1.
Bacteriorhodopsin
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Bacteriorhodopsin is a protein used by Archaea, most notably by Halobacteria, a class of the Euryarchaeota. It acts as a pump, that is, it captures light energy. The resulting proton gradient is subsequently converted into chemical energy, the repeating element of the hexagonal lattice is composed of three identical protein chains, each rotated by 120 degrees relative to the others. Each chain has seven alpha helices and contains one molecule of retinal buried deep within. It is the molecule that changes its conformation when absorbing a photon, resulting in a conformational change of the surrounding protein. It is covalently linked to Lys216 in the chromophore by Schiff base action, after photoisomerization of the retinal molecule, Asp85 becomes a proton acceptor of the donor proton from the retinal molecule. This releases a proton from a site into the extracellular side of the membrane. Reprotonation of the molecule by Asp96 restores its original isomerized form. This results in a second proton being released to the EC side, Asp85 releases its proton into the holding site, where a new cycle may begin. The bacteriorhodopsin molecule is purple and is most efficient at absorbing green light, bacteriorhodopsin has a broad excitation spectrum. For a detection wavelength between 700 and 800 nm, it has an appreciable detected emission for excitation wavelengths between 470 nm and 650 nm, when pumped at 633 nm, the emission spectrum has appreciable intensity between 650 nm and 850 nm. Bacteriorhodopsin belongs to the microbial rhodopsins and they have similarities to vertebrate rhodopsins, the pigments that sense light in the retina. Rhodopsins also contain retinal, however, the functions of rhodopsin and bacteriorhodopsin are different, both rhodopsin and bacteriorhodopsin belong to the 7TM receptor family of proteins, but rhodopsin is a G protein-coupled receptor and bacteriorhodopsin is not. In the first use of electron crystallography to obtain a protein structure. It was then used as a template to build models of G protein-coupled receptors before crystallographic structures were also available for these proteins, many molecules have homology to bacteriorhodopsin, including the light-driven chloride pump halorhodopsin, and some directly light-activated channels like channelrhodopsin. All other phototrophic systems in bacteria, algae, and plants use chlorophylls or bacteriochlorophylls rather than bacteriorhodopsin and these also produce a proton gradient, but in a quite different and more indirect way involving an electron transfer chain consisting of several other proteins. Furthermore, chlorophylls are aided in capturing light energy by other known as antennas. It is possible that phototrophy independently evolved at least twice, once in bacteria and once in archaea
2.
Haloarchaea
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Halobacteria are a class of the Euryarchaeota, found in water saturated or nearly saturated with salt. Halobacteria are now recognized as archaea, rather than bacteria, the name halobacteria was assigned to this group of organisms before the existence of the domain Archaea was realized, and remains valid according to taxonomic rules. In a non-taxonomic context, halophilic archaea are referred to as haloarchaea to distinguish them from halophilic bacteria and these microorganisms are members of the halophile community, in that they require high salt concentrations to grow. They are an evolutionary branch of the Archaea, and are generally considered extremophiles. Haloarchaea can grow aerobically or anaerobically, Haloarchaea have a potential to solubilized phosphorus. P- solubilizing halophilic archaea may play a role in P nutrition to growing in hypersaline soils. Haloarchaea may have application as inoculants for crop growing in hypersaline regions, the extremely halophilic, aerobic members of Archaea are classified within the family Halobacteriaceae, order Halobacteriales in Class III. As of May 2016, the family Halobacteriaceae comprises 50 genera 213 species, haloarculaceae Halapricum, Haloarcula, Halomicroarcula, Halomicrobium, Halorientalis, Halorhabdus, Halosimplex. Haloferacales Haloferacaceae Halabellus, Haloferax, Halogeometricum, Halopelagius, Haloplanus, Haloquadratum, halorubraceae Halobaculum, Halohasta, Halolamina, Halonotius, Halopenitus, Halorubrum, Salinigranum. Haloarchaea require salt concentrations in excess of 2 M to grow, however, Haloarchaea can grow up to saturation. Haloarchaea are found mainly in lakes and solar salterns. Their high densities in the water lead to pink or red colourations of the water. Bacteriorhodopsin is used to light, which provides energy to transport protons across the cellular membrane. The concentration gradient generated from this process can then be used to synthesize ATP, the process is unrelated to other forms of photosynthesis involving electron transport however, and haloarchaea are incapable of fixing carbon from carbon dioxide. Haloarchaea are often considered pleomorphic, or able to take on a range of shapes—even within a single species and this makes identification by microscopic means difficult, and it is now more common to use gene sequencing techniques for identification instead. One of the unusually shaped Haloarchaea is the Square Haloarchaeon of Walsby. It was classified in 2004 using a very low nutrition solution to growth along with a high salt concentration, square in shape. This shape is only permitted by the high osmolarity of the water, permitting cell shapes that would be difficult, if not impossible
3.
Cargill
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Cargill, Inc. is an American privately held global corporation based in Minnetonka, Minnesota, a Minneapolis suburb, but incorporated in Wilmington, Delaware. Founded in 1865, it is now the largest privately held corporation in the United States in terms of revenue, if it were a public company, it would rank, as of 2015, number 12 on the Fortune 500, behind McKesson and ahead of AT&T. Cargill also operates a financial services arm, which manages financial risks in the commodity markets for the company. In 2003, it split off a portion of its operations into a hedge fund called Black River Asset Management, with about $10 billion of assets. It owned 2/3 of the shares of The Mosaic Company, one of the leading producers and marketers of concentrated phosphate. Cargill declared revenues of $136.7 billion and earnings of $2.31 billion in the 2013 fiscal year, employing over 140,000 employees in 66 countries, it is responsible for 25% of all United States grain exports. The company also supplies about 22% of the US domestic meat market, all of the eggs used in McDonalds restaurants in the US pass through Cargills plants. It is the producer of Alberger process salt in the US. Cargill remains a business, as the descendants of the founder own over 90% of the company. As a result, most of its growth has been due to reinvestment of the companys own earnings rather than public financing, Gregory R. Page, who is not part of either the Cargill or MacMillan families, is the executive chairman of Cargill. He succeeded former CEO Warren Staley in mid-2007, as Staley reached Cargills mandatory retirement age of 65, Cargill was founded in 1865 by William W. Cargill when he bought a grain flat house in Conover, Iowa. A year later William was joined by his brother, Sam, together, they built grain flat houses and opened a lumberyard. In 1875, Cargill moved to La Crosse, Wisconsin, and brother, James, joined the family business. The city of La Crosse was strategically located on the Mississippi near the junctions of the La Crosse River, Dubuque, Sam Cargill left La Crosse in 1887 and moved to Minneapolis to manage the office there, which was identified as an important emerging grain center. Three years later, the Minneapolis operation incorporated under Cargill Elevator Co. years after that the La Crosse operation was incorporated under W. W, Cargill Company of La Crosse, Wisconsin. In 1898, John H. MacMillan, Sr. and his brother, Daniel, John MacMillan then married William Cargills eldest daughter, Edna. Upon Sam Cargills death in 1903, William Cargill became the owner of the La Crosse office. John MacMillan was named as manager of Cargill Elevator Company
4.
Salt evaporation pond
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Salt evaporation ponds, also called salterns, salt works or salt pans, are shallow artificial ponds designed to extract salts from sea water or other brines. The seawater or brine is fed into large ponds and water is drawn out through natural evaporation which allows the salt to be subsequently harvested, the ponds also provide a productive resting and feeding ground for many species of waterbirds, which may include endangered species. The ponds are separated by levees. Natural salt pans are geological formations that are created by water evaporating and leaving behind salts. Due to variable algal concentrations, vivid colors – from pale green to bright red – are created in the evaporation ponds, the color indicates the salinity of the ponds. Microorganisms change their hues as the salinity of the pond increases, in low- to mid-salinity ponds, green algae such as Dunaliella salina are predominant, although these algae can also take on an orange hue. In middle- to high-salinity ponds, Halobacteria, which is actually a group of halophilic Archaea, shift the colour to pink, red, other bacteria such as Stichococcus also contribute tints. Notable salt ponds include, the Salterns of Guérande, in Brittany, France, until World War II, salt was extracted from sea water in a unique way in Egypt near Alexandria. Posts were set out on the pans and covered with several feet of sea water. In time the sea water evaporated, leaving the salt behind on the post, salt pans are shallow open, often metal, pans used to evaporate brine for the production of salts. They are usually close to the source of the salt. In this case, extra heat is provided by lighting fires underneath
5.
