for Units, part of the CIPM, recommended a preference for the usage of the dalton over the atomic mass unit as it is shorter. In 2005, the International Union of Pure and Applied Physics endorsed the use of the dalton as an alternative to the atomic mass unit
8.
Fluorescence
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Fluorescence is the emission of light by a substance that has absorbed light or other electromagnetic radiation. It is a form of luminescence, in most cases, the emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation. Fluorescent materials cease to glow immediately when the radiation source stops, unlike phosphorescence, Fluorescence also occurs frequently in nature in some minerals and in various biological states in many branches of the animal kingdom. An early observation of fluorescence was described in 1560 by Bernardino de Sahagún and it was derived from the wood of two tree species, Pterocarpus indicus and Eysenhardtia polystachya. The chemical compound responsible for this fluorescence is matlaline, which is the product of one of the flavonoids found in this wood. The name was derived from the fluorite, some examples of which contain traces of divalent europium. In a key experiment he used a prism to isolate ultraviolet radiation from sunlight, the specific frequencies of exciting and emitted light are dependent on the particular system. S0 is called the state of the fluorophore, and S1 is its first excited singlet state. A molecule in S1 can relax by various competing pathways and it can undergo non-radiative relaxation in which the excitation energy is dissipated as heat to the solvent. Excited organic molecules can also relax via conversion to a triplet state, relaxation from S1 can also occur through interaction with a second molecule through fluorescence quenching. Molecular oxygen is an extremely efficient quencher of fluorescence just because of its unusual triplet ground state, in most cases, the emitted light has a longer wavelength, and therefore lower energy, than the absorbed radiation, this phenomenon is known as the Stokes shift. The emitted radiation may also be of the wavelength as the absorbed radiation. Molecules that are excited through light absorption or via a different process can transfer energy to a second sensitized molecule, the fluorescence quantum yield gives the efficiency of the fluorescence process. It is defined as the ratio of the number of photons emitted to the number of photons absorbed, Φ = Number of photons emitted Number of photons absorbed The maximum fluorescence quantum yield is 1.0, each photon absorbed results in a photon emitted. Compounds with quantum yields of 0.10 are still considered quite fluorescent, thus, if the rate of any pathway changes, both the excited state lifetime and the fluorescence quantum yield will be affected. Fluorescence quantum yields are measured by comparison to a standard, the quinine salt quinine sulfate in a sulfuric acid solution is a common fluorescence standard. The fluorescence lifetime refers to the time the molecule stays in its excited state before emitting a photon. This is an instance of exponential decay, various radiative and non-radiative processes can de-populate the excited state
9.
Ultraviolet
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Ultraviolet is an electromagnetic radiation with a wavelength from 10 nm to 400 nm, shorter than that of visible light but longer than X-rays. UV radiation constitutes about 10% of the light output of the Sun. It is also produced by electric arcs and specialized lights, such as lamps, tanning lamps. Consequently, the effects of UV are greater than simple heating effects. Suntan, freckling and sunburn are familiar effects of over-exposure, along with risk of skin cancer. Living things on dry land would be damaged by ultraviolet radiation from the Sun if most of it were not filtered out by the Earths atmosphere. More-energetic, shorter-wavelength extreme UV below 121 nm ionizes air so strongly that it is absorbed before it reaches the ground, Ultraviolet is also responsible for the formation of bone-strengthening vitamin D in most land vertebrates, including humans. The UV spectrum thus has both beneficial and harmful to human health. Ultraviolet rays are invisible to most humans, the lens in a human eye ordinarily filters out UVB frequencies or higher, and humans lack color receptor adaptations for ultraviolet rays. Under some conditions, children and young adults can see ultraviolet down to wavelengths of about 310 nm, near-UV radiation is visible to some insects, mammals, and birds. Small birds have a fourth color receptor for ultraviolet rays, this gives birds true UV vision, reindeer use near-UV radiation to see polar bears, who are poorly visible in regular light because they blend in with the snow. UV also allows mammals to see urine trails, which is helpful for animals to find food in the wild. The males and females of some species look identical to the human eye. Ultraviolet means beyond violet, violet being the color of the highest frequencies of visible light, Ultraviolet has a higher frequency than violet light. He called them oxidizing rays to emphasize chemical reactivity and to them from heat rays. The terms chemical and heat rays were eventually dropped in favour of ultraviolet and infrared radiation, in 1878 the effect of short-wavelength light on sterilizing bacteria was discovered. By 1903 it was known the most effective wavelengths were around 250 nm, in 1960, the effect of ultraviolet radiation on DNA was established. The discovery of the ultraviolet radiation below 200 nm, named vacuum ultraviolet because it is absorbed by air, was made in 1893 by the German physicist Victor Schumann
10.
Jellyfish
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Jellyfish or jellies are softbodied, free-swimming aquatic animals with a gelatinous umbrella-shaped bell and trailing tentacles. The bell can pulsate to acquire propulsion and locomotion, the tentacles may be utilized to capture prey or defend against predators by emitting toxins in a painful sting. Jellyfish species are classified in the subphylum Medusozoa which makes up a part of the phylum Cnidaria. Jellyfish are found in ocean, from the surface to the deep sea. Scyphozoans are exclusively marine, but some live in freshwater. Large, often colorful, jellyfish are common in coastal zones worldwide, Jellyfish have roamed the seas for at least 500 million years, and possibly 700 million years or more, making them the oldest multi-organ animal. The popular English name jellyfish has been in use since 1796 and it has traditionally also been applied to other animals sharing a superficial resemblance, for example ctenophores were included as jellyfishes. Even some scientists include the phylum ctenophora when they are referring to jellyfish, other scientists prefer to use the more all-encompassing term gelatinous zooplankton, when referring to these, together with other soft-bodied animals in the water column. As jellyfish are not true fish, which are vertebrates, the jellyfish is considered by some to be a misnomer. Public aquaria often use the terms jellies or sea jellies instead, the term jellies may have become more popular than jellyfish. In scientific literature, jelly and jellyfish are often used interchangeably, some sources may use the term jelly to refer to organisms in this taxon, as jellyfish may be considered inappropriate. Many textbooks and sources refer to only scyphozoans as true jellyfish, a group of jellyfish is sometimes called a bloom or a swarm. Bloom is usually used for a group of jellyfish that gather in a small area. Another collective name for a group of jellyfish is a smack, using swarm usually implies some kind of active ability to stay together, which a few species such as Aurelia, the moon jelly, demonstrate. Medusa jellyfish may be classified as scyphomedusae, stauromedusae, cubomedusae, or hydromedusae, the term medusa was coined by Linnaeus in 1752, alluding to the tentacled head of Medusa in Greek mythology. This term refers exclusively to the non-polyp life-stage which occurs in many cnidarians, all medusa-producing species belong to the sub-phylum Medusozoa. In biology, a medusa is a form of cnidarian in which the body is shaped like an umbrella, medusae vary from bell-shaped to the shape of a thin disk, scarcely convex above and only slightly concave below. The digestive cavity consists of the cavity and radiating canals which extend toward the margin, these canals may be simple or branching
11.
