1.
Grand Prismatic Spring
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It is located in the Midway Geyser Basin. Grand Prismatic Spring was noted by geologists working in the Hayden Geological Survey of 1871 and its colors match the rainbow dispersion of white light by an optical prism, red, orange, yellow, green, and blue. The first records of the spring are from early European explorers and surveyors. In 1839, a group of fur trappers from the American Fur Company crossed the Midway Geyser Basin and made note of a lake, most likely the Grand Prismatic Spring. In 1870 the Washburn–Langford–Doane Expedition visited the spring, noting a 50-foot geyser nearby, the vivid colors in the spring are the result of microbial mats around the edges of the mineral-rich water. The mats produce colors ranging from green to red, the amount of color in the microbial mats depends on the ratio of chlorophyll to carotenoids, in the summer, the mats tend to be orange and red, whereas in the winter the mats are usually dark green. The center of the pool is due to extreme heat. The deep blue color of the water in the center of the results from the scattering of blue light by particles suspended in the water. This effect is visible in the center of the spring due to the lack of archaea that live in the center. The spring is approximately 370 feet in diameter and is 160 feet deep, the spring discharges an estimated 560 US gallons of 160 °F water per minute. Media related to Grand Prismatic Spring at Wikimedia Commons
2.
Yellowstone National Park
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Yellowstone National Park is a national park located in the U. S. states of Wyoming, Montana and Idaho. It was established by the U. S. Congress and signed into law by President Ulysses S. Grant on March 1,1872. Yellowstone was the first National Park in the U. S. and is widely held to be the first national park in the world. The park is known for its wildlife and its many features, especially Old Faithful Geyser. It has many types of ecosystems, but the subalpine forest is the most abundant and it is part of the South Central Rockies forests ecoregion. Native Americans have lived in the Yellowstone region for at least 11,000 years, aside from visits by mountain men during the early-to-mid-19th century, organized exploration did not begin until the late 1860s. Management and control of the park fell under the jurisdiction of the Secretary of the Interior. However, the U. S. Army was subsequently commissioned to oversee management of Yellowstone for a 30-year period between 1886 and 1916, in 1917, administration of the park was transferred to the National Park Service, which had been created the previous year. Hundreds of structures have been built and are protected for their architectural and historical significance, Yellowstone National Park spans an area of 3,468.4 square miles, comprising lakes, canyons, rivers and mountain ranges. Yellowstone Lake is one of the largest high-elevation lakes in North America and is centered over the Yellowstone Caldera, the caldera is considered an active volcano. It has erupted with tremendous force several times in the last two million years, half of the worlds geothermal features are in Yellowstone, fueled by this ongoing volcanism. Lava flows and rocks from volcanic eruptions cover most of the area of Yellowstone. The park is the centerpiece of the Greater Yellowstone Ecosystem, the largest remaining nearly-intact ecosystem in the Earths northern temperate zone, hundreds of species of mammals, birds, fish, and reptiles have been documented, including several that are either endangered or threatened. The vast forests and grasslands also include species of plants. Yellowstone Park is the largest and most famous location in the Continental United States. Grizzly bears, wolves, and free-ranging herds of bison and elk live in the park, the Yellowstone Park bison herd is the oldest and largest public bison herd in the United States. Forest fires occur in the each year, in the large forest fires of 1988. Yellowstone has numerous opportunities, including hiking, camping, boating, fishing and sightseeing
3.
Extremophile
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An extremophile is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. In contrast, organisms that live in moderate environments may be termed mesophiles or neutrophiles. Some scientists even concluded that life may have begun on Earth in hydrothermal vents far under the oceans surface. According to astrophysicist Dr. Steinn Sigurdsson, There are viable bacterial spores that have found that are 40 million years old on Earth—and we know theyre very hardened to radiation. On 6 February 2013, scientists reported that bacteria were found living in the cold, on 17 March 2013, researchers reported data that suggested microbial life forms thrive in the Mariana Trench, the deepest spot on the Earth. Other researchers reported related studies that microbes thrive inside rocks up to 1900 feet below the sea floor under 8500 feet 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 domain Archaea contains renowned examples, but extremophiles are present in numerous and diverse genetic lineages of bacteria and archaeans. Furthermore, it is erroneous to use the term extremophile to encompass all archaeans, neither are all extremophiles unicellular, protostome animals found in similar environments include the Pompeii worm, the psychrophilic Grylloblattidae and Antarctic krill. Their chances of dying increase the longer they are exposed to the extreme environment, There are many classes of extremophiles that range all around the globe, each corresponding to the way its environmental niche differs from mesophilic conditions. Many extremophiles fall under multiple categories and are classified as polyextremophiles, for example, organisms living inside hot rocks deep under Earths surface are thermophilic and barophilic such as Thermococcus barophilus. A polyextremophile living at the summit of a mountain in the Atacama Desert might be a radioresistant xerophile, a psychrophile, polyextremophiles are well known for their ability to tolerate both high and low pH levels. Two sub-types exist, facultative anaerobe and obligate anaerobe, in it, microbial ecologists, astronomers, planetary scientists, geochemists, philosophers, and explorers cooperate constructively to guide the search for life on other planets. Astrobiologists are particularly interested in studying extremophiles, as many organisms of this type are capable of surviving in environments similar to known to exist on other planets. For example, Mars may have regions in its deep subsurface permafrost that could harbor endolith communities, the subsurface water ocean of Jupiters moon Europa may harbor life, especially at hypothesized hydrothermal vents at the ocean floor. Recent research carried out on extremophiles in Japan involved a variety of bacteria including Escherichia coli, the bacteria were cultivated while being rotated in an ultracentrifuge at high speeds corresponding to 403,627 g. Analysis showed that the size of prokaryotic cells is essential for successful growth under hypergravity. The research has implications on the feasibility of panspermia, on 19 May 2014, scientists announced that numerous microbes, like Tersicoccus phoenicis, may be resistant to methods usually used in spacecraft assembly clean rooms. Its not currently known if such resistant microbes could have withstood space travel and are present on the Curiosity rover now on the planet Mars, on 20 August 2014, scientists confirmed the existence of microorganisms living half a mile below the ice of Antarctica
4.
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
5.
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
6.
Geothermal gradient
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Geothermal gradient is the rate of increasing temperature with respect to increasing depth in the Earths interior. Away from tectonic plate boundaries, it is about 25 °C per km of depth near the surface in most of the world, strictly speaking, geo-thermal necessarily refers to the Earth but the concept may be applied to other planets. A line tracing the gradient through the body is called a geotherm on Earth. On the Moon it is called a selenotherm, the Earths internal heat comes from a combination of residual heat from planetary accretion, heat produced through radioactive decay, and possibly heat from other sources. The major heat-producing isotopes in the Earth are potassium-40, uranium-238, uranium-235, at the center of the planet, the temperature may be up to 7,000 K and the pressure could reach 360 GPa. Temperature within the Earth increases with depth, the heat content of the Earth is 1031 joules. Much of the heat is created by decay of radioactive elements. An estimated 45 to 90 percent of the heat escaping from the Earth originates from decay of elements mainly located in the mantle. Heat of impact and compression released during the formation of the Earth by accretion of in-falling meteorites. Heat released as abundant heavy metals descended to the Earths core, latent heat released as the liquid outer core crystallizes at the inner core boundary. Heat may be generated by tidal force on the Earth as it rotates, since rock cannot flow as readily as water it compresses and distorts, in Earths continental crust, the decay of natural radioactive isotopes has had significant involvement in the origin of geothermal heat. The continental crust is abundant in lower density minerals but also contains significant concentrations of heavier lithophilic minerals such as uranium, because of this, it holds the largest global reservoir of radioactive elements found in the Earth. Especially in layers closer to Earths surface, naturally occurring isotopes are enriched in the granite and these high levels of radioactive elements are largely excluded from the Earths mantle due to their inability to substitute in mantle minerals and consequent enrichment in partial melts. The mantle is made up of high density minerals with high contents of atoms that have relatively small atomic radii such as magnesium, titanium. Heat flows constantly from its sources within the Earth to the surface, total heat loss from the Earth is estimated at 44.2 TW. Mean heat flow is 65 mW/m2 over continental crust and 101 mW/m2 over oceanic crust and this is 0.087 watt/square meter on average, but is much more concentrated in areas where thermal energy is transported toward the crust by convection such as along mid-ocean ridges and mantle plumes. The Earths crust effectively acts as an insulating blanket which must be pierced by fluid conduits in order to release the heat underneath. More of the heat in the Earth is lost through plate tectonics, the final major mode of heat loss is by conduction through the lithosphere, the majority of which occurs in the oceans due to the crust there being much thinner and younger than under the continents
7.
Earth
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Earth, otherwise known as the World, or the Globe, is the third planet from the Sun and the only object in the Universe known to harbor life. It is the densest planet in the Solar System and the largest of the four terrestrial planets, according to radiometric dating and other sources of evidence, Earth formed about 4.54 billion years ago. Earths gravity interacts with objects in space, especially the Sun. During one orbit around the Sun, Earth rotates about its axis over 365 times, thus, Earths axis of rotation is tilted, producing seasonal variations on the planets surface. The gravitational interaction between the Earth and Moon causes ocean tides, stabilizes the Earths orientation on its axis, Earths lithosphere is divided into several rigid tectonic plates that migrate across the surface over periods of many millions of years. About 71% of Earths surface is covered with water, mostly by its oceans, the remaining 29% is land consisting of continents and islands that together have many lakes, rivers and other sources of water that contribute to the hydrosphere. The majority of Earths polar regions are covered in ice, including the Antarctic ice sheet, Earths interior remains active with a solid iron inner core, a liquid outer core that generates the Earths magnetic field, and a convecting mantle that drives plate tectonics. Within the first billion years of Earths history, life appeared in the oceans and began to affect the Earths atmosphere and surface, some geological evidence indicates that life may have arisen as much as 4.1 billion years ago. Since then, the combination of Earths distance from the Sun, physical properties, in the history of the Earth, biodiversity has gone through long periods of expansion, occasionally punctuated by mass extinction events. Over 99% of all species that lived on Earth are extinct. Estimates of the number of species on Earth today vary widely, over 7.4 billion humans live on Earth and depend on its biosphere and minerals for their survival. Humans have developed diverse societies and cultures, politically, the world has about 200 sovereign states, the modern English word Earth developed from a wide variety of Middle English forms, which derived from an Old English noun most often spelled eorðe. It has cognates in every Germanic language, and their proto-Germanic root has been reconstructed as *erþō, originally, earth was written in lowercase, and from early Middle English, its definite sense as the globe was expressed as the earth. By early Modern English, many nouns were capitalized, and the became the Earth. More recently, the name is simply given as Earth. House styles now vary, Oxford spelling recognizes the lowercase form as the most common, another convention capitalizes Earth when appearing as a name but writes it in lowercase when preceded by the. It almost always appears in lowercase in colloquial expressions such as what on earth are you doing, the oldest material found in the Solar System is dated to 4. 5672±0.0006 billion years ago. By 4. 54±0.04 Gya the primordial Earth had formed, the formation and evolution of Solar System bodies occurred along with the Sun
8.
