1.
Transmission electron microscopy
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Transmission electron microscopy is a microscopy technique in which a beam of electrons is transmitted through an ultra-thin specimen, interacting with the specimen as it passes through it. TEMs are capable of imaging at a higher resolution than light microscopes. This enables the user to examine fine detail—even as small as a single column of atoms. TEM forms a major analysis method in a range of scientific fields, TEMs find application in cancer research, virology, materials science as well as pollution, nanotechnology and semiconductor research. At smaller magnifications TEM image contrast is due to absorption of electrons in the material, due to the thickness, at higher magnifications complex wave interactions modulate the intensity of the image, requiring expert analysis of observed images. The first TEM was built by Max Knoll and Ernst Ruska in 1931, with this group developing the first TEM with resolution greater than that of light in 1933, in 1986, Ruska was awarded the Nobel Prize in physics for the development of transmission electron microscopy. Developments into ultraviolet microscopes, led by Köhler and Rohr, allowed for an increase in resolving power of about a factor of two, however this required more expensive quartz optical components, due to the absorption of UV by glass. At this point it was believed that obtaining an image with sub-micrometer information was simply due to this wavelength constraint. It had earlier recognized by Plücker in 1858 that the deflection of cathode rays was possible by the use of magnetic fields. This effect had been utilized to build primitive cathode ray oscilloscopes as early as 1897 by Ferdinand Braun, indeed, in 1891 it was recognized by Riecke that the cathode rays could be focused by these magnetic fields, allowing for simple lens designs. Later this theory was extended by Hans Busch in his published in 1926. The team consisted of several PhD students including Ernst Ruska and Bodo von Borries, in 1931 the group successfully generated magnified images of mesh grids placed over the anode aperture. The device used two lenses to achieve higher magnifications, arguably the first electron microscope. In that same year, Reinhold Rudenberg, the director of the Siemens company, had patented an electrostatic lens electron microscope. At this time the nature of electrons, which were considered charged matter particles, had not been fully realized until the publication of the De Broglie hypothesis in 1927. In April 1932, Ruska suggested the construction of a new microscope for direct imaging of specimens inserted into the microscope. This goal was achieved in September 1933, using images of cotton fibers, research continued on the electron microscope at Siemens in 1936, the aim of the research was the development improvement of TEM imaging properties, particularly with regard to biological specimens. At this time electron microscopes were being fabricated for specific groups, in 1939 the first commercial electron microscope, pictured, was installed in the Physics department of IG Farben-Werke
2.
Micrograph
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A micrograph or photomicrograph is a photograph or digital image taken through a microscope or similar device to show a magnified image of an item. This is opposed to an image, which is at a scale that is visible to the naked eye. Micrography is the practice or art of using microscopes to make photographs, a micrograph contains extensive details that form the features of a microstructure. The neuropathologist Solomon C. Fuller designed and created the first photomicrograph in 1900, micrographs are widely used in all fields of microscopy. A light micrograph or photomicrograph is a micrograph prepared using an optical microscope, at a basic level, photomicroscopy may be performed simply by hooking up a regular camera to a microscope, thereby enabling the user to take photographs at reasonably high magnification. Roman Vishniac was a pioneer in the field of photomicroscopy, specializing in the photography of living creatures in full motion and he also made major developments in light-interruption photography and color photomicroscopy. An electron micrograph is a micrograph prepared using an electron microscope, however, the term electron micrograph is not used in electron microscopy. Digital micrography is a digital picture obtained either directly with a microscope or by scanning of a photomicrograph, digital micrographs are now commonly obtained using a USB microscope attached directly to a home computer or laptop. Today, an add-on three-in-one macro lens which has capability to take wide-angle, fish-eye and macro with 7x, 14x, micrographs usually have micron bars, or magnification ratios, or both. Magnification is a ratio between size of object on a picture and its real size, unfortunately, magnification is somewhat a misleading parameter. It depends on a size of a printed picture. Editors of journals and magazines routinely resize a figure to fit the page, a scale bar, or micron bar, is a bar of known length displayed on a picture. The bar can be used for measurements on a picture, when a picture is resized a bar is also resized. If a picture has a bar, the magnification can be easily calculated, ideally, all pictures destined for publication/presentation should be supplied with a scale bar, the magnification ratio is optional. All but one of the micrographs presented on this page do not have a bar, supplied magnification ratios are likely incorrect. The microscope has been used for scientific discovery. It has also linked to the arts since its invention in the 17th century. At first scientists used the microscope to view and draw objects not visible with the unaided eye, early adopters of the microscope, such as Robert Hooke and Antonie van Leeuwenhoek, were excellent illustrators
3.