San Francisco Bay
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San Francisco Bay is a shallow estuary in the U. S. state of California. It is surrounded by a region known as the San Francisco Bay Area, dominated by the large cities San Francisco, Oakland. San Francisco Bay drains water from approximately 40 percent of California and it then connects to the Pacific Ocean via the Golden Gate strait. However, this group of interconnected bays is often called the San Francisco Bay. The bay was designated a Ramsar Wetland of International Importance on February 2,2013, the bay covers somewhere between 400 and 1,600 square miles, depending on which sub-bays, estuaries, wetlands, and so on are included in the measurement. The main part of the bay measures 3 to 12 miles wide east-to-west and it is the largest Pacific estuary in the Americas. Later, wetlands and inlets were filled in, reducing the Bays size since the mid-19th century by as much as one third. Recently, large areas of wetlands have been restored, further confusing the issue of the Bays size, despite its value as a waterway and harbor, many thousands of acres of marshy wetlands at the edges of the bay were, for many years, considered wasted space. As a result, soil excavated for building projects or dredged from channels was often dumped onto the wetlands, from the mid-19th century through the late 20th century, more than a third of the original bay was filled and often built on. The idea was, and remains, controversial, there are five large islands in San Francisco Bay. Alameda, the largest island, was created when a shipping lane was cut in 1901 and it is now predominantly a bedroom community. Angel Island was known as Ellis Island West because it served as the point for immigrants from East Asia. It is now a park accessible by ferry. Mountainous Yerba Buena Island is pierced by a tunnel linking the east and west spans of the San Francisco–Oakland Bay Bridge, attached to the north is the artificial and flat Treasure Island, site of the 1939 Golden Gate International Exposition. From the Second World War until the 1990s, both served as military bases and are now being redeveloped. Isolated in the center of the Bay is Alcatraz, the site of the federal penitentiary. The federal prison on Alcatraz Island no longer functions, but the complex is a popular tourist site, despite its name, Mare Island in the northern part of the bay is a peninsula rather than an island. During the last ice age, the now filled by the bay was a large linear valley with small hills
6.
Newark, California
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Newark is a city in Alameda County, California, United States. It was incorporated as a city in September 1955, Newark is an enclave, surrounded by the city of Fremont. The three cities of Newark, Fremont, and Union City make up the Tri-City area and its population was 44,205 in 2015. The southern end of the San Francisco Bay lies near the edge of the city. State Route 84 runs through the city, and continues as the Dumbarton Bridge to cross the San Francisco Bay to reach Menlo Park, interstate 880 serves as the eastern boundary with Fremont. According to the United States Census Bureau, the city has an area of 13.9 square miles. Newark was named after Newark Castle, Port Glasgow in Scotland by J. Barr Robertson, before it was settled by Europeans, Newark was home to the Ohlone Native American Peoples. The first European settlement in the area was by the Spanish missionaries of Mission San José, whose territory covered much of the present day cities of Newark, Fremont, and Union City. In 1878 land belonging to Washington Township of Alameda County was purchased by The Pacific Land Investment Company, Newark was incorporated in September 1955. The 2010 United States Census reported that Newark had a population of 42,574, the population density was 3,063.2 people per square mile. The racial makeup of Newark was 17,567 White,2,002 Black,279 Native American,11,571 Asian,621 Pacific Islander,7,735 from other races, hispanic or Latino of any race were 14,994 persons. The Census reported that 42,428 people lived in households,145 lived in non-institutionalized group quarters, there were 659 unmarried opposite-sex partnerships, and 93 same-sex married couples or partnerships. 1,942 households were made up of individuals and 705 had someone living alone who was 65 years of age or older, the average household size was 3.27. There were 10,334 families, the family size was 3.60. The median age was 35.4 years, for every 100 females there were 99.3 males. For every 100 females age 18 and over, there were 96.8 males, there were 13,414 housing units at an average density of 965.2 per square mile, of which 8,942 were owner-occupied, and 4,030 were occupied by renters. The homeowner vacancy rate was 1. 0%, the vacancy rate was 4. 0%. 28,489 people lived in owner-occupied housing units and 13,939 people lived in housing units
7.
Photochemistry
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Photochemistry is the branch of chemistry concerned with the chemical effects of light. Generally, this term is used to describe a chemical reaction caused by absorption of ultraviolet, in nature, photochemistry is of immense importance as it is the basis of photosynthesis, vision, and the formation of vitamin D with sunlight. Photochemical reactions proceed differently than temperature-driven reactions, photochemistry is also destructive, as illustrated by the photodegradation of plastics. Photoexcitation is the first step in a process where the reactant is elevated to a state of higher energy. The first law of photochemistry, known as the Grotthuss–Draper law, when a molecule in the ground state absorbs light, one electron is excited to a higher orbital level. This electron maintains its spin according to the selection rule. The excitation to a singlet state can be from HOMO to LUMO or to a higher orbital, so that singlet excitation states S1, S2. Kashas rule stipulates that higher singlet states would quickly relax by radiationless decay or internal conversion to S1, thus, S1 is usually, but not always, the only relevant singlet excited state. This excited state S1 can further relax to S0 by IC, but also by an allowed radiative transition from S1 to S0 that emits a photon, this process is called fluorescence. Alternatively, it is possible for the excited state S1 to undergo spin inversion and this violation of the spin selection rule is possible by intersystem crossing of the vibrational and electronic levels of S1 and T1. According to Hunds rule of multiplicity, this T1 state would be somewhat more stable than S1. This triplet state can relax to the ground state S0 by radiationless IC or by a pathway called phosphorescence. This process implies a change of spin, which is forbidden by spin selection rules. Thus, triplet states generally have longer lifetimes than singlet states and these transitions are usually summarized in a state energy diagram or Jablonski diagram, the paradigm of molecular photochemistry. These excited species, either S1 or T1, have a half empty low-energy orbital, but at the same time, they have an electron in a high energy orbital, and are thus more reducing. In general, excited species are prone to participate in electron transfer processes, Photochemical reactions require a light source that emits wavelengths corresponding to an electronic transition in the reactant. In the early experiments, sunlight was the source, although it is polychromatic. Mercury-vapor lamps are common in the laboratory
8.
Membrane protein
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Membrane proteins are proteins that interact with, or are part of, biological membranes. The integral membrane proteins are classified as transmembrane proteins that span across the membrane, Membrane proteins are a common type of proteins along with soluble globular proteins, fibrous proteins, and disordered proteins. They are targets of over 50% of all modern medicinal drugs and it is estimated that 20–30% of all genes in most genomes encode membrane proteins. Membrane proteins perform a variety of functions vital to the survival of organisms, transport proteins move molecules and ions across the membrane. They can be categorized according to the Transporter Classification database, Membrane enzymes may have many activities, such as oxidoreductase, transferase or hydrolase. Cell adhesion molecules allow cells to each other and interact. For example, proteins involved in immune response, integral membrane proteins are permanently attached to the membrane. Such proteins can be separated from the biological membranes only using detergents, nonpolar solvents and these proteins may have different transmembrane topology. Integral monotopic proteins are membrane proteins that are attached to only one side of the membrane. Peripheral membrane proteins are attached either to the lipid bilayer or to integral proteins by a combination of hydrophobic, electrostatic. Peripheral proteins dissociate following treatment with a reagent, such as a solution with an elevated pH or high salt concentrations. Integral and peripheral proteins may be modified, with added fatty acid or prenyl chains, or GPI. Polypeptide toxins and many antibacterial peptides, such as colicins or hemolysins and these proteins are water-soluble but can aggregate and associate irreversibly with the lipid bilayer and become reversibly or irreversibly membrane-associated. A large fraction of all proteins are thought to be membrane proteins, for instance, about 1000 of the ~4200 proteins of E. coli are thought to be membrane proteins. The membrane localization has been confirmed for more than 600 of them experimentally, the localization of proteins in membranes can be predicted very reliably using hydrophobicity analyses of protein sequences, i. e. the localization of hydrophobic amino acid sequences. Approximate positions of membrane boundary planes were calculated for each PDB entry
9.
Transmembrane protein
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A transmembrane protein is a type of integral membrane protein that spans the entirety of the biological membrane to which it is permanently attached. Many transmembrane proteins function as gateways to permit the transport of substances across the biological membrane. They frequently undergo significant conformational changes to move a substance through the membrane, Transmembrane proteins are polytopic proteins that aggregate and precipitate in water. They require detergents or nonpolar solvents for extraction, although some of them can be extracted using denaturing agents. The other type of membrane protein is the integral monotopic protein that is also permanently attached to the cell membrane. There are two types of transmembrane proteins, alpha-helical and beta-barrels. Alpha-helical proteins are present in the membranes of bacterial cells or the plasma membrane of eukaryotes. This is the category of transmembrane proteins. In humans, 27% of all proteins have been estimated to be membrane proteins. Beta-barrel proteins are so far only in outer membranes of gram-negative bacteria, cell wall of gram-positive bacteria. All beta-barrel transmembrane proteins have simplest up-and-down topology, which may reflect their evolutionary origin. This classification refers to the position of the N- and C-terminal domains, types I, II, and III are single-pass molecules, while type IV are multiple-pass molecules. Type I transmembrane proteins are anchored to the membrane with a stop-transfer anchor sequence and have their N-terminal domains targeted to the ER lumen during synthesis. Type IV is subdivided into IV-A, with their N-terminal domains targeted to the cytosol and IV-B, Membrane protein structures can be determined by X-ray crystallography, electron microscopy or NMR spectroscopy. The most common structures of these proteins are transmembrane helix bundle. The portion of the proteins that are attached to the lipid bilayer consist mostly of hydrophobic amino acids. Membrane proteins have hydrophobic surfaces, are flexible and are expressed at relatively low levels. This creates difficulties in obtaining protein and then growing crystals
10.