Deep sea
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The deep sea or deep layer is the lowest layer in the ocean, existing below the thermocline and above the seabed, at a depth of 1000 fathoms or more. Little or no light penetrates this part of the ocean, for this reason, scientists once assumed that life would be sparse in the deep ocean, but virtually every probe has revealed that, on the contrary, life is abundant in the deep ocean. From the time of Pliny until the nineteenth century. humans believed there was no life in the deep. It took an expedition in the ship Challenger between 1872 and 1876 to prove Pliny wrong, its deep-sea dredges and trawls brought up living things from all depths that could be reached. Yet even in the century scientists continued to imagine that life at great depth was insubstantial. The eternal dark, the almost inconceivable pressure, and the cold that exist below one thousand meters were, they thought, so forbidding as to have all. The reverse is in fact true, lies the largest habitat on earth. In 1960, the Bathyscaphe Trieste descended to the bottom of the Mariana Trench near Guam, at 10,911 m, if Mount Everest were submerged there, its peak would be more than a mile beneath the surface. The Trieste was retired, and for a while the Japanese remote-operated vehicle Kaikō was the vessel capable of reaching this depth. It was lost at sea in 2003, in May and June 2009, the hybrid-ROV Nereus returned to the Challenger Deep for a series of three dives to depths exceeding 10900 meters. It has been suggested that more is known about the Moon than the deepest parts of the ocean, little was known about the extent of life on the deep ocean floor until the discovery of thriving colonies of shrimps and other organisms around hydrothermal vents in the late 1970s. Before the discovery of the vents, it had been accepted that almost all life on earth obtained its energy from the sun. The new discoveries revealed groups of creatures that obtained nutrients and energy directly from thermal sources, the revolutionary discovery that life can exist under these extreme conditions changed opinions about the chances of there being life elsewhere in the universe. Scientists now speculate that Europa, one of Jupiters moons, may be able to support life beneath its icy surface, natural light does not penetrate the deep ocean, with the exception of the upper parts of the mesopelagic. Since photosynthesis is not possible, plants cannot live in this zone, since plants are the primary producers of almost all of earths ecosystems, life in this area of the ocean must depend on energy sources from elsewhere. Except for the close to the hydrothermal vents, this energy comes from organic material drifting down from the photic zone. The sinking organic material is composed of algal particulates, detritus, and other forms of biological waste, because pressure in the ocean increases by about 1 atmosphere for every 10 meters of depth, the amount of pressure experienced by many marine organisms is extreme. With the advent of traps that incorporate a special pressure-maintaining chamber, salinity is remarkably constant throughout the deep sea, at about 35 parts per thousand
9.
Hydrothermal vent
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A hydrothermal vent is a fissure in a planets surface from which geothermally heated water issues. Hydrothermal vents are found near volcanically active places, areas where tectonic plates are moving apart, ocean basins. Hydrothermal vents exist because the earth is both active and has large amounts of water on its surface and within its crust. Common land types include hot springs, fumaroles and geysers, under the sea, hydrothermal vents may form features called black smokers. Chemosynthetic bacteria and archaea form the base of the chain, supporting diverse organisms, including giant tube worms, clams, limpets. Active hydrothermal vents are believed to exist on Jupiters moon Europa, and Saturns moon Enceladus, Hydrothermal vents in the deep ocean typically form along the mid-ocean ridges, such as the East Pacific Rise and the Mid-Atlantic Ridge. These are locations where two plates are diverging and new crust is being formed. The proportion of each varies from location to location, in contrast to the approximately 2 °C ambient water temperature at these depths, water emerges from these vents at temperatures ranging from 60 to as high as 464 °C. Due to the hydrostatic pressure at these depths, water may exist in either its liquid form or as a supercritical fluid at such temperatures. The critical point of water is 375 °C at a pressure of 218 atmospheres, however, introducing salinity into the fluid raises the critical point to higher temperatures and pressures. The critical point of seawater is 407 °C and 298.5 bars, accordingly, if a hydrothermal fluid with a salinity of 3.2 wt. % NaCl vents above 407 °C and 298.5 bars, furthermore, the salinity of vent fluids have been shown to vary widely due to phase separation in the crust. The critical point for lower salinity fluids is at lower temperature and pressure conditions than that for seawater, for example, a vent fluid with a 2.24 wt. % NaCl salinity has the point at 400 °C and 280.5 bars. Thus, water emerging from the hottest parts of some hydrothermal vents can be a supercritical fluid, examples of supercritical venting are found at several sites. Sister Peak vents low salinity phase-separated, vapor-type fluids, sustained venting was not found to be supercritical but a brief injection of 464 °C was well above supercritical conditions. A nearby site, Turtle Pits, was found to vent low salinity fluid at 407 °C, which is above the critical point of the fluid at that salinity. A vent site in the Cayman Trough named Beebe, which is the worlds deepest known hydrothermal site at ~5000 m below sea level, has shown sustained supercritical venting at 401 °C and 2.3 wt% NaCl
10.
Peat bogs
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A bog is a wetland that accumulates peat, a deposit of dead plant material—often mosses, and in a majority of cases, sphagnum moss. It is one of the four types of wetlands. Other names for bogs include mire, quagmire, and muskeg and they are frequently covered in ericaceous shrubs rooted in the sphagnum moss and peat. The gradual accumulation of decayed plant material in a bog functions as a carbon sink, Bogs occur where the water at the ground surface is acidic and low in nutrients. In some cases, the water is derived entirely from precipitation, water flowing out of bogs has a characteristic brown colour, which comes from dissolved peat tannins. In general, the low fertility and cool climate results in relatively slow plant growth, large areas of landscape can be covered many metres deep in peat. Bogs have distinctive assemblages of animal, fungal and plant species, Bogs are widely distributed in cold, temperate climes, mostly in boreal ecosystems in the Northern Hemisphere. The worlds largest wetland is the bogs of the Western Siberian Lowlands in Russia. Large peat bogs also occur in North America, particularly the Hudson Bay Lowland and they are less common in the Southern Hemisphere, with the largest being the Magellanic moorland, comprising some 44,000 square kilometres. Sphagnum bogs were widespread in northern Europe but have often been cleared and drained for agriculture, a 2014 expedition leaving from Itanga village, Republic of the Congo discovered a peat bog as big as England which stretches into neighboring Democratic Republic of Congo. There are many highly specialised animals, fungi and plants associated with bog habitat, most are capable of tolerating the combination of low nutrient levels and waterlogging. Sphagnum moss is generally abundant, along with ericaceous shrubs, the shrubs are often evergreen, which is understood to assist in conservation of nutrients. In drier locations, evergreen trees can occur, in case the bog blends into the surrounding expanses of boreal evergreen forest. Sedges are one of the more common herbaceous species, carnivorous plants such as sundews and pitcher plants have adapted to the low-nutrient conditions by using invertebrates as a nutrient source. Orchids have adapted to these conditions through the use of fungi to extract nutrients. Some shrubs such as Myrica gale have root nodules in which nitrogen fixation occurs, Bogs are recognized as a significant/specific habitat type by a number of governmental and conservation agencies. They can provide habitat for mammals, such as caribou, moose, the United Kingdom in its Biodiversity Action Plan establishes bog habitats as a priority for conservation. Russia has a reserve system in the West Siberian Lowland
11.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase
12.
Molecular biology
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Writing in Nature in 1961, William Astbury described molecular biology as. It is concerned particularly with the forms of biological molecules and is predominantly three-dimensional and structural—which does not mean, however and it must at the same time inquire into genesis and function. Researchers in molecular biology use specific techniques native to molecular biology but increasingly combine these techniques and ideas from genetics. There is not a line between these disciplines. Biochemists focus heavily on the role, function, and structure of biomolecules, the study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry. Genetics is the study of the effect of differences on organisms. This can often be inferred by the absence of a normal component, the study of mutants – organisms which lack one or more functional components with respect to the so-called wild type or normal phenotype. Genetic interactions can often confound simple interpretations of such knockout studies, molecular biology is the study of molecular underpinnings of the processes of replication, transcription, translation, and cell function. This picture, however, is undergoing revision in light of emerging novel roles for RNA, much of molecular biology is quantitative, and recently much work has been done at its interface with computer science in bioinformatics and computational biology. In the early 2000s, the study of structure and function. There is also a tradition of studying biomolecules from the ground up in biophysics. One of the most basic techniques of molecular biology to study protein function is molecular cloning, in this technique, DNA coding for a protein of interest is cloned using PCR and/or restriction enzymes into a plasmid. A vector has 3 distinctive features, an origin of replication, a multiple cloning site, the origin of replication will have promoter regions upstream from the replication/transcription start site. This plasmid can be inserted into either bacterial or animal cells, introducing DNA into bacterial cells can be done by transformation via uptake of naked DNA, conjugation via cell-cell contact or by transduction via viral vector. Introducing DNA into eukaryotic cells, such as cells, by physical or chemical means is called transfection. Several different transfection techniques are available, such as calcium phosphate transfection, electroporation, microinjection, the plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection. DNA coding for a protein of interest is now inside a cell, a variety of systems, such as inducible promoters and specific cell-signaling factors, are available to help express the protein of interest at high levels. Large quantities of a protein can then be extracted from the bacterial or eukaryotic cell, polymerase chain reaction is an extremely versatile technique for copying DNA
13.