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
4.
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
5.
Firmicutes
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The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and they have round cells, called cocci, or rod-like forms. Many Firmicutes produce endospores, which are resistant to desiccation and can survive extreme conditions and they are found in various environments, and the group includes some notable pathogens. Those in one family, the heliobacteria, produce energy through photosynthesis, Firmicutes play an important role in beer, wine, and cider spoilage. The group is divided into the Clostridia, which are anaerobic, the Bacilli, which are obligate or facultative aerobes. On phylogenetic trees, the first two show up as paraphyletic or polyphyletic, as do their main genera, Clostridium. The division Firmicutes as part of the gut flora has been shown to be involved in energy resorption, presence of Christensenella, in class Clostridia and also isolated from human faeces, has been found to correlate with lower body mass index. The presence of Firmicutes can be detected with polymerase chain reaction techniques. Phylum Firmicutes - J. P. Euzéby, List of Prokaryotic names with Standing in Nomenclature
6.
Bacilli
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Bacilli refers to a taxonomic class of bacteria. It includes two orders, Bacillales and Lactobacillales, which contain several well-known pathogens such as Bacillus anthracis, several related concepts make use of similar words, and the ambiguity can create considerable confusion. The term Bacillus is also the name of a genus that, among other genera. Also, bacillus can be a term to describe the morphology of any rod-shaped bacterium. This general term does not mean that the subject is a member of class Bacilli or genus Bacillus, thus, it does not necessarily imply a similar group of characteristics. Not all members of class Bacilli are rod-shaped, and many other rod-shaped bacteria that do not fall within that class exist, moreover, the general term bacillus does not necessarily indicate the Gram-positive staining common to class Bacilli. For example, E. coli is a bacterium that could, therefore, be described as a bacillus. Some microbiologists have forsaken the general term because of the confusion it can create
7.
Bacillaceae
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The Bacillaceae are a family of Gram-positive, heterotrophic, rod-shaped bacteria that may produce endospores. Motile members of family are characterized by peritrichous flagella. Some Bacillaceae are aerobic, while others are facultative or strict anaerobes, most are not pathogenic, but Bacillus species are known to cause disease in humans. Some Bacillaceae, such as the genera Filobacillus, Lentibacillus, and Halobacillus, stain Gram-negative or Gram-variable, genera within this family are sometimes colloquially identified as bacilli. However, this term is a misnomer because it does not distinguish between class Bacilli, order Bacillales, family Bacillaceae, and genus Bacillus
8.
Bacillus
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Bacillus is a genus of gram-positive, rod-shaped bacteria and a member of the phylum Firmicutes. Bacillus species can be obligate aerobes, or facultative anaerobes and they will test positive for the enzyme catalase when there has been oxygen used or present. Ubiquitous in nature, Bacillus includes both free-living and parasitic pathogenic species and these characteristics originally defined the genus, but not all such species are closely related, and many have been moved to other genera of the Firmicutes. Many species of Bacillus can produce copious amounts of enzymes which are use of in different industries. B. subtilis has proved a model for research. Other species of Bacillus are important pathogens, causing anthrax and food poisoning, many Bacillus species are able to secrete large quantities of enzymes. A portion of the Bacillus thuringiensis genome was incorporated into corn crops, the resulting GMOs are therefore resistant to some insect pests. Bacillus subtilis is one of the best understood prokaryotes, in terms of molecular and cellular biology and its superb genetic amenability and relatively large size have provided the powerful tools required to investigate a bacterium from all possible aspects. Recent improvements in fluorescent microscopy techniques have provided insight into the dynamic structure of a single cell organism. Bacillus species are almost ubiquitous in nature, e. g. in soil, B. thuringiensis produces a toxin that can kill insects and thus has been used as insecticide. Two Bacillus species are considered significant, B. anthracis, which causes anthrax, and B. cereus. A third species, B. thuringiensis, is an important insect pathogen, the type species is B. subtilis, an important model organism. It is also a notable food spoiler, causing ropiness in bread, some environmental and commercial strains of B. coagulans may play a role in food spoilage of highly acidic, tomato-based products. An easy way to isolate Bacillus species is by placing nonsterile soil in a test tube with water, shaking, placing in melted mannitol salt agar, colonies are usually large, spreading, and irregularly shaped. Under the microscope, the Bacillus cells appear as rods, the cell wall is composed of teichoic and teichuronic acids. The role of the cytoskeleton in shape generation and maintenance is important The genus Bacillus was named in 1835 by Christian Gottfried Ehrenberg and he had seven years earlier named the genus Bacterium. Bacillus was later amended by Ferdinand Cohn to further describe them as spore-forming, Gram-positive, like other genera associated with the early history of microbiology, such as Pseudomonas and Vibrio, the 266 species of Bacillus are ubiquitous. The genus has a very large ribosomal 16S diversity and is environmentally diverse, several studies have tried to reconstruct the phylogeny of the genus
9.