Alpha helix
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This secondary structure is also sometimes called a classic Pauling–Corey–Branson α-helix. The name 3. 613-helix is also used for type of helix, denoting the average number of residues per helical turn. Among types of structure in proteins, the α-helix is the most regular. In the early 1930s, William Astbury showed that there were changes in the X-ray fiber diffraction of moist wool or hair fibers upon significant stretching. The data suggested that the unstretched fibers had a molecular structure with a characteristic repeat of ~5.1 ångströms. Astbury initially proposed a structure for the fibers. He later joined other researchers in proposing that, the protein molecules formed a helix the stretching caused the helix to uncoil. Hans Neurath was the first to show that Astburys models could not be correct in detail, neuraths paper and Astburys data inspired H. S. Taylor, Maurice Huggins and Bragg and collaborators to propose models of keratin that somewhat resemble the modern α-helix. The pivotal moment came in the spring of 1948, when Pauling caught a cold. Being bored, he drew a polypeptide chain of roughly correct dimensions on a strip of paper and folded it into a helix, after a few attempts, he produced a model with physically plausible hydrogen bonds. Pauling then worked with Corey and Branson to confirm his model before publication. The amino acids in an α-helix are arranged in a helical structure where each amino acid residue corresponds to a 100° turn in the helix. Dunitz describes how Paulings first article on the theme in fact shows a left-handed helix, short pieces of left-handed helix sometimes occur with a large content of achiral glycine amino acids, but are unfavorable for the other normal, biological L-amino acids. The pitch of the alpha-helix is 5.4 Å, which is the product of 1.5 and 3.6, the alpha-helices can be identified in protein structure using several computational methods, one of which being DSSP. Similar structures include the 310 helix and the π-helix, the subscripts refer to the number of atoms in the closed loop formed by the hydrogen bond. Residues in α-helices typically adopt backbone dihedral angles around, as shown in the image at right, in more general terms, they adopt dihedral angles such that the ψ dihedral angle of one residue and the φ dihedral angle of the next residue sum to roughly -105°. As a consequence, α-helical dihedral angles, in general, fall on a stripe on the Ramachandran diagram. For comparison, the sum of the angles for a 310 helix is roughly -75°
11.
Retinal
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Retinal is also known as retinaldehyde. It was originally called retinene, and renamed after it was discovered to be vitamin A aldehyde, retinal is one of the many forms of vitamin A. Retinal is a chromophore, bound to proteins called opsins. Retinal allows certain microorganisms to convert light into metabolic energy, vertebrate animals ingest retinal directly from meat, or they produce retinal from carotenoids, either from one of two carotenes or from β-cryptoxanthin, a type of xanthophyll. These carotenoids must be obtained from plants or other photosynthetic organisms, no other carotenoids can be converted by animals to retinal, and some carnivores cannot convert any carotenoids at all. The other main forms of vitamin A, retinol, and an active form, retinoic acid. Invertebrates such as insects and squid use hydroxylated forms of retinal in their visual systems, living organisms produce retinal by irreversible oxidative cleavage of carotenoids. For example, beta-carotene + O2 →2 retinal catalyzed by a beta-carotene 15, 15-monooxygenase or a beta-carotene 15, vision begins with the photoisomerization of retinal. When the 11-cis-retinal chromophore absorbs a photon it isomerizes from the 11-cis state to the all-trans state, the absorbance spectrum of the chromophore depends on its interactions with the opsin protein to which it is bound, different opsins produce different absorbance spectra. Opsins are proteins and the visual pigments found in the photoreceptor cells in the retinas of eyes. An opsin is arranged into a bundle of seven transmembrane alpha-helices connected by six loops, in rod cells the opsin molecules are embedded in the membranes of the disks which are entirely inside of the cell. The N-terminus head of the molecule extends into the interior of the disk, in cone cells the disks are defined by the cells plasma membrane so that the N-terminus head extends outside of the cell. Retinal binds covalently to a lysine on the transmembrane helix nearest the C-terminus of the protein through a Schiff base linkage, formation of the Schiff base linkage involves removing the oxygen atom from retinal and two hydrogen atoms from the free amino group of lysine, giving H2O. Retinylidene is the divalent group formed by removing the oxygen atom from retinal, opsins are prototypical G protein-coupled receptors. Bovine rhodopsin, the opsin of the rod cells of cattle, was the first GPCR to have its X-ray structure determined, bovine rhodopsin contains 348 amino acid residues. The retinal chromophore binds at Lys296, although mammals use retinal exclusively as the opsin chromophore, other groups of animals additionally use four chromophores closely related to retinal. These are 3, 4-didehydroretinal, -3-hydroxyretinal, -3-hydroxyretinal, and -4-hydroxyretinal, many fish and amphibians use 3, 4-didehydroretinal, also called dehydroretinal. With the exception of the dipteran suborder Cyclorrhapha, the higher flies
12.
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
13.
Ion channels
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Not to be confused with, Ion Television or Ion implantation. Ion channels are present in the membranes of all cells, Ion channels are one of the two classes of ionophoric proteins, along with ion transporters. Their classification as molecules is referred to as channelomics, there are two distinctive features of ion channels that differentiate them from other types of ion transporter proteins, The rate of ion transport through the channel is very high. Ions pass through channels down their electrochemical gradient, which is a function of ion concentration and membrane potential, downhill, Ion channels are located within the membrane of most cells and of many intracellular organelles. They are often described as narrow, water-filled tunnels that allow only ions of a certain size and/or charge to pass through and this characteristic is called selective permeability. The archetypal channel pore is just one or two atoms wide at its narrowest point and is selective for specific species of ion, such as sodium or potassium. However, some channels may be permeable to the passage of more than one type of ion, typically sharing a common charge, ions often move through the segments of the channel pore in single file nearly as quickly as the ions move through free solution. In many ion channels, passage through the pore is governed by a gate, Ion channels are integral membrane proteins, typically formed as assemblies of several individual proteins. Such multi-subunit assemblies usually involve an arrangement of identical or homologous proteins closely packed around a water-filled pore through the plane of the membrane or lipid bilayer. For most voltage-gated ion channels, the pore-forming subunit are called the α subunit, while the auxiliary subunits are denoted β, γ, because channels underlie the nerve impulse and because transmitter-activated channels mediate conduction across the synapses, channels are especially prominent components of the nervous system. Indeed, numerous toxins that organisms have evolved for shutting down the nervous systems of predators, in the search for new drugs, ion channels are a frequent target. There are over 300 types of ion channels in a living cell, Ion channels may be classified by the nature of their gating, the species of ions passing through those gates, the number of gates and localization of proteins. Further heterogeneity of ion channels arises when channels with different constitutive subunits give rise to a kind of current. Absence or mutation of one or more of the types of channel subunits can result in loss of function and, potentially. Ion channels may be classified by gating, i. e. what opens, Voltage-gated ion channels open or close depending on the voltage gradient across the plasma membrane, while ligand-gated ion channels open or close depending on binding of ligands to the channel. Voltage-gated ion channels open and close in response to membrane potential, Voltage-gated sodium channels, This family contains at least 9 members and is largely responsible for action potential creation and propagation. The pore-forming α subunits are very large and consist of four repeat domains each comprising six transmembrane segments for a total of 24 transmembrane segments. The members of family also coassemble with auxiliary β subunits
14.
Archaea
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The Archaea constitute a domain and kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells, Archaea were initially classified as bacteria, receiving the name archaebacteria, but this classification is outdated. Archaeal cells have unique properties separating them from the two domains of life, Bacteria and Eukaryota. The Archaea are further divided into multiple recognized phyla, classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment. Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat, other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more energy sources than eukaryotes, these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea use sunlight as a source, and other species of archaea fix carbon, however, unlike plants and cyanobacteria. Archaea reproduce asexually by fission, fragmentation, or budding, unlike bacteria and eukaryotes. They are also found in the colon, oral cavity. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet, Archaea are a major part of Earths life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, one example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures. For much of the 20th century, prokaryotes were regarded as a group of organisms and classified based on their biochemistry, morphology. For example, microbiologists tried to classify based on the structures of their cell walls, their shapes. In 1965, Emile Zuckerkandl and Linus Pauling proposed instead using the sequences of the genes in different prokaryotes to work out how they are related to each other and this approach, known as phylogenetics, is the main method used today. Archaea were first classified as a group of prokaryotes in 1977 by Carl Woese. These two groups were named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese. Woese argued that group of prokaryotes is a fundamentally different sort of life
15.
