1.
Scanning electron microscope
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A scanning electron microscope is a type of electron microscope that produces images of a sample by scanning it with a focused beam of electrons. The electrons interact with atoms in the sample, producing various signals that contain information about the surface topography. The electron beam is scanned in a raster scan pattern. SEM can achieve better than 1 nanometer. Specimens can be observed in vacuum, in low vacuum, in wet conditions. The most common SEM mode is detection of electrons emitted by atoms excited by the electron beam. The number of electrons that can be detected depends, among other things. By scanning the sample and collecting the electrons that are emitted using a special detector. An account of the history of SEM has been presented by McMullan. Ardenne applied the principle not only to achieve magnification but also to purposefully eliminate the chromatic aberration otherwise inherent in the electron microscope. He further discussed the various modes, possibilities and theory of SEM. The types of produced by an SEM include secondary electrons, reflected or back-scattered electrons, photons of characteristic X-rays and light, absorbed current. Secondary electron detectors are standard equipment in all SEMs, but it is rare that a machine would have detectors for all other possible signals. The signals result from interactions of the beam with atoms at various depths within the sample. In the most common or standard detection mode, ie secondary electron imaging or SEI, consequently, SEM can produce very high-resolution images of a sample surface, revealing details less than 1 nm in size. Back-scattered electrons are beam electrons that are reflected from the sample by elastic scattering and they emerge from deeper locations within the specimen and consequently the resolution of BSE images is generally poorer than SE images. BSE images can provide information about the distribution of different elements in the sample, characteristic X-rays are emitted when the electron beam removes an inner shell electron from the sample, causing a higher-energy electron to fill the shell and release energy. These characteristic X-rays are used to identify the composition and measure the abundance of elements in the sample, due to the very narrow electron beam, SEM micrographs have a large depth of field yielding a characteristic three-dimensional appearance useful for understanding the surface structure of a sample
2.
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
3.
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
4.
Proteobacteria
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The Proteobacteria are a major phylum of Gram-negative bacteria. The name of the phylum has never been published as no type genus has been proposed. They include a variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia. Others are free-living, and include many of the responsible for nitrogen fixation. Carl Woese established this grouping in 1987, calling it informally the purple bacteria, the Alphaproteobacteria grow at very low levels of nutrients and have unusual morphology such as stalks and buds. They include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants, the type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter. The Betaproteobacteria are highly diverse and contain chemolithoautotrophs, photoautotrophs. The type order is the Burkholderiales, comprising a range of metabolic diversity. The Gammaproteobacteria are the largest class in terms of species with validly published names, the type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter. The Deltaproteobacteria include bacteria that are predators on other bacteria and are important contributors to the side of the sulfur cycle. The type order is the Myxococcales, which includes organisms with self-organising abilities such as Myxococcus spp, the Epsilonproteobacteria are often slender, Gram-negative rods that are helical or curved. The type order is the Campylobacterales, which includes important food pathogens such as Campylobacter spp, the type order is the Oligoflexales, which contains the genus Oligoflexus. The Acidithiobacillia contain only sulfur-oxidising autotrophs, the type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp. All Proteobacteria are Gram-negative, though some may stain Gram-positive or Gram-variable in practice, many move about using flagella, but some are nonmotile or rely on bacterial gliding. The last include the Myxobacteriales, an order of bacteria that can aggregate to form fruiting bodies. Also, a variety in the types of metabolism exists. Most members are facultatively or obligately anaerobic, Chemolithoautotrophic, and heterotrophic, a variety of genera, which are not closely related to each other, convert energy from light through photosynthesis. Proteobacteria are associated with the imbalance of microbiota of the reproductive tract of women
5.
Gammaproteobacteria
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Gammaproteobacteria are a class of several medically, ecologically, and scientifically important groups of bacteria. An exceeding number of important pathogens belong to this class, like all Proteobacteria, the Gammaproteobacteria are Gram-negative. The Gammaproteobacteria comprise several medically and scientifically important groups of bacteria, such as the Enterobacteriaceae, Vibrionaceae, a number of important pathogens belong to this class, e. g. Salmonella spp. Yersinia pestis, Vibrio cholerae, Pseudomonas aeruginosa, and Escherichia coli, important plant pathogens such as Xanthomonas axonopodis pv. citri and Pseudomonas syringae pv. actinidiae are also Gammaproteobacteria. Members of Chromatium are photosynthetic and oxidize hydrogen sulfide instead of water, some Gammaproteobacteria are methane oxidizers, and many are symbiotic with geothermic ocean vent-dwelling animals. Due to a genus, Acidithiobacillus, the Gammaproteobacteria class is paraphyletic to Betaproteobacteria. A number of bacteria have been described as members of Gammaproteobacteria, Betaproteobacteria Proteobacteria Gammaproteobacteria at the US National Library of Medicine Medical Subject Headings
6.
Vibrionaceae
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The Vibrionaceae are a family of Proteobacteria given their own order. Inhabitants of fresh or salt water, several species are pathogenic, including the type species Vibrio cholerae, most bioluminescent bacteria belong to this family, and are typically found as symbionts of deep-sea animals. Vibrionaceae are Gram-negative organisms and facultative anaerobes, capable of fermentation and they contain oxidase and have one or more flagella, which are generally polar. Originally, these characteristics defined the family, which was divided into four genera, two of these, Vibrio and Photobacterium, correspond to the modern group, although several new genera have been defined. Genetic studies have shown the two original members—Aeromonas and Plesiomonas—belong to separate families. As mentioned above, Vibrionaceae bacteria are in symbiosis with marine organisms. A characteristic of the family is the broad host range susceptible to infection by vibrios, pathogens of man, other than V. cholerae, include V. parahemolyticus, a cause of gastroenteritis and V. vulnificus that can lead to acute and fatal septicaemia. Species such as V. tubiashii cause disease in larval stages of Pacific oyster while V. harveyi causes luminous vibriosis in penaeid shrimps. The extent of the host range is seen with such as V. mediterranei and V. coralliilyticus, which can infect zooxanthellae. These species of Vibrio are thought to be a cause of coral bleaching
7.