DNA polymerase
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In molecular biology, DNA polymerases are enzymes that synthesize DNA molecules from deoxyribonucleotides, the building blocks of DNA. These enzymes are essential to DNA replication and usually work in pairs to two identical DNA strands from a single original DNA molecule. During this process, DNA polymerase reads the existing DNA strands to create two new strands that match the existing ones. Every time a cell divides, DNA polymerases are required to duplicate the cells DNA. In this way, genetic information is passed down generation to generation. Before replication can take place, an enzyme called helicase unwinds the DNA molecule from its tightly woven form and this opens up or unzips the double-stranded DNA to give two single strands of DNA that can be used as templates for replication. In 1956, Arthur Kornberg and colleagues discovered DNA polymerase I and they described the DNA replication process by which DNA polymerase copies the base sequence of a template DNA strand. Kornberg was later awarded the Nobel Prize in Physiology or Medicine in 1959 for this work, DNA polymerase II was also discovered by Thomas Kornberg and Malcolm E. Gefter in 1970 while further elucidating the role of Pol I in E. coli DNA replication. The main function of DNA polymerase is to synthesize DNA from deoxyribonucleotides, the DNA copies are created by the pairing of nucleotides to bases present on each strand of the original DNA molecule. This pairing always occurs in specific combinations, with cytosine along with guanine, by contrast, RNA polymerases synthesize RNA from ribonucleotides from either RNA or DNA. When synthesizing new DNA, DNA polymerase can add free nucleotides only to the 3 end of the newly forming strand and this results in elongation of the newly forming strand in a 5-3 direction. No known DNA polymerase is able to begin a new chain, it can add a nucleotide onto a pre-existing 3-OH group. Primers consist of RNA or DNA bases, in DNA replication, the first two bases are always RNA, and are synthesized by another enzyme called primase. It is important to note that the directionality of the newly forming strand is opposite to the direction in which DNA polymerase moves along the template strand. Since DNA polymerase requires a free 3 OH group for initiation of synthesis, hence, DNA polymerase moves along the template strand in a 3-5 direction, and the daughter strand is formed in a 5-3 direction. This difference enables the resultant double-strand DNA formed to be composed of two DNA strands that are antiparallel to each other, the function of DNA polymerase is not quite perfect, with the enzyme making about one mistake for every billion base pairs copied. Error correction is a property of some, but not all DNA polymerases and this process corrects mistakes in newly synthesized DNA. When an incorrect base pair is recognized, DNA polymerase moves backwards by one pair of DNA
14.
Polymerase chain reaction
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It is an easy, cheap, and reliable way to repeatedly replicate a focused segment of DNA, a concept which is applicable to numerous fields in modern biology and related sciences. Developed in 1983 by Kary Mullis, PCR is now a common and often indispensable technique used in clinical, in 1993, Mullis was awarded the Nobel Prize in Chemistry along with Michael Smith for his work on PCR. Primers containing sequences complementary to the region, along with a DNA polymerase, after which the method is named, enable selective. As PCR progresses, the DNA generated is used as a template for replication. The simplicity of the principle underlying PCR means it can be extensively modified to perform a wide array of genetic manipulations. PCR is not generally considered to be a recombinant DNA method, as it does not involve cutting and pasting DNA, almost all PCR applications employ a heat-stable DNA polymerase, such as Taq polymerase, an enzyme originally isolated from the thermophilic bacterium Thermus aquaticus. In the first step, the two strands of the DNA double helix are physically separated at a temperature in a process called DNA melting. In the second step, the temperature is lowered and the two DNA strands become templates for DNA polymerase to amplify the target DNA. The selectivity of PCR results from the use of primers that are complementary to the DNA region targeted for amplification under specific thermal cycling conditions, PCR amplifies a specific region of a DNA strand. Most PCR methods amplify DNA fragments of between 0.1 and 10 kilo base pairs, although some techniques allow for amplification of fragments up to 40 kbp in size. The amount of amplified product is determined by the available substrates in the reaction, the thermal cycler heats and cools the reaction tubes to achieve the temperatures required at each step of the reaction. Many modern thermal cyclers make use of the Peltier effect, which permits both heating and cooling of the holding the PCR tubes simply by reversing the electric current. Thin-walled reaction tubes permit favorable thermal conductivity to allow for rapid thermal equilibration, most thermal cyclers have heated lids to prevent condensation at the top of the reaction tube. Older thermal cyclers lacking a heated lid require a layer of oil on top of the mixture or a ball of wax inside the tube. Typically, PCR consists of a series of 20–40 repeated temperature changes, called cycles, the cycling is often preceded by a single temperature step at a very high temperature, and followed by one hold at the end for final product extension or brief storage. The individual steps common to most PCR methods are as follows, Initialization and it consists of heating the reaction chamber to a temperature of 94–96 °C, or 98 °C if extremely thermostable polymerases are used, which is then held for 1–10 minutes. Denaturation, This step is the first regular cycling event and consists of heating the reaction chamber to 94–98 °C for 20–30 seconds and this causes DNA melting, or denaturation, of the double-stranded DNA template by breaking the hydrogen bonds between complementary bases, yielding two single-stranded DNA molecules. Annealing, In the next step, the temperature is lowered to 50–65 °C for 20–40 seconds
15.
Greek language
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Greek is an independent branch of the Indo-European family of languages, native to Greece and other parts of the Eastern Mediterranean. It has the longest documented history of any living language, spanning 34 centuries of written records and its writing system has been the Greek alphabet for the major part of its history, other systems, such as Linear B and the Cypriot syllabary, were used previously. The alphabet arose from the Phoenician script and was in turn the basis of the Latin, Cyrillic, Armenian, Coptic, Gothic and many other writing systems. Together with the Latin texts and traditions of the Roman world, during antiquity, Greek was a widely spoken lingua franca in the Mediterranean world and many places beyond. It would eventually become the official parlance of the Byzantine Empire, the language is spoken by at least 13.2 million people today in Greece, Cyprus, Italy, Albania, Turkey, and the Greek diaspora. Greek roots are used to coin new words for other languages, Greek. Greek has been spoken in the Balkan peninsula since around the 3rd millennium BC, the earliest written evidence is a Linear B clay tablet found in Messenia that dates to between 1450 and 1350 BC, making Greek the worlds oldest recorded living language. Among the Indo-European languages, its date of earliest written attestation is matched only by the now extinct Anatolian languages, the Greek language is conventionally divided into the following periods, Proto-Greek, the unrecorded but assumed last ancestor of all known varieties of Greek. The unity of Proto-Greek would have ended as Hellenic migrants entered the Greek peninsula sometime in the Neolithic era or the Bronze Age, Mycenaean Greek, the language of the Mycenaean civilisation. It is recorded in the Linear B script on tablets dating from the 15th century BC onwards, Ancient Greek, in its various dialects, the language of the Archaic and Classical periods of the ancient Greek civilisation. It was widely known throughout the Roman Empire, after the Roman conquest of Greece, an unofficial bilingualism of Greek and Latin was established in the city of Rome and Koine Greek became a first or second language in the Roman Empire. The origin of Christianity can also be traced through Koine Greek, Medieval Greek, also known as Byzantine Greek, the continuation of Koine Greek in Byzantine Greece, up to the demise of the Byzantine Empire in the 15th century. Much of the written Greek that was used as the language of the Byzantine Empire was an eclectic middle-ground variety based on the tradition of written Koine. Modern Greek, Stemming from Medieval Greek, Modern Greek usages can be traced in the Byzantine period and it is the language used by the modern Greeks, and, apart from Standard Modern Greek, there are several dialects of it. In the modern era, the Greek language entered a state of diglossia, the historical unity and continuing identity between the various stages of the Greek language is often emphasised. Greek speakers today still tend to regard literary works of ancient Greek as part of their own rather than a foreign language and it is also often stated that the historical changes have been relatively slight compared with some other languages. According to one estimation, Homeric Greek is probably closer to demotic than 12-century Middle English is to modern spoken English, Greek is spoken by about 13 million people, mainly in Greece, Albania and Cyprus, but also worldwide by the large Greek diaspora. Greek is the language of Greece, where it is spoken by almost the entire population
16.
Mickey Hot Springs
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Mickey Hot Springs is a small hot spring system at the north end of Alvord Desert just east of Steens Mountain in southeastern Oregon, United States. There are several natural bubbling mudpots and steam vents, the system contains at least 60 vents,11 of which are dry. The hydrothermal system is in its stages of existence. Each vent has a temperature ranging from 25 °C to 100 °C with the average about 77 °C. The water pH is neutral to slightly alkaline, an ecosystem of thermophilic organisms exist in the springs, separated by temperature stratum. Extent and location of the aquifer in the Alvord Basin, Harney County, Oregon, A study based on Strontium Isotope Geochemistry of rocks
17.