Bacteria
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
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Eukaryote
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A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota, the presence of a nucleus gives eukaryotes their name, which comes from the Greek εὖ and κάρυον. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular or multicellular, only eukaryotes form multicellular organisms consisting of many kinds of tissue made up of different cell types. Eukaryotes can reproduce asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two identical cells. In meiosis, DNA replication is followed by two rounds of division to produce four daughter cells each with half the number of chromosomes as the original parent cell. These act as sex cells resulting from genetic recombination during meiosis, the domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features, eukaryotes represent a tiny minority of all living things. However, due to their larger size, eukaryotes collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1. 6–2.1 billion years ago, in 1905 and 1910, the Russian biologist Konstantin Mereschkowsky argued three things about the origin of nucleated cells. Firstly, plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, secondly, the host had earlier in evolution formed by symbiosis between an amoeba-like host and a bacteria-like cell that formed the nucleus. Thirdly, plants inherited photosynthesis from cyanobacteria, the split between the prokaryotes and eukaryotes was introduced in the 1960s. The concept of the eukaryote has been attributed to the French biologist Edouard Chatton, the terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1938 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in one paragraph, and the idea was effectively ignored until Chattons statement was rediscovered by Stanier. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in cells in her paper. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA and this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts
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Multicellular organism
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Multicellular organisms are organisms that consist of more than one cell, in contrast to unicellular organisms. Multicellular organisms arise in different ways, for example by cell division or by aggregation of many single cells. Colonial organisms are the result of identical individuals joining together to form a colony. Multicellularity has evolved independently at least 46 times, including in some prokaryotes, like cyanobacteria, myxobacteria, actinomycetes, however, complex multicellular organisms evolved only in six eukaryotic groups, animals, fungi, brown algae, red algae, green algae, and land plants. It evolved repeatedly for Chloroplastida, once or twice for animals, once for brown algae, the first evidence of multicellularity is from cyanobacteria-like organisms that lived 3–3.5 billion years ago. To reproduce, true multicellular organisms must solve the problem of regenerating a whole organism from germ cells, animals have evolved a considerable diversity of cell types in a multicellular body, compared with 10–20 in plants and fungi. Loss of multicellularity occurred in some groups, fungi are predominantly multicellular, though early diverging lineages are largely unicellular and there have been numerous reversions to unicellularity across fungi. It may also have occurred in some red algae, but it is possible that they are primitively unicellular), loss of multicellularity is also considered probable in some green algae. In other groups, generally parasites, a reduction of multicellularity occurred, multicellular organisms, especially long-living animals, face the challenge of cancer, which occurs when cells fail to regulate their growth within the normal program of development. Changes in tissue morphology can be observed during this process, cancer in animals has often been described as a loss of multicellularity. There is a discussion about the possibility of existence of cancer in other organisms or even in protozoa. For example, plant galls have been characterized as tumors but some argue that plants do not develop cancer. In some multicellular groups, which are called Weismannists, a separation between a sterile somatic cell line and a cell line evolved. However, Weismannist development is relatively rare, as part of species have the capacity for somatic embryogenesis. One hypothesis for the origin of multicellularity is that a group of function-specific cells aggregated into a mass called a grex. This is essentially what slime molds do, another hypothesis is that a primitive cell underwent nucleus division, thereby becoming a coenocyte. A membrane would then form around each nucleus, thereby resulting in a group of connected cells in one organism and this is what plant and animal embryos do as well as colonial choanoflagellates. Because the first multicellular organisms were simple, soft organisms lacking bone, shell or other body parts
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Rhodopsin
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Rhodopsin is a light-sensitive receptor protein involved in visual phototransduction. It is named after ancient Greek ῥόδον for “rose”, due to its pinkish color, Rhodopsin is a biological pigment found in the rods of the retina and is a G-protein-coupled receptor. Rhodopsin is extremely sensitive to light, and thus enables vision in low-light conditions, when rhodopsin is exposed to light, it immediately photobleaches. In humans, it is regenerated fully in about 30 minutes, Rhodopsin was discovered by Franz Christian Boll in 1876. Rhodopsin consists of a protein moiety also called scotopsin, which binds covalently a cofactor called retinal, opsins are G protein coupled receptors and have seven transmembrane domains. The seven transmembrane domains form a pocket, where the retinal binds to a residue in the seventh transmembrane domain. The retinal lies horizontally to the cell membrane, and the cell membrane lipid bilayer embeds half of the rhodopsin. Thousands of rhodopsin molecules are found in outer segment disc of the host rod cell. Retinol is produced in the retina from Vitamin A, from dietary beta-carotene, Rhodopsin of the rods most strongly absorbs green-blue light and, therefore, appears reddish-purple, which is why it is also called visual purple. It is responsible for vision in the dark. Several closely related opsins exist that only in a few amino acids. Humans have eight different other opsins besides rhodopsin, as well as cryptochrome, the photopsins are found in the different types of the cone cells of the retina and are the basis of color vision. They have absorption maxima for yellowish-green, green, and bluish-violet light, the remaining opsin is found in photosensitive ganglion cells and absorbs blue light most strongly. In rhodopsin, the group of retinal is covalently linked to the amino group of a lysine residue on the protein in a protonated Schiff base. The intermediates formed during this process were first investigated in the laboratory of George Wald, the photoisomerization dynamics has been subsequently investigated with time-resolved IR spectroscopy and UV/Vis spectroscopy. A first photoproduct called photorhodopsin forms within 200 femtoseconds after irradiation and this intermediate can be trapped and studied at cryogenic temperatures, and was initially referred to as prelumirhodopsin. In subsequent intermediates lumirhodopsin and metarhodopsin I, the Schiffs base linkage to all-trans retinal remains protonated, the structure of rhodopsin has been studied in detail via x-ray crystallography on rhodopsin crystals. Several models attempt to explain how the group can change its conformation without clashing with the enveloping rhodopsin protein pocket
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Biological pigment
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Biological pigments, also known simply as pigments or biochromes, are substances produced by living organisms that have a color resulting from selective color absorption. Biological pigments include plant pigments and flower pigments, many biological structures, such as skin, eyes, feathers, fur and hair contain pigments such as melanin in specialized cells called chromatophores. For example, butterfly wings typically contain structural color, although many butterflies have cells that contain pigment as well, see conjugated systems for electron bond chemistry that causes these molecules to have pigment. Other functions of pigments in plants include attracting insects to flowers to encourage pollination, plant pigments include a variety of different kinds of molecule, including porphyrins, carotenoids, anthocyanins and betalains. All biological pigments selectively absorb certain wavelengths of light while reflecting others, the principal pigments responsible are, Chlorophyll is the primary pigment in plants, it is a chlorin that absorbs yellow and blue wavelengths of light while reflecting green. It is the presence and relative abundance of chlorophyll that gives plants their green color, all land plants and green algae possess two forms of this pigment, chlorophyll a and chlorophyll b. Kelps, diatoms, and other photosynthetic heterokonts contain chlorophyll c instead of b, all chlorophylls serve as the primary means plants use to intercept light in order to fuel photosynthesis. Carotenoids are red, orange, or yellow tetraterpenoids, during the process of photosynthesis, they have functions in light-harvesting, in photoprotection, and also serve as protein structural elements. In higher plants, they serve as precursors to the plant hormone abscisic acid. Plants, in general, contain six ubiquitous carotenoids, neoxanthin, violaxanthin, antheraxanthin, zeaxanthin, lutein, lutein is a yellow pigment found in fruits and vegetables and is the most abundant carotenoid in plants. Lycopene is the red pigment responsible for the color of tomatoes, other less common carotenoids in plants include lutein epoxide, lactucaxanthin, and alpha carotene. In cyanobacteria, many other carotenoids exist such as canthaxanthin, myxoxanthophyll, synechoxanthin, algal phototrophs such as dinoflagellates use peridinin as a light harvesting pigment. Anthocyanins are water-soluble flavonoid pigments that appear red to blue, according to pH and they occur in all tissues of higher plants, providing color in leaves, plant stem, roots, flowers, and fruits, though not always in sufficient quantities to be noticeable. Anthocyanins are most visible in the petals of flowers of many species, betalains are red or yellow pigments. Like anthocyanins they are water-soluble, but unlike anthocyanins they are synthesized from tyrosine and this class of pigments is found only in the Caryophyllales, and never co-occur in plants with anthocyanins. Betalains are responsible for the red color of beets. Chlorophylls degrade into colorless tetrapyrroles known as nonfluorescent chlorophyll catabolites, as the predominant chlorophylls degrade, the hidden pigments of yellow xanthophylls and orange beta-carotene are revealed. These pigments are present throughout the year, but the red pigments, pigmentation is used by many animals for protection, by means of camouflage, mimicry, or warning coloration
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Vertebrate