Vibrio
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Vibrio is a genus of Gram-negative bacteria, possessing a curved-rod shape, several species of which can cause foodborne infection, usually associated with eating undercooked seafood. Typically found in water, Vibrio species are facultative anaerobes that test positive for oxidase. All members of the genus are motile and have polar flagella with sheaths, Vibrio species typically possess two chromosomes, which is unusual for bacteria. Each chromosome has a distinct and independent origin of replication, and are conserved together over time in the genus, recent phylogenies have been constructed based on a suite of genes. O. F. Müller described eight species of the genus Vibrio, some of the other species are today assigned to eukaryote taxa, e. g. to the euglenoid Peranema or to the diatom Bacillaria. However, Vibrio Müller,1773 became regarded as the name of a genus. Filippo Pacini isolated micro-organisms he called vibrions from cholera patients in 1854, several species of Vibrio are pathogens. Most disease-causing strains are associated with gastroenteritis, but can also infect open wounds and they can be carried by numerous marine animals, such as crabs or prawns, and have been known to cause fatal infections in humans during exposure. Pathogenic Vibrio species include V. cholerae, V. parahaemolyticus, V. cholerae is generally transmitted by contaminated water. Pathogenic Vibrio species can cause illness, usually associated with eating undercooked seafood. The pathogenic features can be linked to quorum sensing where bacteria are able to express their virulence factor via their signalling molecules, V. vulnificus outbreaks commonly occur in warm climates and small, generally lethal, outbreaks occur regularly. An outbreak occurred in New Orleans after Hurricane Katrina, and several cases occur most years in Florida. As of 2013 in the United States, Vibrio infections as a whole were up 43% when compared with the rates observed in 2006-2008, V. vulnificus, the most severe strain, has not increased. Foodborne Vibrio infections are most often associated with eating raw shellfish, many Vibrio species are also zoonotic. They cause disease in fish and shellfish, and are causes of mortality among domestic marine life. Medical care depends on the presentation and the presence of underlying medical conditions. Because Vibrio gastroenteritis is self-limited in most patients, no medical therapy is required. Patients who cannot tolerate oral fluid replacement may require intravenous fluid therapy, although most Vibrio species are sensitive to antibiotics such as doxycycline or quinolones, antibiotic therapy does not shorten the course of the illness or the duration of pathogen excretion
8.
Binomial nomenclature
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Such a name is called a binomial name, a binomen, binominal name or a scientific name, more informally it is also called a Latin name. The first part of the name identifies the genus to which the species belongs, for example, humans belong to the genus Homo and within this genus to the species Homo sapiens. The formal introduction of system of naming species is credited to Carl Linnaeus. But Gaspard Bauhin, in as early as 1623, had introduced in his book Pinax theatri botanici many names of genera that were adopted by Linnaeus. Although the general principles underlying binomial nomenclature are common to these two codes, there are differences, both in the terminology they use and in their precise rules. Similarly, both parts are italicized when a binomial name occurs in normal text, thus the binomial name of the annual phlox is now written as Phlox drummondii. In scientific works, the authority for a name is usually given, at least when it is first mentioned. In zoology Patella vulgata Linnaeus,1758, the original name given by Linnaeus was Fringilla domestica, the parentheses indicate that the species is now considered to belong in a different genus. The ICZN does not require that the name of the person who changed the genus be given, nor the date on which the change was made, in botany Amaranthus retroflexus L. – L. is the standard abbreviation used in botany for Linnaeus. – Linnaeus first named this bluebell species Scilla italica, Rothmaler transferred it to the genus Hyacinthoides, the ICN does not require that the dates of either publication be specified. Prior to the adoption of the binomial system of naming species. Together they formed a system of polynomial nomenclature and these names had two separate functions. First, to designate or label the species, and second, to be a diagnosis or description, such polynomial names may sometimes look like binomials, but are significantly different. For example, Gerards herbal describes various kinds of spiderwort, The first is called Phalangium ramosum, Branched Spiderwort, is aptly termed Phalangium Ephemerum Virginianum, Soon-Fading Spiderwort of Virginia. The Latin phrases are short descriptions, rather than identifying labels, the Bauhins, in particular Caspar Bauhin, took some important steps towards the binomial system, by pruning the Latin descriptions, in many cases to two words. The adoption by biologists of a system of binomial nomenclature is due to Swedish botanist and physician Carl von Linné. It was in his 1753 Species Plantarum that he first began using a one-word trivial name together with a generic name in a system of binomial nomenclature. This trivial name is what is now known as an epithet or specific name
9.