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
10.
Christian Gottfried Ehrenberg
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Christian Gottfried Ehrenberg, German naturalist, zoologist, comparative anatomist, geologist, and microscopist, was one of the most famous and productive scientists of his time. The son of a judge, Christian Gottfried Ehrenberg was born in Delitzsch and he first studied theology at the University of Leipzig, then medicine and natural sciences in Berlin and became a friend of the famous explorer Alexander von Humboldt. In 1818, he completed his dissertation on fungi, Sylvae mycologicae Berolinenses. In 1820–1825, on an expedition to the Middle East with his friend Wilhelm Hemprich, he collected thousands of specimens of plants. He investigated parts of Egypt, the Libyan Desert, the Nile valley and the coasts of the Red Sea. Subsequently parts of Syria, Arabia and Abyssinia were examined, some results of these travels and of the important collections that had been made were reported on by Humboldt in 1826. While in Sudan he designed the mansion of the governor of Dongola. After his return, Ehrenberg published several papers on insects and corals and two volumes Symbolae physicae, in many particulars of the mammals, birds, insects. Other observations were communicated to scientific societies, Ehrenberg was appointed professor of medicine at Berlin University in 1827. In 1829 he accompanied Humboldt through eastern Russia to the Chinese frontier, after his return he began to concentrate his studies on microscopic organisms, which until then had not been systematically studied. He was particularly interested in a group of protists called diatoms, but he also studied. Until Ehrenberg took up the study it was not known that considerable masses of rock were composed of forms of animals or plants. He also demonstrated that the phosphorescence of the sea was due to organisms and he was a member of the Royal Swedish Academy of Sciences from 1836 and a foreign member of the Royal Society of London from 1837. In 1839, he won the Wollaston Medal, the highest award granted by the Geological Society of London, Ehrenberg was elected a Foreign Honorary Member of the American Academy of Arts and Sciences in 1849. He continued until late in life to investigate the microscopic organisms of the deep sea and he died in Berlin on 27 June 1876. After his death in 1876, his collections of organisms were deposited in the Museum für Naturkunde at the University of Berlin. The Ehrenberg Collection includes 40,000 microscope preparations,5,000 raw samples,3,000 pencil and ink drawings and his collection of scorpions, and other arachnids from the Middle East, is also held in the Berlin Museum. He was also the first winner of the Leeuwenhoek Medal in 1877, in his hometown, Delitzsch, the highest A-Level school, the Ehrenberg-Gymnasium is named after him
11.
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
12.
