1.
Spiral bacteria
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Spiral bacteria, bacteria of spiral shape, form the third major morphological category of prokaryotes along with the rod-shaped bacilli and round cocci. Spiral bacteria can be subclassified by the number of twists per cell, cell thickness, cell flexibility, a spirillum is a rigid spiral bacterium that is Gram-negative and frequently amphitrichous or lophotrichous. Owing to their properties, spirochetes are difficult to Gram-stain. Examples include, Members of the phylum Spirochaetes Leptospira species, which cause leptospirosis, examples include, Vibrio cholerae, a marine bacterium that causes cholera Vibrio fluvialis, a marine bacterium that causes another infectious diarrhea
2.
Gram stain
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Gram staining or Gram stain, also called Grams method, is a method of staining used to differentiate bacterial species into two large groups. The name comes from the Danish bacteriologist Hans Christian Gram, who developed the technique, Gram staining differentiates bacteria by the chemical and physical properties of their cell walls by detecting peptidoglycan, which is present in the cell wall of Gram-positive bacteria. Both Gram-positive bacteria and Gram-negative bacteria pick up the counterstain, the counterstain, however, is unseen on Gram-positive bacteria because of the darker crystal violet stain. The Gram stain is almost always the first step in the identification of a bacterial organism. While Gram staining is a diagnostic tool in both clinical and research settings, not all bacteria can be definitively classified by this technique. This gives rise to gram-variable and gram-indeterminate groups, the method is named after its inventor, the Danish scientist Hans Christian Gram, who developed the technique while working with Carl Friedländer in the morgue of the city hospital in Berlin in 1884. Gram devised his technique not for the purpose of distinguishing one type of bacterium from another and he published his method in 1884, and included in his short report the observation that the typhus bacillus did not retain the stain. Gram staining is a laboratory technique used to differentiate bacterial species into two large groups based on the physical properties of their cell walls. Gram staining is not used to classify archaea, formerly archaeabacteria, the Gram stain is not an infallible tool for diagnosis, identification, or phylogeny, and it is of extremely limited use in environmental microbiology. It is used mainly to make a preliminary morphologic identification or to establish that there are significant numbers of bacteria in a clinical specimen. It cannot identify bacteria to the level, and for most medical conditions. In clinical microbiology laboratories, it is used in combination with other traditional, some organisms are gram-variable, some are not stained with either dye used in the Gram technique and are not seen. Gram staining has been suggested to be as effective a tool as PCR in one primary research report regarding gonococcal urethritis. Gram stains are performed on body fluid or biopsy when infection is suspected, there are four basic steps of the Gram stain, Applying a primary stain to a heat-fixed smear of a bacterial culture. Carbol fuchsin is sometimes substituted for safranin since it more intensely stains anaerobic bacteria, crystal violet dissociates in aqueous solutions into CV+ and chloride ions. These ions penetrate through the wall and cell membrane of both gram-positive and gram-negative cells. The CV+ ion interacts with negatively charged components of bacterial cells, iodide interacts with CV+ and forms large complexes of crystal violet and iodine within the inner and outer layers of the cell. Iodine is often referred to as a mordant, but is an agent that prevents the removal of the CV–I complex and, therefore
3.
Treponema pallidum
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Treponema pallidum is a spirochaete bacterium with subspecies that cause treponemal diseases such as syphilis, bejel, pinta, and yaws. The treponemes have a cytoplasmic and an outer membrane, using light microscopy, treponemes are visible only by using dark field illumination. They are Gram negative, but some regard them as too thin to be Gram stained, the cause of pinta is sometimes described as Treponema carateum, rather than a subspecies of T. pallidum, even when the subspecies convention is used for the other agents. This bacterium can be detected with special stains, such as the Dieterle stain, T. pallidum is also detected by serology, including nontreponemal VDRL, rapid plasma reagin, and treponemal antibody tests, T. pallidum immobilization reaction, and syphilis TPHA test). The organism can also be transmitted to a fetus by transplacental passage during the stages of pregnancy. The helical structure of T. p. pallidum allows it to move in a motion through mucous membranes or enter minuscule breaks in the skin. In women the initial lesion is usually on the labia, the walls of the vagina, or the cervix and it gains access to the hosts blood and lymph systems through tissue and mucous membranes. The genome of T. pallidum was sequenced in 1998, the recent sequencing of the genomes of several spirochetes permits a thorough analysis of the similarities and differences within this bacterial phylum. The shape of T. pallidum is flat and wavy, unlike the other spirochetes, no vaccine for syphilis is available as of 2015. The outer membrane of T. pallidum has too few surface proteins for an antibody to be effective, epidemic cycles driven by host behaviour. Journal of the Royal Society Interface, centers for Disease Control and Prevention. Centers for Disease Control and Prevention
4.
Taxonomy (biology)
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Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. The exact definition of taxonomy varies from source to source, but the core of the remains, the conception, naming. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, the broadest meaning of taxonomy is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique, the term alpha taxonomy is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, ideals can, it may be said, never be completely realized. They have, however, a value of acting as permanent stimulants. Some of us please ourselves by thinking we are now groping in a beta taxonomy, turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy, thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. This activity is what the term denotes, it is also referred to as beta taxonomy. How species should be defined in a group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy, by extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in scientific thinking. Early taxonomy was based on criteria, the so-called artificial systems. Later came systems based on a complete consideration of the characteristics of taxa, referred to as natural systems, such as those of de Jussieu, de Candolle and Bentham. The publication of Charles Darwins Origin of Species led to new ways of thinking about classification based on evolutionary relationships and this was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler and Engler, the advent of molecular genetics and statistical methodology allowed the creation of the modern era of phylogenetic systems based on cladistics, rather than morphology alone. Taxonomy has been called the worlds oldest profession, and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate
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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.