Oregon
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Oregon is a state in the Pacific Northwest region of the United States. Oregon is bordered on the west by the Pacific Ocean, on the north by Washington, on the south by California, on the east by Idaho, the Columbia River delineates much of Oregons northern boundary, and the Snake River delineates much of the eastern boundary. The parallel 42° north delineates the boundary with California and Nevada. Oregon was inhabited by indigenous tribes before Western traders, explorers. An autonomous government was formed in the Oregon Country in 1843 before the Oregon Territory was created in 1848, Oregon became the 33rd state on February 14,1859. Today, at 98,000 square miles, Oregon is the ninth largest and, with a population of 4 million, the capital of Oregon is Salem, the second most populous of its cities, with 164,549 residents. Portland is Oregons most populous city, with 632,309 residents, Portlands metro population of 2,389,228 ranks the 23rd largest metro in the nation. The Willamette Valley in western Oregon is the states most densely populated area, the tall conifers, mainly Douglas fir, along Oregons rainy west coast contrast with the lighter-timbered and fire-prone pine and juniper forests covering portions to the east. Abundant alders in the west fix nitrogen for the conifers, stretching east from central Oregon are semi-arid shrublands, prairies, deserts, steppes, and meadows. At 11,249 feet, Mount Hood is the states highest point, Oregons only national park, Crater Lake National Park, comprises the caldera surrounding Crater Lake, the deepest lake in the United States. The state is home to the single largest organism in the world, Armillaria ostoyae. Because of its landscapes and waterways, Oregons economy is largely powered by various forms of agriculture, fishing. It is also the top timber-producer of the lower 48 states, Technology is another one of the states major economic forces, which began in the 1970s with the establishment of the Silicon Forest and the expansion of Tektronix and Intel. Sportswear company Nike, Inc. headquartered in Beaverton, is the states largest public corporation with a revenue of $30.6 billion. The earliest evidence of the name Oregon has Spanish origins and this chronicle is the first topographical and linguistic source with respect to the place name Oregon. There are also two other sources with Spanish origins such as the name Oregano which grows in the part of the region. Another early use of the name, spelled Ouragon, was in a 1765 petition by Major Robert Rogers to the Kingdom of Great Britain, the term referred to the then-mythical River of the West. By 1778 the spelling had shifted to Oregon, in his 1765 petition, Rogers wrote, The rout. is from the Great Lakes towards the Head of the Mississippi, and from thence to the River called by the Indians Ouragon
18.
Sulfur
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Sulfur or sulphur is a chemical element with symbol S and atomic number 16. It is abundant, multivalent, and nonmetallic, under normal conditions, sulfur atoms form cyclic octatomic molecules with chemical formula S8. Elemental sulfur is a yellow crystalline solid at room temperature. Chemically, sulfur reacts with all elements except for gold, platinum, iridium, tellurium, though sometimes found in pure, native form, sulfur usually occurs as sulfide and sulfate minerals. Being abundant in native form, sulfur was known in ancient times, being mentioned for its uses in ancient India, ancient Greece, China, in the Bible, sulfur is called brimstone. Today, almost all elemental sulfur is produced as a byproduct of removing sulfur-containing contaminants from natural gas, the greatest commercial use of the element is the production of sulfuric acid for sulfate and phosphate fertilizers, and other chemical processes. The element sulfur is used in matches, insecticides, and fungicides, many sulfur compounds are odoriferous, and the smells of odorized natural gas, skunk scent, grapefruit, and garlic are due to organosulfur compounds. Hydrogen sulfide gives the characteristic odor to rotting eggs and other biological processes, sulfur is an essential element for all life, but almost always in the form of organosulfur compounds or metal sulfides. Three amino acids and two vitamins are organosulfur compounds, many cofactors also contain sulfur including glutathione and thioredoxin and iron–sulfur proteins. Disulfides, S–S bonds, confer mechanical strength and insolubility of the keratin, found in outer skin, hair. Sulfur is one of the chemical elements needed for biochemical functioning and is an elemental macronutrient for all organisms. Sulfur is derived from the Latin word sulpur, which was Hellenized to sulphur, the spelling sulfur appears toward the end of the Classical period. In 12th-century Anglo-French, it was sulfre, in the 14th century the Latin ph was restored, for sulphre, the parallel f~ph spellings continued in Britain until the 19th century, when the word was standardized as sulphur. Sulfur was the form chosen in the United States, whereas Canada uses both, the IUPAC adopted the spelling sulfur in 1990, as did the Nomenclature Committee of the Royal Society of Chemistry in 1992, restoring the spelling sulfur to Britain. Sulfur forms polyatomic molecules with different chemical formulas, the best-known allotrope being octasulfur, cyclo-S8. The point group of cyclo-S8 is D4d and its dipole moment is 0 D. Octasulfur is a soft, bright-yellow solid that is odorless and it melts at 115.21 °C, boils at 444.6 °C and sublimes easily. At 95.2 °C, below its melting temperature, cyclo-octasulfur changes from α-octasulfur to the β-polymorph, the structure of the S8 ring is virtually unchanged by this phase change, which affects the intermolecular interactions. At higher temperatures, the viscosity decreases as depolymerization occurs, molten sulfur assumes a dark red color above 200 °C
19.
Anaerobic organism
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An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It may react negatively or even die if oxygen is present, an anaerobic organism may be unicellular or multicellular. Van Leeuwenhoek sealed one of the tubes by using a flame. In 1913 Martinus Beijerinck repeated Van Leeuwenhoeks experiment and identified Clostridium butyricum as a prominent anaerobic bacterium in the sealed pepper infusion tube liquid. That Leeuwenhoek, one hundred years before the discovery of oxygen, for practical purposes, there are three categories of anaerobe, Obligate anaerobes, which are harmed by the presence of oxygen. Aerotolerant organisms, which use oxygen for growth, but tolerate its presence. Facultative anaerobes, which can grow without oxygen but use oxygen if it is present, some obligate anaerobes use fermentation, while others use anaerobic respiration. In the presence of oxygen, facultative anaerobes use aerobic respiration, without oxygen, some of them ferment, there are many anaerobic fermentative reactions. This is only 5% of the energy per molecule that the typical aerobic reaction generates. Since normal microbial culturing occurs in air, which is an aerobic environment. Hydrogen then reacts with oxygen gas on a palladium catalyst to more water. The issue with the Gaspak method is that a reaction can take place where the bacteria may die. The thioglycollate supplies a medium mimicking that of a dicot, thus providing not only an anaerobic environment, complex multicellular life that does not need oxygen is said to be rare, however there are examples of such organisms. Some organisms metabolise primarily using glycogen, for example the Nereid s and some polychaetes, or the juvenile Trichinella spiralis parasites. )
20.
Oxygen
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Oxygen is a chemical element with symbol O and atomic number 8. It is a member of the group on the periodic table and is a highly reactive nonmetal. By mass, oxygen is the third-most abundant element in the universe, after hydrogen, at standard temperature and pressure, two atoms of the element bind to form dioxygen, a colorless and odorless diatomic gas with the formula O2. This is an important part of the atmosphere and diatomic oxygen gas constitutes 20. 8% of the Earths atmosphere, additionally, as oxides the element makes up almost half of the Earths crust. Most of the mass of living organisms is oxygen as a component of water, conversely, oxygen is continuously replenished by photosynthesis, which uses the energy of sunlight to produce oxygen from water and carbon dioxide. Oxygen is too reactive to remain a free element in air without being continuously replenished by the photosynthetic action of living organisms. Another form of oxygen, ozone, strongly absorbs ultraviolet UVB radiation, but ozone is a pollutant near the surface where it is a by-product of smog. At low earth orbit altitudes, sufficient atomic oxygen is present to cause corrosion of spacecraft, the name oxygen was coined in 1777 by Antoine Lavoisier, whose experiments with oxygen helped to discredit the then-popular phlogiston theory of combustion and corrosion. One of the first known experiments on the relationship between combustion and air was conducted by the 2nd century BCE Greek writer on mechanics, Philo of Byzantium. In his work Pneumatica, Philo observed that inverting a vessel over a burning candle, Philo incorrectly surmised that parts of the air in the vessel were converted into the classical element fire and thus were able to escape through pores in the glass. Many centuries later Leonardo da Vinci built on Philos work by observing that a portion of air is consumed during combustion and respiration, Oxygen was discovered by the Polish alchemist Sendivogius, who considered it the philosophers stone. In the late 17th century, Robert Boyle proved that air is necessary for combustion, English chemist John Mayow refined this work by showing that fire requires only a part of air that he called spiritus nitroaereus. From this he surmised that nitroaereus is consumed in both respiration and combustion, Mayow observed that antimony increased in weight when heated, and inferred that the nitroaereus must have combined with it. Accounts of these and other experiments and ideas were published in 1668 in his work Tractatus duo in the tract De respiratione. Robert Hooke, Ole Borch, Mikhail Lomonosov, and Pierre Bayen all produced oxygen in experiments in the 17th and the 18th century but none of them recognized it as a chemical element. This may have been in part due to the prevalence of the philosophy of combustion and corrosion called the phlogiston theory, which was then the favored explanation of those processes. Established in 1667 by the German alchemist J. J. Becher, one part, called phlogiston, was given off when the substance containing it was burned, while the dephlogisticated part was thought to be its true form, or calx. The fact that a substance like wood gains overall weight in burning was hidden by the buoyancy of the combustion products
21.
Cellular respiration
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Respiration is one of the key ways a cell releases chemical energy to fuel cellular activity. Cellular respiration is considered an exothermic reaction which releases heat. The overall reaction occurs in a series of steps, most of which are redox reactions themselves. Nutrients that are used by animal and plant cells in respiration include sugar, amino acids and fatty acids. The chemical energy stored in ATP can then be used to drive processes requiring energy, including biosynthesis, aerobic respiration requires oxygen in order to create ATP. The potential of NADH and FADH2 is converted to more ATP through a transport chain with oxygen as the terminal electron acceptor. Most of the ATP produced by cellular respiration is made by oxidative phosphorylation. This works by the released in the consumption of pyruvate being used to create a chemiosmotic potential by pumping protons across a membrane. This potential is used to drive ATP synthase and produce ATP from ADP. Biology textbooks often state that 38 ATP molecules can be made per oxidised glucose molecule during cellular respiration, aerobic metabolism is up to 15 times more efficient than anaerobic metabolism. They share the pathway of glycolysis but aerobic metabolism continues with the Krebs cycle. The post-glycolytic reactions take place in the mitochondria in eukaryotic cells, glycolysis is a metabolic pathway that takes place in the cytosol of cells in all living organisms. This pathway can function with or without the presence of oxygen, in humans, aerobic conditions produce pyruvate and anaerobic conditions produce lactate. In aerobic conditions, the process converts one molecule of glucose into two molecules of pyruvate, generating energy in the form of two net molecules of ATP, four molecules of ATP per glucose are actually produced, however, two are consumed as part of the preparatory phase. The initial phosphorylation of glucose is required to increase the reactivity in order for the molecule to be cleaved into two molecules by the enzyme aldolase. During the pay-off phase of glycolysis, four groups are transferred to ADP by substrate-level phosphorylation to make four ATP. Glycogen can be converted into glucose 6-phosphate as well with the help of glycogen phosphorylase, during energy metabolism, glucose 6-phosphate becomes fructose 6-phosphate. An additional ATP is used to phosphorylate fructose 6-phosphate into fructose 1, fructose 1, 6-diphosphate then splits into two phosphorylated molecules with three carbon chains which later degrades into pyruvate
22.