Gram-positive bacteria
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Gram-positive bacteria are bacteria that give a positive result in the Gram stain test. Gram-positive bacteria take up the crystal violet stain used in the test and this is because the thick peptidoglycan layer in the bacterial cell wall retains the stain after it is washed away from the rest of the sample, in the decolorization stage of the test. Their peptidoglycan layer is thinner and sandwiched between an inner cell membrane and a bacterial outer membrane, causing them to take up the counterstain. Despite their thicker peptidoglycan layer, gram-positive bacteria are more receptive to antibiotics than gram-negative, peptidoglycan chains are cross-linked to form rigid cell walls by a bacterial enzyme DD-transpeptidase. A much smaller volume of periplasm than that in gram-negative bacteria, only some species have a capsule usually consisting of polysaccharides. Also only some species are flagellates, and when they do have flagella they only have two basal body rings to support them, both gram-positive and gram-negative bacteria commonly have a surface layer called an S-layer. In gram-positive bacteria, the S-layer is attached to the peptidoglycan layer, specific to gram-positive bacteria is the presence of teichoic acids in the cell wall. Some of these are lipoteichoic acids, which have a component in the cell membrane that can assist in anchoring the peptidoglycan. Along with cell shape, Gram staining is a method used to differentiate bacterial species. Historically, the kingdom Monera was divided into four divisions based primarily on Gram staining, based on molecular studies of the 16S sequences, Woese recognised twelve bacterial phyla. Two of these were both gram-positive and were divided on the proportion of the guanine and cytosine content in their DNA, the high G + C phylum was made up of the Actinobacteria and the low G + C phylum contained the Firmicutes. The Actinobacteria include the Corynebacterium, Mycobacterium, Nocardia and Streptomyces genera, the Firmicutes, have a 45–60% GC content, but this is lower than that of the Actinobacteria. The gram-positive and gram-negative staining response is not a reliable characteristic as these two kinds of bacteria do not form phylogenetic coherent groups. All gram-positive bacteria are bounded by a lipid membrane, and, in general. For the bacterial cells bounded by a cell membrane, the term monoderm bacteria or monoderm prokaryotes has been proposed. The presence of inner and outer cell membranes defines a new compartment in these cells and these bacteria have been designated as diderm bacteria. The distinction between the monoderm and diderm bacteria is supported by conserved signature indels in a number of important proteins, of these two structurally distinct groups of bacteria, monoderms are indicated to be ancestral. In general, gram-positive bacteria are monoderms and have a lipid bilayer whereas gram-negative bacteria are diderms and have two bilayers
13.
Catalase
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Catalase is a common enzyme found in nearly all living organisms exposed to oxygen. It catalyzes the decomposition of hydrogen peroxide to water and oxygen and it is a very important enzyme in protecting the cell from oxidative damage by reactive oxygen species. Likewise, catalase has one of the highest turnover numbers of all enzymes, one molecule can convert millions of hydrogen peroxide molecules to water. Catalase is a tetramer of four chains, each over 500 amino acids long. It contains four heme groups that allow the enzyme to react with the hydrogen peroxide. The optimum pH for human catalase is approximately 7, and has a broad maximum. The pH optimum for other catalases varies between 4 and 11 depending on the species, the optimum temperature also varies by species. Human catalase forms a tetramer composed of four subunits, each of which can be divided into four domains. The extensive hydrophobic core of each subunit is generated by an eight-stranded antiparallel b-barrel, with nearest neighbor connectivity capped by b-barrel loops on one side and a9 on the other. A helical domain at one face of the b-barrel is composed of four C-terminal helices, catalase was not noticed until 1818 when Louis Jacques Thénard, who discovered H2O2, suggested its breakdown is caused by an unknown substance. In 1900, Oscar Loew was the first to give it the name catalase, in 1937 catalase from beef liver was crystallised by James B. Sumner and Alexander Dounce and the weight was found in 1938. In 1969, the amino acid sequence of bovine catalase was discovered, then in 1981, the three-dimensional structure of the protein was revealed. The formation of bubbles, oxygen, indicates a positive result and this easy assay, which can be seen with the naked eye, without the aid of instruments, is possible because catalase has a very high specific activity, which produces a detectable response. Alternative splicing may result in different protein variants, Fe-E is a mesomeric form of Fe-E, meaning the iron is not completely oxidized to +V, but receives some stabilising electron density from the heme ligand. This heme has to be drawn then as a radical cation, as hydrogen peroxide enters the active site, it interacts with the amino acids Asn148 and His75, causing a proton to transfer between the oxygen atoms. The free oxygen atom coordinates, freeing the newly formed water molecule, Fe=O reacts with a second hydrogen peroxide molecule to reform Fe-E and produce water and oxygen. The reactivity of the center may be improved by the presence of the phenolate ligand of Tyr358 in the fifth iron ligand
14.
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
15.