Filippo Pacini
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Filippo Pacini was an Italian anatomist, posthumously famous for isolating the cholera bacillus Vibrio cholerae in 1854, well before Robert Kochs more widely accepted discoveries 30 years later. Pacini was born in Pistoia, Tuscany, to a humble family, however, in 1830, he was given a scholarship to the most venerable medical school in Pistoia. He learned his trade as a physician, and learned to dissect, in 1831, during a dissection class, Pacini discovered small sensory organs in the nervous system which can detect pressure and vibrations. He studied them closely from 1833 on, and first discussed them in 1835 at the Società medico-fisica in Florence, within just a few years, the work was widely known in Europe and the bodies had become known as Pacinian corpuscles. He served as an assistant to Paolo Savi in Pisa from 1840 to 1843, the Asiatic cholera pandemic of 1846-63, was the time period when Pacini made his discovery the cholera bacillus. Cholera came to Florence in 1854 during the Asiatic Cholera Pandemic of 1846-63, Pacini became very interested in the disease. Immediately following the death of patients, he performed an autopsy and with his microscope. During such studies, Pacini first discovered a comma-shaped bacillus which he described as a Vibrio and he published a paper in 1854 entitled, Microscopical observations and pathological deductions on cholera in which he described the organism and its relation to the disease. His microscopic slides of the organism were clearly labeled, identifying the date, john Snow, who disproved the miasma theory, and Robert Koch, widely and erroneously credited with the discovery of the bacillum 30 years later. Pacinis work was repeatedly Published in the community and readily available in translation via The British. The British and Foreign Medico-chirurgical Review Or Quarterly, volume 38, July 1866 printed Pacinis work in the English language. In 1965, the committee on nomenclature adopted the formal name Vibrio cholera pacini Pacini 1854 to honor his work. During his career, Pacini also published studies on the retina of the human eye, the electric organs in electric fishes, the structure of bone. Pacini did not marry, and spent most of the money remaining after his investigations on the long-term care of his two ailing sisters. He died nearly penniless in Florence on July 9,1883, in 1935, his remains were transferred to the church of Santa Maria delle Grazie, along with the remains of Atto Tigri and Filippo Civinini, two other noted anatomists
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
11.
Bacterium
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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
12.
Brackish water
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Brackish water or briny water is water that has more salinity than fresh water, but not as much as seawater. It may result from mixing of seawater with fresh water, as in estuaries, the word comes from the Middle Dutch root brak. Brackish water is also the primary product of the salinity gradient power process. Because brackish water is hostile to the growth of most terrestrial plant species, without appropriate management it is damaging to the environment. Technically, brackish water contains between 0.5 and 30 grams of salt per litre—more often expressed as 0.5 to 30 parts per thousand, thus, brackish covers a range of salinity regimes and is not considered a precisely defined condition. It is characteristic of many brackish surface waters that their salinity can vary considerably over space and/or time, brackish water condition commonly occurs when fresh water meets seawater. In fact, the most extensive brackish water habitats worldwide are estuaries, the River Thames flowing through London is a classic river estuary. A similar pattern of replacement can be observed with the aquatic plants and this type of ecological succession from a freshwater to marine ecosystem is typical of river estuaries. Salmon are anadromous, meaning live in the sea but ascend rivers to spawn, eels are catadromous, living in rivers and streams. Besides the species migrate through estuaries, there are many other fish that use them as nursery grounds for spawning or as places young fish can feed. Herring and plaice are two commercially important species that use the Thames Estuary for this purpose, estuaries are also commonly used as fishing grounds, and as places for fish farming or ranching. Another important brackish water habitat is the swamp or mangal. Many, though not all, mangrove swamps fringe estuaries and lagoons where the salinity changes with each tide, like estuaries, mangrove swamps are extremely important breeding grounds for many fish, with species such as snappers, halfbeaks, and tarpon spawning or maturing among them. Mangroves represent important nesting site for numerous birds groups such as herons, storks, spoonbills, ibises, kingfishers, the Sundarbans and Bhitarkanika Mangroves are two of the large mangrove forests in the world, both on the coast of the Bay of Bengal. Some seas and lakes are brackish, the Baltic Sea is a brackish sea adjoining the North Sea. Because the salt water coming in from the sea is denser than freshwater, limited mixing occurs because of the lack of tides and storms, with the result that the fish fauna at the surface is freshwater in composition while that lower down is more marine. Cod are an example of a species found in deep water in the Baltic. The Caspian Sea is the worlds largest lake and contains brackish water with a salinity about one-third that of normal seawater, the Caspian is famous for its peculiar animal fauna, including one of the few non-marine seals and the great sturgeons, a major source of caviar
13.
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
14.
Pilus
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A pilus is a hair-like appendage found on the surface of many bacteria. The terms pilus and fimbria can be used interchangeably, although some researchers reserve the term pilus for the appendage required for bacterial conjugation, all pili in the latter sense are primarily composed of pilin proteins, which are oligomeric. Dozens of these structures can exist on the bacteria, some bacterial viruses or bacteriophages attach to receptors on pili at the start of their reproductive cycle. They are also fragile and constantly replaced, sometimes with pili of different composition, specific host responses to old pili structure are not effective on the new structure. Recombination genes of pili code for variable and constant regions of the pili, conjugative pili allow for the transfer of DNA between bacteria, in the process of bacterial conjugation. They are sometimes called sex pili, in analogy to sexual reproduction, perhaps the most well-studied is the F pilus of Escherichia coli, encoded by the F plasmid or fertility factor. A pilus is typically 6 to 7 nm in diameter, not all bacteria can make conjugative pili, but conjugation can occur between bacteria of different species. Some pili, called type IV pili, generate motile forces, movement produced by type IV pili is typically jerky, so it is called twitching motility, as distinct from other forms of bacterial motility, such as that produced by flagella. However, some bacteria, for example Myxococcus xanthus, exhibit gliding motility, Bacterial type IV pilins are similar in structure to the component flagellins of archaeal flagella. Genetic transformation is the process by which a recipient bacterial cell takes up DNA from a neighboring cell, in Neisseria meningitidis, DNA transformation requires the presence of short DNA uptake sequences which are 9-10 monomers residing in coding regions of the donor DNA. Specific recognition of DUSs is mediated by a type IV pilin, menningococcal type IV pili bind DNA through the minor pilin ComP via an electropositive stripe that is predicted to be exposed on the filaments surface. ComP displays an exquisite binding preference for selective DUSs, the distribution of DUSs within the N. meningitides genome favors certain genes, suggesting that there is a bias for genes involved in genomic maintenance and repair. Attachment of bacteria to host surfaces is required for colonization during infection or to formation of a biofilm. A fimbria is a short pilus that is used to attach the bacterium to a surface and they are sometimes called attachment pili. Fimbriae are either located at the poles of a cell, or are spread over its entire surface. Mutant bacteria that lack fimbriae cannot adhere to their usual target surfaces, the lectins are necessary to adhere to target cells because they can recognize oligosaccharide units on the surface of these target cells. Other fimbriae bind to components of the extracellular matrix, fimbriae are found in Gram-negative bacteria. In Gram-positive bacteria, the subunits are covalently linked
15.