Aequorea victoria
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Aequorea victoria, also sometimes called the crystal jelly, is a bioluminescent hydrozoan jellyfish, or hydromedusa, that is found off the west coast of North America. The species is best known as the source of two involved in bioluminescence, aequorin, a photoprotein, and green fluorescent protein. Their discoverers, Osamu Shimomura and colleagues, won the 2008 Nobel Prize in Chemistry for their work on GFP, the bell margin is surrounded by uneven tentacles, up to 150 of them in fully-grown specimens. The tentacles possess nematocysts that aid in capture, although they have no effect on humans. The bell margin is ringed with the velum, which is typical of hydromedusae. Larger specimens are found with symbiotic hyperiid amphipods attached to the subumbrella. Aequorea victoria are found along the North American west coast of the Pacific Ocean from the Bering Sea to southern California, the medusa part of the life cycle is a pelagic organism, which is budded off a bottom-living polyp in late spring. The medusae can be floating and swimming both nearshore and offshore in the eastern Pacific Ocean, this species is particularly common in Puget Sound. In September 2009, Aequorea victoria was spotted in the Moray Firth, the specimen was put on display in Macduff Marine Aquarium in Aberdeenshire, Scotland. These features are fairly plastic, and the numbers of tentacles, one other species is occasionally found in the same geographical range as Aequorea victoria, this other form has been called Aequorea coerulescens. While A. coerulescens is apparently generally found offshore in the eastern Pacific Ocean, rare specimens have been collected in central California and in Friday Harbor, while morphologically similar to Aequorea victoria, the Aequorea coerulescens form is larger with many more radial canals. Animals of sizes intermediate between two forms are also rather intermediate in appearance, making morphological identifications difficult. This species is thought to be synonymous with Aequorea aequorea of Osamu Shimomura, Shimomura together with Martin Chalfie and Roger Y. Tsien were awarded the 2008 Nobel Prize in Chemistry for the discovery, originally the A. victoria name was used to designate the variant found in the Pacific, and the A. aequorea designation was used for specimens found in the Atlantic and Mediterranean. The species name used in GFP purification was later disputed by M. N, arai and A. Brinckmann-Voss, who decided to separate them on the basis of 40 specimens collected from around Vancouver Island. Aequorea victoria have a life history, alternating between asexual benthic polyps and sexual planktonic medusae in a seasonal pattern. Aequorea victoria juvenile medusae are asexually budded off hydroid colonies in late spring, the medusa spends its first stage of life growing quickly, and after reaching approximately 3 cm will begin producing gametes for reproduction. Each medusa is either a male or a female, the hydroids live on hard or rocky substrates on the bottom, where they asexually bud new tiny jellyfish each springtime in response to some environmental cue
12.
Fluorescence spectroscopy
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Fluorescence spectroscopy is a type of electromagnetic spectroscopy that analyzes fluorescence from a sample. A complementary technique is absorption spectroscopy, in the special case of single molecule fluorescence spectroscopy, intensity fluctuations from the emitted light are measured from either single fluorophores, or pairs of fluorophores. Devices that measure fluorescence are called fluorometers, molecules have various states referred to as energy levels. Fluorescence spectroscopy is concerned with electronic and vibrational states. Generally, the species being examined has an electronic state of interest. Within each of these states there are various vibrational states. In fluorescence, the species is first excited, by absorbing a photon, collisions with other molecules cause the excited molecule to lose vibrational energy until it reaches the lowest vibrational state of the excited electronic state. This process is often visualized with a Jablonski diagram, the molecule then drops down to one of the various vibrational levels of the ground electronic state again, emitting a photon in the process. As molecules may drop down into any of several levels in the ground state, the emitted photons will have different energies. For atomic species, the process is similar, however, since atomic species do not have energy levels. This process of re-emitting the absorbed photon is resonance fluorescence and while it is characteristic of atomic fluorescence, is seen in molecular fluorescence as well, an emission map is measured by recording the emission spectra resulting from a range of excitation wavelengths and combining them all together. This is a three dimensional surface data set, emission intensity as a function of excitation and emission wavelengths, both types use the following scheme, the light from an excitation source passes through a filter or monochromator, and strikes the sample. A proportion of the incident light is absorbed by the sample, the fluorescent light is emitted in all directions. Various light sources may be used as sources, including lasers, LED. A laser only emits light of high irradiance at a narrow wavelength interval, typically under 0.01 nm. The disadvantage of this method is that the wavelength of a laser cannot be changed by much, a mercury vapor lamp is a line lamp, meaning it emits light near peak wavelengths. By contrast, an arc has a continuous emission spectrum with nearly constant intensity in the range from 300-800 nm. Filters and/or monochromators may be used in fluorimeters, a monochromator transmits light of an adjustable wavelength with an adjustable tolerance
13.
Wavelength
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In physics, the wavelength of a sinusoidal wave is the spatial period of the wave—the distance over which the waves shape repeats, and thus the inverse of the spatial frequency. Wavelength is commonly designated by the Greek letter lambda, the concept can also be applied to periodic waves of non-sinusoidal shape. The term wavelength is also applied to modulated waves. Wavelength depends on the medium that a wave travels through, examples of wave-like phenomena are sound waves, light, water waves and periodic electrical signals in a conductor. A sound wave is a variation in air pressure, while in light and other electromagnetic radiation the strength of the electric, water waves are variations in the height of a body of water. In a crystal lattice vibration, atomic positions vary, wavelength is a measure of the distance between repetitions of a shape feature such as peaks, valleys, or zero-crossings, not a measure of how far any given particle moves. For example, in waves over deep water a particle near the waters surface moves in a circle of the same diameter as the wave height. The range of wavelengths or frequencies for wave phenomena is called a spectrum, the name originated with the visible light spectrum but now can be applied to the entire electromagnetic spectrum as well as to a sound spectrum or vibration spectrum. In linear media, any pattern can be described in terms of the independent propagation of sinusoidal components. The wavelength λ of a sinusoidal waveform traveling at constant speed v is given by λ = v f, in a dispersive medium, the phase speed itself depends upon the frequency of the wave, making the relationship between wavelength and frequency nonlinear. In the case of electromagnetic radiation—such as light—in free space, the speed is the speed of light. Thus the wavelength of a 100 MHz electromagnetic wave is about, the wavelength of visible light ranges from deep red, roughly 700 nm, to violet, roughly 400 nm. For sound waves in air, the speed of sound is 343 m/s, the wavelengths of sound frequencies audible to the human ear are thus between approximately 17 m and 17 mm, respectively. Note that the wavelengths in audible sound are much longer than those in visible light, a standing wave is an undulatory motion that stays in one place. A sinusoidal standing wave includes stationary points of no motion, called nodes, the upper figure shows three standing waves in a box. The walls of the box are considered to require the wave to have nodes at the walls of the box determining which wavelengths are allowed, the stationary wave can be viewed as the sum of two traveling sinusoidal waves of oppositely directed velocities. Consequently, wavelength, period, and wave velocity are related just as for a traveling wave, for example, the speed of light can be determined from observation of standing waves in a metal box containing an ideal vacuum. In that case, the k, the magnitude of k, is still in the same relationship with wavelength as shown above
14.
Visible spectrum
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The visible spectrum is the portion of the electromagnetic spectrum that is visible to the human eye. Electromagnetic radiation in this range of wavelengths is called light or simply light. A typical human eye will respond to wavelengths from about 390 to 700 nm, in terms of frequency, this corresponds to a band in the vicinity of 430–770 THz. The spectrum does not, however, contain all the colors that the human eyes, unsaturated colors such as pink, or purple variations such as magenta, are absent, for example, because they can be made only by a mix of multiple wavelengths. Colors containing only one wavelength are called pure colors or spectral colors. Visible wavelengths pass through the window, the region of the electromagnetic spectrum that allows wavelengths to pass largely unattenuated through the Earths atmosphere. An example of this phenomenon is that clean air scatters blue light more than red wavelengths, the optical window is also referred to as the visible window because it overlaps the human visible response spectrum. The near infrared window lies just out of the vision, as well as the Medium Wavelength IR window. In the 13th century, Roger Bacon theorized that rainbows were produced by a process to the passage of light through glass or crystal. In the 17th century, Isaac Newton discovered that prisms could disassemble and reassemble white light and he was the first to use the word spectrum in this sense in print in 1671 in describing his experiments in optics. The result is red light is bent less sharply than violet as it passes through the prism. Newton divided the spectrum into seven named colors, red, orange, yellow, green, blue, indigo, the human eye is relatively insensitive to indigos frequencies, and some people who have otherwise-good vision cannot distinguish indigo from blue and violet. For this reason, some commentators, including Isaac Asimov, have suggested that indigo should not be regarded as a color in its own right. However, the evidence indicates that what Newton meant by indigo, comparing Newtons observation of prismatic colors to a color image of the visible light spectrum shows that indigo corresponds to what is today called blue, whereas blue corresponds to cyan. In the 18th century, Goethe wrote about optical spectra in his Theory of Colours, Goethe used the word spectrum to designate a ghostly optical afterimage, as did Schopenhauer in On Vision and Colors. Goethe argued that the spectrum was a compound phenomenon. Where Newton narrowed the beam of light to isolate the phenomenon, Goethe observed that a wider aperture produces not a spectrum but rather reddish-yellow, the spectrum appears only when these edges are close enough to overlap. Young was the first to measure the wavelengths of different colors of light, the connection between the visible spectrum and color vision was explored by Thomas Young and Hermann von Helmholtz in the early 19th century
15.