Ruminant
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Ruminants are mammals that are able to acquire nutrients from plant-based food by fermenting it in a specialized stomach prior to digestion, principally through microbial actions. The process typically requires the fermented ingesta to be regurgitated and chewed again, the process of rechewing the cud to further break down plant matter and stimulate digestion is called rumination. The word ruminant comes from the Latin ruminare, which means to chew over again, the roughly 150 species of ruminants includes both domestic and wild species. Ruminating mammals include cattle, goats, sheep, giraffes, yaks, deer, antelope and it has also been suggested that notoungulates also relied on rumination, as opposed to other antlantogenates that relied on the more typical hindgut fermentation, though this is not entirely certain. Taxonomically, the suborder Ruminantia is a lineage of herbivorous artiodactyls that includes the most advanced, the term ruminant is not synonymous with Ruminantia. The suborder Ruminantia includes many ruminant species, but does not include tylopods, the primary difference between a ruminant and nonruminant is that ruminants have a four-compartment stomach. The four parts are the rumen, reticulum, omasum, in the first two chambers, the rumen and the reticulum, the food is mixed with saliva and separates into layers of solid and liquid material. Solids clump together to form the cud or bolus, the cud is then regurgitated and chewed to completely mix it with saliva and to break down the particle size. Fiber, especially cellulose and hemicellulose, is broken down in these chambers by microbes into the three volatile fatty acids, acetic acid, propionic acid, and butyric acid. Protein and nonstructural carbohydrate are also fermented, though the rumen and reticulum have different names, they represent the same functional space as digesta can move back and forth between them. Together, these chambers are called the reticulorumen, after this, the digesta is moved to the true stomach, the abomasum. The abomasum is the equivalent of the monogastric stomach. Digesta is finally moved into the intestine, where the digestion and absorption of nutrients occurs. Microbes produced in the reticulorumen are also digested in the small intestine, fermentation continues in the large intestine in the same way as in the reticulorumen. Only small amounts of glucose are absorbed from dietary carbohydrates, most dietary carbohydrates are fermented into VFAs in the rumen. The VFA propionate is used for around 70% of the glucose and glycogen produced, also, some mammals are pseudoruminants, which have a three-compartment stomach instead of four like ruminants. Pseudoruminants, like traditional ruminants, are foregut fermentors and most ruminate or chew cud, however, their anatomy and method of digestion differs significantly from that of a four-chambered ruminant. Monogastric herbivores, such as rhinoceroses, horses, and rabbits, are not ruminants and these hindgut fermenters digest cellulose in an enlarged cecum through the reingestion of the cecotrope
16.
Genus
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A genus is a taxonomic rank used in the biological classification of living and fossil organisms in biology. In the hierarchy of classification, genus comes above species. In binomial nomenclature, the name forms the first part of the binomial species name for each species within the genus. Felis catus and Felis silvestris are two species within the genus Felis, Felis is a genus within the family Felidae. The composition of a genus is determined by a taxonomist, the standards for genus classification are not strictly codified, so different authorities often produce different classifications for genera. Moreover, genera should be composed of units of the same kind as other genera. The term comes from the Latin genus, a noun form cognate with gignere, linnaeus popularized its use in his 1753 Species Plantarum, but the French botanist Joseph Pitton de Tournefort is considered the founder of the modern concept of genera. The scientific name of a genus may be called the name or generic epithet. It plays a role in binomial nomenclature, the system of naming organisms. The rules for the names of organisms are laid down in the Nomenclature Codes. The standard way of scientifically describing species and other lower-ranked taxa is by binomial nomenclature, the generic name forms its first half. For example, the gray wolfs binomial name is Canis lupus, with Canis being the name shared by the wolfs close relatives. The specific name is written in lower-case and may be followed by names in zoology or a variety of infraspecific names in botany. Especially with these names, when the generic name is known from context. Because animals are typically only grouped within subspecies, it is written as a trinomen with a third name. Dog breeds, meanwhile, are not scientifically distinguished, there are several divisions of plant species and therefore their infraspecific names generally include contractions explaining the relation. For example, the genus Hibiscus includes hundreds of other species apart from the Rose of Sharon or common garden hibiscus, Rose of Sharon doesnt have subspecies but has cultivars that carry desired traits, such as the bright white H. syriaca Diana. Hawaiian hibiscus, meanwhile, includes several separate species, since not all botanists agree on the divisions or names between species, it is common to specify the source of the name using author abbreviations
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Endospore