Robert Koch
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Robert Heinrich Hermann Koch was a celebrated German physician and pioneering microbiologist. In addition to his studies on these diseases, Koch created and improved laboratory technologies and techniques in the field of microbiology. As a result of his research on tuberculosis, Koch received the Nobel Prize in Physiology or Medicine in 1905. Robert Koch was born in Clausthal, Hanover, Germany, on 11 December 1843, to Hermann Koch, Koch excelled in academics from an early age. Before entering school in 1848, he had taught himself how to read and he graduated from high school in 1862, having excelled in science and maths. At the age of 19, Koch entered the University of Göttingen, however, after three semesters, Koch decided to change his area of study to medicine, as he aspired to be a physician. During his fifth semester of school, Jacob Henle, an anatomist who had published a theory of contagion in 1840. In his sixth semester, Koch began to research at the Physiological Institute. This would eventually form the basis of his dissertation, in January 1866, Koch graduated from medical school, earning honors of the highest distinction. Several years after his graduation in 1866, he worked as a surgeon in the Franco-Prussian War, from 1880-1885, Koch held a position as government advisor with the Imperial Department of Health. Koch began conducting research on microorganisms in a laboratory connected to his patient examination room, koch’s early research in this laboratory yielded one of his major contributions to the field of microbiology, as he developed the technique of growing bacteria. Furthermore, he managed to isolate and grow selected pathogens in pure laboratory culture, from 1885 to 1890, he served as an administrator and professor at Berlin University. For this he accepted harsh conditions, the Prussian Ministry of Health insisted after the scandal with tuberculin, that any of Kochs inventions would unconditionally belong to the government and not compensated. Koch lost the right to apply for patent protection, in an attempt to grow bacteria, Koch began to use solid nutrients such as potato slices. Through these initial experiments, Koch observed individual colonies of identical and he found that potato slices were not suitable media for all organisms, and later began to use nutrient solutions with gelatin. Koch’s discovery of the agent of anthrax led to the formation of a generic set of postulates which can be used in the determination of the cause of most infectious diseases. The organism must be isolated from a host containing the disease, samples of the organism taken from pure culture must cause the same disease when inoculated into a healthy, susceptible animal in the laboratory. The organism must be isolated from the animal and must be identified as the same original organism first isolated from the originally diseased host
16.
Protein
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Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
17.
Management of dehydration
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The management of dehydration typically involves the use of oral rehydration solution. Standard home solutions such as salted rice water, salted yogurt drinks, vegetable, clean plain water can also be one of several fluids given. There are commercial solutions such as Pedialyte, and relief agencies such as UNICEF widely distribute packets of salts, the World Health Organization describes a homemade ORS with one liter water with one teaspoon salt and six teaspoons sugar added. The WHO, however, does not generally recommend homemade solutions as how to make them is easily forgotten. Rehydration Project recommends adding the amount of sugar but only one-half a teaspoon of salt. Both agree that drinks with too much sugar or salt can make dehydration worse, in what the World Health Organization terms some dehydration, the child or adult is restless and irritable, is thirsty, and will drink eagerly. WHO recommends that if there is vomiting, don’t stop, but do pause for 5–10 minutes, with the older WHO solution, also give some clean water during rehydration. With the newer reduced-osmolarity, more dilute solution, this is not necessary, begin to offer food after the initial four-hour rehydration period with children and adults. With infants, continue to breastfeed even during rehydration as long as the infant will breastfeed, begin zinc supplementation after initial four-hour rehydration to reduce severity and duration of episode. If available, zinc supplementation should be continued for 10 to 14 days, during the initial period of rehydration, the patient should be re-assessed at least every four hours. The family should be provided with at least two days worth of ORS packets, in severe dehydration, the person may be lethargic or unconscious, drinks poorly, or may not be able to drink. Malnourished patients should receive a modified ORS which has less sodium, more potassium, for patients not malnourished, rehydration should be performed relatively rapidly by means of intravenous solution. Patients who can drink, even poorly, should be given Oral Rehydration Solution by mouth until the IV drip is running. In addition, all patients should start to receive some ORS when they are able to drink without difficulty, ORS provides additional base and potassium which may not be adequately supplied by IV fluid. Ideally, patients should be reassessed every fifteen to thirty minutes until a radial pulse is present. Hopefully, patients will graduate to the medium dehydration or some dehydration category, inadequate replacement of potassium losses during diarrhea can lead to potassium depletion and hypokalaemia especially in children with malnutrition. This can potentially cause muscle weakness, impaired kidney function, hypokalaemia is worsened when base is given to treat acidosis without simultaneously providing potassium, as happens in standard IVs including Ringers Lactate Solution. ORS can help correct potassium deficit, as can giving foods rich in potassium during diarrhea, as in above sections, for all patients, supplemental zinc can help to reduce the severity and duration of diarrhea
18.