Sea pansy
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The sea pansy is a colonial cnidarian native to warm continental shelf waters of the Western Hemisphere. It is frequently found washed ashore on northeast Florida beaches following northeasterly winds or rough surf conditions and it also can often be found living intertidally completely buried in the sand. Its predator is the sea slug, Armina tigrina. The sea pansy is a collection of polyps with different forms, a single, giant polyp up to two inches in diameter forms the anchoring stem. This peduncle can be distended to better anchor the colony in the substrate, the pansy-like body bears many small, anemone-like feeding polyps. A cluster of tentacleless polyps form an outlet valve that releases water to deflate the colony, if the colony is on a sand bar at low tide, it usually deflates and becomes covered with a thin film of silty sand. Small white dots between the polyps are polyps that act as pumps to expand the deflated colony. The feeding polyps secrete a sticky mucus to trap tiny organisms suspended in the water, the colony’s rigidity and purple color come from calcium carbonate spicules throughout the polyps tissues. The sea pansy is strikingly bioluminescent when disturbed because of the interplay between a luciferase and green fluorescent protein, both molecules have recently become extremely important in biology. Discussion of green fluorescent protein in the sea pansy http, //150.176.130. 202/species/seapansy. htm Whitney laboratory for Marine Bioscience Bill Frank, Jacksonville, Florida
16.
Chromophore
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A chromophore is the part of a molecule responsible for its color. The color that is seen by our eyes is the one not absorbed within a certain spectrum of visible light. The chromophore is a region in the molecule where the difference between two separate molecular orbitals falls within the range of the visible spectrum. Visible light that hits the chromophore can thus be absorbed by exciting an electron from its state into an excited state. In biological molecules that serve to capture or detect light energy, in the conjugated chromophores, the electrons jump between energy levels that are extended pi orbitals, created by a series of alternating single and double bonds, often in aromatic systems. Common examples include retinal, various food colorings, fabric dyes, pH indicators, lycopene, β-carotene, various factors in a chromophores structure go into determining at what wavelength region in a spectrum the chromophore will absorb. Lengthening or extending a conjugated system with more unsaturated bonds in a molecule will tend to shift absorption to longer wavelengths, woodward-Fieser rules can be used to approximate ultraviolet-visible maximum absorption wavelength in organic compounds with conjugated pi-bond systems. Some of these are metal complex chromophores, which contain a metal in a complex with ligands. Examples are chlorophyll, which is used by plants for photosynthesis and hemoglobin, the highly conjugated pi-bonding system of the macrocycle ring absorbs visible light. The nature of the metal can also influence the absorption spectrum of the metal-macrocycle complex or properties such as excited state lifetime. The tetrapyrrole moiety in organic compounds which is not macrocyclic but still has a conjugated pi-bond system still acts as a chromophore, examples of such compounds include bilirubin and urobilin, which exhibit a yellow color. An auxochrome is a group of atoms attached to the chromophore which modifies the ability of the chromophore to absorb light. Halochromism occurs when a substance changes color as the pH changes and this is a property of pH indicators, whose molecular structure changes upon certain changes in the surrounding pH. This change in structure affects a chromophore in the pH indicator molecule, because of their limited extent, the aromatic rings only absorb light in the ultraviolet region, and so the compound appears colorless in the 0-8 pH range. However, as the pH increases beyond 8.2, that central carbon becomes part of a double bond becoming sp2 hybridized and this makes the three rings conjugate together to form an extended chromophore absorbing longer wavelength visible light to show a fuchsia color. At pH ranges outside 0-12, other molecular structure changes result in other color changes, visual phototransduction Woodwards rules Chromatophore Pigment Photophore Fluorophore Litmus Biological pigment Causes of Color, physical mechanisms by which color is generated. High Speed Nano-Sized Electronics May be Possible with Chromophores - Azonano. com
17.
Cofactor (biochemistry)
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A cofactor is a non-protein chemical compound or metallic ion that is required for a proteins biological activity to happen. These proteins are enzymes, and cofactors can be considered helper molecules that assist in biochemical transformations. A coenzyme that is tightly or even covalently bound is termed a prosthetic group, the two subcategories under coenzyme are cosubstrates and prosthetic groups. Cosubstrates are transiently bound to the protein and will be released at some point, the prosthetic groups, on the other hand, are bound permanently to the protein. Both of them have the function, which is to facilitate the reaction of enzymes. Additionally, some sources also limit the use of the cofactor to inorganic substances. An inactive enzyme without the cofactor is called an apoenzyme, while the enzyme with cofactor is called a holoenzyme. Some enzymes or enzyme complexes require several cofactors, organic cofactors are often vitamins or made from vitamins. Many contain the nucleotide adenosine monophosphate as part of their structures, such as ATP, coenzyme A, FAD and this common structure may reflect a common evolutionary origin as part of ribozymes in an ancient RNA world. It has been suggested that the AMP part of the molecule can be considered to be a kind of handle by which the enzyme can grasp the coenzyme to switch it between different catalytic centers. Cofactors can be divided into two groups, organic cofactors, such as flavin or heme, and inorganic cofactors, such as the metal ions Mg2+, Cu+, Mn2+. Organic cofactors are sometimes divided into coenzymes and prosthetic groups. The term coenzyme refers specifically to enzymes and, as such, on the other hand, prosthetic group emphasizes the nature of the binding of a cofactor to a protein and, thus, refers to a structural property. Different sources give different definitions of coenzymes, cofactors. It should be noted that terms are often used loosely. However, the author could not arrive at a single all-encompassing definition of a coenzyme, the study of these cofactors falls under the area of bioinorganic chemistry. In nutrition, the list of essential trace elements reflects their role as cofactors, in humans this list commonly includes iron, magnesium, manganese, cobalt, copper, zinc, and molybdenum. Although chromium deficiency causes impaired glucose tolerance, no human enzyme that uses this metal as a cofactor has been identified, iodine is also an essential trace element, but this element is used as part of the structure of thyroid hormones rather than as an enzyme cofactor
18.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
19.
Cell biology
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Cell biology is a branch of biology that studies the different structures and functions of the cell and focuses mainly on the idea of the cell as the basic unit of life. This is done both on a microscopic and molecular level as it encompasses prokaryotic cells and eukaryotic cells, knowing the components of cells and how cells work is fundamental to all biological sciences, it is also essential for research in bio-medical fields such as cancer, and other diseases. Research in cell biology is closely related to genetics, biochemistry, molecular biology, immunology, and developmental biology. The study of the cell is done on a level, however, most of the processes within the cell are made up of a mixture of small organic molecules, inorganic ions, hormones. Approximately 75-85% of the volume is due to water making it an indispensable solvent as a result of its polarity. These molecules within the cell, which operate as substrates, provide an environment for the cell to carry out metabolic reactions. The cell shape varies among the different types of organisms, and are then classified into two categories, eukaryotes and prokaryotes. Cell biology focuses more on the study of cells, and their signalling pathways. This environment of the cell is made up of hydrophilic and hydrophobic regions which allows for the exchange of the above-mentioned molecules and ions. The hydrophilic regions of the cell are mainly on the inside and outside of the cell, the cell membrane consists of lipids and proteins which accounts for its hydrophobicity as a result of being non-polar substances. Therefore, in order for these molecules to participate in reactions, within the cell and they accomplish this process of gaining access to the cell via, osmotic pressure, diffusion, concentration gradients, and membrane channels. Inside of the cell are extensive internal sub-cellular membrane-bounded compartments called organelles, cytoplasm - contents of the main fluid-filled space inside cells, chemical reactions also happen in this jelly-like substance. Nuclear Architecture is important for dictating nuclear function, vacuole - contain cell sap or other storage material. Vesicle - small membrane-bounded spheres inside cells which transport substances, the growth process of the cell does not refer to the size of the cell, but instead the density of the number of cells present in the organism at a given time. Cell growth pertains to the increase in the number of cells present in an organism as it grows and develops, Cells are the foundation of all organisms, they are the fundamental unit of life. The growth and development of the cell are essential for the maintenance of the host, for this process the cell goes through the steps of the cell cycle and development which involves cell growth, DNA replication, cell division, regeneration, specialization, and cell death. The cell cycle is divided into four phases, G1, S, G2. The G phases – which is the growth phase - makes up approximately 95% of the cycle
20.