Spirochaete
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A spirochaete or spirochete is a member of the phylum Spirochaetes, which contains distinctive diderm bacteria, most of which have long, helically coiled cells. Spirochaetes stain gram-negative and are chemoheterotrophic in nature, with lengths between 3 and 500 µm and diameters around 0.09 to at least 3 µm and these cause a twisting motion which allows the spirochaete to move about. When reproducing, a spirochaete will undergo asexual transverse binary fission, most spirochaetes are free-living and anaerobic, but there are numerous exceptions. Spirochaetes bacteria are diverse in their capacity, the ecological niches that they inhabit, as well as molecular characteristics including GC content. Many organisms within the Spirochaetes phylum are causative agents of prevalent diseases, Brachyspira pilosicoli and Brachyspira aalborgi, which cause intestinal spirochaetosis Spirochetes may also cause dementia and may be involved in the pathogenesis of Alzheimers disease. Salvarsan, the first partially organic synthetic antimicrobial drug in history, was effective against spirochaetes only and was primarily used to cure syphilis. The class currently consists of 14 validly named genera across 4 orders and 5 families, the orders Brachyspirales, Brevinematales and Leptospirales each contain a single family, Brachyspiraceae, Brevinemataceae and Leptospiraceae, respectively. The Spirochaetales order harbours two families, Spirochaetaceae and Borreliaceae, additional CSIs have been found exclusively shared by each family within the Spirochaetales. These molecular markers are in agreement with the phylogenetic tree branching of two monophyletic clades within the Spirochaetales order. A conserved signature indel has also found exclusively shared by all Spirochaetes species. This CSI is a 3 amino acid insert in the basal body rod protein FlgC which is an important part of the unique endoflagellar structure shared by Spirochaetes species. Given that the CSI is exclusively shared by members within this phylum, historically, the all families belonging to the Spirochaetes phylum were assigned to a single order, the Spirochaetales. These synapomorphic characteristics justify the phylogenetic divisions and are a means to identify each order/family within the phylum, the phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature, phylum Spirochaetes Garrity & Holt 2001 Class Spirochaetae Cavalier-Smith 2002 Order Leptospirales Gupta et al.2014 Family Leptospiraceae Hovind-Hougen 1979 emend. Levett et al.2005 Genus Leptonema Hovind-Hougen 1983 Genus Leptospira Noguchi 1917 emend, faine and Stallman 1982 Genus Turneriella Levett et al.2005 Order Brachyspirales corrig. Gupta et al.2013 Genus Exilispira Imachi et al.2008 Family Borreliaceae Gupta et al.2014 Genus Borreliella Adeolu & Gupta 2015 Genus Borrelia Swellengrebel 1907 emend. Pikuta et al.2009 Genus Treponema Schaudinn 1905 emend Abt et al.2013 Notes, ♦ Type strain lost or not available ♪ Prokaryotes where no pure cultures are isolated or available, i
7.
Synonym (taxonomy)
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For example, Linnaeus was the first to give a scientific name to the Norway spruce, which he called Pinus abies. This name is no longer in use, it is now a synonym of the current scientific name which is Picea abies, unlike synonyms in other contexts, in taxonomy a synonym is not interchangeable with the name of which it is a synonym. In taxonomy, synonyms are not equals, but have a different status, for any taxon with a particular circumscription, position, and rank, only one scientific name is considered to be the correct one at any given time. A synonym cannot exist in isolation, it is always an alternative to a different scientific name, given that the correct name of a taxon depends on the taxonomic viewpoint used a name that is one taxonomists synonym may be another taxonomists correct name. Synonyms may arise whenever the same taxon is described and named more than once, independently. They may also arise when existing taxa are changed, as when two taxa are joined to one, a species is moved to a different genus. To the general user of scientific names, in such as agriculture, horticulture, ecology, general science. A synonym is a name that was used as the correct scientific name but which has been displaced by another scientific name. Thus Oxford Dictionaries Online defines the term as a name which has the same application as another. In handbooks and general texts, it is useful to have mentioned as such after the current scientific name. Synonyms used in this way may not always meet the strict definitions of the synonym in the formal rules of nomenclature which govern scientific names. Changes of scientific name have two causes, they may be taxonomic or nomenclatural, a name change may be caused by changes in the circumscription, position or rank of a taxon, representing a change in taxonomic, scientific insight. A name change may be due to purely nomenclatural reasons, that is, based on the rules of nomenclature, the earliest such name is called the senior synonym, while the later name is the junior synonym. One basic principle of zoological nomenclature is that the earliest correctly published name, synonyms are important because if the earliest name cannot be used, then the next available junior synonym must be used for the taxon. Objective synonyms refer to taxa with the type and same rank. For example, John Edward Gray published the name Antilocapra anteflexa in 1855 for a species of pronghorn, however, it is now commonly accepted that his specimen was an unusual individual of the species Antilocapra americana published by George Ord in 1815. Ords name thus takes precedence, with Antilocapra anteflexa being a subjective synonym. Objective synonyms are common at the level of genera, because for various reasons two genera may contain the type species, these are objective synonyms
8.