Cholera vaccine
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Cholera vaccines are vaccines that are effective at preventing cholera. For the first six months after vaccination they provide about 85% protection, after two years the level of protection decreases to less than 50%. When enough of the population is immunized, it may protect those who have not been immunized, the World Health Organization recommends the use of cholera vaccines in combination with other measures among those at high risk. With the oral vaccine, two or three doses are typically recommended, a single dose vaccine is avaliable for those traveling to an area were cholera is common. In some countries an injectable cholera vaccine is available, the available types of oral vaccine are generally safe. Mild abdominal pain or diarrhea may occur and they are safe in pregnancy and in those with poor immune function. They are licensed for use in more than 60 countries, in countries where the disease is common, the vaccine appears to be cost effective. The first vaccines used against cholera were developed in the late 1800s and they were the first widely used vaccine that was made in a laboratory. Oral vaccines were first introduced in the 1990s and it is on the World Health Organizations List of Essential Medicines, the most effective and safe medicines needed in a health system. The cost to immunize against cholera is between 0.1 and 4.0 USD, since licensure of Dukoral and Shanchol, over a million doses of these vaccines have been deployed in various mass oral cholera campaigns around the world. The cholera vaccine is used by backpackers and persons visiting locations where there is a high risk of cholera infection. Although the protection observed has been described as moderate, herd immunity can multiply the effectiveness of vaccination, Dukoral has been licensed for children 2 years of age and older, Shanchol for children 1 year of age and older. The administration of the vaccine to adults confers additional indirect protection to children, vaccination should not disrupt the provision of other high priority health interventions to control or prevent cholera outbreaks. The WHO as of late 2013 established a revolving stockpile of 2 million OCV doses. The supply is increasing to 6 million as a South Korean companies has gone into production, GAVI Alliance donated $115 million to help pay for expansions. The oral vaccines are generally of two forms, inactivated and attenuated, inactivated oral vaccines provide protection in 52% of cases the first year following vaccination and in 62% of cases the second year. Two variants of the oral vaccine currently are in use, WC-rBS. WC-rBS is a monovalent inactivated vaccine containing killed whole cells of V. cholerae O1 plus additional recombinant cholera toxin B subunit, BivWC is a bivalent inactivated vaccine containing killed whole cells of V. cholerae O1 and V. cholerae O139
19.
Chromosome
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A chromosome is a DNA molecule with part or all of the genetic material of an organism. Prokaryotes usually have one single circular chromosome, whereas most eukaryotes are diploid, chromosomes in eukaryotes are composed of chromatin fiber. Chromatin fiber is made of nucleosomes, a nucleosome is a histone octamer with part of a longer DNA strand attached to and wrapped around it. Chromatin fiber, together with associated proteins is known as chromatin, chromatin is present in most cells, with a few exceptions, for example, red blood cells. Occurring only in the nucleus of cells, chromatin contains the vast majority of DNA, except for a small amount inherited maternally. Chromosomes are normally visible under a microscope only when the cell is undergoing the metaphase of cell division. Before this happens every chromosome is copied once, and the copy is joined to the original by a centromere resulting in an X-shaped structure, the original chromosome and the copy are now called sister chromatids. During metaphase, when a chromosome is in its most condensed state, in this highly condensed form chromosomes are easiest to distinguish and study. In prokaryotic cells, chromatin occurs free-floating in cytoplasm, as these cells lack organelles, the main information-carrying macromolecule is a single piece of coiled double-helix DNA, containing many genes, regulatory elements and other noncoding DNA. The DNA-bound macromolecules are proteins that serve to package the DNA, chromosomes vary widely between different organisms. Some species such as certain bacteria also contain plasmids or other extrachromosomal DNA and these are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. Chromosomal recombination during meiosis and subsequent sexual reproduction plays a significant role in genetic diversity. In prokaryotes and viruses, the DNA is often densely packed and organized, in the case of archaea, by homologs to eukaryotic histones, small circular genomes called plasmids are often found in bacteria and also in mitochondria and chloroplasts, reflecting their bacterial origins. Some use the term chromosome in a sense, to refer to the individualized portions of chromatin in cells. However, others use the concept in a sense, to refer to the individualized portions of chromatin during cell division. The word chromosome comes from the Greek χρῶμα and σῶμα, describing their strong staining by particular dyes, schleiden, Virchow and Bütschli were among the first scientists who recognized the structures now so familiar to everyone as chromosomes. The term was coined by von Waldeyer-Hartz, referring to the term chromatin, in a series of experiments beginning in the mid-1880s, Theodor Boveri gave the definitive demonstration that chromosomes are the vectors of heredity. His two principles were the continuity of chromosomes and the individuality of chromosomes and it is the second of these principles that was so original
20.
Base pair
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A base pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the blocks of the DNA double helix. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs allow the DNA helix to maintain a regular helical structure that is dependent on its nucleotide sequence. The complementary nature of this structure provides a backup copy of all genetic information encoded within double-stranded DNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes, intramolecular base pairs can occur within single-stranded nucleic acids. The size of a gene or an organisms entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of base pairs is equal to the number of nucleotides in one of the strands. The haploid human genome is estimated to be about 3.2 billion bases long and to contain 20, a kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC. Hydrogen bonding is the interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen donors and acceptors allows only the right pairs to form stably. Purine-pyrimidine base pairing of AT or GC or UA results in proper duplex structure, the only other purine-pyrimidine pairings would be AC and GT and UG, these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two bonds, does occur fairly often in RNA. Higher GC content results in higher melting temperatures, it is, therefore, on the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must also be taken into account when designing primers for PCR reactions, the following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5 end to the 3 end, thus and this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine, most intercalators are large polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine, an unnatural base pair is a designed subunit of DNA which is created in a laboratory and does not occur in nature
21.
DNA
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Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids, alongside proteins, lipids and complex carbohydrates, most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are termed polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases—cytosine, guanine, adenine, or thymine —a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison the total mass of the biosphere has been estimated to be as much as 4 trillion tons of carbon. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information and this information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences, the two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases and it is the sequence of these four nucleobases along the backbone that encodes biological information. RNA strands are created using DNA strands as a template in a process called transcription, under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells DNA is organized into structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, eukaryotic organisms store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast prokaryotes store their DNA only in the cytoplasm, within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed, DNA was first isolated by Friedrich Miescher in 1869. DNA is used by researchers as a tool to explore physical laws and theories, such as the ergodic theorem. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro-, among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a polymer made from repeating units called nucleotides
22.