Lithotroph
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Lithotrophs are a diverse group of organisms using inorganic substrate to obtain reducing equivalents for use in biosynthesis or energy conservation via aerobic or anaerobic respiration. Known chemolithotrophs are exclusively microorganisms, no known macrofauna possesses the ability to utilize inorganic compounds as energy sources, macrofauna and lithotrophs can form symbiotic relationships, in which case the lithotrophs are called prokaryotic symbionts. An example of this is chemolithotrophic bacteria in giant tube worms or plastids, lithotrophs belong to either the kingdom Bacteria or the kingdom Archaea. The term lithotroph was created from the Greek terms lithos and troph, many lithoautotrophs are extremophiles, but this is not universally so. Different from a lithotroph is an organotroph, an organism which obtains its reducing agents from the catabolism of organic compounds, the term was suggested in 1946 by Lwoff and collaborators. A chemolithotroph is able to use reduced compounds as a source of energy. This process is accomplished through oxidation and ATP synthesis, the majority of chemolithotrophs are able to fix carbon dioxide through the Calvin cycle, a metabolic pathway in which carbon enters as CO2 and leaves as glucose. For some substrates, the cells must cull through large amounts of substrate to secure just a small amount of energy. This makes their metabolic process inefficient in many places and hinders them from thriving and this group of organisms includes sulfur oxidizers, nitrifying bacteria, iron oxidizers, and hydrogen oxidizers. The term chemolithotrophy refers to an acquisition of energy from the oxidation of inorganic compounds. This form of metabolism is believed to only in prokaryotes and was first characterized by Russian microbiologist Sergei Winogradsky. The survival of these bacteria is dependent on the physiochemical conditions of their environment. The most important requirement for life is an abundant source of rich inorganic compounds. These compounds are crucial for chemolithotrophs because they provide a suitable energy source/electron donor from which the microorganisms can fix CO2, since chemosynthesis can take place in the absence of sunlight, these organisms are found mostly around hydrothermal vents and other locations rich in inorganic substrate. The energy obtained from inorganic oxidation varies depending on the substrate, for example, the oxidation of hydrogen sulfide to elemental sulfur produces far less energy than the oxidation of elemental sulfur to sulfate. The majority of lithotrophs fix carbon dioxide through the Calvin cycle, for some substrates, such as ferrous iron, the cells must cull through large amounts of inorganic substrate to secure just a small amount of energy. This makes their metabolic process inefficient in many places and hinders them from thriving, there is a fairly large variation in the types of inorganic substrates that these microorganisms can use to produce energy. The chemolithotrophs that are best documented are aerobic respirers, meaning that they use oxygen in their metabolic process, the list of these microorganisms that employ anaerobic respiration though is growing
23.
Sulfuric acid
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Sulfuric acid is a highly corrosive strong mineral acid with the molecular formula H2SO4 and molecular weight 98.079 g/mol. It is a pungent-ethereal, colorless to slightly yellow liquid that is soluble in water at all concentrations. Sometimes, it is dyed dark brown during production to alert people to its hazards, the historical name of this acid is oil of vitriol. Sulfuric acid is an acid and shows different properties depending upon its concentration. Its corrosiveness on other materials, like metals, living tissues or even stones, can be ascribed to its strong acidic nature and, if concentrated. It is also hygroscopic, readily absorbing water vapour from the air, Sulfuric acid at a high concentration can cause very serious damage upon contact, since not only does it cause chemical burns via hydrolysis, but also secondary thermal burns through dehydration. It can lead to permanent blindness if splashed onto eyes and irreversible damage if swallowed, Sulfuric acid has a wide range of applications including in domestic acidic drain cleaners, as an electrolyte in lead-acid batteries and in various cleaning agents. It is also a central substance in the chemical industry, principal uses include mineral processing, fertilizer manufacturing, oil refining, wastewater processing, and chemical synthesis. It is widely produced with different methods, such as process, wet sulfuric acid process, lead chamber process. The study of vitriol, a category of glassy minerals from which the acid can be derived, sumerians had a list of types of vitriol that they classified according to the substances color. Some of the earliest discussions on the origin and properties of vitriol is in the works of the Greek physician Dioscorides, galen also discussed its medical use. Ibn Sina focused on its uses and different varieties of vitriol. Sulfuric acid was called oil of vitriol by medieval European alchemists because it was prepared by roasting green vitriol in an iron retort, there are references to it in the works of Vincent of Beauvais and in the Compositum de Compositis ascribed to Saint Albertus Magnus. A passage from Pseudo-Geber´s Summa Perfectionis was long considered to be the first recipe for sulfuric acid, in the seventeenth century, the German-Dutch chemist Johann Glauber prepared sulfuric acid by burning sulfur together with saltpeter, in the presence of steam. As saltpeter decomposes, it oxidizes the sulfur to SO3, in 1736, Joshua Ward, a London pharmacist, used this method to begin the first large-scale production of sulfuric acid. This process allowed the effective industrialization of sulfuric acid production, after several refinements, this method, called the lead chamber process or chamber process, remained the standard for sulfuric acid production for almost two centuries. Sulfuric acid created by John Roebucks process approached a 65% concentration, later refinements to the lead chamber process by French chemist Joseph Louis Gay-Lussac and British chemist John Glover improved concentration to 78%. However, the manufacture of dyes and other chemical processes require a more concentrated product
24.
PH
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In chemistry, pH is a numeric scale used to specify the acidity or basicity of an aqueous solution. It is approximately the negative of the base 10 logarithm of the concentration, measured in units of moles per liter. More precisely it is the negative of the logarithm to base 10 of the activity of the hydrogen ion, solutions with a pH less than 7 are acidic and solutions with a pH greater than 7 are basic. Pure water is neutral, at pH7, being neither an acid nor a base, contrary to popular belief, the pH value can be less than 0 or greater than 14 for very strong acids and bases respectively. The pH scale is traceable to a set of standard solutions whose pH is established by international agreement, the pH of aqueous solutions can be measured with a glass electrode and a pH meter, or an indicator. In the first papers, the notation had the H as a subscript to the p, as so. The exact meaning of the p in pH is disputed, but according to the Carlsberg Foundation and it has also been suggested that the p stands for the German Potenz, others refer to French puissance. Another suggestion is that the p stands for the Latin terms pondus hydrogenii, potentia hydrogenii and it is also suggested that Sørensen used the letters p and q simply to label the test solution and the reference solution. Currently in chemistry, the p stands for decimal cologarithm of, PH is defined as the decimal logarithm of the reciprocal of the hydrogen ion activity, aH+, in a solution. P H = − log 10 = log 10 For example and this definition was adopted because ion-selective electrodes, which are used to measure pH, respond to activity. For H+ number of electrons transferred is one and it follows that electrode potential is proportional to pH when pH is defined in terms of activity. The reference electrode may be a silver chloride electrode or a calomel electrode, the hydrogen-ion selective electrode is a standard hydrogen electrode. Reference electrode | concentrated solution of KCl || test solution | H2 | Pt Firstly, the cell is filled with a solution of hydrogen ion activity. Then the emf, EX, of the cell containing the solution of unknown pH is measured. PH = pH + E S − E X z The difference between the two measured emf values is proportional to pH and this method of calibration avoids the need to know the standard electrode potential. The proportionality constant, 1/z is ideally equal to 12.303 R T / F the Nernstian slope, to apply this process in practice, a glass electrode is used rather than the cumbersome hydrogen electrode. A combined glass electrode has a reference electrode. It is calibrated against buffer solutions of hydrogen ion activity
25.