Molecular biology
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Writing in Nature in 1961, William Astbury described molecular biology as. It is concerned particularly with the forms of biological molecules and is predominantly three-dimensional and structural—which does not mean, however and it must at the same time inquire into genesis and function. Researchers in molecular biology use specific techniques native to molecular biology but increasingly combine these techniques and ideas from genetics. There is not a line between these disciplines. Biochemists focus heavily on the role, function, and structure of biomolecules, the study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry. Genetics is the study of the effect of differences on organisms. This can often be inferred by the absence of a normal component, the study of mutants – organisms which lack one or more functional components with respect to the so-called wild type or normal phenotype. Genetic interactions can often confound simple interpretations of such knockout studies, molecular biology is the study of molecular underpinnings of the processes of replication, transcription, translation, and cell function. This picture, however, is undergoing revision in light of emerging novel roles for RNA, much of molecular biology is quantitative, and recently much work has been done at its interface with computer science in bioinformatics and computational biology. In the early 2000s, the study of structure and function. There is also a tradition of studying biomolecules from the ground up in biophysics. One of the most basic techniques of molecular biology to study protein function is molecular cloning, in this technique, DNA coding for a protein of interest is cloned using PCR and/or restriction enzymes into a plasmid. A vector has 3 distinctive features, an origin of replication, a multiple cloning site, the origin of replication will have promoter regions upstream from the replication/transcription start site. This plasmid can be inserted into either bacterial or animal cells, introducing DNA into bacterial cells can be done by transformation via uptake of naked DNA, conjugation via cell-cell contact or by transduction via viral vector. Introducing DNA into eukaryotic cells, such as cells, by physical or chemical means is called transfection. Several different transfection techniques are available, such as calcium phosphate transfection, electroporation, microinjection, the plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection. DNA coding for a protein of interest is now inside a cell, a variety of systems, such as inducible promoters and specific cell-signaling factors, are available to help express the protein of interest at high levels. Large quantities of a protein can then be extracted from the bacterial or eukaryotic cell, polymerase chain reaction is an extremely versatile technique for copying DNA
21.
Gene
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A gene is a locus of DNA which is made up of nucleotides and is the molecular unit of heredity. The transmission of genes to an offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes, genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions, genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotypical traits, usage of the term having a gene typically refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection or survival of the fittest of the alleles, the concept of a gene continues to be refined as new phenomena are discovered. For example, regulatory regions of a gene can be far removed from its coding regions, some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. The existence of discrete inheritable units was first suggested by Gregor Mendel, from 1857 to 1864, in Brno, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring. He described these mathematically as 2n combinations where n is the number of differing characteristics in the original peas, although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured the distinction between genotype and phenotype, charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan and genesis / genos. Darwin used the term gemmule to describe hypothetical particles that would mix during reproduction, de Vries called these units pangenes, after Darwins 1868 pangenesis theory. In 1909 the Danish botanist Wilhelm Johannsen shortened the name to gene, advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid was shown to be the repository of genetic information by experiments in the 1940s to 1950s. In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities, indivisible by recombination, collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, which is transcribed from DNA. This dogma has since shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics, in 1972, Walter Fiers and his team at the University of Ghent were the first to determine the sequence of a gene, the gene for Bacteriophage MS2 coat protein. The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing, an automated version of the Sanger method was used in early phases of the Human Genome Project. The theories developed in the 1930s and 1940s to integrate molecular genetics with Darwinian evolution are called the evolutionary synthesis
22.
Reporter gene
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In molecular biology, a reporter gene is a gene that researchers attach to a regulatory sequence of another gene of interest in bacteria, cell culture, animals or plants. Certain genes are chosen as reporters because the characteristics they confer on organisms expressing them are identified and measured. Reporter genes are used as an indication of whether a certain gene has been taken up by or expressed in the cell or organism population. To introduce a gene into an organism, scientists place the reporter gene. For bacteria or prokaryotic cells in culture, this is usually in the form of a circular DNA molecule called a plasmid, commonly used reporter genes that induce visually identifiable characteristics usually involve fluorescent and luminescent proteins. The GUS gene has been used in plants but luciferase. A common reporter in bacteria is the E. coli lacZ gene and this enzyme causes bacteria expressing the gene to appear blue when grown on a medium that contains the substrate analog X-gal. An example of a selectable-marker which is also a reporter in bacteria is the chloramphenicol acetyltransferase gene, thus, a method for identifying those few successful gene uptake events is necessary. In the case of selectable-marker reporters such as CAT, the population of bacteria can be grown on a substrate that contains chloramphenicol. Only those cells that have taken up the construct containing the CAT gene will survive. Reporter genes can also be used to assay for the expression of the gene of interest, in these cases, the reporter is directly attached to the gene of interest to create a gene fusion. The two genes are under the promoter elements and are transcribed into a single messenger RNA molecule. The mRNA is then translated into protein, in these cases it is important that both proteins be able to properly fold into their active conformations and interact with their substrates despite being fused. Reporter genes can be used to assay for the activity of a promoter in a cell or organism. In this case there is no separate gene of interest, the gene is simply placed under the control of the target promoter. The results are normally reported relative to the activity under a consensus promoter known to induce gene expression. A more complex use of reporter genes on a scale is in two-hybrid screening. GUS reporter system Research highlights and updated information on reporter genes, staining Whole Mouse Embryos for β-Galactosidase Activity
23.
Biosensor
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A biosensor is an analytical device, used for the detection of an analyte, that combines a biological component with a physicochemical detector. The sensitive biological element is a biologically derived material or biomimetic component that interacts with the analyte under study, the biologically sensitive elements can also be created by biological engineering. The biosensor reader device with the electronics or signal processors that are primarily responsible for the display of the results in a user-friendly way. This sometimes accounts for the most expensive part of the device, however it is possible to generate a user friendly display that includes transducer. The readers are usually custom-designed and manufactured to suit the different working principles of biosensors, a biosensor typically consists of a bio-recognition component, biotransducer component, and electronic system which include a signal amplifier, processor, and display. Transducers and electronics can be combined, e. g. in CMOS-based microsensor systems, the recognition component, often called a bioreceptor, uses biomolecules from organisms or receptors modeled after biological systems to interact with the analyte of interest. This interaction is measured by the biotransducer which outputs a signal proportional to the presence of the target analyte in the sample. The general aim of the design of a biosensor is to enable quick, in a biosensor, the bioreceptor is designed to interact with the specific analyte of interest to produce an effect measurable by the transducer. High selectivity for the analyte among a matrix of other chemical or biological components is a key requirement of the bioreceptor, an immunosensor utilizes the very specific binding affinity of antibodies for a specific compound or antigen. The specific nature of the interaction is analogous to a lock. Binding events result in a change that in combination with a tracer, such as a fluorescent molecules, enzymes, or radioisotopes. There are limitations with using antibodies in sensors,1. The antibody binding capacity is dependent on assay conditions and 2. The antibody-antigen interaction is generally irreversible, however, it has been shown that binding can be disrupted by chaotropic reagents, organic solvents, or even ultrasonic radiation. The use of antibodies as the component of biosensors has several drawbacks. They have high molecular weights and limited stability, contain essential disulfide bonds and are expensive to produce, in one approach to overcome these limitations, recombinant binding fragments or domains of antibodies have been engineered. The elements of the family that specifically bind to a target antigen, are often selected in vitro by display techniques, phage display, ribosome display. They are thus especially suitable to create biosensors, the specific binding capabilities and catalytic activity of enzymes make them popular bioreceptors. Notably, since enzymes are not consumed in reactions, the biosensor can easily be used continuously, the catalytic activity of enzymes also allows lower limits of detection compared to common binding techniques
24.