Gene
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A gene is a locus of DNA which is made up of nucleotides and is the molecular unit of heredity. The transmission of genes to an offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes, genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions, genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotypical traits, usage of the term having a gene typically refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection or survival of the fittest of the alleles, the concept of a gene continues to be refined as new phenomena are discovered. For example, regulatory regions of a gene can be far removed from its coding regions, some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. The existence of discrete inheritable units was first suggested by Gregor Mendel, from 1857 to 1864, in Brno, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring. He described these mathematically as 2n combinations where n is the number of differing characteristics in the original peas, although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured the distinction between genotype and phenotype, charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan and genesis / genos. Darwin used the term gemmule to describe hypothetical particles that would mix during reproduction, de Vries called these units pangenes, after Darwins 1868 pangenesis theory. In 1909 the Danish botanist Wilhelm Johannsen shortened the name to gene, advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid was shown to be the repository of genetic information by experiments in the 1940s to 1950s. In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities, indivisible by recombination, collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, which is transcribed from DNA. This dogma has since shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics, in 1972, Walter Fiers and his team at the University of Ghent were the first to determine the sequence of a gene, the gene for Bacteriophage MS2 coat protein. The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing, an automated version of the Sanger method was used in early phases of the Human Genome Project. The theories developed in the 1930s and 1940s to integrate molecular genetics with Darwinian evolution are called the evolutionary synthesis
23.
Bacteriophage
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A bacteriophage /ˈbækˈtɪər. i. oʊˌfeɪdʒ/ is a virus that infects and replicates within a bacterium. The term is derived from bacteria and the Greek, φαγεῖν, bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have relatively simple or elaborate structures. Their genomes may encode as few as four genes, and as many as hundreds of genes, phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere, phages are widely distributed in locations populated by bacterial hosts, such as soil or the intestines of animals. They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Central Europe and they are seen as a possible therapy against multi-drug-resistant strains of many bacteria. Bacteriophages occur abundantly in the biosphere, with different virions, genomes, phages are classified by the International Committee on Taxonomy of Viruses according to morphology and nucleic acid. Nineteen families are recognized by the ICTV that infect bacteria. Of these, only two families have RNA genomes, and only five families are enveloped, of the viral families with DNA genomes, only two have single-stranded genomes. Eight of the families with DNA genomes have circular genomes while nine have linear genomes. Nine families infect bacteria only, nine infect archaea only, in 1915, British bacteriologist Frederick Twort, superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria. He believed the agent must be one of the following, a stage in the cycle of the bacteria. Tworts work was interrupted by the onset of World War I, for d’Hérelle, there was no question as to the nature of his discovery, In a flash I had understood, what caused my clear spots was in fact an invisible microbe … a virus parasitic on bacteria. DHérelle called the virus a bacteriophage or bacteria-eater and he also recorded a dramatic account of a man suffering from dysentery who was restored to good health by the bacteriophages. It was DHerelle who conducted research into bacteriophages and introduced the concept of phage therapy. In 1969, Max Delbrück, Alfred Hershey and Salvador Luria were awarded the Nobel Prize in Physiology and Medicine for their discoveries of the replication of viruses and their genetic structure. Phages were discovered to be agents and were used in the former Soviet Republic of Georgia. They had widespread use, including treatment of soldiers in the Red Army, however, they were abandoned for general use in the West for several reasons, Medical trials were carried out, but a basic lack of understanding of phages made these invalid. Antibiotics were discovered and marketed widely and they were easier to make, store and to prescribe
24.
Horizontal gene transfer
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Horizontal gene transfer or lateral gene transfer is the movement of genetic material between unicellular and/or multicellular organisms other than by the transmission of DNA from parent to offspring. HGT is an important factor in the evolution of many organisms and it often involves temperate bacteriophages and plasmids. Most thinking in genetics has focused upon vertical transfer, but horizontal gene transfer is important, artificial horizontal gene transfer is a form of genetic engineering. Inter-bacterial gene transfer was first described in Japan in a 1959 publication that demonstrated the transfer of resistance between different species of bacteria. In the mid-1980s, Syvanen predicted that lateral gene transfer existed, had biological significance, as Jian, Rivera and Lake put it, Increasingly, studies of genes and genomes are indicating that considerable horizontal transfer has occurred between prokaryotes. The phenomenon appears to have had significance for unicellular eukaryotes as well. As Bapteste et al. observe, additional evidence suggests that gene transfer might also be an important evolutionary mechanism in protist evolution, there is some evidence that even higher plants and animals have been affected and this has raised concerns for safety. Grafting of one plant to another can transfer chloroplasts, mitochondrial DNA, some Lepidoptera have been genetically modified by horizontal gene transfer from the wasp bracovirus. Bites from the insect Reduviidae can, via a parasite, infect humans with the trypanosomal Chagas disease and it has been suggested that lateral gene transfer to humans from bacteria may play a role in cancer. Richardson and Palmer state, Horizontal gene transfer has played a role in bacterial evolution and is fairly common in certain unicellular eukaryotes. However, the prevalence and importance of HGT in the evolution of multicellular eukaryotes remain unclear, some have argued that the process may be a hidden hazard of genetic engineering as it could allow transgenic DNA to spread from species to species. There are several mechanisms for horizontal gene transfer, Transformation, the alteration of a cell resulting from the introduction, uptake. This process is common in bacteria, but less so in eukaryotes. Transformation is often used in laboratories to insert genes into bacteria for experiments or for industrial or medical applications. See also molecular biology and biotechnology, transduction, the process in which bacterial DNA is moved from one bacterium to another by a virus. Bacterial conjugation, a process involves the transfer of DNA via a plasmid from a donor cell to a recombinant recipient cell during cell-to-cell contact. Gene transfer agents, virus-like elements encoded by the host that are found in the alphaproteobacteria order Rhodobacterales. A transposon is a segment of DNA that can sometimes pick up a resistance gene and insert it into a plasmid or chromosome
25.