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Vertebrates /ˈvɜːrtᵻbrᵻts/ comprise all species of animals within the subphylum Vertebrata /-ɑː/. Vertebrates represent the majority of the phylum Chordata, with currently about 66,000 species described. Vertebrates include the fish and the jawed vertebrates, which include the cartilaginous fish. A bony fish known as the lobe-finned fishes is included with tetrapods, which are further divided into amphibians, reptiles, mammals. Extant vertebrates range in size from the frog species Paedophryne amauensis, at as little as 7.7 mm, to the blue whale, vertebrates make up less than five percent of all described animal species, the rest are invertebrates, which lack vertebral columns. The vertebrates traditionally include the hagfish, which do not have proper vertebrae due to their loss in evolution, though their closest living relatives, hagfish do, however, possess a cranium. For this reason, the vertebrate subphylum is sometimes referred to as Craniata when discussing morphology, molecular analysis since 1992 has suggested that hagfish are most closely related to lampreys, and so also are vertebrates in a monophyletic sense. Others consider them a group of vertebrates in the common taxon of craniata. The word origin of vertebrate derives from the Latin word vertebratus, the Proto-Indo-European language origins are still unclear. Vertebrate is derived from the vertebra, which refers to any of the bones or segments of the spinal column. All vertebrates are built along the basic body plan, a stiff rod running through the length of the animal, with a hollow tube of nervous tissue above it. In all vertebrates, the mouth is found at, or right below, the remaining part of the body continuing after the anus forms a tail with vertebrae and spinal cord, but no gut. However, a few vertebrates have secondarily lost this anatomy, retaining the notochord into adulthood, such as the sturgeon, jawed vertebrates are typified by paired appendages, but this trait is not required in order for an animal to be a vertebrate. All basal vertebrates breathe with gills, the gills are carried right behind the head, bordering the posterior margins of a series of openings from the pharynx to the exterior. Each gill is supported by a cartilagenous or bony gill arch, the bony fish have three pairs of arches, cartilaginous fish have five to seven pairs, while the primitive jawless fish have seven. The vertebrate ancestor no doubt had more arches than this, as some of their relatives have more than 50 pairs of gills. In amphibians and some primitive fishes, the larvae bear external gills. These are reduced in adulthood, their function taken over by the gills proper in fishes, some amphibians retain the external larval gills in adulthood, the complex internal gill system as seen in fish apparently being irrevocably lost very early in the evolution of tetrapods
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Scotopic vision
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Scotopic vision is the vision of the eye under low light conditions. The term comes from Greek skotos meaning darkness and -opia meaning a condition of sight, scotopic vision is dominated by retina amacrine cells, specifically all-amacrine cells. AII-amacrine cells capture rod bipolar cell input and redistribute it to cone bipolar cells since rod-driven bipolar cells do not synapse on ganglion cells, scotopic vision occurs at luminance levels of 10−3 to 10−6 cd/m². Other species are not universally color blind in low-light conditions, the Elephant Hawk-moth displays advanced color discrimination even in dim starlight. Mesopic vision occurs in intermediate lighting conditions and is effectively a combination of scotopic and photopic vision and this however gives inaccurate visual acuity and color discrimination. In normal light, the vision of cone cells dominates and is photopic vision, there is good visual acuity and color discrimination. In scientific literature, one encounters the term scotopic lux which corresponds to photopic lux. The normal human observer’s relative wavelength sensitivity will not change due to background illumination change under scotopic vision, the wavelength sensitivity is determined by the rhodopsin photopigment. This is a red pigment and can be seen at the back of eye of animals that have a background to their eye called Tapetum lucidum. The pigment is not noticeable under photopic and mesopic conditions, the principle that the wavelength sensitivity does not change during scotopic vision led to the ability to detect two functional cone classes in individuals. If two cone classes are present, then their relative sensitivity will change the wavelength sensitivity. ”For adaption to occur at very low levels. This leads to the eye being unable to resolve high spatial frequencies in low light since the observer is spatially averaging the light signal. The behavior of the rhodopsin photopigment explains why the human eye cannot resolve lights with different spectral power distributions under low light, the reaction of this single photopigment will give the same quanta for 400 nm light and 700 nm light. Therefore, this photopigment only maps the rate of absorption and does not encode information about the spectral composition of the light. Another reason that vision is poor under scotopic vision is that rods and this many-to-one ratio leads to poor spatial frequency sensitivity. Photopic vision Mesopic vision Adaptation Averted vision Night vision Purkinje effect Rod cell Spatial frequency Marc, R. E. Anderson, J. R. Jones, B. W. Sigulinsky, C. L. Lauritzen, the AII amacrine cell connectome, A dense network hub
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Rod cell
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Rod cells are photoreceptor cells in the retina of the eye that can function in less intense light than the other type of visual photoreceptor, cone cells. Rods are usually concentrated at the outer edges of the retina and are used in peripheral vision. On average, there are approximately 90 million rod cells in the human retina, Rod cells are more sensitive than cone cells and are almost entirely responsible for night vision. However, rods have little role in vision, which is one of the main reasons why colors are much less apparent in darkness. Rods are a longer and leaner than cones but have the same structural basis. The opsin or pigment is on the side, lying on the Retinal pigment epithelium. This epithelium end contains many stacked disks, rods have a high area for visual pigment and thus substantial efficiency of light absorption. Rods are much more common than cones, with about 100 million rod cells compared to 7 million cone cells, like cones, rod cells have a synaptic terminal, an inner segment, and an outer segment. The synaptic terminal forms a synapse with another neuron, for example a septo cell, the inner and outer segments are connected by a cilium, which lines the distal segment. The inner segment contains organelles and the nucleus, while the rod outer segment. A human rod cell is about 2 microns in diameter and 100 microns long, rods are not all morphologically the same, in mice, rods close to the outer plexiform synaptic layer display a reduced length and due to short synaptic body. Those rods also have different synaptic organizations, in vertebrates, activation of a photoreceptor cell is a hyperpolarization of the cell. When they are not being stimulated, such as in the dark, rod cells and cone cells depolarize and this neurotransmitter hyperpolarizes the bipolar cell. Bipolar cells exist between photoreceptors and ganglion cells and act to transmit signals from the photoreceptors to the ganglion cells, as a result of the bipolar cell being hyperpolarized, it does not release its transmitter at the bipolar-ganglion synapse and the synapse is not excited. Depolarization of rod cells occurs because in the dark, cells have a high concentration of cyclic guanosine 3-5 monophosphate. Glutamate can depolarize some neurons and hyperpolarize others, allowing photoreceptors to interact in an antagonistic manner, when light hits photoreceptive pigments within the photoreceptor cell, the pigment changes shape. The pigment, called rhodopsin comprises a large protein called opsin, attached to which is a covalently bound prosthetic group, the retinal exists in the 11-cis-retinal form when in the dark, and stimulation by light causes its structure to change to all-trans-retinal. This structural change causes an increased affinity for the protein called transducin
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Homology (biology)
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In biology, homology is the existence of shared ancestry between a pair of structures, or genes, in different taxa. Evolutionary biology explains homologous structures adapted to different purposes as the result of descent with modification from a common ancestor, examples include the legs of a centipede, the maxillary palp and labial palp of an insect, and the spinous processes of successive vertebrae in a vertebral column. Sequence homology between protein or DNA sequences is defined in terms of shared ancestry. Two segments of DNA can have shared ancestry because of either an event or a duplication event. Homology among proteins or DNA is inferred from their sequence similarity, significant similarity is strong evidence that two sequences are related by divergent evolution from a common ancestor. Alignments of multiple sequences are used to discover the homologous regions, the word homology, coined in about 1656, derives from the Greek ὁμόλογος homologos from ὁμός homos same and λόγος logos relation. Homology is the relationship between biological structures or sequences that are derived from a common ancestor, for example, many insects possess two pairs of flying wings. In beetles, the first pair of wings has evolved into a pair of hard wing covers, the same major forearm bones are found in fossils of lobe-finned fish such as Eusthenopteron. The opposite of homologous organs are analogous organs which do similar jobs in two taxa that were not present in their last common ancestor but rather evolved separately. For example, the wings of insects and birds evolved independently in widely separated groups, similarly, the wings of a sycamore maple seed and the wings of a bird are analogous but not homologous, as they develop from quite different structures. A structure can be homologous at one level, but only analogous at another, for example, in the pterosaurs, the wing involves both the forelimb and the hindlimb. Analogy is called homoplasy in cladistics, and convergent or parallel evolution in evolutionary biology, specialised terms are used in taxonomic research. Primary homology is that initially conjectured by a researcher based on similar structure or anatomical connections, secondary homology is implied by parsimony analysis, where a character that only occurs once on a tree is taken to be homologous. As implied in this definition, many cladists consider homology to be synonymous with synapomorphy, homologies provide the fundamental basis for all biological classification, although some may be highly counter-intuitive. The homologies between these have been discovered by comparing genes in evolutionary developmental biology, among insects, the stinger of the female honey bee is a modified ovipositor, homologous with ovipositors in other insects such as the Orthoptera, Hemiptera, and those Hymenoptera without stingers. The three small bones in the ear of mammals including humans, the malleus, incus. The malleus and incus develop in the embryo from structures that form jaw bones in lizards, both lines of evidence show that these bones are homologous, sharing a common ancestor. Among the many homologies in mammal reproductive systems, ovaries and testicles are homologous, in many plants, defensive or storage structures are made by modifications of the development of primary leaves, stems, and roots
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Halobacterium salinarum