Volcanism
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It includes all phenomena resulting from and causing magma within the crust or mantle of the body, to rise through the crust and form volcanic rocks on the surface. Magma from the mantle or lower crust rises through its crust towards the surface, if magma reaches the surface, its behavior depends on the viscosity of the molten constituent rock. Viscous magma produces volcanoes characterised by explosive eruptions, while non-viscous magma produce volcanoes characterised by effusive eruptions pouring large amounts of lava onto the surface, in some cases, rising magma can cool and solidify without reaching the surface. Instead, the cooled and solidified igneous mass crystallises within the crust to form an igneous intrusion, as magma cools the chemicals in the crystals formed are effectively removed from the main mix of the magma, so the chemical content of the remaining magma evolves as it solidifies slowly. Fresh unevolved magma injections can remobilise more evolved magmas, allowing eruptions from more viscous magmas, movement of molten rock in the mantle, caused by thermal convection currents, coupled with gravitational effects of changes on the earths surface drive plate tectonic motion and ultimately volcanism. Volcanoes are places where magma reaches the earths surface, the type of volcano depends on the location of the eruption and the consistency of the magma. These are formed where magma pushes between existing rock, intrusions can be in the form of batholiths, dikes, sills, earthquakes are generally associated with plate tectonic activity, but some earthquakes are generated as a result of volcanic activity. These are formed where water interacts with volcanism and these include geysers, fumaroles, hotsprings and mudpots, they are often used as a source of geothermal energy. The amount of gas and ash emitted by volcanic eruptions has a significant effect on the Earths climate, large eruptions correlate well with some significant climate change events. When the magma cools it solidifies and forms rocks, the type of rock formed depends on the composition of the magma. Magma that reaches the surface to become lava cools rapidly resulting in rocks with small crystals such as basalt, some of this magma may cool extremely rapidly and will form volcanic glass such as obsidian. Magma that remains trapped below ground in thin intrusions cools slower than magma exposed to the surface, magma that remains trapped in large quantities below ground cools most slowly resulting in rocks with larger crystals - such as granite and gabbro. Existing rocks that come into contact with magma may be melted and assimilated into the magma, other rocks adjacent to the magma may be altered by contact metamorphism or metasomatism as they are affected by the heat and escaping or externally circulating hydrothermal fluids. Volcanism is not confined only to Earth, but is thought to be found on any body having a solid crust, evidence of volcanism should still be found on any body that has had volcanism at some point in its history. It can be surmised that volcanism exists on planets and moons of this type in other systems as well. In 2014, scientists found 70 lava flows which formed on the Moon in the last 100 million years, bimodal volcanism Continental drift Hotspot Volcanic arc Glossary of Volcanic Terms. G. J. Hudak, University of Wisconsin Oshkosh,2001, crumpler, L. S. and Lucas, S. G. Volcanoes of New Mexico, An Abbreviated Guide For Non-Specialists. New Mexico Museum of Natural History and Science Bulletin, archived from the original on 2007-03-21
26.
Hot springs
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A hot spring is a spring produced by the emergence of geothermally heated groundwater that rises from the Earths crust. There are geothermal hot springs in many locations all over the crust of the earth, while some of these springs contain water that is a safe temperature for bathing, others are so hot that immersion can result in injury or death. The water temperature of a hot spring is usually 6.5 °C or more above mean air temperature, note that by this definition, thermal spring is not synonymous with the term hot spring a spring whose hot water is brought to the surface. The water temperature of the spring is usually 8.3 °C or more above the air temperature. A spring with water above the human body temperature –36.7 °C. suggest that the phrase warm spring is not useful. In general, the temperature of rocks within the earth increases with depth, the rate of temperature increase with depth is known as the geothermal gradient. If water percolates deeply enough into the crust, it will be heated as it comes into contact with hot rocks, the water from hot springs in non-volcanic areas is heated in this manner. In active volcanic zones such as Yellowstone National Park, water may be heated by coming into contact with magma, the high temperature gradient near magma may cause water to be heated enough that it boils or becomes superheated. If the water becomes so hot that it builds steam pressure and erupts in a jet above the surface of the Earth, if the water only reaches the surface in the form of steam, it is called a fumarole. If the water is mixed with mud and clay, it is called a mud pot, note that hot springs in volcanic areas are often at or near the boiling point. People have been seriously scalded and even killed by accidentally or intentionally entering these springs, Warm springs are sometimes the result of hot and cold springs mixing. They may occur within an area or outside of one. One example of a warm spring is Warm Springs, Georgia. Hot springs range in flow rate from the tiniest seeps to veritable rivers of hot water, sometimes there is enough pressure that the water shoots upward in a geyser, or fountain. There are many claims in the literature about the rates of hot springs. It should be noted there are many more high flow non-thermal springs than geothermal springs. For example, there are 33 recognized magnitude one springs (having a flow in excess of 2,800 L/s in Florida alone, silver Springs, Florida has a flow of more than 21,000 L/s. Springs with high flow rates include, The Excelsior Geyser Crater in Yellowstone National Park yields about 4,000 U. S. gal/min
27.
Geyser
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A geyser is a spring characterized by intermittent discharge of water ejected turbulently and accompanied by steam. As a fairly rare phenomenon, the formation of geysers is due to particular hydrogeological conditions that exist in only a few places on Earth, generally all geyser field sites are located near active volcanic areas, and the geyser effect is due to the proximity of magma. Generally, surface water works its way down to a depth of around 2,000 metres where it contacts hot rocks. The resultant boiling of the water results in the geyser effect of hot water. Over one thousand known geysers exist worldwide, at least 1,283 geysers have erupted in Yellowstone National Park, Wyoming, United States, and an average of 465 geysers are active there in a given year. Like many other phenomena, geysers are not unique to planet Earth. Jet-like eruptions, often referred to as cryogeysers, have been observed on several of the moons of the solar system. Due to the low ambient pressures, these eruptions consist of vapor without liquid, they are more easily visible by particles of dust. Water vapor jets have been observed near the pole of Saturns moon Enceladus. There are also signs of carbon dioxide eruptions from the polar ice cap of Mars. In the latter two cases, instead of being driven by energy, the eruptions seem to rely on solar heating via a solid-state greenhouse effect. The word geyser comes from Geysir, the name of a spring at Haukadalur, Iceland, that name, in turn, comes from the Icelandic verb geysa, to gush. Geysers are generally associated with volcanic areas, as the water boils, the resulting pressure forces a superheated column of steam and water to the surface through the geysers internal plumbing. The formation of geysers specifically requires the combination of three conditions that are usually found in volcanic terrain. The heat needed for geyser formation comes from magma that needs to be near the surface of the earth, the fact that geysers need heat much higher than normally found near the earths surface is the reason they are associated with volcanoes or volcanic areas. The pressures encountered at the areas where the water is heated make the point of the water much higher than at normal atmospheric pressures. The water ejected from a geyser travels underground through deep, pressurized fissures in the Earths crust, in order for the heated water to form a geyser, a plumbing system made of fractures, fissures, porous spaces, and sometimes cavities is required. This includes a reservoir to hold the water while it is being heated, Geysers are generally aligned along faults
28.
Fumarole
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A fumarole is an opening in a planets crust, often in areas surrounding volcanoes, which emits steam and gases such as carbon dioxide, sulfur dioxide, hydrogen chloride, and hydrogen sulfide. The steam forms when superheated water vaporizes as its pressure drops when it emerges from the ground, the name solfatara, from the Italian solfo, sulfur, is given to fumaroles that emit sulfurous gases. Fumaroles may occur along tiny cracks or long fissures, in clusters or fields. A fumarole field is an area of springs and gas vents where magma or hot igneous rocks at shallow depth release gases or interact with groundwater. From the perspective of groundwater, a fumarole could be described as a hot spring that boils off all its water before the water reaches the surface. Fumaroles may persist for decades or centuries if located above a persistent heat source, the Valley of Ten Thousand Smokes, for example, was formed during the 1912 eruption of Novarupta in Alaska. Initially, thousands of fumaroles occurred in the ash from the eruption. An estimated four thousand fumaroles exist within the boundaries of Yellowstone National Park in the United States, in April 2006 fumarole emissions killed three ski-patrol workers east of Chair 3 at Mammoth Mountain Ski Area in California. The workers were overpowered by toxic fumes that had accumulated in a crevasse they had fallen into, another example is an array of fumaroles in the Valley of Desolation in Morne Trois Pitons National Park in Dominica. Boiling Lake Mazuku Mofetta Mudpot Mud volcano USGS Photo Glossary, Fumarole Sulfur Mining on Gunung Welirang Volcano Chisholm, Hugh, ed. Fumarole
29.
Photosynthesis
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Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that can later be released to fuel the organisms activities. In most cases, oxygen is released as a waste product. Most plants, most algae, and cyanobacteria perform photosynthesis, such organisms are called photoautotrophs, in plants, these proteins are held inside organelles called chloroplasts, which are most abundant in leaf cells, while in bacteria they are embedded in the plasma membrane. In these light-dependent reactions, some energy is used to strip electrons from suitable substances, such as water, in the Calvin cycle, atmospheric carbon dioxide is incorporated into already existing organic carbon compounds, such as ribulose bisphosphate. Using the ATP and NADPH produced by the light-dependent reactions, the compounds are then reduced and removed to form further carbohydrates. Cyanobacteria appeared later, the oxygen they produced contributed directly to the oxygenation of the Earth. Today, the rate of energy capture by photosynthesis globally is approximately 130 terawatts. Photosynthetic organisms also convert around 100–115 thousand million tonnes of carbon into biomass per year. Photosynthetic organisms are photoautotrophs, which means that they are able to synthesize food directly from carbon dioxide, however, not all organisms that use light as a source of energy carry out photosynthesis, photoheterotrophs use organic compounds, rather than carbon dioxide, as a source of carbon. In plants, algae, and cyanobacteria, photosynthesis releases oxygen and this is called oxygenic photosynthesis and is by far the most common type of photosynthesis used by living organisms. Although there are differences between oxygenic photosynthesis in plants, algae, and cyanobacteria, the overall process is quite similar in these organisms. There are also varieties of anoxygenic photosynthesis, used mostly by certain types of bacteria. Carbon dioxide is converted into sugars in a process called carbon fixation, photosynthesis provides the energy in the form of free electrons that are used to split carbon from carbon dioxide that is then used to fix that carbon once again as carbohydrate. Carbon fixation is a redox reaction, so photosynthesis supplies the energy that drives both process. In the first stage, light-dependent reactions or light reactions capture the energy of light and use it to make the energy-storage molecules ATP, during the second stage, the light-independent reactions use these products to capture and reduce carbon dioxide. Most organisms that utilize oxygenic photosynthesis use visible light for the light-dependent reactions, some organisms employ even more radical variants of photosynthesis. Some archea use a method that employs a pigment similar to those used for vision in animals. The bacteriorhodopsin changes its configuration in response to sunlight, acting as a proton pump and this produces a proton gradient more directly, which is then converted to chemical energy
30.