Proof of concept
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A proof of concept is usually small and may or may not be complete. The appearance of the terms in news archives suggests it might have been in use as long ago as 1967. In 1969 Committee on Science and Astronautics, the column also provided definitions for the related but distinct terms breadboard, prototype, engineering prototype, and brassboard. Sky Captain and the World of Tomorrow,300, and Sin City were all shot in front of a greenscreen with almost all backgrounds, all three used proof-of-concept short films. In the case of Sin City, the film became the prologue of the final film. Pixar sometimes creates short animated films use a difficult or untested technique. Their short film Geris Game used techniques for animation of cloth, in engineering and technology, a rough prototype of a new idea is often constructed as a proof of concept. For example, a concept of an electrical device may be constructed using a breadboard. A patent application often requires a demonstration of functionality prior to being filed, some universities have proof of concept centers to fill the funding gap for seed-stage investing and accelerate the commercialization of university innovations. Proof of concept centers provide seed funding to novel, early stage research that most often would not be funded by any other conventional source, in the field of business development and sales, a vendor may allow a prospect customer to trial a product. In these cases, the proof of concept may mean the use of specialized sales engineers to ensure that the vendor makes a best-possible effort. Winzapper was a proof of concept which possessed the bare minimum of capabilities needed to remove an item from the Windows Security Log. Once a vendor is satisfied, a prototype is developed which is used to seek funding or to demonstrate to prospective customers. A steel thread is technical proof of concept that all of the technologies in a solution. By contrast, a proof of technology aims to determine the solution to some problem or to demonstrate that a given configuration can achieve a certain throughput. No business users need be involved in a proof of technology, a pilot project refers to an initial roll-out of a system into production, targeting a limited scope of the intended final solution. The scope may be limited by the number of users who can access the system, the business processes affected, the purpose of a pilot project is to test, often in a production environment. Although not suggested by natural language, and in contrast to usage in other areas, Proof of Principle, a third term, Proof of Mechanism, is closely related and is also described here
25.
Genetic engineering
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Genetic engineering, also called genetic modification, is the direct manipulation of an organisms genome using biotechnology. It is a set of used to change the genetic makeup of cells, including the transfer of genes within. Genes may be removed, or knocked out, using a nuclease, gene targeting is a different technique that uses homologous recombination to change an endogenous gene, and can be used to delete a gene, remove exons, add a gene, or introduce point mutations. An organism that is generated through genetic engineering is considered to be a modified organism. The first GMOs were bacteria generated in 1973 and GM mice in 1974, insulin-producing bacteria were commercialized in 1982 and genetically modified food has been sold since 1994. GloFish, the first GMO designed as a pet, was first sold in the United States in December 2003, Genetic engineering techniques have been applied in numerous fields including research, agriculture, industrial biotechnology, and medicine. However the European Commission has also defined genetic engineering broadly as including selective breeding, cloning and stem cell research, although not considered genetic engineering, are closely related and genetic engineering can be used within them. Synthetic biology is a discipline that takes genetic engineering a step further by introducing artificially synthesized material from raw materials into an organism. If genetic material from another species is added to the host, if genetic material from the same species or a species that can naturally breed with the host is used the resulting organism is called cisgenic. Genetic engineering can also be used to remove material from the target organism. In Europe genetic modification is synonymous with genetic engineering while within the United States of America it can refer to conventional breeding methods. The Canadian regulatory system is based on whether a product has novel features regardless of method of origin, within the scientific community, the term genetic engineering is not commonly used, more specific terms such as transgenic are preferred. Plants, animals or micro organisms that have changed through genetic engineering are termed genetically modified organisms or GMOs, bacteria were the first organisms to be genetically modified. Plasmid DNA containing new genes can be inserted into the bacterial cell and these genes can code for medicines or enzymes that process food and other substrates. Plants have been modified for insect protection, herbicide resistance, virus resistance, enhanced nutrition, tolerance to environmental pressures, most commercialised GMOs are insect resistant and/or herbicide tolerant crop plants. Genetically modified animals have used for research, model animals. The genetically modified animals include animals with genes knocked out, increased susceptibility to disease, hormones for extra growth, humans have altered the genomes of species for thousands of years through selective breeding, or artificial selection as contrasted with natural selection, and more recently through mutagenesis. Genetic engineering as the manipulation of DNA by humans outside breeding
26.
Roger Y. Tsien
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Roger Yonchien Tsien was an American biochemist. Tsien was also a pioneer of calcium imaging, Tsien was born in New York, in 1952. He grew up in Livingston, New Jersey and attended Livingston High School there, Tsien suffered from asthma as a child, and as a result, he was often indoors. He spent hours conducting chemistry experiments in his basement laboratory, when he was 16, he won first prize in the nationwide Westinghouse Talent Search with a project investigating how metals bind to thiocyanate. Tsien attended Harvard College on a National Merit Scholarship, where he was elected to Phi Beta Kappa as a junior and he graduated summa cum laude with a Bachelor of Science in chemistry and physics in 1972. According to his roommate, economist and Iowa politician Herman Quirmbach. Nd I have met a lot of brilliant people, Tsien was a Research Fellow at Gonville and Caius College, Cambridge from 1977 to 1981. He was appointed to the faculty at the University of California, Berkeley and he also developed fluorescent indicators of calcium ions and other ions important in biological processes. In 2008, Tsien shared the Nobel Prize in Chemistry with Osamu Shimomura and Martin Chalfie for the fluorescent protein, discovery, expression. The multicolored fluorescent proteins developed in Tsiens lab are used by scientists to track where and this is such a popular technique that it has added a new dimension to the fields of molecular biology, cell biology, and biochemistry. Since the discovery of the wild type GFP, numerous different mutants of GFP have been engineered and tested, the first significant leap forward was a single point mutation reported by Tsien in 1995 in Nature. This mutation dramatically improved the fluorescent and spectral characteristics of GFP, all these then largely amplified the practicality of using GFP by scientists in their research. Tsien mainly contributed to much of our understanding of how GFP works and for developing new techniques, former trainees include Atsushi Miyawaki and Alice Y. Ting. Timelines of GFP-development involved by Tsien,1994, Tsien showed the mechanism that GFP chromophore is formed in a reaction which requires oxygen. 1994–1998, Tsien and collaborators made various GFP mutants by genetic modification, newly created variants of GFP can shine more brightly and show different colours, such as yellow, cyan, and blue. 2000–2002, Tsien produced monomeric variants of DsRED, which can glow in shades of red, pink, remarkably, since then complicated marcromolecular networks of living organisms can be labelled or marked by using all the colours of the rainbow. Other detailed highlights involved by Tsien,2002, The critical structural difference between GFP and DsRed was revealed, one extra double-bond in the chromophore of DsRed extends its conjugation thus causes the red-shift. 2002, Monomeric DsRed was first developed,2004, New fruit FPs were generated
27.