American and British English spelling differences
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Many of the differences between American and British English date back to a time when spelling standards had not yet developed. For instance, some spellings seen as American today were once used in Britain. But English-language spelling reform has rarely been adopted otherwise, and thus modern English orthography varies somewhat between countries and is far from phonemic in any country, in the early 18th century, English spelling was inconsistent. These differences became noticeable after the publishing of influential dictionaries, todays British English spellings mostly follow Johnsons A Dictionary of the English Language, while many American English spellings follow Websters An American Dictionary of the English Language. Webster was a proponent of English spelling reform for reasons both philological and nationalistic, in A Companion to the American Revolution, John Algeo notes, it is often assumed that characteristically American spellings were invented by Noah Webster. He was very influential in popularizing certain spellings in America, rather he chose already existing options such as center, color and check for the simplicity, analogy or etymology. William Shakespeares first folios, for example, used spellings like center and color as much as centre, Webster did attempt to introduce some reformed spellings, as did the Simplified Spelling Board in the early 20th century, but most were not adopted. In Britain, the influence of those who preferred the Norman spellings of words proved to be decisive, later spelling adjustments in the United Kingdom had little effect on todays American spellings and vice versa. For the most part, the systems of most Commonwealth countries. Australian spelling has also strayed slightly from British spelling, with some American spellings incorporated as standard, New Zealand spelling is almost identical to British spelling, except in the word fiord. There is also an increasing use of macrons in words that originated in Māori, most words ending in an unstressed -our in British English end in -or in American English. Wherever the vowel is unreduced in pronunciation, e. g. contour, velour, paramour and troubadour the spelling is the same everywhere, most words of this kind came from Latin, where the ending was spelled -or. They were first adopted into English from early Old French, after the Norman conquest of England, the ending became -our to match the Old French spelling. The -our ending was not only used in new English borrowings, however, -or was still sometimes found, and the first three folios of Shakespeares plays used both spellings before they were standardised to -our in the Fourth Folio of 1685. After the Renaissance, new borrowings from Latin were taken up with their original -or ending, Websters 1828 dictionary had only -or and is given much of the credit for the adoption of this form in the United States. Johnson, unlike Webster, was not an advocate of spelling reform and he preferred French over Latin spellings because, as he put it, the French generally supplied us. In Jeffersons original draft it is spelled honour, Honor and honour were equally frequent in Britain until the 17th century, honor still is, in the UK, the usual spelling as a persons name and appears in Honor Oak, a district of London. In derivatives and inflected forms of the words, British usage depends on the nature of the suffix used
9.
Phylum (biology)
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In biology, a phylum is a taxonomic rank below kingdom and above class. Traditionally, in botany the term division was used instead of phylum, although from 1993 the International Code of Nomenclature for algae, fungi, depending on definitions, the kingdom Animalia contains approximately 35 phyla, Plantae contains about 12, and Fungi contains around 7. Current research in phylogenetics is uncovering the relationships between phyla, which are contained in larger clades, like Ecdysozoa and Embryophyta, the definitions of zoological phyla have changed from their origins in the six Linnaean classes and the four embranchements of Georges Cuvier. Haeckel introduced the term phylum, based on the Greek word phylon, in plant taxonomy, Eichler classified plants into five groups, named divisions. Informally, phyla can be thought of as grouping organisms based on general specialization of body plan, the most important objective measure in the above definitions is the certain degree—how unrelated do organisms need to be to be members of different phyla. The minimal requirement is that all organisms in a phylum should be more closely related to one another than to any other group. So phyla can be merged or split if it becomes apparent that they are related to one another or not, a definition of a phylum based on body plan has been proposed by paleontologists Graham Budd and Sören Jensen. By Budd and Jensens definition, a phylum is defined by a set of shared by all its living representatives. This approach brings some small problems—for instance, ancestral characters common to most members of a phylum may have been lost by some members, also, this definition is based on an arbitrary point of time, the present. However, as it is based, it is easy to apply to the fossil record. A greater problem is that it relies on a decision about which groups of organisms should be considered as phyla. However, proving that a fossil belongs to the group of a phylum is difficult. Furthermore, organisms in the group of a phylum can possess the body plan of the phylum without all the characteristics necessary to fall within it. This weakens the idea that each of the phyla represents a body plan. A classification using this definition may be affected by the chance survival of rare groups. Representatives of many modern phyla did not appear until long after the Cambrian, the kingdom Plantae is defined in various ways by different biologists. All definitions include the living embryophytes, to which may be added the two green algae divisions, Chlorophyta and Charophyta, to form the clade Viridiplantae. The table below follows the influential Cavalier-Smith system in equating Plantae with Archaeplastida, a group containing Viridiplantae, the definition and classification of plants at the division level also varies from source to source, and has changed progressively in recent years
10.