Open reading frame
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In molecular genetics, an open reading frame is the part of a reading frame that has the potential to be translated. An ORF is a stretch of codons that do not contain a stop codon. An ATG codon within the ORF may indicate where translation starts, the transcription termination site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, a protein would be made during translation. In eukaryotic genes with multiple exons, ORFs span intron/exon regions, one common use of closed reading frames is as one piece of evidence to assist in gene prediction. Long ORFs are often used, along with evidence, to initially identify candidate protein-coding regions or functional RNA-coding regions in a DNA sequence. The presence of an CRF does not necessarily mean that the region is never translated, for example, in a randomly generated DNA sequence with an equal percentage of each nucleotide, a stop-codon would be expected once every 21 codons. By itself even an open reading frame is not conclusive evidence for the presence of a gene. On the other hand, it has proven that some short ORFs that lack the classical hallmarks of protein-coding genes can produce functional peptides. 5’NTR of about 50% of mammal mRNAs are known to one or several sORFs. 64-75% of experimentally found translation initiation sites of sORFs are conservative in the genomes of human, such kind of situation is characteristic of SLAMF1 gene, for example. Since DNA is interpreted in groups of three nucleotides, a DNA strand has three reading frames. The double helix of a DNA molecule has two anti-parallel strands so, with the two strands having three reading frames each, there are six possible frame translations. ORF Finder, The ORF Finder is an analysis tool which finds all open reading frames of a selectable minimum size in a users sequence or in a sequence already in the database. This tool identifies all open reading frames using the standard or alternative genetic codes, the deduced amino acid sequence can be saved in various formats and searched against the sequence database using the BLAST server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions and it is also packaged with the Sequin sequence submission software. The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their single letter amino acid code, the pairwise global alignment between the sequences makes it convenient to detect the different mutations, including single nucleotide polymorphism. Needleman and Wunsch algorithms are used for the gene alignment, the ORF Investigator is written in the portable Perl programming language, and is therefore available to users of all common operating systems
26.
Transcription (biology)
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Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme RNA polymerase. Both DNA and RNA are nucleic acids, which use base pairs of nucleotides as a complementary language, during transcription, a DNA sequence is read by an RNA polymerase, which produces a complementary, antiparallel RNA strand called a primary transcript. Transcription proceeds in the general steps, RNA polymerase, together with one or more general transcription factors. RNA polymerase creates a bubble, which separates the two strands of the DNA helix. This is done by breaking the bonds between complementary DNA nucleotides. RNA sugar-phosphate backbone forms with assistance from RNA polymerase to form an RNA strand, hydrogen bonds of the RNA–DNA helix break, freeing the newly synthesized RNA strand. If the cell has a nucleus, the RNA may be further processed and this may include polyadenylation, capping, and splicing. The RNA may remain in the nucleus or exit to the cytoplasm through the pore complex. The stretch of DNA transcribed into an RNA molecule is called a transcription unit, if the gene encodes a protein, the transcription produces messenger RNA, the mRNA, in turn, serves as a template for the proteins synthesis through translation. Alternatively, the gene may encode for either non-coding RNA, ribosomal RNA, transfer RNA. Overall, RNA helps synthesize, regulate, and process proteins, in virology, the term may also be used when referring to mRNA synthesis from an RNA molecule. For instance, the genome of a negative-sense single-stranded RNA virus may be template for a positive-sense single-stranded RNA and this is because the positive-sense strand contains the information needed to translate the viral proteins for viral replication afterwards. This process is catalyzed by a viral RNA replicase, the regulatory sequence before the coding sequence is called the five prime untranslated region, the sequence after the coding sequence is called the three prime untranslated region. As opposed to DNA replication, transcription results in an RNA complement that includes the nucleotide uracil in all instances where thymine would have occurred in a DNA complement, only one of the two DNA strands serve as a template for transcription. The antisense strand of DNA is read by RNA polymerase from the 3 end to the 5 end during transcription. The complementary RNA is created in the direction, in the 5 →3 direction. This directionality is because RNA polymerase can only add nucleotides to the 3 end of the growing mRNA chain and this use of only the 3 →5 DNA strand eliminates the need for the Okazaki fragments that are seen in DNA replication. This also removes the need for an RNA primer to initiate RNA synthesis, the non-template strand of DNA is called the coding strand, because its sequence is the same as the newly created RNA transcript
27.