Osamu Shimomura
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Osamu Shimomura is a Japanese organic chemist and marine biologist, and Professor Emeritus at Marine Biological Laboratory in Woods Hole, Massachusetts and Boston University School of Medicine. Born in Fukuchiyama, Kyoto in 1928, Shimomura was brought up in Manchukuo and Osaka, later, his family moved to Isahaya, Nagasaki,25 km from the epicenter of the August 1945 atomic bombing of the city. He recalls hearing, as a 16-year-old boy, the bomber plane Bockscar before the bomb exploded. The explosion flash blinded Shimomura for about thirty seconds, and he was drenched by the black rain bomb fallout. He overcame great odds in the following 11 years to earn an education, Shimomuras education opportunities were starkly limited in devastated, post-war Japan. Although he later recalled having no interest in the subject, he enrolled in the College of Pharmaceutical Sciences of Nagasaki Medical College, the Medical College campus had been entirely destroyed by the atomic bomb blast, forcing the pharmacy school to relocate to a temporary campus near Shimomuras home. This proximity was the reason he embarked upon the studies. Shimomura was awarded a BS degree in pharmacy in 1951, Shimomuras mentor at Nagasaki helped him find employment as an assistant to Professor Yoshimasa Hirata at Nagoya University in 1956. At Nagoya, Hirata assigned Shimomura the challenging task of determining what made the remains of a type of crustacean glow when moistened with water. The article caught the attention of Professor Frank Johnson at Princeton University and his wife, Akemi, whom Shimomura met at Nagasaki University, is also an organic chemist and a partner in his research activities. Their son, Tsutomu Shimomura, is a security expert who was involved in the arrest of Kevin Mitnick. List of Japanese Nobel laureates Nobel Prize in Chemistry,2008
28.
Martin Chalfie
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Martin Lee Chalfie is an American scientist. He is University Professor at Columbia University and he shared the 2008 Nobel Prize in Chemistry along with Osamu Shimomura and Roger Y. Tsien for the discovery and development of the fluorescent protein. He holds a Ph. D. in neurobiology from Harvard University, Chalfie grew up in Chicago, Illinois, son of the guitarist Eli Chalfie and owner of an apparel store Vivian Chalfie. His maternal grandfather, Meyer L. Friedlen, immigrated to Chicago from Moscow at an age, his paternal grandparents, Benjamin and Esther Chalfie. He matriculated at Harvard University in 1965, intending to be a major, but he switched to biochemistry because it combined his interests in chemistry, math. He spent the summer after his junior year working in the laboratory of Klaus Weber at Harvard, as a result, in his senior year, he completed his major and took courses in law, theater, and Russian literature. He also competed on the team at Harvard and was named captain in his senior year. At the time, swimming coach Bill Brooks said, Marty will make an excellent captain because he has the admiration of the entire team, following the announcement of Chalfies Nobel award, his freshman-year roommate observed of Chalfie, “He would always identify himself as a swimmer. In the summer of 1971, his research at the laboratory of Jose Zadunaisky at Yale University resulted in his first publication, with revived confidence, he returned to Harvard for graduate studies under Robert Perlman, and received his Ph. D. in 1977. He conducted his research at the LMB with Sidney Brenner and John Sulston. Chalfie then left the LMB in 1982 to join the faculty of Columbia University in the department of biological sciences and she later joined him on the faculty of Columbia University. Chalfie and his wife had a daughter, Sarah, in July 1992, Chalfie was elected to the National Academy of Sciences in 2004. He slept through the call from the Nobel Prize Committee. When he woke up, he knew the prize would have been announced already, so he said Okay, and so he opened up his laptop, got to the Nobel Prize site and found out that he was the schnook. Chalfies lab uses the nematode C. elegans to investigate aspects of cell development. The wealth of developmental, anatomical, genetic, and molecular information available for C. elegans provides a powerful and he has published over 100 papers of which at least 25 have over 100 citations. Chalfie won a Golden Goose Award for this work in 2012
29.
Nobel Prize in Chemistry
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The Nobel Prize in Chemistry is awarded annually by the Royal Swedish Academy of Sciences to scientists in the various fields of chemistry. It is one of the five Nobel Prizes established by the will of Alfred Nobel in 1895, awarded for outstanding contributions in chemistry, physics, literature, peace, and physiology or medicine. This award is administered by the Nobel Foundation and awarded by Royal Swedish Academy of Sciences on proposal of the Nobel Committee for Chemistry which consists of five elected by Academy. The award is presented in Stockholm at a ceremony on December 10. The first Nobel Prize in Chemistry was awarded in 1901 to Jacobus Henricus van t Hoff, of the Netherlands, for his discovery of the laws of chemical dynamics and osmotic pressure in solutions. From 1901 to 2016, the award has been bestowed on a total of 174 individuals, though Nobel wrote several wills during his lifetime, the last was written a little over a year before he died, and signed at the Swedish-Norwegian Club in Paris on 27 November 1895. Nobel bequeathed 94% of his assets,31 million Swedish kronor, to establish. Due to the level of surrounding the will, it was not until April 26,1897 that it was approved by the Storting. The executors of his will were Ragnar Sohlman and Rudolf Lilljequist, the members of the Norwegian Nobel Committee that were to award the Peace Prize were appointed shortly after the will was approved. The prize-awarding organisations followed, the Karolinska Institutet on June 7, the Swedish Academy on June 9, the Nobel Foundation then reached an agreement on guidelines for how the Nobel Prize should be awarded. In 1900, the Nobel Foundations newly created statutes were promulgated by King Oscar II, according to Nobels will, The Royal Swedish Academy of Sciences were to award the Prize in Chemistry. The committee and institution serving as the board for the prize typically announce the names of the laureates in October. The prize is awarded at formal ceremonies held annually on December 10. The highlight of the Nobel Prize Award Ceremony in Stockholm is when each Nobel Laureate steps forward to receive the prize from the hands of His Majesty the King of Sweden, the Nobel Laureate receives three things, a diploma, a medal and a document confirming the prize amount. Later the Nobel Banquet is held in Stockholm City Hall, a maximum of three laureates and two different works may be selected. The award can be given to a maximum of three recipients per year and it consists of a gold medal, a diploma, and a cash grant. The Nobel Laureates in chemistry are selected by a committee that consists of five elected by the Royal Swedish Academy of Sciences. In its first stage, several people are asked to nominate candidates
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Aequorin
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Aequorin is a calcium-activated photoprotein isolated from the hydrozoan Aequorea victoria. Though the bioluminescence was studied decades before, the protein was isolated from the animal by Osamu Shimomura. In the animals, the protein together with the Green fluorescent protein to produce green light by resonant energy transfer. Work on aequorin began with E. Newton Harvey in 1921, later, Osamu Shimomura began work into the bioluminescence of Aequorea in 1961. This involved tedious harvesting of tens of thousands of jellyfish from the docks in Friday Harbor and it was determined that light could be produced from extracts with seawater, and more specifically, with calcium. It was also noted during the extraction the animal creates green light due to the presence of the fluorescent protein. This is to say, apoaequorin is the enzyme produced in the photocytes of the animal, when coelenterazine is bound, it is called aequorin. Notably, the protein contains three EF hand motifs that function as binding sites for Ca2+ ions, the protein is a member of the superfamily of the calcium-binding proteins of which there are some 66 subfamilies. The crystal structure revealed that aequorin binds coelenterazine and oxygen in the form of a peroxide, coelenterazine-2-hydroperoxide, the binding site for the first two calcium atoms show a 20X greater affinity for calcium than the third site. However, earlier claims that only two EF-hands bind calcium, were questioned when later structures indicated that all three site indeed can bind calcium, thus, titration studies show that all three calcium-binding sites are active but only two ions are needed to trigger the enzymatic reaction. Other studies have shown the presence of an internal cysteine bond that maintains the structure of aequorin, chemical characterization of aequorin indicates the protein is somewhat resilient to harsh treatments. Held at 95⁰C for 2 minutes the protein lost only 25% activity, denaturants 6M-urea or 4M-guanidine hydrochloride did not destroy the protein. Aequorin is presumably encoded in the genome of Aequorea, at least four copies of the gene were recovered as cDNA from the animal. Because the genome has not been sequenced, it is if the cDNA variants can account for all of the isoforms of the protein. Early studies of the bioluminescence of Aequorea by E. Newton Harvey had noted that the bioluminescence appears as a ring around the bell and this was remarkable because most bioluminescence reactions appeared to require oxygen, and led to the idea that the animals somehow store oxygen. It was later discovered that the apoprotein can stably bind coelenterazine, however, in the presence of calcium ions, the protein undergoes a conformational change and through oxidation converts its prosthetic group, coelenterazine, into excited coelenteramide and CO2. As the excited coelenteramide relaxes to the state, blue light is emitted. Before coelenteramide is exchanged out, the protein is still fluorescent blue