Gram-negative bacteria
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Gram-negative bacteria are a group of bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane. Gram-negative bacteria are spread worldwide, in all environments that support life. Several classes of antibiotics target gram-negative bacteria specifically, including aminoglycosides, historically, the kingdom Monera was divided into four divisions based on Gram staining, Firmacutes, Gracillicutes, Mollicutes and Mendocutes. Since 1987, the monophyly of the bacteria has been disproven with molecular studies. However some authors, such as Cavalier-Smith still treat them as a monophyletic taxon, bacteria are traditionally divided into the two groups, gram-positive and gram-negative, based on their Gram stain retention. These groups are thought of as lineages, with gram-negative bacteria more closely related to one another than to gram-positive bacteria. While this is true, the classification system breaks down in some cases. A given bacterias Gram stain result, bacterial membrane organization, as such, the Gram stain cannot be reliably used to assess familial relationships of bacteria. That said, Gram staining does often give information about the composition of the cell membrane. Of these two distinct groups of prokaryotic organisms, monoderm prokaryotes are indicated to be ancestral. In addition, a number of taxa that are either part of the phylum Firmicutes or branches in its proximity are also found to possess a diderm cell structure. Other notable groups of bacteria include the cyanobacteria, spirochaetes, green sulfur. Medically relevant gram-negative cocci include the four types that cause a sexually transmitted disease, a meningitis, medically relevant gram-negative bacilli include a multitude of species. Some of them cause primarily respiratory problems, primarily urinary problems, 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. One of the unique characteristics of gram-negative bacteria is the structure of the bacterial outer membrane. The outer leaflet of this comprises a complex lipopolysaccharide whose lipid portion acts as an endotoxin
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Chemoheterotroph
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Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environments. These molecules can be organic or inorganic, the chemotroph designation is in contrast to phototrophs, which utilize solar energy. Chemotrophs can be either autotrophic or heterotrophic, chemotrophs are commonly found in ocean floors where sunlight cannot reach them because they are not dependent on solar energy. Ocean floors often contain underwater volcanos that can provide heat to substitute sunlight for warmth, originally used with a different meaning, the term took its current definition after Lwoff and collaborators. Chemoautotrophs, in addition to deriving energy from chemical reactions, synthesize all necessary organic compounds from carbon dioxide, chemoautotrophs use inorganic energy sources, such as hydrogen sulfide, elemental sulfur, ferrous iron, and also molecular hydrogen, and ammonia. Most are bacteria or archaea that live in environments such as deep sea vents and are the primary producers in such ecosystems. Chemoautotrophs generally fall into groups, methanogens, halophiles, sulfur oxidizers and reducers, nitrifiers, anammox bacteria. An example of one of these prokaryotes would be Sulfolobus, chemolithotrophic growth can be dramatically fast, such as Thiomicrospira crunogena with a doubling time around one hour. Later, the term would also the chemoorganoautotrophy, that is. Chemoheterotrophs are unable to fix carbon to form their own organic compounds, in the deep oceans, iron-oxidizing bacteria derive their energy needs by oxidizing iron to iron. The extra electron obtained from this powers the cells, replacing or augmenting traditional phototrophism. In general, iron-oxidizing bacteria can exist only in areas with high iron concentrations, most of the ocean is devoid of iron, due to both the oxidative effect of dissolved oxygen in the water and the tendency of prokaryotes to take up the iron. Lava beds supply bacteria with iron straight from the Earths mantle, in addition, because oxygen is necessary for the reaction, these bacteria are much more common in the upper ocean, where oxygen is more abundant. What is still unknown is how exactly iron bacteria extract iron from rock and it is accepted that some mechanism exists that eats away at the rock, perhaps through specialized enzymes or compounds that bring more FeO to the surface. It has been debated about how much of the weathering of the rock is due to biotic components. Hydrothermal vents also release large quantities of dissolved iron into the deep ocean, in addition, the high thermal gradient around vent systems means a wide variety of bacteria can coexist, each with its own specialized temperature niche. Manganese-oxidizing bacteria also use of igneous lava rocks in much the same way. Manganese is much rarer than iron in oceanic crust, but is easier for bacteria to extract from igneous glass
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Flagellum
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A flagellum is a lash-like appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells. The word flagellum in Latin means whip, the primary role of the flagellum is locomotion, but it also often has function as a sensory organelle, being sensitive to chemicals and temperatures outside the cell. Flagella are organelles defined by function rather than structure, large differences occur between different types of flagella, the prokaryotic and eukaryotic flagella differ greatly in protein composition, structure, and mechanism of propulsion. However, both can be used for swimming, an example of a flagellated bacterium is the ulcer-causing Helicobacter pylori, which uses multiple flagella to propel itself through the mucus lining to reach the stomach epithelium. An example of a eukaryotic cell is the mammalian sperm cell. Eukaryotic flagella are structurally identical to eukaryotic cilia, although distinctions are made according to function and/or length. Fimbriae and pili are also thin appendages, but have different functions and are usually smaller, three types of flagella have so far been distinguished, bacterial, archaeal, and eukaryotic. The main differences among these three types are, Bacterial flagella are helical filaments, each with a motor at its base which can turn clockwise or counterclockwise. They provide two of several kinds of bacterial motility, archaeal flagella are superficially similar to bacterial flagella, but are different in many details and considered non-homologous. Eukaryotic flagella—those of animal, plant, and protist cells—are complex cellular projections that lash back, eukaryotic flagella are classed along with eukaryotic motile cilia as undulipodia to emphasize