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An endospore is a dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum. The name endospore is suggestive of a spore or seed-like form and it is a stripped-down, dormant form to which the bacterium can reduce itself. Endospore formation is triggered by a lack of nutrients. In endospore formation, the bacterium divides within its cell wall, one side then engulfs the other. Endospores enable bacteria to lie dormant for extended periods, even centuries, revival of spores millions of years old has been claimed. When the environment becomes more favorable, the endospore can reactivate itself to the vegetative state, most types of bacteria cannot change to the endospore form. Examples of bacteria that can form endospores include Bacillus and Clostridium, the endospore consists of the bacteriums DNA, ribosomes and large amounts of dipicolinic acid. Dipicolinic acid is a chemical that appears to help in the ability for endospores to maintain dormancy. This chemical comprises up to 10% of the dry weight. They are resistant to radiation, desiccation, high temperature, extreme freezing. Thermo-resistant endospores were first hypothesized by Ferdinand Cohn after studying Bacillus subtilis growth on cheese after boiling the cheese and his notion of spores being the reproductive mechanism for the growth was a large blow to the previous suggestions of spontaneous generation. Astrophysicist Steinn Sigurdsson said There are viable bacterial spores that have found that are 40 million years old on Earth –. Common anti-bacterial agents that work by destroying vegetative cell walls do not affect endospores, endospores are commonly found in soil and water, where they may survive for long periods of time. A variety of different microorganisms form spores or cysts, but the endospores of low G+C gram-positive bacteria are by far the most resistant to harsh conditions, some classes of bacteria can turn into exospores, also known as microbial cysts, instead of endospores. Exospores and endospores are two kinds of hibernating or dormant stages seen in classes of microorganisms. Bacteria produce a single endospore internally, the spore is sometimes surrounded by a thin covering known as the exosporium, which overlies the spore coat. The spore coat, which acts like a sieve that excludes large toxic molecules like lysozyme, is resistant to many toxic molecules, the cortex lies beneath the spore coat and consists of peptidoglycan. The core wall lies beneath the cortex and surrounds the protoplast or core of the endospore, the core contains the spore chromosomal DNA which is encased in chromatin-like proteins known as SASPs, that protect the spore DNA from UV radiation and heat
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Obligate aerobe
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An obligate aerobe is an organism that requires oxygen to grow. Through cellular respiration, these organisms use oxygen to metabolise substances, like sugars or fats, in this type of respiration, oxygen serves as the terminal electron acceptor for the electron transport chain. Aerobic respiration has the advantage of yielding more energy than fermentation or anaerobic respiration, examples of obligately aerobic bacteria include Mycobacterium tuberculosis and Nocardia asteroides. With the exception of the yeasts, most fungi are obligate aerobes, also, almost all algae are obligate aerobes. Aerobic respiration Anaerobic respiration Fermentation Obligate anaerobe Facultative anaerobe Microaerophile
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Model organism
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Model organisms are in vivo models and are widely used to research human disease when human experimentation would be unfeasible or unethical. This strategy is made possible by the descent of all living organisms. Studying model organisms can be informative, but care must be taken when extrapolating from one organism to another, in researching human disease, model organisms allow for better understanding the disease process without the added risk of harming an actual human. The species chosen will usually meet a determined taxonomic equivalency to humans, although biological activity in a model organism does not ensure an effect in humans, many drugs, treatments and cures for human diseases are developed in part with the guidance of animal models. There are three types of disease models, homologous, isomorphic and predictive. Homologous animals have the same causes, symptoms and treatment options as would humans who have the same disease, isomorphic animals share the same symptoms and treatments. Predictive models are similar to a human disease in only a couple of aspects. The use of animals in research dates back to ancient Greece, with Aristotle, research using animal models has been central to most of the achievements of modern medicine. It has contributed most of the knowledge in fields such as human physiology and biochemistry. For example, the results have included the near-eradication of polio and the development of organ transplantation, from 1910 to 1927, Thomas Hunt Morgans work with the fruit fly Drosophila melanogaster identified chromosomes as the vector of inheritance for genes. Drosophila became one of the first, and for some time the most widely used, model organisms, D. melanogaster remains one of the most widely used eukaryotic model organisms. The mouse has since been used extensively as an organism and is associated with many important biological discoveries of the 20th. In the late 19th century, Emil von Behring isolated the diphtheria toxin and he went on to develop an antitoxin against diphtheria in animals and then in humans, which resulted in the modern methods of immunization and largely ended diphtheria as a threatening disease. The diphtheria antitoxin is famously commemorated in the Iditarod race, which is modeled after the delivery of antitoxin in the 1925 serum run to Nome. The success of animal studies in producing the diphtheria antitoxin has also attributed as a cause for the decline of the early 20th-century opposition to animal research in the United States. This led to the 1922 discovery of insulin and its use in treating diabetes, modern general anaesthetics, such as halothane and related compounds, were also developed through studies on model organisms, and are necessary for modern, complex surgical operations. In the 1940s, Jonas Salk used rhesus monkey studies to isolate the most virulent forms of the polio virus, the vaccine, which was made publicly available in 1955, reduced the incidence of polio 15-fold in the United States over the following five years. It has been estimated that developing and producing the vaccines required the use of 100,000 rhesus monkeys, models are those organisms with a wealth of biological data that make them attractive to study as examples for other species and/or natural phenomena that are more difficult to study directly