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Calcium
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Calcium is a chemical element with symbol Ca and atomic number 20. Calcium is a soft grayish-yellow alkaline earth metal, fifth-most-abundant element by mass in the Earths crust, the ion Ca2+ is also the fifth-most-abundant dissolved ion in seawater by both molarity and mass, after sodium, chloride, magnesium, and sulfate. Free calcium metal is too reactive to occur in nature, Calcium is produced in supernova nucleosynthesis. Calcium is a trace element in living organisms. It is the most abundant metal by mass in animals, and it is an important constituent of bone, teeth. In cell biology, the movement of the calcium ion into, Calcium carbonate and calcium citrate are often taken as dietary supplements. Calcium is on the World Health Organizations List of Essential Medicines, Calcium has a wide variety of applications, almost all of which are associated with calcium compounds and salts. Calcium metal is used as a deoxidizer, desulfurizer, and decarbonizer for production of ferrous and nonferrous alloys. In steelmaking and production of iron, Ca reacts with oxygen, Calcium carbonate is used in manufacturing cement and mortar, lime, limestone and aids in production in the glass industry. It also has chemical and optical uses as mineral specimens in toothpastes, Calcium hydroxide solution is used to detect the presence of carbon dioxide in a gas sample bubbled through a solution. The solution turns cloudy where CO2 is present, Calcium arsenate is used in insecticides. Calcium carbide is used to make acetylene gas and various plastics, Calcium chloride is used in ice removal and dust control on dirt roads, as a conditioner for concrete, as an additive in canned tomatoes, and to provide body for automobile tires. Calcium citrate is used as a food preservative, Calcium cyclamate is used as a sweetening agent in several countries. In the United States, it has been outlawed as a suspected carcinogen, Calcium gluconate is used as a food additive and in vitamin pills. Calcium hypochlorite is used as a swimming pool disinfectant, as an agent, as an ingredient in deodorant. Calcium permanganate is used in rocket propellant, textile production, as a water sterilizing agent. Calcium phosphate is used as a supplement for animal feed, fertilizer, in production for dough and yeast products, in the manufacture of glass. Calcium phosphide is used in fireworks, rodenticide, torpedoes, Calcium sulfate is used as common blackboard chalk, as well as, in its hemihydrate form, Plaster of Paris
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Complementary DNA
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In genetics, complementary DNA is double-stranded DNA synthesized from a single stranded RNA template in a reaction catalyzed by the enzyme reverse transcriptase. CDNA is often used to clone genes in prokaryotes. When scientists want to express a protein in a cell that does not normally express that protein. CDNA is also produced naturally by retroviruses and then integrated into the hosts genome, the term cDNA is also used, typically in a bioinformatics context, to refer to an mRNA transcripts sequence, expressed as DNA bases rather than RNA bases. The number of introns present in a cDNA is zero, since it is derived from eukaryotic mRNA which does not contain introns, although there are several methods for doing so, cDNA is most often synthesized from mature mRNA using the enzyme reverse transcriptase. This enzyme, which occurs in retroviruses, operates on a single strand of mRNA. To obtain eukaryotic cDNA whose introns have been removed, A eukaryotic cell transcribes the DNA into RNA, the same cell processes the pre-mRNA strands by removing introns, and adding a poly-A tail and 5’ Methyl-Guanine cap This mixture of mature mRNA strands is extracted from the cell. The Poly-A tail of the post-transcription mRNA can be taken advantage of with oligo beads in an affinity chromatography assay and this synthesizes one complementary strand of DNA hybridized to the original mRNA strand. To synthesize an additional DNA strand, traditionally one would digest the RNA of the strand, using an enzyme like RNase H. After digestion of the RNA, a single stranded DNA is left and because single stranded nucleic acids are hydrophobic and it is likely that the ssDNA forms a hairpin loop at the 3 end. From the hairpin loop, a DNA polymerase can use it as a primer to transcribe a complementary sequence for the ss cDNA. Now, you should be left with a double stranded cDNA with identical sequence as the mRNA of interest, Complementary DNA is often used in gene cloning or as gene probes or in the creation of a cDNA library. Partial sequences of cDNAs are often obtained as expressed sequence tags and this is achieved by designing sequence-specific DNA primers that hybridize to the 5 and 3 ends of a cDNA region coding for a protein. Once amplified, the sequence can be cut at each end with nucleases, such vectors allow for self-replication, inside the cells, and potentially integration in the host DNA. They typically also contain a promoter to drive transcription of the target cDNA into mRNA. Some viruses also use cDNA to turn their viral RNA into mRNA, the mRNA is used to make viral proteins to take over the host cell. CDNA library cDNA microarray RNA-Seq H-Invitational Database Functional Annotation of the Mouse database Complementary DNA tool
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Escherichia coli
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Escherichia coli is a gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes can cause food poisoning in their hosts. The harmless strains are part of the flora of the gut, and can benefit their hosts by producing vitamin K2. E. coli is expelled into the environment within fecal matter, the bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards. E. coli and other facultative anaerobes constitute about 0. 1% of gut flora, cells are able to survive outside the body for a limited amount of time, which makes them potential indicator organisms to test environmental samples for fecal contamination. A growing body of research, though, has examined environmentally persistent E. coli which can survive for extended periods outside of a host, the bacterium can be grown and cultured easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is a chemoheterotroph whose chemically defined medium must include a source of carbon, under favorable conditions, it takes only 20 minutes to reproduce. E. coli is a Gram-negative, facultative anaerobic and nonsporulating bacterium, cells are typically rod-shaped, and are about 2.0 μm long and 0. 25–1.0 μm in diameter, with a cell volume of 0. 6–0.7 μm3. E. coli stains Gram-negative because its cell wall is composed of a peptidoglycan layer. During the staining process, E. coli picks up the color of the counterstain safranin, the outer membrane surrounding the cell wall provides a barrier to certain antibiotics such that E. coli is not damaged by penicillin. Strains that possess flagella are motile, the flagella have a peritrichous arrangement. E. coli can live on a variety of substrates and uses mixed-acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate. Optimum growth of E. coli occurs at 37 °C, and it uses oxygen when it is present and available. It can, however, continue to grow in the absence of oxygen using fermentation or anaerobic respiration, the ability to continue growing in the absence of oxygen is an advantage to bacteria because their survival is increased in environments where water predominates. The bacterial cell cycle is divided into three stages, the B period occurs between the completion of cell division and the beginning of DNA replication. The C period encompasses the time it takes to replicate the chromosomal DNA, the D period refers to the stage between the conclusion of DNA replication and the end of cell division. The doubling rate of E. coli is higher when more nutrients are available, However, the length of the C and D periods do not change, even when the doubling time becomes less than the sum of the C and D periods. At the fastest growth rates, replication begins before the round of replication has completed, resulting in multiple replication forks along the DNA
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Caenorhabditis elegans
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Caenorhabditis elegans is a free-living, transparent nematode, about 1 mm in length, that lives in temperate soil environments. The name is a blend of the Greek caeno-, rhabditis, in 1900, Maupas initially named it Rhabditides elegans, Osche placed it in the subgenus Caenorhabditis in 1952, and in 1955, Dougherty raised it to the status of genus. C. elegans is an unsegmented pseudocoelomate, and lacks a respiratory and it possesses gut granules which emit a brilliant blue fluorescence, a wave of which is seen at death in a death fluorescence. The majority of these nematodes are hermaphrodites, males have specialised tails for mating that include spicules. In 1963, Sydney Brenner proposed research into C. elegans primarily in the area of neuronal development, in 1974, he began research into the molecular and developmental biology of C. elegans, which has since been extensively used as a model organism. C. elegans was the first multicellular organism to have its genome sequenced, and as of 2012. It is the species of its genus. C. elegans is unsegmented, vermiform, and bilaterally symmetrical and it has a cuticle, four main epidermal cords, and a fluid-filled pseudocoelom. It also has some of the organ systems as larger animals. About one in an individuals is male and the rest are hermaphrodites. The basic anatomy of C. elegans includes a mouth, pharynx, intestine, gonad, like all nematodes, they have neither a circulatory nor a respiratory system. When a wave of dorsal/ventral muscle contractions proceeds from the back to the front of the animal, when wave of contractions is initiated at the front and proceeds posteriorly along the body, the animal is propelled forwards. Because of this bias in body bends, any normal living, moving individual tends to lie on either its left side or its right side when observed crossing a horizontal surface. A set of ridges on the sides of the body cuticle. The pharynx is a muscular food pump in the head of C. elegans and this grinds food and transports it directly to the intestine. A set of valve cells connects the pharynx to the intestine, after digestion, the contents of the intestine are released via the rectum, as is the case with all other nematodes. No direct connection exists between the pharynx and the canal, which functions in the release of liquid urine. Males have a single-lobed gonad, a vas deferens, and a tail specialized for mating, hermaphrodites have two ovaries, oviducts, spermatheca, and a single uterus