their distinctive wavy appendage role in cellular function or motility. Primary cilia are immotile, and are not undulipodia, they have a structurally different 9+0 axoneme rather than the 9+2 axoneme found in both flagella and motile cilia undulipodia, the bacterial flagellum is made up of the protein flagellin. Its shape is a 20-nanometer-thick hollow tube and it is helical and has a sharp bend just outside the outer membrane, this hook allows the axis of the helix to point directly away from the cell. A shaft runs between the hook and the body, passing through protein rings in the cells membrane that act as bearings. Gram-positive organisms have two of these basal body rings, one in the layer and one in the plasma membrane. The filament ends with a capping protein, the flagellar filament is the long, helical screw that propels the bacterium when rotated by the motor, through the hook. Each protofilament is a series of protein chains. However, Campylobacter jejuni has seven protofilaments, the basal body has several traits in common with some types of secretory pores, such as the hollow, rod-like plug in their centers extending out through the plasma membrane. The bacterial flagellum is driven by an engine made up of protein
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Bacterial outer membrane
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The bacterial outer membrane is found in gram-negative bacteria. Coli it is linked to the cells peptidoglycan by Brauns lipoprotein, porins can be found in this layer. If lipid A, part of the LPS, enters the system it causes a toxic reaction by activating TLR4. Lipid A is very pathogenic and not immunogenic, however, the polysaccharide component is very immunogenic, but not pathogenic, causing an aggressive response by the immune system. The sufferer will have a temperature and respiration rate and a low blood pressure. This may lead to shock, which may be fatal. The machinery and the source that drive this process are not yet fully understood. O-antigen repeat units are then polymerised in the periplasm by the Wzy polymerase, the LPS transport machinery is composed of LptA, LptB, LptC, LptD, LptE. This supported by the fact that depletion of any one of these blocks the LPS assembly pathway. Moreover, the location of at least one of five proteins in every cellular compartment suggests a model for how the LPS assembly pathway is organised and ordered in space. LptC is required for the translocation of lipopolysaccharide from the membrane to the outer membrane. LptE forms a complex with LptD, which is involved in the assembly of LPS in the leaflet of the outer membrane and is essential for envelope biogenesis
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Periplasm
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The periplasm is a concentrated gel-like matrix in the space between the inner cytoplasmic membrane and the bacterial outer membrane called the periplasmic space in gram-negative bacteria. It has been found using cryo-electron microscopy, that a much smaller periplasmic space is present in gram-positive bacteria, the periplasm may constitute up to 40% of the total cell volume of gram-negative bacteria, and this is a much smaller percentage in gram-positive bacteria. These bacteria are distinguished from each other based on the presence or absence of a lipid membrane. All gram-positive bacteria are bounded by a single unit lipid membrane, for the bacterial cells that are bounded by a single cell membrane the term monoderm bacteria or monoderm prokaryotes has been proposed. The presence of inner and outer cell membranes forms and define the periplasmic space or periplasmic compartment. These bacterial cells with two membranes have been designated as diderm bacteria, the distinction between the monoderm and diderm prokaryotes is supported by conserved signature indels in a number of important proteins. In diderm bacteria, the contains a thin cell wall composed of peptidoglycan. Importantly, the periplasm is devoid of ATP, D. White, The Physiology and Biochemistry of Prokaryotes, Oxford University Press, Oxford,2000, pp.22
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Fission (biology)
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In biology, fission is the division of a single entity into two or more parts and the regeneration of those parts into separate entities resembling the original. The object experiencing fission is usually a cell, but the term may refer to how organisms, bodies, populations. The fission may be binary fission, in which a single entity produces two parts, or multiple fission, in which a single entity produces multiple parts, organisms in the domains of Archaea and Bacteria reproduce with binary fission. This form of reproduction and cell division is also used by some organelles within eukaryotic organisms. Binary fission results in the reproduction of a prokaryotic cell by dividing the cell into two parts, each with the potential to grow to the size of the original. Unlike the process of mitosis used by cells, binary fission takes place without the formation of a spindle apparatus in the cell. The single DNA molecule first replicates, then attaches each copy to a different part of the cell membrane, when the cell begins to pull apart, the replicated and original chromosomes are separated. The consequence of this method of reproduction is that all the cells are genetically identical. The process of fission in bacteria involves the following steps. First, the cells DNA is replicated, the replicated DNA copies then move to opposite poles of the cell in an energy-dependent process. Then, the plate of the cell constricts and separates the plasma membrane such that each new cell has exactly the same genetic material. More specifically, the following occur, The bacterium before binary fission is when the DNA is tightly coiled. The DNA of the bacterium has uncoiled and duplicated, the DNA is pulled to the separate poles of the bacterium as it increases size to prepare for splitting. The growth of a new cell wall begins to separate the bacterium, the new cell wall fully develops, resulting in the complete split of the bacterium. The new daughter cells have tightly coiled DNA rods, ribosomes, and plasmids, binary fission is generally rapid though its speed varies between species. For E. coli, cells typically divide about every 20 minutes at 37 °C and this time period can therefore be referred to as the doubling time. Some species other than E. coli may have faster or slower doubling times, some organelles in eukaryotic cells reproduce using binary fission. Mitochondrial fission occurs frequently within the cell, even when the cell is not actively undergoing mitosis, binary fission in organisms can occur in four ways, irregular, longitudinal, transverse, oblique
16.
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. )
17.
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%
18.