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Halobacterium salinarum is an extremely halophilic marine Gram-negative obligate aerobic archaeon. Despite its name, this microorganism is not a bacterium, and it is found in salted fish, hides, hypersaline lakes, and salterns. As these salterns reach the minimum salinity limits for extreme halophiles, H. salinarum has also been found in high-salt food such as salt pork, marine fish, and sausages. The ability of H. salinarum to survive at high salt concentrations has led to its classification as an extremophile. Halobacteria are single-celled, rod-shaped microorganisms that are among the most ancient forms of life, the membrane consists of a single lipid monolayer surrounded by an S-layer. The S-layer is made of a glycoprotein, which accounts for approximately 50% of the cell surface proteins. These proteins form a lattice in the membrane, sulfate residues are abundant on the glycan chains of the glycoprotein, giving it a negative charge. The negative charge is believed to stabilize the lattice in high-salt conditions, amino acids are the main source of chemical energy for H. salinarum, particularly arginine and aspartate, though they are able to metabolize other amino acids, as well. H. salinarum have been reported to not be able to grow on sugars, although H. salinarum is unable to catabolize glucose, the transcription factor TrmB has been proven to regulate the gluconeogenic production of sugars found on the S-layer glycoprotein. To survive in extremely salty environments, this archaeon—as with other halophilic Archaeal species—utilizes compatible solutes to reduce osmotic stress, potassium levels are not at equilibrium with the environment, so H. salinarum expresses multiple active transporters which pump potassium into the cell. At extremely high salt concentrations protein precipitation will occur, to prevent the salting out of proteins, H. salinarum encodes mainly acidic proteins. The average isoelectric point of H. salinarum proteins is 5.03 and these highly acidic proteins are overwhelmingly negative in charge and are able to remain in solution even at high salt concentrations. H. salinarum can grow to such densities in ponds that oxygen is quickly depleted. Though it is an obligate aerobe, it is able to survive in conditions by utilizing light-energy. H. salinarum express the membrane protein bacteriorhodopsin which acts as a proton pump. It consists of two parts, the 7-transmembrane protein, bacterioopsin, and the cofactor, retinal. Upon absorption of a photon, retinal changes conformation, causing a change in the bacterioopsin protein which drives proton transport. The proton gradient which is formed can then be used to generate energy by ATP synthase
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Channelrhodopsin
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Channelrhodopsins are a subfamily of retinylidene proteins that function as light-gated ion channels. They serve as sensory photoreceptors in unicellular algae, controlling phototaxis. Expressed in cells of organisms, they enable light to control electrical excitability, intracellular acidity, calcium influx. Channelrhodopsin-1 and Channelrhodopsin-2 from the model organism Chlamydomonas reinhardtii are the first discovered channelrhodopsins, variants have been cloned from other algal species, and more are expected. In terms of structure, channelrhodopsins are retinylidene proteins and they are seven-transmembrane proteins like rhodopsin, and contain the light-isomerizable chromophore all-trans-retinal. The retinal chromophore is covalently linked to the rest of the protein through a protonated Schiff base, whereas most 7-transmembrane proteins are G protein-coupled receptors that open other ion channels indirectly via second messengers, channelrhodopsins directly form ion channels. This makes cellular depolarization extremely fast, robust, and useful for bioengineering and neuroscience applications, the natural ChR2 absorbs blue light with an absorption and action spectrum maximum at 480 nm. When the all-trans-retinal complex absorbs a photon, it induces a change from all-trans to 13-cis-retinal. This change introduces a one in the transmembrane protein, opening the pore to at least 6 Å. Within milliseconds, the retinal relaxes back to the form, closing the pore. Most natural channelrhodopsins are nonspecific cation channels, conducting H+, Na+, K+, recently, anion-conducting channelrhodopsins have been discovered. Channelrhodopsins are key tools in optogenetics, the C-terminal end of Channelrhodopsin-2 extends into the intracellular space and can be replaced by fluorescent proteins without affecting channel function. This kind of fusion construct can be useful to visualize the morphology of ChR2 expressing cells, point mutations close to the retinal binding pocket have been shown to affect the biophysical properties of the channelrhodopsin, resulting in a variety of different tools. Closing of the channel after optical activation can be delayed by mutating the protein residues C128 or D156. This modification results in super-sensitive channelrhodopsins that can be opened by a light pulse. Mutating the E123 residue accelerates channel kinetics, and the resulting ChR2 mutants have been used to spike neurons at up to 200 Hz, in general, channelrhodopsins with slow kinetics are more light-sensitive on the population level, as open channels accumulate over time even at low light levels. H134R and T159C mutants display increased photocurrents, and a combination of T159 and E123 has slightly larger photocurrents, among ChR variants, ChIEF, a chimera and point mutant of ChR1 and ChR2, demonstrates the largest photocurrents and the least desensitization and has kinetics similar to wild-type ChR2. Chimeric channelrhodopsins have been developed by combining transmembrane helices from ChR1 and VChR1, reaChR has improved membrane trafficking and strong expression in mammalian cells, and has been used for minimally invasive, transcranial activation of brainstem motoneurons
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Sensory rhodopsin II
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Sensory rhodopsin II, also known as pharaonis phoborhodopsin, is a membrane protein of archaea, responsible for generation of phototaxis signal. Sensory rhodopsin II is found in Halobacterium salinarum and Natronomonas pharaonis Structure of sensory rhodopsin II is typical for microbial rhodopsin and it consists of seven transmembrane a-helices with retinal molecule connected via Schiff base to K205. Notable feature of sensory rhodopsin II is presence of charged residue Y199 on the surface of the hydrophobic region and this residue is responsible for binding of sensory rhodopsin II transducer protein - HtrII. HtrII consists of two helices, two HAMP-domains and methyl-accepting signalling domain. In case of Halobacterium salinarum HtrII also comprises extracellular chemosensor region, SRII in the plasma membrane binds its transducer via a number of bonds. Photon absorption induces structural changes in SRII, which when conducted to HtrII, HtrII in turn regulates level of unbound kinases in cytoplasm. Kinases regulate rotation of flagella via phosphorilation, thus phototaxis signal is converted in bacteria motion. Engelhard, M. Microbial Rhodopsins, Scaffolds for Ion Pumps, Channels, results and Problems in Cell Differentiation. Sasaki, J. Spudich, J. Signal transfer in haloarchaeal sensory rhodopsin- transducer complexes
27.
Catalysis
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Catalysis is the increase in the rate of a chemical reaction due to the participation of an additional substance called a catalyst. In most cases, reactions occur faster with a catalyst because they require less activation energy, furthermore, since they are not consumed in the catalyzed reaction, catalysts can continue to act repeatedly. Often only tiny amounts are required in principle, in the presence of a catalyst, less free energy is required to reach the transition state, but the total free energy from reactants to products does not change. A catalyst may participate in multiple chemical transformations, the effect of a catalyst may vary due to the presence of other substances known as inhibitors or poisons or promoters. Catalyzed reactions have an activation energy than the corresponding uncatalyzed reaction, resulting in a higher reaction rate at the same temperature. However, the mechanics of catalysis is complex. Usually, the catalyst participates in this slowest step, and rates are limited by amount of catalyst, in heterogeneous catalysis, the diffusion of reagents to the surface and diffusion of products from the surface can be rate determining. A nanomaterial-based catalyst is an example of a heterogeneous catalyst, analogous events associated with substrate binding and product dissociation apply to homogeneous catalysts. Although catalysts are not consumed by the reaction itself, they may be inhibited, deactivated, in heterogeneous catalysis, typical secondary processes include coking where the catalyst becomes covered by polymeric side products. Additionally, heterogeneous catalysts can dissolve into the solution in a system or sublimate in a solid–gas system. The production of most industrially important chemicals involves catalysis, similarly, most biochemically significant processes are catalysed. Research into catalysis is a field in applied science and involves many areas of chemistry, notably organometallic chemistry. Catalysis is relevant to aspects of environmental science, e. g. the catalytic converter in automobiles. Many transition metals and transition metal complexes are used in catalysis as well, Catalysts called enzymes are important in biology. A catalyst works by providing a reaction pathway to the reaction product. The rate of the reaction is increased as this route has a lower activation energy than the reaction route not mediated by the catalyst. The disproportionation of hydrogen peroxide creates water and oxygen, as shown below,2 H2O2 →2 H2O + O2 This reaction is preferable in the sense that the reaction products are more stable than the starting material, though the uncatalysed reaction is slow. In fact, the decomposition of hydrogen peroxide is so slow that hydrogen peroxide solutions are commercially available and this reaction is strongly affected by catalysts such as manganese dioxide, or the enzyme peroxidase in organisms
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N-terminus
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The N-terminus is the start of a protein or polypeptide terminated by an amino acid with a free amine group. By convention, peptide sequences are written N-terminus to C-terminus, left to right in LTR languages and this correlates the translation direction to the text direction. Each amino acid has a group and a carboxylic group. The chain has two ends - an amine group, the N-terminus, and a carboxyl group, the C-terminus. When a protein is translated from messenger RNA, it is created from N-terminus to C-terminus, the amino end of an amino acid during the elongation stage of translation, attaches to the carboxyl end of the growing chain. Since the start codon of the genetic codes for the amino acid methionine. However, some proteins are modified posttranslationally, for example, by cleavage from a protein precursor, the N-terminus is the first part of the protein that exits the ribosome during protein biosynthesis. It often contains signal peptide sequences, intracellular postal codes that direct delivery of the protein to the proper organelle, the signal peptide is typically removed at the destination by a signal peptidase. The N-terminal amino acid of a protein is an important determinant of its half-life and this is called the N-end rule. The N-terminal signal peptide is recognized by the signal recognition particle, in eukaryotic cells, these proteins are synthesized at the rough endoplasmic reticulum. In prokaryotic cells, the proteins are exported across the cell membrane, in chloroplasts, signal peptides target proteins to the thylakoids. The N-terminal mitochondrial targeting peptide allows for the protein to be imported into the mitochondrion, the N-terminal chloroplast targeting peptide allows for the protein to be imported into the chloroplast. Protein N-termini can be modified co - or posttranslationally and it has been suggested that N-terminal acetylation can prevent a protein from following a secretory pathway. The N-terminus can be modified by the addition of a myristoyl anchor, proteins that are modified this way contain a consensus motif at their N-terminus as a modification signal. The N-terminus can also be modified by the addition of a fatty acid anchor to form N-acylated proteins, the most common form of such modification is the addition of a palmitoyl group. TopFIND, a database covering proteases, their cleavage site specificity, substrates, inhibitors
29.