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Indole
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Indole is an aromatic heterocyclic organic compound with formula C8H7N. It has a structure, consisting of a six-membered benzene ring fused to a five-membered nitrogen-containing pyrrole ring. Indole is widely distributed in the environment and can be produced by a variety of bacteria. As an intercellular signal molecule, indole regulates various aspects of physiology, including spore formation, plasmid stability, resistance to drugs, biofilm formation. The amino acid tryptophan is a derivative and the precursor of the neurotransmitter serotonin. Indole is a solid at room temperature, Indole can be produced by bacteria as a degradation product of the amino acid tryptophan. It occurs naturally in feces and has an intense fecal odor. At very low concentrations, however, it has a flowery smell and it also occurs in coal tar. The corresponding substituent is called indolyl, Indole undergoes electrophilic substitution, mainly at position 3. Substituted indoles are structural elements of the tryptophan-derived tryptamine alkaloids like the neurotransmitter serotonin, other indolic compounds include the plant hormone auxin, tryptophol, the anti-inflammatory drug indomethacin, the betablocker pindolol, and the naturally occurring hallucinogen dimethyltryptamine. The name indole is a portmanteau of the indigo and oleum. Indole chemistry began to develop with the study of the dye indigo, indigo can be converted to isatin and then to oxindole. Then, in 1866, Adolf von Baeyer reduced oxindole to indole using zinc dust, in 1869, he proposed a formula for indole. Certain indole derivatives were important dyestuffs until the end of the 19th century, in the 1930s, interest in indole intensified when it became known that the indole substituent is present in many important alkaloids, and it remains an active area of research today. It condenses with serine by Michael addition of indole to PLP-aminoacrylate, as an intercellular signal molecule, indole regulates various aspects of bacterial physiology, including spore formation, plasmid stability, resistance to drugs, biofilm formation, and virulence. The amino acid tryptophan is a derivative and the precursor of the neurotransmitter serotonin. Indole is a constituent of coal tar, and the 220–260 °C distillation fraction is the main industrial source of the material. Indole and its derivatives can also be synthesized by a variety of methods, the main industrial routes start from aniline via vapor-phase reaction with ethylene glycol in the presence of catalysts, In general, reactions are conducted between 200 and 500 °C
36.
Synaptobrevin
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Synaptobrevins are small integral membrane proteins of secretory vesicles with molecular weight of 18 kilodalton that are part of the vesicle-associated membrane protein family. Synaptobrevin is one of the SNARE proteins involved in formation of the SNARE complexes, out of four α-helices of the core SNARE complex one is contributed by synaptobrevin, one by syntaxin, and two by SNAP-25. SNARE proteins are the key components of the machinery that drives fusion of membranes in exocytosis. Their function however is subject to fine-tuning by various regulatory proteins collectively referred to as SNARE masters, Synaptobrevin is degraded by tetanospasmin, a protein derived from the bacterium Clostridium tetani, which causes tetanus. A related bacterium, Clostridium botulinum, produces botulinum toxin that also hydrolyzes synaptobrevin, sEC22A, SEC22B, SYBL1, VAMP1, VAMP2, VAMP3, VAMP4, VAMP5, VAMP8, YKT6, Synaptobrevin at the US National Library of Medicine Medical Subject Headings
37.
Redox
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Redox is a chemical reaction in which the oxidation states of atoms are changed. Any such reaction involves both a process and a complementary oxidation process, two key concepts involved with electron transfer processes. Redox reactions include all chemical reactions in which atoms have their oxidation state changed, in general, the chemical species from which the electron is stripped is said to have been oxidized, while the chemical species to which the electron is added is said to have been reduced. It can be explained in terms, Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom. Reduction is the gain of electrons or a decrease in state by a molecule, atom. As an example, during the combustion of wood, oxygen from the air is reduced, the reaction can occur relatively slowly, as in the case of rust, or more quickly, as in the case of fire. Redox is a portmanteau of reduction and oxidation, the word oxidation originally implied reaction with oxygen to form an oxide, since dioxygen was historically the first recognized oxidizing agent. Later, the term was expanded to encompass oxygen-like substances that accomplished parallel chemical reactions, ultimately, the meaning was generalized to include all processes involving loss of electrons. The word reduction originally referred to the loss in weight upon heating a metallic ore such as an oxide to extract the metal. In other words, ore was reduced to metal, antoine Lavoisier showed that this loss of weight was due to the loss of oxygen as a gas. Later, scientists realized that the atom gains electrons in this process. The meaning of reduction then became generalized to all processes involving gain of electrons. Even though reduction seems counter-intuitive when speaking of the gain of electrons, it help to think of reduction as the loss of oxygen. Since electrons are charged, it is also helpful to think of this as reduction in electrical charge. The electrochemist John Bockris has used the words electronation and deelectronation to describe reduction and oxidation processes respectively when they occur at electrodes and these words are analogous to protonation and deprotonation, but they have not been widely adopted by chemists. The term hydrogenation could be used instead of reduction, since hydrogen is the agent in a large number of reactions. But, unlike oxidation, which has been generalized beyond its root element, the word redox was first used in 1928. The processes of oxidation and reduction occur simultaneously and cannot happen independently of one another, the oxidation alone and the reduction alone are each called a half-reaction, because two half-reactions always occur together to form a whole reaction
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Palmitoylation
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Palmitoylation is the covalent attachment of fatty acids, such as palmitic acid, to cysteine and less frequently to serine and threonine residues of proteins, which are typically membrane proteins. The precise function of palmitoylation depends on the protein being considered. Palmitoylation enhances the hydrophobicity of proteins and contributes to their membrane association, Palmitoylation also appears to play a significant role in subcellular trafficking of proteins between membrane compartments, as well as in modulating protein–protein interactions. In contrast to prenylation and myristoylation, palmitoylation is usually reversible, the reverse reaction is catalysed by palmitoyl protein thioesterases. An example of a protein that undergoes palmitoylation is hemagglutinin, a membrane glycoprotein used by influenza to attach to host cell receptors. The palmitoylation cycles of an array of enzymes have been characterized in the past few years, including H-Ras, Gsα, the β2-adrenergic receptor. Another example is the major signaling protein Wnt, which is modified by a group at a serine. This is a type of O-acylation and is mediated by a membrane-bound O-acyltransferase, scientists have appreciated the significance of attaching long hydrophobic chains to specific proteins in cell signaling pathways. A good example of its significance is in the clustering of proteins in the synapse, a major mediator of protein clustering in the synapse is the postsynaptic density protein PSD-95. When this protein is palmitoylated it is restricted to the membrane and this restriction to the membrane allows it to bind to and cluster ion channels in the postsynaptic membrane. Also, in the neuron, palmitoylation of SNAP-25 directs it to partition in the cell membrane. This provides a role for palmitoylation in regulating neurotransmitter release, Palmitoylation of delta catenin seems to coordinate activity-dependent changes in synaptic adhesion molecules, synapse structure, and receptor localizations that are involved in memory formation. Resh, M. Palmitoylation of Ligands, Receptors, and Intracellular Signaling Molecules, linder M, Deschenes R. Palmitoylation, policing protein stability and traffic
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