Translation (biology)
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In molecular biology and genetics, translation is the process in which ribosomes in a cells cytoplasm create proteins, following transcription of DNA to RNA in the cells nucleus. The entire process is a part of gene expression, in translation, messenger RNA is decoded by a ribosome, outside the nucleus, to produce a specific amino acid chain, or polypeptide. The polypeptide later folds into a protein and performs its functions in the cell. The ribosome facilitates decoding by inducing the binding of complementary tRNA anticodon sequences to mRNA codons, the tRNAs carry specific amino acids that are chained together into a polypeptide as the mRNA passes through and is read by the ribosome. Translation proceeds in three phases, Initiation, The ribosome assembles around the target mRNA, the first tRNA is attached at the start codon. Elongation, The tRNA transfers an amino acid to the corresponding to the next codon. The ribosome then moves to the next mRNA codon to continue the process, termination, When a stop codon is reached, the ribosome releases the polypeptide. In bacteria, translation occurs in the cytoplasm, where the large, in eukaryotes, translation occurs in the cytosol or across the membrane of the endoplasmic reticulum in a process called vectorial synthesis. Many types of transcribed RNA, such as transfer RNA, ribosomal RNA, a number of antibiotics act by inhibiting translation. These include anisomycin, cycloheximide, chloramphenicol, tetracycline, streptomycin, erythromycin, prokaryotic ribosomes have a different structure from that of eukaryotic ribosomes, and thus antibiotics can specifically target bacterial infections without any harm to a eukaryotic hosts cells. The basic process of production is addition of one amino acid at a time to the end of a protein. This operation is performed by a ribosome, a ribosome is made up of two subunits, a small subunit and a large subunit. These subunits come together before translation of mRNA into a protein to provide a location for translation to be carried out, the choice of amino acid type to add is determined by an mRNA molecule. Each amino acid added is matched to a three nucleotide subsequence of the mRNA, for each such triplet possible, the corresponding amino acid is accepted. The successive amino acids added to the chain are matched to successive nucleotide triplets in the mRNA, in this way the sequence of nucleotides in the template mRNA chain determines the sequence of amino acids in the generated amino acid chain. Addition of an amino acid occurs at the C-terminus of the peptide, the mRNA carries genetic information encoded as a ribonucleotide sequence from the chromosomes to the ribosomes. The ribonucleotides are read by translational machinery in a sequence of nucleotide triplets called codons, each of those triplets codes for a specific amino acid. The ribosome molecules translate this code to a sequence of amino acids
28.
Plasmid
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A plasmid is a small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently. They are most commonly found in bacteria as small circular, double-stranded DNA molecules, however, plasmids are sometimes present in archaea, in nature, plasmids often carry genes that may benefit the survival of the organism, for example antibiotic resistance. Artificial plasmids are used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. Plasmids are considered replicons, a unit of DNA capable of replicating autonomously within a suitable host, however, plasmids, like viruses, are not generally classified as life. Plasmids can be transmitted from one bacterium to another via three mechanisms, transformation, transduction, and conjugation. This host-to-host transfer of material is called horizontal gene transfer. Unlike viruses, plasmids are naked DNA and do not encode genes necessary to encase the genetic material for transfer to a new host, however, some classes of plasmids encode the conjugative sex pilus necessary for their own transfer. The size of the plasmid varies from 1 to over 200 kbp, rather, plasmids provide a mechanism for horizontal gene transfer within a population of microbes and typically provide a selective advantage under a given environmental state. In order for plasmids to replicate independently within a cell, they must possess a stretch of DNA that can act as an origin of replication, the self-replicating unit, in this case the plasmid, is called a replicon. Smaller plasmids make use of the host replicative enzymes to make copies of themselves, a few types of plasmids can also insert into the host chromosome, and these integrative plasmids are sometimes referred to as episomes in prokaryotes. Plasmids almost always carry at least one gene, many of the genes carried by a plasmid are beneficial for the host cells, for example, enabling the host cell to survive in an environment that would otherwise be lethal or restrictive for growth. Plasmids can also provide bacteria with the ability to fix nitrogen, some plasmids, however, have no observable effect on the phenotype of the host cell or its benefit to the host cells cannot be determined, and these plasmids are called cryptic plasmids. Naturally occurring plasmids vary greatly in their physical properties and their size can range from very small mini-plasmids of less than a 1 kilobase pairs, to very large megaplasmids of several megabase pairs. At the upper end, little can differentiate between a megaplasmid and a minichromosome, Plasmids are generally circular, however examples of linear plasmids are also known. These linear plasmids require specialized mechanisms to replicate their ends, Plasmids may be present in an individual cell in varying number, ranging from one to several hundreds. The normal number of copies of plasmid that may be found in a cell is called the copy number, and is determined by how the replication initiation is regulated. Larger plasmids tend to have lower copy numbers, low-copy-number plasmids that exist only as one or a few copies in each bacterium are, upon cell division, in danger of being lost in one of the segregating bacteria. Such single-copy plasmids have systems that attempt to distribute a copy to both daughter cells
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Lysis
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Lysis refers to the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a lysate, many species of bacteria are subject to lysis by the enzyme lysozyme, found in animal saliva, egg white, and other secretions. Phage lytic enzymes produced during infection are responsible for the ability of these viruses to lyse bacterial cells. Penicillin and related β-lactam antibiotics cause the death of bacteria through enzyme-mediated lysis that occurs after the causes the bacterium to form a defective cell wall. If cell wall is completely lost, the bacterium is referred as a protoplast if penicillin was used on gram-positive bacteria, cytolysis occurs when a cell bursts due to an osmotic imbalance that has caused excess water to move into the cell. Cytolysis can be prevented by several different mechanisms, including the contractile vacuole that exists in some paramecia, oncolysis refers to the destruction of neoplastic cells or of a tumour. Its also used to refer to the reduction of any swelling, plasmolysis is the contraction of cells within plants due to the loss of water through osmosis. In a hypertonic environment, the cell membrane peels off of the cell wall and these cells will eventually wilt and die unless the flow of water caused by osmosis can stop the contraction of the cell membrane. Erythrocytes hemoglobin release free radicals in response to pathogens when lysed by them, cell lysis is used in laboratories to break open cells and purify or further study their contents. Lysis in the laboratory may be affected by enzymes or detergents or other chaotropic agents, mechanical disruption of cell membranes, as by repeated freezing and thawing, sonication, pressure, or filtration may also be referred to as lysis. The unprocessed solution immediately after lysis but before any further extraction steps is referred to as a crude lysate. For example, lysis is used in western and Southern blotting to analyze the composition of proteins, lipids. Depending on the detergent used, either all or some membranes are lysed, for example, if only the cell membrane is lysed then gradient centrifugation can be used to collect certain organelles. Lysis is also used for purification, DNA extraction. Cell disruption Crenation Hemolysis Lysogenic Pitted keratolysis
. PMID 6419937.