C-terminus
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The C-terminus is the end of an amino acid chain, terminated by a free carboxyl group. When the protein is translated from messenger RNA, it is created from N-terminus to C-terminus, the convention for writing peptide sequences is to put the C-terminal end on the right and write the sequence from N- to C-terminus. Each amino acid has a group and an amine group. Amino acids link to one another to form a chain by a reaction which joins the amine group of one amino acid to the carboxyl group of the next. Thus polypeptide chains have an end with a carboxyl group, the C-terminus, and an end with an unbound amine group. Proteins are naturally synthesized starting from the N-terminus and ending at the C-terminus, while the N-terminus of a protein often contains targeting signals, the C-terminus can contain retention signals for protein sorting. The most common ER retention signal is the amino acid sequence -KDEL or -HDEL at the C-terminus and this keeps the protein in the endoplasmic reticulum and prevents it from entering the secretory pathway. One form of C-terminal modification is prenylation, during prenylation, a farnesyl- or geranylgeranyl-isoprenoid membrane anchor is added to a cysteine residue near the C-terminus. Small, membrane-bound G proteins are modified this way. Another form of C-terminal modification is the addition of a phosphoglycan, glycosylphosphatidylinositol, the GPI anchor is attached to the C-terminus after proteolytic cleavage of a C-terminal propeptide. The most prominent example for this type of modification is the prion protein, the C-terminal domain of some proteins has specialized functions. In humans, the CTD of RNA polymerase II typically consists of up to 52 repeats of the sequence Tyr-Ser-Pro-Thr-Ser-Pro-Ser and this allows other proteins to bind to the C-terminal domain of RNA polymerase in order to activate polymerase activity. These domains then involved in the initiation of DNA transcription, the capping of the RNA transcript, N-terminus TopFIND, a scientific database covering proteases, their cleavage site specificity, substrates, inhibitors and protein termini originating from their activity
30.
Photoreceptor cell
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A photoreceptor cell is a specialized type of cell found in the retina that is capable of phototransduction. The great biological importance of photoreceptors is that they convert light signals that can stimulate biological processes. To be more specific, photoreceptor proteins in the cell absorb photons, there are currently three known types of photoreceptor cells in mammalian eyes, rods, cones, and photosensitive retinal ganglion cells. The two classic photoreceptor cells are rods and cones, each contributing information used by the system to form a representation of the visual world. The rods are narrower than the cones and distributed differently across the retina, a third class of mammalian photoreceptor cell was discovered during the 1990s, the photosensitive ganglion cells. These cells do not contribute to sight directly, but are thought to support circadian rhythms, there are major functional differences between the rods and cones. Rods are extremely sensitive, and can be triggered by a single photon, at very low light levels, visual experience is based solely on the rod signal. This explains why colors cannot be seen at low light levels, cones require significantly brighter light in order to produce a signal. In humans, there are three different types of cell, distinguished by their pattern of response to different wavelengths of light. Color experience is calculated from three distinct signals, perhaps via an opponent process. The three types of cone cell respond to light of short, medium, and long wavelengths, note that, due to the principle of univariance, the firing of the cell depends upon only the number of photons absorbed. The different responses of the three types of cells are determined by the likelihoods that their respective photoreceptor proteins will absorb photons of different wavelengths. So, for example, an L cone cell contains a protein that more readily absorbs long wavelengths of light. Light of a wavelength can also produce the same response. The human retina contains about 120 million rod cells, and 6 million cone cells, the number and ratio of rods to cones varies among species, dependent on whether an animal is primarily diurnal or nocturnal. Certain owls, such as the owl, have a tremendous number of rods in their retinae. In addition, there are about 2.4 million to 3 million ganglion cells in the visual system,1 to 2% of them photosensitive. The axons of cells form the two optic nerves
31.
Anabaena
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A plant genus of the Euphorbiaceae, see its synonym Romanoa. Anabaena is a genus of cyanobacteria that exist as plankton. They are known for nitrogen-fixing abilities, and they form symbiotic relationships with certain plants and they are one of four genera of cyanobacteria that produce neurotoxins, which are harmful to local wildlife, as well as farm animals and pets. Production of these neurotoxins is assumed to be an input into its symbiotic relationships, a DNA sequencing project was undertaken in 1999, which mapped the complete genome of Anabaena, which is 7.2 million base pairs long. The study focused on heterocysts, which convert nitrogen into ammonia, certain species of Anabaena have been used on rice paddy fields, proving to be an effective natural fertilizer. Under nitrogen-limiting conditions, vegetative cells differentiate into heterocysts at semiregular intervals along the filaments, heterocyst cells are terminally specialized for nitrogen fixation. The interior of cells is micro-oxic as a result of increased respiration, inactivation of O2-producing photosystem II. Carbohydrate, probably in the form of glurose, is synthesized in vegetative cells, in return, nitrogen fixed in heterocysts moves into the vegetative cells, at least in part in the form of amino acids. Anabaena is used as an organism to study simple vision. The process in which changes the shape of molecules in the retina, thereby driving the cellular reactions. Anabaena sensory rhodopsin, a specific light-sensitive membrane protein, is central to this research, mishra, Yogesh, Bhargava, Poonam, Chaurasia, Neha, Rai, Lal Chand. Proteomic evaluation of the non-survival of Anabaena doliolum at elevated temperatures, processes Impacts 04/2015, DOI,10. 1039/C5EM00097A Sequenced Anabaena Genomes Guiry, M. D. Guiry, G. M. World-wide electronic publication, National University of Ireland, Galway
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Neurospora crassa
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Neurospora crassa is a type of red bread mold of the phylum Ascomycota. The genus name, meaning nerve spore refers to the striations on the spores. The first published account of fungus was from an infestation of French bakeries in 1843. N. crassa is used as a model organism because it is easy to grow and has a life cycle that makes genetic analysis simple since recessive traits will show up in the offspring. Analysis of genetic recombination is facilitated by the arrangement of the products of meiosis in Neurospora ascospores. Its entire genome of seven chromosomes has been sequenced, Neurospora was used by Edward Tatum and George Wells Beadle in their experiments for which they won the Nobel Prize in Physiology or Medicine in 1958. Beadle and Tatum exposed N. crassa to x-rays, causing mutations and they then observed failures in metabolic pathways caused by errors in specific enzymes. This led them to propose the one gene, one enzyme hypothesis that specific code for specific proteins. Their hypothesis was elaborated to enzyme pathways by Norman Horowitz. As Norman Horowitz reminisced in 2004 “These experiments founded the science of what Beadle and Tatum called ‘biochemical genetics’. In actuality, they proved to be the gun in what became molecular genetics and all developments that have followed from that. ”In the 24 April 2003 issue of Nature. The genome is about 43 megabases long and includes approximately 10,000 genes, there is a project underway to produce strains containing knockout mutants of every N. crassa gene. In its natural environment, N. crassa lives mainly in tropical and sub-tropical regions and it can be found growing on dead plant matter after fires. Neurospora is actively used in research around the world, like other Ascomycetes, N. crassa has two mating types that, in this case, are symbolized by A and a. There is no evident morphological difference between the A and a mating type strains, both can form abundant protoperithecia, the female reproductive structure. Protoperithecia are formed most readily in the laboratory when growth occurs on solid synthetic medium with a relatively low source of nitrogen, nitrogen starvation appears to be necessary for expression of genes involved in sexual development. The protoperithecium consists of an ascogonium, a coiled multicellular hypha that is enclosed in an aggregation of hyphae. A branched system of slender hyphae, called the trichogyne, extends from the tip of the ascogonium projecting beyond the sheathing hyphae into the air, the sexual cycle is initiated when a cell of opposite mating type contacts a part of the trichogyne
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Chlamydomonas reinhardtii
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Chlamydomonas reinhardtii is a single-cell green alga about 10 micrometres in diameter that swims with two flagella. It has a wall made of hydroxyproline-rich glycoproteins, a large cup-shaped chloroplast, a large pyrenoid. Chlamydomonas species are distributed worldwide in soil and fresh water. Chlamydomonas reinhardtii is a well studied biological model organism, partly due to its ease of culturing. When illuminated, C. reinhardtii can grow photoautotrophically, but it can grow in the dark if supplied with organic carbon. Commercially, C. reinhardtii is of interest for producing biopharmaceuticals and biofuel, the C. reinhardtii wild-type laboratory strain c137 originates from an isolate made near Amherst, Massachusetts, in 1945 by Gilbert M. Smith. Chlamydomonas is used as an organism for research on fundamental questions in cell and molecular biology such as. How do cells respond to light, how do cells recognize one another. How do cells generate regular, repeatable flagellar waveforms, how do cells regulate their proteome to control flagellar length. How do cells respond to changes in mineral nutrition, there are many known mutants of C. reinhardtii. These mutants are useful tools for studying a variety of processes, including flagellar motility, photosynthesis. Since Chlamydomonas species are haploid, the effects of mutations are seen immediately without further crosses. In 2007, the nuclear genome sequence of C. reinhardtii was published. Channelrhodopsin-1 and Channelrhodopsin-2, proteins that function as light-gated cation channels, were isolated from C. reinhardtii. These proteins and others like them are widely used in the field of optogenetics. Vegetative cells of the species are haploid with 17 small chromosomes. Under nitrogen starvation, vegetative cells differentiate into haploid gametes, there are two mating types, identical in appearance, thus isogamous, and known as mt and mt, which can fuse to form a diploid zygote. The zygote is not flagellated, and it serves as a dormant form of the species in the soil, in the light, the zygote undergoes meiosis and releases four flagellated haploid cells that resume the vegetative lifecycle
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Schiff base
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A Schiff base is a compound with the general structure R2C=NR. They can be considered a sub-class of imines, being either secondary ketimines or secondary depending on their structure. The term is synonymous with azomethine which refers specifically to secondary aldimines. A number of naming systems exist for these compounds. For instance a Schiff base derived from an aniline, where R3 is a phenyl or a substituted phenyl, can be called an anil, the term Schiff base is normally applied to these compounds when they are being used as ligands to form coordination complexes with metal ions. Such complexes do occur naturally, for instance in Corrin, but the majority of Schiff bases are artificial and are used to form many important catalysts, such as Jacobsens catalyst. Schiff bases can be synthesized from an aliphatic or aromatic amine, the common enzyme cofactor PLP forms a Schiff base with a lysine residue and is transaldiminated to the substrate. Similarly, the cofactor retinal forms a Schiff base in rhodopsins, including human rhodopsin, an example where the substrate forms a Schiff base to the enzyme is in the fructose 1, 6-bisphosphate aldolase catalyzed reaction during glycolysis and in the metabolism of amino acids. Schiff bases are common ligands in coordination chemistry, the imine nitrogen is basic and exhibits pi-acceptor properties. The ligands are derived from alkyl diamines and aromatic aldehydes. Chiral Schiff bases were one of the first ligands used for asymmetric catalysis, in 1968 Ryōji Noyori developed a copper-Schiff base complex for the metal-carbenoid cyclopropanation of styrene. For this work he was awarded a share of the 2001 Nobel Prize in Chemistry. Their simple and clean chemistry make them a candidate as a low cost alternative to currently used conjugated materials. Schiff base chemistry is used to prepare covalent organic framework
35.