GC-content
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In molecular biology and genetics, GC-content is the percentage of nitrogenous bases on a DNA or RNA molecule that are either guanine or cytosine. This may refer to a fragment of DNA or RNA. When it refers to a fragment of the material, it may denote the GC-content of section of a gene, single gene, group of genes. G and C undergo a specific hydrogen bonding, whereas A bonds specifically with T or U, the GC pair is bound by three hydrogen bonds, while AT and AU pairs are bound by two hydrogen bonds. To emphasize this difference in the number of bonds, the base pairings can be represented as respectively G≡C versus A=T. In spite of the higher thermostability conferred to the material, it is envisaged that cells with DNA of high GC-content undergo autolysis. However, it has shown that there is a strong correlation between the prokaryotic optimal growth at higher temperatures and the GC content of structured RNAs. In PCR experiments, the GC-content of primers are used to predict their annealing temperature to the template DNA, a higher GC-content level indicates a higher melting temperature. GC content is expressed as a percentage value, but sometimes as a ratio. GC-content percentage is calculated as G + C A + T + G + C whereas the AT/GC ratio is calculated as A + T G + C. The absorbance of DNA at a wavelength of 260 nm increases fairly sharply when the double-stranded DNA separates into two single strands when sufficiently heated, the most commonly used protocol for determining GC ratios uses flow cytometry for large number of samples. GC ratios within a genome is found to be markedly variable and these variations in GC ratio within the genomes of more complex organisms result in a mosaic-like formation with islet regions called isochores. This results in the variations in staining intensity in the chromosomes, gC-rich isochores include in them many protein coding genes, and thus determination of ratio of these specific regions contributes in mapping gene-rich regions of the genome. Within a long region of sequence, genes are often characterised by having a higher GC-content in contrast to the background GC-content for the entire genome. Evidence of GC ratio with that of length of the region of a gene has shown that the length of the coding sequence is directly proportional to higher G+C content. This has been pointed to the fact that the stop codon has a bias towards A and T nucleotides, and, thus, for example, the Actinobacteria are characterised as high GC-content bacteria. In Streptomyces coelicolor A3, GC content is 72%, the GC-content of Yeast is 38%, and that of another common model organism, Thale Cress, is 36%. Because of the nature of the code, it is virtually impossible for an organism to have a genome with a GC-content approaching either 0% or 100%
31.
Homologous recombination
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Homologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks. Homologous recombination also produces new combinations of DNA sequences during meiosis and these new combinations of DNA represent genetic variation in offspring, which in turn enables populations to adapt during the course of evolution. Homologous recombination is used in horizontal gene transfer to exchange genetic material between different strains and species of bacteria and viruses. Although homologous recombination varies widely among different organisms and cell types, after a double-strand break occurs, sections of DNA around the 5 ends of the break are cut away in a process called resection. In the strand invasion step that follows, an overhanging 3 end of the broken DNA molecule then invades a similar or identical DNA molecule that is not broken. After strand invasion, the sequence of events may follow either of two main pathways discussed below, the DSBR pathway or the SDSA pathway. Homologous recombination that occurs during DNA repair tends to result in non-crossover products, homologous recombination is conserved across all three domains of life as well as viruses, suggesting that it is a nearly universal biological mechanism. Since their dysfunction has been associated with increased susceptibility to several types of cancer. Homologous recombination is used in gene targeting, a technique for introducing genetic changes into target organisms. In the early 1900s, William Bateson and Reginald Punnett found an exception to one of the principles of inheritance originally described by Gregor Mendel in the 1860s. Two decades later, Barbara McClintock and Harriet Creighton demonstrated that chromosomal crossover occurs during meiosis and this work established E. coli as a model organism in genetics, and helped Lederberg win the 1958 Nobel Prize in Physiology or Medicine. In 1983, Jack Szostak and colleagues presented a model now known as the DSBR pathway, homologous recombination is essential to cell division in eukaryotes like plants, animals, fungi and protists. In cells that divide through mitosis, homologous recombination repairs double-strand breaks in DNA caused by ionizing radiation or DNA-damaging chemicals, left unrepaired, these double-strand breaks can cause large-scale rearrangement of chromosomes in somatic cells, which can in turn lead to cancer. It does so by facilitating chromosomal crossover, in regions of similar. This creates new, possibly beneficial combinations of genes, which can give offspring an evolutionary advantage, chromosomal crossover often begins when a protein called Spo11 makes a targeted double-strand break in DNA. The absence of a recombination hotspot between two genes on the same chromosome often means that those genes will be inherited by future generations in equal proportion and this represents linkage between the two genes greater than would be expected from genes that independently assort during meiosis. Double-strand breaks can be repaired through homologous recombination or through non-homologous end joining, NHEJ is a DNA repair mechanism which, unlike homologous recombination, does not require a long homologous sequence to guide repair
32.
Transformation (genetics)
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Transformation is one of three processes for horizontal gene transfer, in which exogenous genetic material passes from bacterium to another, the other two being conjugation and transduction. In transformation, the material passes through the intervening medium. Transformation in bacteria was first demonstrated in 1928 by British bacteriologist Frederick Griffith, Griffith discovered that a strain of Streptococcus pneumoniae could be made virulent after being exposed to heat-killed virulent strains. Griffith hypothesized that some transforming principle from the strain was responsible for making the harmless strain virulent. In 1944 this transforming principle was identified as being genetic by Oswald Avery, Colin MacLeod and they isolated DNA from a virulent strain of S. pneumoniae and using just this DNA were able to make a harmless strain virulent. They called this uptake and incorporation of DNA by bacteria transformation, the results of Avery et al. It was originally thought that Escherichia coli, a used laboratory organism, was refractory to transformation. However, in 1970, Morton Mandel and Akiko Higa showed that E. coli may be induced to take up DNA from bacteriophage λ without the use of helper phage after treatment with calcium chloride solution. Two years later in 1972, Stanley Norman Cohen, Annie Chang, the method of transformation by Mandel and Higa was later improved upon by Douglas Hanahan. Transformation of animal and plant cells was also investigated with the first transgenic mouse being created by injecting a gene for a rat growth hormone into an embryo in 1982. In 1907 a bacterium that caused plant tumors, Agrobacterium tumefaciens, was discovered, not all plant cells are susceptible to infection by A. tumefaciens, so other methods were developed, including electroporation and micro-injection. Particle bombardment was possible with the invention of the Biolistic Particle Delivery System by John Sanford in the 1980s. In transformation, the material passes through the intervening medium. Competence refers to a state of being able to take up exogenous DNA from the environment. Natural genetic transformation appears to be an adaptation for repair of DNA damage that also generates genetic diversity and it has also been reported in at least 30 species of Proteobacteria distributed in the classes alpha, beta, gamma and epsilon. Naturally competent bacteria carry sets of genes that provide the protein machinery to bring DNA across the cell membrane, the DNA first binds to the surface of the competent cells on a DNA receptor, and passes through the cytoplasmic membrane via DNA translocase. Only single-stranded DNA may pass through, the other strand being degraded by nucleases in the process, the translocated single-stranded DNA may then be integrated into the bacterial chromosomes by a RecA-dependent process. In Gram-negative cells, due to the presence of an extra membrane, pilin may be required for competence, but its role is uncertain
33.
Anaerobic digestion
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Anaerobic digestion is a collection of processes by which microorganisms break down biodegradable material in the absence of oxygen. The process is used for industrial or domestic purposes to waste or to produce fuels. Much of the fermentation used industrially to produce food and drink products, as well as home fermentation, anaerobic digestion occurs naturally in some soils and in lake and oceanic basin sediments, where it is usually referred to as anaerobic activity. This is the source of marsh gas methane as discovered by Volta in 1776, the digestion process begins with bacterial hydrolysis of the input materials. Insoluble organic polymers, such as carbohydrates, are broken down to soluble derivatives that become available for other bacteria, acidogenic bacteria then convert the sugars and amino acids into carbon dioxide, hydrogen, ammonia, and organic acids. These bacteria convert these resulting organic acids into acetic acid, along with ammonia, hydrogen. Finally, methanogens convert these products to methane and carbon dioxide, the methanogenic archaea populations play an indispensable role in anaerobic wastewater treatments. Anaerobic digestion is used as part of the process to treat biodegradable waste, as part of an integrated waste management system, anaerobic digestion reduces the emission of landfill gas into the atmosphere. Anaerobic digesters can also be fed with energy crops, such as maize. Anaerobic digestion is used as a source of renewable energy. The process produces a biogas, consisting of methane, carbon dioxide and this biogas can be used directly as fuel, in combined heat and power gas engines or upgraded to natural gas-quality biomethane. The nutrient-rich digestate also produced can be used as fertilizer, many microorganisms affect anaerobic digestion, including acetic acid-forming bacteria and methane-forming archaea. These organisms promote a number of processes in converting the biomass to biogas. Gaseous oxygen is excluded from the reactions by physical containment, anaerobes utilize electron acceptors from sources other than oxygen gas. These acceptors can be the material itself or may be supplied by inorganic oxides from within the input material. When the oxygen source in a system is derived from the organic material itself, the intermediate end products are primarily alcohols, aldehydes. In the presence of specialised methanogens, the intermediates are converted to the end products of methane, carbon dioxide. In an anaerobic system, the majority of the energy contained within the starting material is released by methanogenic bacteria as methane
34.