Leptospira
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Leptospira is a genus of spirochaete bacteria, including a small number of pathogenic and saprophytic species. Leptospira was first observed in 1907 in kidney tissue slices of a victim who was described as having died of yellow fever. Leptospira, together with the genera Leptonema and Turneria, is a member of the family Leptospiraceae, the genus Leptospira is divided into 20 species based on DNA hybridization studies. Pathogenic Leptospira Leptospira alstoni Smythe et al.2013 Leptospira interrogans Wenyon 1926 emend, there are currently over 200 recognized serovars. A few serovars are found in more than one species of Leptospira, at its 2002 meeting, the Committee on the Taxonomy of Leptospira of the International Union of Microbiological Societies approved the following nomenclature for serovars of Leptospira. Genus and species must of course be italicized, with the name not italicized. Although over 200 serotypes of Leptospira have been described, all members of the genus have similar morphology, Leptospira are spiral-shaped bacteria that are 6-20 μm long and 0.1 μm in diameter with a wavelength of about 0.5 μm. One or both ends of the spirochete are usually hooked, because they are so thin, live Leptospira are best observed by darkfield microscopy. The bacteria have a number of degrees of freedom, when ready to proliferate via binary fission, Leptospira have a Gram-negative-like cell envelope consisting of a cytoplasmic and outer membrane. However, the layer is associated with the cytoplasmic rather than the outer membrane. The two flagella of Leptospira extend from the membrane at the ends of the bacteria into the periplasmic space and are necessary for the motility of Leptospira. The outer membrane contains a variety of lipoproteins and transmembrane outer membrane proteins, as expected, the protein composition of the outer membrane differs when comparing Leptospira growing in artificial medium with Leptospira present in an infected animal. Several leptospiral outer membrane proteins have shown to attach to the host extracellular matrix. These proteins may be important for adhesion of Leptospira to host tissues and in resisting complement, the outer membrane of Leptospira, like those of most other Gram-negative bacteria, contains lipopolysaccharide. Differences in the highly immunogenic LPS structure account for the numerous serovars of Leptospira, leptospiral LPS has low endotoxin activity. An unusual feature of leptospiral LPS is that it activates host cells via TLR2 rather than TLR4, the unique structure of the lipid A portion of the LPS molecule may account for this observation. Finally, the LPS O antigen content of L. interrogans differs in an acutely infected versus a chronically infected animal, the role of O antigen changes in the establishment or maintenance of acute or chronic infection, if any, is unknown. Leptospira, both pathogenic and saprophytic, can occupy diverse environments, habitats and life cycles, these bacteria are found throughout the world, except in Antarctica
19.
Borrelia burgdorferi
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Borrelia burgdorferi is a bacterial species of the spirochete class of the genus Borrelia. B. burgdorferi exists in North America and Europe and is the predominant causative agent of Lyme disease in the United States, Borrelia species are considered diderm bacteria rather than Gram-positive or negative. Borrelia burgdorferi is named after the researcher Willy Burgdorfer, who first isolated the bacterium in 1982, B. burgdorferi resembles other spirochetes in that it has an outer membrane and inner membrane with a thin layer of peptidoglycan in between. However, the outer membrane lacks lipopolysaccharide and its shape is a flat wave. It is about 0.3 μm wide and 5 to 20 μm in length, B. B. burgdorferi is a slow-growing microaerophilic spirochete with a doubling time of 24 to 48 hours. B. burgdorferi circulates between Ixodes ticks and a vertebrate host in an enzootic cycle, B. burgdorferi living in a tick cannot be passed to its offspring. Therefore, tick larvae must feed on the blood of an animal to acquire B. burgdorferi. The spirochetes survive as the larvae molts into a nymph and persist in the nutrient-poor midgut as the nymph overwinters, infected nymphs then transmit B. burgdorferi by feeding on another vertebrate to complete the cycle. Ticks can transmit B. burgdorferi to humans, but humans are dead-end hosts, nymphs molt into adult ticks, which usually feed on larger mammals that are not able to support the survival of B. burgdorferi. Lyme disease is a zoonotic, vector-borne disease transmitted by the Ixodes tick, the infected nymphal tick transmits B. burgdorferi via its saliva to the human during its blood meal. B. burgdorferi is truly associated with PCBCL, then there is wide geographic variability, progression of the disease follows from 3 stages. Stage 1 affects the area around the bite, with a rash or swelling possible, stage 2 occurs weeks to months after, if left untreated, the bacteria spread through the body and affect the heart, bones, and nervous system. Stage 3 occurs years after and chronic arthritis and neurological complications develop, anaplasmosis and babesiosis are also common tick borne pathogens that infect humans similarly to Borrelia burgdorferi. Consequently, it is possible for an Ixodes tick to coinfect a host with two or all other diseases. In addition, they tend to acquire a range of secondary symptoms. More studies and research must be done to determine the effect of co-infection. So far, there are three factors that may contribute to the severity of the manifestation of Lyme Disease. The presence of ribosomal spacers, plasmids, and the surface protein C are indicators of the severity of the infection
20.
Intestinal spirochetosis
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Intestinal spirochetosis, also intestinal spirochetes, colonic spirochetosis and colonic spirochetes, is an infection of the colonic-type mucosa with spirochete microorganisms. No clear association exists with complaints, however, potential associations exist with include watery diarrhea and abdominal pain, which may be seen with blood, these findings are not specific, i. e. may be seen due to number of other causes. Human intestinal spirochetosis is caused by Brachyspira pilosicoli and Brachyspira aalborgi, porcine and avian intestinal spirochetosis are caused by Brachyspira pilosicoli. It is diagnosed by examination of tissue, i. e. biopsy
21.