Opsin
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Opsins are a group of light-sensitive proteins found in photoreceptor cells of the retina. Five classical groups of opsins are involved in vision, mediating the conversion of a photon of light into an electrochemical signal, another opsin found in the mammalian retina, melanopsin, is involved in circadian rhythms and pupillary reflex but not in image-forming. Opsins can be classified several ways, including function, type of chromophore, molecular structure, signal output, there are two groups of protein termed opsins. Type I opsins are employed by prokaryotes and by algae and fungi. No opsins have been found outside these groups, at one time it was thought that type I and type II were related because of structural and functional similarities. With the advent of genetic sequencing it became apparent that sequence identity was no greater than could be accounted for by random chance, however, in recent years new methods have been developed specific to deep phylogeny. Like type II opsins, type I opsins have a seven transmembrane domain structure similar to found in eukaryotic G-protein coupled receptors. Type I opsins are found in all three domains of life, Archaea, Bacteria, and Eukaryota, in Eukaryota, type I opsins are found mainly in unicellular organisms such as green algae, and in fungi. In most complex multicellular eukaryotes, type I opsins have been replaced with other molecules such as cryptochrome and phytochrome in plants. Microbial opsins are often known by the form of the molecule. Several type I opsins, such as proteo- and bacteriorhodopsin, are used by various groups to harvest energy from light to carry out metabolic processes using a non-chlorophyll-based pathway. Beside that, halorhodopsins of Halobacteria and channelrhodopsins of some algae, e. g. Volvox, serve them as light-gated ion channels, sensory rhodopsins exist in Halobacteria that induce a phototactic response by interacting with transducer membrane-embedded proteins that have no relation to G proteins. Type I opsins are used in optogenetics to switch on or off neuronal activity, type I opsins are preferred if the neuronal activity should be modulated at higher frequency, because they respond faster than type II opsins. Type II opsins are seven-transmembrane proteins belonging to the G protein-coupled receptor superfamily, type II opsins fall phylogenetically into four groups, C-opsins, Cnidops, R-opsins, and Go/RGR opsins. The Go/RGR opsins are divided into four sub-clades, Go-opsins, RGR, Peropsins, C-opsins, R-opsins, and the Go/RGR opsins are found only in Bilateria. Type II visual opsins are traditionally classified as either ciliary or rhabdomeric, ciliary opsins, found in vertebrates and cnidarians, attach to ciliary structures such as rods and cones. Rhabdomeric opsins are attached to light-gathering organelles called rhabdomeres and this classification cuts across phylogenetic categories so that both the terms ciliary and rhabdomeric can be ambiguous. Here, C-opsins refers to a clade found exclusively in Bilateria, similarly, R-opsin includes melanopsin even though it does not occur on rhabdomeres in vertebrates
36.
International Standard Serial Number
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An International Standard Serial Number is an eight-digit serial number used to uniquely identify a serial publication. The ISSN is especially helpful in distinguishing between serials with the same title, ISSN are used in ordering, cataloging, interlibrary loans, and other practices in connection with serial literature. The ISSN system was first drafted as an International Organization for Standardization international standard in 1971, ISO subcommittee TC 46/SC9 is responsible for maintaining the standard. When a serial with the content is published in more than one media type. For example, many serials are published both in print and electronic media, the ISSN system refers to these types as print ISSN and electronic ISSN, respectively. The format of the ISSN is an eight digit code, divided by a hyphen into two four-digit numbers, as an integer number, it can be represented by the first seven digits. The last code digit, which may be 0-9 or an X, is a check digit. Formally, the form of the ISSN code can be expressed as follows, NNNN-NNNC where N is in the set, a digit character. The ISSN of the journal Hearing Research, for example, is 0378-5955, where the final 5 is the check digit, for calculations, an upper case X in the check digit position indicates a check digit of 10. To confirm the check digit, calculate the sum of all eight digits of the ISSN multiplied by its position in the number, the modulus 11 of the sum must be 0. There is an online ISSN checker that can validate an ISSN, ISSN codes are assigned by a network of ISSN National Centres, usually located at national libraries and coordinated by the ISSN International Centre based in Paris. The International Centre is an organization created in 1974 through an agreement between UNESCO and the French government. The International Centre maintains a database of all ISSNs assigned worldwide, at the end of 2016, the ISSN Register contained records for 1,943,572 items. ISSN and ISBN codes are similar in concept, where ISBNs are assigned to individual books, an ISBN might be assigned for particular issues of a serial, in addition to the ISSN code for the serial as a whole. An ISSN, unlike the ISBN code, is an identifier associated with a serial title. For this reason a new ISSN is assigned to a serial each time it undergoes a major title change, separate ISSNs are needed for serials in different media. Thus, the print and electronic versions of a serial need separate ISSNs. Also, a CD-ROM version and a web version of a serial require different ISSNs since two different media are involved, however, the same ISSN can be used for different file formats of the same online serial
37.
International Standard Book Number
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The International Standard Book Number is a unique numeric commercial book identifier. An ISBN is assigned to each edition and variation of a book, for example, an e-book, a paperback and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, the method of assigning an ISBN is nation-based and varies from country to country, often depending on how large the publishing industry is within a country. The initial ISBN configuration of recognition was generated in 1967 based upon the 9-digit Standard Book Numbering created in 1966, the 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108. Occasionally, a book may appear without a printed ISBN if it is printed privately or the author does not follow the usual ISBN procedure, however, this can be rectified later. Another identifier, the International Standard Serial Number, identifies periodical publications such as magazines, the ISBN configuration of recognition was generated in 1967 in the United Kingdom by David Whitaker and in 1968 in the US by Emery Koltay. The 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108, the United Kingdom continued to use the 9-digit SBN code until 1974. The ISO on-line facility only refers back to 1978, an SBN may be converted to an ISBN by prefixing the digit 0. For example, the edition of Mr. J. G. Reeder Returns, published by Hodder in 1965, has SBN340013818 -340 indicating the publisher,01381 their serial number. This can be converted to ISBN 0-340-01381-8, the check digit does not need to be re-calculated, since 1 January 2007, ISBNs have contained 13 digits, a format that is compatible with Bookland European Article Number EAN-13s. An ISBN is assigned to each edition and variation of a book, for example, an ebook, a paperback, and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, a 13-digit ISBN can be separated into its parts, and when this is done it is customary to separate the parts with hyphens or spaces. Separating the parts of a 10-digit ISBN is also done with either hyphens or spaces, figuring out how to correctly separate a given ISBN number is complicated, because most of the parts do not use a fixed number of digits. ISBN issuance is country-specific, in that ISBNs are issued by the ISBN registration agency that is responsible for country or territory regardless of the publication language. Some ISBN registration agencies are based in national libraries or within ministries of culture, in other cases, the ISBN registration service is provided by organisations such as bibliographic data providers that are not government funded. In Canada, ISBNs are issued at no cost with the purpose of encouraging Canadian culture. In the United Kingdom, United States, and some countries, where the service is provided by non-government-funded organisations. Australia, ISBNs are issued by the library services agency Thorpe-Bowker
38.
PubMed Identifier
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
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