Sulfolobus
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Sulfolobus is a genus of microorganism in the family Sulfolobaceae. It belongs to the archaea domain, Sulfolobus species grow in volcanic springs with optimal growth occurring at pH 2-3 and temperatures of 75-80 °C, making them acidophiles and thermophiles respectively. Sulfolobus cells are shaped and flagellar. Species of Sulfolobus are generally named after the location from which they were first isolated, other species can be found throughout the world in areas of volcanic or geothermal activity, such as geological formations called mud pots, which are also known as solfatare. In 2001, the first genome sequence of Sulfolobus, Sulfolobus solfataricus P2, was published, in P2s genome, the genes related to chromosome replication were likewise found to be more related to those in eukaryotes. These genes include DNA polymerase, primase, MCM, CDC6/ORC1, RPA, RPC, in 2004, the origins of DNA replication of Sulfolobus solfataricus and Sulfolobus acidocaldarius were identified. It showed that both contained two origins in their genome. This was the first time more than a single origin of DNA replication had been shown to be used in a prokaryotic cell. The mechanism of DNA replication in archaea is evolutionary conserved, Sulfolobus is now used as a model to study the molecular mechanisms of DNA replication in Archaea. Sulfolobus proteins are of interest for biotechnology and industrial use due to their thermostable nature, one application is the creation of artificial derivatives from S. acidocaldarius proteins, named affitins. Intracellular proteins are not necessarily stable at low pH however, as Sulfolobus species maintain a significant pH gradient across the outer membrane, for example, S. tokodaii is known to oxidize hydrogen sulfide to sulfate intracellularly. The complete genomes have been sequenced for S. acidocaldarius DSM639, S. solfataricus P2, the archaeon Sulfolobus solfataricus has a circular chromosome that consists of 2,992,245 bp. Another sequenced species, S. tokodaii has a circular chromosome as well but is smaller with 2,694,756 bp. Both species lack the genes ftsZ and minD, which has been characteristic of sequenced Crenarchaeota and they also code for citrate synthase and two subunits of 2-oxoacid, ferredoxin oxidoreductase, which plays the same role as alpha-ketoglutarate dehydrogenase in the TCA cycle. This indicates that Sulfolobus has a TCA cycle system similar to found in mitochondria of eukaryotes. Other genes in the chain which partake in the production of ATP were not similar to what is found in eukaryotes. Cytochrome c is one example that plays an important role in electron transfer to oxygen in eukaryotes. This was also found in A. pernix K1, since this step is important for an aerobic microorganism like Sulfolobus, it probably uses a different molecule for the same function or has a different pathway
35.
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
36.
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
37.
Alkaliphile
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Alkaliphiles are a class of extremophilic microbes capable of survival in alkaline environments, growing optimally around a pH of 10. These bacteria can be categorized as obligate alkaliphiles, facultative alkaliphiles and haloalkaliphiles. Microbial growth in alkaline conditions presents several complications to normal activity and reproduction. For example, alkalinity can lead to denaturation of DNA, instability of the membrane and inactivation of cytosolic enzymes. To determine which of the above possibilities an alkaliphile uses, experimentation has demonstrated that alkaliphilic enzymes possess relatively normal pH optimums. Because the cytosolic pH must remain neutral, alkaliphiles must have one or more mechanisms of acidifying the cytosol when in the presence of a highly alkaline environment. Alkaliphiles maintain cytosolic acidification through both passive and active means, in addition, the peptidoglycan in alkaliphilic B. subtilis has been observed to contain higher levels of hexosamines and amino acids as compared to its neutrophilic counterpart. When alkaliphiles lose these acidic residues in the form of induced mutations, the most characterized method of active acidification is in the form of Na+/H+ antiporters. In this model, H+ ions are first extruded through the transport chain in respiring cells. This proton accumulation leads to a lowering of cytosolic pH, the extruded Na+ can be used for solute symport, which are necessary for cellular processes. It has been noted that Na+/H+ antiport is required for alkaliphilic growth, if Na+/H+ antiporters are disabled through mutation or another means, the bacteria are rendered neutrophilic. The sodium required for this system is the reason some alkaliphiles can only grow in saline environments. In addition to the method of proton extrusion discussed above, it is believed that the method of cellular respiration is different in obligate alkaliphiles as compared to neutrophiles. Generally, ATP production operates by establishing a proton gradient and an electrical potential. However, since alkaliphiles have a reversed pH gradient, it would seem that ATP production—which is based on a proton motive force—would be severely reduced. It has been proposed that while the pH gradient has been reversed and this increase in charge causes the production of greater amounts of ATP by each translocated proton when driven through an ATPase. Research in this area is ongoing, alkaliphiles promise several interesting uses for biotechnology and future research. Alkaliphilic methods of regulating pH and producing ATP are of interest in the scientific community and it is hoped that further research into alkaliphilic enzymes will allow scientists to harvest alkaliphiles enzymes for use in basic conditions
38.
Capnophile
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Capnophiles are microorganisms that thrive in the presence of high concentrations of carbon dioxide. Some capnophiles may have a requirement for carbon dioxide, while others merely compete more successfully for resources under these conditions. The term is a descriptive one and has less relevance as a means of establishing a taxonomic or evolutionary relationship among organisms with this characteristic. For example, the ability of capnophiles to tolerate the amount of oxygen that is also in their environment may vary widely, in 2004, a capnophilic bacterium was characterized that appears to require carbon dioxide. This organism, Mannheimia succiniciproducens, has a unique metabolism involving carbon fixation, there are currently at least two relatively well characterized capnophilic groups of microorganisms that include human pathogens. Campylobacter species can cause intestinal disorders, other capnophilic pathogens occur in the Gram-negative Aggregatibacter spp. found in the mouth. These are a cause of aggressive juvenile periodontitis, however, capnophiles are also normal flora in some ruminants. Mannheimia succiniciproducens, in particular, was isolated from a bovine rumen and its unusual biochemistry and benign characteristics have attracted commercial interest
39.
Endolith
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An endolith is an organism that lives inside rock, coral, animal shells, or in the pores between mineral grains of a rock. Many are extremophiles, living in places previously thought inhospitable to life and they are of particular interest to astrobiologists, who theorize that endolithic environments on Mars and other planets constitute potential refugia for extraterrestrial microbial communities. The main threat to their survival seems not to result from the pressure at such depth, but from the increased temperature. Judging from hyperthermophile organisms, the limit is at about 120 °C, which limits the possible depth to 4-4.5 km below the continental crust. Endolithic organisms have also found in surface rocks in regions of low humidity and low temperature, including the Dry Valleys and permafrost of Antarctica, the Alps. Endoliths can survive by feeding on traces of iron, potassium, whether they metabolize these directly from the surrounding rock, or rather excrete an acid to dissolve them first, remains to be seen. The Ocean Drilling Program found microscopic trails in basalt from the Atlantic, Indian, photosynthetic endoliths have also been discovered. As water and nutrients are rather sparse in the environment of the endolith, early data suggests that some only engage in cell division once every hundred years. In August 2013 researchers reported evidence of endoliths in the floor with a generation time of 10,000 years. Most of their energy is spent repairing cell damage caused by cosmic rays or racemization and it is thought that they weather long ice ages in this fashion, emerging when the temperature in the area warms. As most endoliths are autotrophs, they can generate organic compounds essential for their survival on their own from inorganic matter, some endoliths have specialized in feeding on their autotroph relatives. The micro-biotope where these different endolithic species live together has been called a Subsurface Lithotrophic Microbial Ecosystem, endolithic fungi have been discovered in shells as early as the year 1889 by Edouard Bornet and Charles Flahault. These two French phycologists specifically provided descriptions for two fungi, Ostracoblabe implexis and Lithopythium gangliiforme, discovery of endolithic fungi, such as Dodgella priscus and Conchyliastrum, has also been made in the beach sand of Australia by George Zembrowski. Findings have also made in coral reefs and have been found to be, at times. According to a study done by Astrid Gunther endoliths were also found in the island of Cozumel, although the rate of thickening of the shells were faster in more infested areas it is not rapid enough to combat the degradation of the mussel shells. Evidence of endolithic fungi were discovered within dinosaur eggshell found in central China, the endolithic fungi that was found within the eggshells were characterized as being “needle-like, ribbon-like, and silk-like. Fungus is seldom fossilized and even when it is preserved it can be difficult to distinguish endolithic hyphae from endolithic cyanobacteria, endolithic microbes can, however, be distinguished based on their distribution, ecology, and morphology. It may also have led to the preservation of dinosaur eggs, endolith Advanced Collection — Compiled for professionals and advanced learners, this endolith collection includes online resources such as journal articles, academic reviews, and surveys
40.
Halophile
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Halophiles are organisms that thrive in high salt concentrations. They are a type of extremophile organisms, the name comes from the Greek word for salt-loving. While most halophiles are classified into the Archaea domain, there are also bacterial halophiles and some eukaryota, some well-known species give off a red color from carotenoid compounds, notably bacteriorhodopsin. Halophiles are categorized as slight, moderate, or extreme, by the extent of their halotolerance. Slight halophiles prefer 0.3 to 0.8 M, moderate halophiles 0.8 to 3.4 M, halophiles require sodium chloride for growth, in contrast to halotolerant organisms, which do not require salt but can grow under saline conditions. High salinity represents an environment to which relatively few organisms have been able to adapt. Most halophilic and all halotolerant organisms expend energy to exclude salt from their cytoplasm to avoid protein aggregation, to survive the high salinities, halophiles employ two differing strategies to prevent desiccation through osmotic movement of water out of their cytoplasm. Both strategies work by increasing the osmolarity of the cell. In the first, organic compounds are accumulated in the cytoplasm — osmoprotectants which are known as compatible solutes and these can be either synthesised or accumulated from the environment. The most common compatible solutes are neutral or zwitterionic, and include amino acids, sugars, polyols, betaines, the second, more radical, adaptation involves the selective influx of potassium ions into the cytoplasm. Of particular note are the extreme halophiles or haloarchaea, a group of archaea and these are the primary inhabitants of salt lakes, inland seas, and evaporating ponds of seawater, such as the deep salterns, where they tint the water column and sediments bright colors. These species most likely if they are exposed to anything other than a very high-concentration. These prokaryotes require salt for growth, the high concentration of sodium chloride in their environment limits the availability of oxygen for respiration. Their cellular machinery is adapted to high concentrations by having charged amino acids on their surfaces. They are heterotrophs that normally respire by aerobic means, most halophiles are unable to survive outside their high-salt native environments. Indeed, many cells are so fragile that when placed in distilled water, halophiles may use a variety of energy sources. They can be aerobic or anaerobic, anaerobic halophiles include phototrophic, fermentative, sulfate-reducing, homoacetogenic, and methanogenic species. The Haloarchaea, and particularly the family Halobacteriaceae, are members of the domain Archaea, currently,15 recognised genera are in the family
. PMID 18664583.