Arsphenamine
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This organoarsenic compound was the first modern chemotherapeutic agent. Arsphenamine was first synthesized in 1907 in Paul Ehrlichs lab by Alfred Bertheim, the antisyphilitic activity of this compound was discovered by Sahachiro Hata in 1909, during a survey of hundreds of newly synthesized organic arsenical compounds. Ehrlich had theorized that by screening many compounds, a drug could be discovered that would have anti-microbial activity, Ehrlichs team began their search for such a magic bullet among chemical derivatives of the dangerously toxic drug atoxyl. Arsphenamine was used to treat the disease syphilis because it is toxic to the bacterium Treponema pallidum, arsphenamine was originally called 606 because it was the sixth in the sixth group of compounds synthesized for testing, it was marketed by Hoechst AG under the trade name Salvarsan in 1910. Salvarsan was the first organic antisyphilitic, and an improvement over the inorganic mercury compounds that had been used previously. It was distributed as a yellow, crystalline, hygroscopic powder that was highly unstable in air, some of the side effects attributed to Salvarsan, including rashes, liver damage, and risks of life and limb, were thought to be caused by improper handling and administration. This caused Ehrlich, who worked assiduously to standardize practices, to observe, Ehrlichs laboratory developed a more soluble arsenical compound, Neosalvarsan, which was easier to prepare, and it became available in 1912. Less severe side-effects such as nausea and vomiting were still common, an additional problem was that both Salvarsan and Neosalvarsan had to be stored in sealed vials under a nitrogen atmosphere to prevent oxidation. These arsenical compounds were supplanted as treatments for syphilis in the 1940s by penicillin, after leaving Ehrlichs laboratory, Hata continued parallel investigation of the new medicines in Japan. Salvarsan has long assumed to have an As=As double bond. However, in 2005, an extensive mass spectral analysis Salvarsan was shown to have As-As single bonds, the drug was also found to be a mixture consisting of cyclo-As3 and cyclo-As5 species. Dr. Ehrlichs Magic Bullet,1940 film about Ehrlichs quest to find a cure for syphilis
22.
Antimicrobial drug
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An antimicrobial is an agent that kills microorganisms or stop their growth. Antimicrobial medicines can be grouped according to the microorganisms they act primarily against, for example, antibiotics are used against bacteria and antifungals are used against fungi. They can also be classified according to their function, agents that kill microbes are called microbicidal, while those that merely inhibit their growth are called biostatic. The use of medicines to treat infection is known as antimicrobial chemotherapy. The main classes of agents are disinfectants, which kill a wide range of microbes on non-living surfaces to prevent the spread of illness, antiseptics. The term antibiotic originally described only those formulations derived from living organisms but is now applied to synthetic antimicrobials, such as the sulphonamides. The term also used to be restricted to antibacterials, but its context has broadened to include all antimicrobials, antibacterial agents can be further subdivided into bactericidal agents, which kill bacteria, and bacteriostatic agents, which slow down or stall bacterial growth. In response, further advancements in technologies have resulted in solutions that can go beyond simply inhibiting microbial growth. Instead, certain types of media have been developed to kill microbes on contact. Use of substances with antimicrobial properties is known to have been common practice for at least 2000 years, ancient Egyptians and ancient Greeks used specific molds and plant extracts to treat infection. More recently, microbiologists such as Louis Pasteur and Jules Francois Joubert observed antagonism between some bacteria and discussed the merits of controlling these interactions in medicine, in 1928, Alexander Fleming became the first to discover a natural antimicrobial fungus known as Penicillium rubens. The substance extracted from the fungus he named penicillin and in 1942 it was used to treat a Streptococcus infection. Penicillin also proved successful in the treatment of other infectious diseases such as gonorrhea, strep throat and pneumonia. Many antimicrobial agents exist, for use against a range of infectious diseases. Antibacterials are used to treat bacterial infections, the toxicity to humans and other animals from antibacterials is generally considered low. However, prolonged use of certain antibacterials can decrease the number of gut flora, after prolonged antibacterial use consumption of probiotics and reasonable eating can help to replace destroyed gut flora. Stool transplants may be considered for patients who are having difficulty recovering from prolonged antibiotic treatment, the discovery, development and clinical use of antibacterials during the 20th century has substantially reduced mortality from bacterial infections. However, since 1980 the introduction of new agents for clinical use has declined
23.
Conserved signature indels
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Conserved signature inserts and deletions in protein sequences provide an important category of molecular markers for understanding phylogenetic relationships. While indels can be arbitrary inserts or deletions, CSIs are defined as only those protein indels that are present within conserved regions of the protein, the CSIs that are restricted to a particular clade or group of species, generally provide good phylogenetic markers of common evolutionary descent. Due to the rarity and highly specific nature of such changes, other confounding factors such as differences in evolutionary rates at different sites or among different species also generally do not affect the interpretation of a CSI. Most CSIs that have identified have been found to exhibit high predictive value. Therefore, based upon their presence or absence, it should be possible to both known and even previously unknown species belonging to these groups in different environments. Group specific CSIs are commonly shared by different species belonging to a particular Taxon and these CSIs were most likely introduced in an ancestor of the group of species before the members of the taxa diverged. They provide molecular means for distinguishing members of a taxon from all other organisms. Figure 1 shows an example of 5aa CSI found in all species belonging to the taxon X and this is a distinctive characteristic of this taxon as it is not found in any other species. This signature was introduced in a common ancestor of the species from this taxon. Similarly other group-specific signatures could be shared by either A1 and A2 or B1 and B2, etc. or even by X1 and X2 or by X3 and X4, etc. The groups A, B, C, D and X, group specific CSIs have been used in the past to determine the phylogenetic relationship of a number of bacterial phyla and subgroups within it. For example a 3 amino acid insert was uniquely shared by members of the phylum Thermotogae in the essential 50S ribosomal protein L7/L12 and this is not present in any other bacteria species and could be used to characterize members of the phylum Thermotogae from all other bacteria. Group specific CSIs were also used to characterize subgroups within the phylum Thermotogae, main-line CSIs are those in which a conserved insert or deletion is shared by several major phyla, but absent from other phyla. Figure 2 shows an example of 5aa CSI found in a region that is commonly present in the species belonging to phyla X, Y and Z. This signature indicates a relationship of taxa X, Y and Z. Main-line CSIs have been used in the past to determine the relationship of a number of bacterial phyla. The large CSI of about 150-180 amino acids within a region of Gyrase B, is commonly shared between various Proteobacteria, Chlamydiales, Planctomycetes and Aquificales species. This CSI is absent in other bacterial phyla as well as Archaea
24.
Basal body
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A basal body is a protein structure found at the base of a eukaryotic undulipodium. It is formed from a centriole and several additional structures, and is, essentially. Basal body serves as a site for the growth of the axoneme microtubules. Centrioles, from which bodies are derived, act as anchoring sites for proteins that in turn anchor microtubules. These microtubules provide structure and facilitate movement of vesicles and organelles within eukaryotic cells. Cilia and basal bodies form during quiescence or the G1 phase of the cell cycle, before the cell enters G1 phase, i. e. before the formation of the cilium, the mother centriole serves as a component of the centrosome. In cells that are destined to have one primary cilium mother centriole differentiates into the basal body upon entry into G1 or quiescence. Thus, basal body in such cell is derived from the centriole, basal body differs from the mother centriole in at least 2 aspects. First, basal bodies have basal feet, which are anchored to cytoplasmic microtubules and are necessary for polarized alignment of the cilium, second, basal bodies have pinwheel-shaped transition fibers that originate from the appendages of mother centriole. In multiciliated cells, however, in many cases basal bodies are not made from centrioles but are generated de novo from a protein structure called the deuterosome. During cell cycle quiescence, basal bodies organize primary cilia and reside at the cortex in proximity to plasma membrane. On cell cycle entry, cilia resorb and the basal body migrates to the nucleus where it functions to organize centrosomes, centrioles, basal bodies, and cilia are important for mitosis, polarity, cell division, protein trafficking, signaling, motility, and sensation. Mutations affecting basal bodies are associated with human diseases, most notably Bardet–Biedl syndrome. Regulation of basal body production and spatial orientation is a function of the domain of γ-tubulin. Plants lack centrioles and only lower plants with motile sperm have flagella, Histology image, 21804loa – Histology Learning System at Boston University - Ultrastructure of the Cell, ciliated epithelium, cilia and basal bodies
25.
Synapomorphy
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In phylogenetics, apomorphy and synapomorphy refer to derived characteristic of a clade. Apomorphy implies a characteristic that is different from the form of an ancestor, i. e. an innovation, synapomorphy is a shared derived character or trait state that distinguishes a clade from other organisms. In other words, it is an apomorphy shared by members of a monophyletic group, and thus assumed to be present in their most recent common ancestor. The word synapomorphy, coined by German entomologist Willi Hennig, is derived from the Greek words σύν, syn = shared, ἀπό, apo = away from, a derived character is a character that is derived from an ancestral character over evolutionary history. Derived characters are used in determining phylogenetic relationships, the concept of synapomorphy is relative to a given clade in the tree of life. What counts as a synapomorphy for one clade may well be a character or plesiomorphy at a less inclusive or nested clade. For example, the presence of mammary glands is a synapomorphy for mammals in relation to tetrapods but is a symplesiomorphy for mammals in relation to one another, rodents and primates, for example
26.
Treponema
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Treponema is a genus of spiral-shaped bacteria. The major treponeme species of human pathogens is Treponema pallidum, whose subspecies are responsible for such as syphilis, bejel. Treponema carateum is the cause of pinta, Treponema paraluiscuniculi is associated with syphilis in rabbits. The phylogeny is based on 16S rRNA-based LTP release 123 by The All-Species Living Tree Project, the currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature and National Center for Biotechnology Information. Candidatus Treponema suis Molbak et al. 1994. Treponema paraluiscuniculi ♦ Smibert 1974. Treponema pertenue ♦ Castellani & Chalmers 1910. Treponema phagedenis ♠ T. p. phagedenis ♠ Brumpt T. p. vaccae ♠ Evans et al
27.
National Center for Biotechnology Information
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The National Center for Biotechnology Information is part of the United States National Library of Medicine, a branch of the National Institutes of Health. The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper, the NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a database for the biomedical literature. Other databases include the NCBI Epigenomics database, all these databases are available online through the Entrez search engine. NCBI is directed by David Lipman, one of the authors of the BLAST sequence alignment program. He also leads a research program, including groups led by Stephen Altschul, David Landsman, Eugene Koonin, John Wilbur, Teresa Przytycka. NCBI is listed in the Registry of Research Data Repositories re3data. org, NCBI has had responsibility for making available the GenBank DNA sequence database since 1992. GenBank coordinates with individual laboratories and other databases such as those of the European Molecular Biology Laboratory. Since 1992, NCBI has grown to other databases in addition to GenBank. The NCBI assigns a unique identifier to each species of organism, the NCBI has software tools that are available by WWW browsing or by FTP. For example, BLAST is a sequence similarity searching program, BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds. RAG2/IL2RG The NCBI Bookshelf is a collection of freely accessible, downloadable, some of the books are online versions of previously published books, while others, such as Coffee Break, are written and edited by NCBI staff. BLAST is a used for calculating sequence similarity between biological sequences such as nucleotide sequences of DNA and amino acid sequences of proteins. BLAST is a tool for finding sequences similar to the query sequence within the same organism or in different organisms. It searches the query sequence on NCBI databases and servers and post the results back to the browser in chosen format. Input sequences to the BLAST are mostly in FASTA or Genbank format while output could be delivered in variety of such as HTML, XML formatting. HTML is the output format for NCBIs web-page. Entrez is both indexing and retrieval system having data from sources for biomedical research
. PMID 8346204.