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Bacillus (shape)
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A bacillus is a rod-shaped bacterium. Bacilli are found in different taxonomic groups of bacteria. However, the name Bacillus, capitalized and italicized, refers to a genus of bacteria. The name Bacilli, capitalized but not italicized, can refer to a less specific taxonomic group of bacteria that includes two orders, one of which contains the genus Bacillus. When the word is formatted with a lowercase and not italicized, bacillus, it will most likely be referring to shape, the shape bacillus can also be called rods. Bacilli usually divide in the plane and are solitary, but can combine to form diplobacilli, streptobacilli. Diplobacilli, Two bacilli arranged side by side each other. Coccobacillus, Oval and similar to coccus, there is no connection between the shape of a bacterium and its color in the Gram staining. MacConkey agar can be used to distinguish among Gram negative bacilli such as E. coli and salmonella
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Ferdinand Cohn
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Ferdinand Julius Cohn was a German biologist. He is one of the founders of bacteriology and microbiology. Ferdinand J. Cohn was born in the Jewish quarter of Breslau in the Prussian Province of Silesia and his father, Issak Cohn, was a successful merchant and manufacturer. At the age of 10 Ferdinand suffered hearing impairment, starting at age 16 he studied botany under Heinrich Goppert at the University of Breslau. Due to Cohns Jewish background he was prevented from taking the degree examinations at Breslau. He then moved to the University of Berlin, at age 19 in 1847 he received a degree in botany at Berlin. He remained studying botany for another couple of years in Berlin, in 1849 he returned to the University of Breslau and he remained at that university for the rest of his career as a teacher and researcher. On his initial return to Breslau in his twenties, his father had bought for him a large. This microscope, which the University of Breslau and most universities did not have, was Ferdinand Cohns main research tool in the 1850s, in the 1850s he studied the growth and division of plant cells. In 1855 he produced papers on the sexuality of Sphaeroplea annulina, in the 1860s he studied plant physiology in several different aspects. From 1870 onward he mostly studied bacteria and he established the use of sterile culture mediums and rediscovered the botanical garden of Lorenz Scholz von Rosenau in Breslau. He published over 150 research reports during his lifetime, the University of Breslau became an innovative center for plant physiology and microbiology while he was there. Cohn was the first to classify algae as plants, and to define what distinguishes them from green plants and his classification of bacteria into four groups based on shape is still in use today. In 1885 he received the Leeuwenhoek Medal, Jewish Encyclopedia entry for Ferdinand Julius Cohn Ferdinand Cohn in the Encyclopedia of World Biography, published by Gale Group
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Flagellate
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A flagellate is a cell or organism with one or more whip-like organelles called flagella. The word flagellate also describes a particular characteristic of many protists. The term presently does not imply any specific relationship or classification of the organisms that possess flagellae, however, the term flagellate is included in other terms which are more formally characterized. Eukaryotic flagella are supported by microtubules in an arrangement, with nine fused pairs surrounding two central singlets. These arise from a basal body, in some flagellates, flagella direct food into a cytostome or mouth, where food is ingested. Flagella often support hairs, called mastigonemes, or contain rods and their ultrastructure plays an important role in classifying eukaryotes. Among protoctists and microscopic animals, a flagellate is an organism with one or more whip-like organelles called flagella, some cells in animals may be flagellate, for instance the spermatozoa of most phyla. Flowering plants do not produce flagellate cells, but ferns, mosses, green algae, likewise, most fungi do not produce cells with flagellae, but the primitive fungal chytrids do. Many protists take the form of single-celled flagellates, flagella are generally used for propulsion. They may also be used to create a current that brings in food, in most such organisms, one or more flagella are located at or near the anterior of the cell, e. g. Euglena. Often there is one directed forwards and one trailing behind, among animals, fungi, and Choanozoa, which make up a group called the opisthokonts, there is a single posterior flagellum. They are from the phylum Mastigophora and they can cause diseases and are typically heterotrophic. They reproduce by binary fission. They spend most of their existence moving or feeding, many parasites that affect human health or economy are flagellates. Flagellates are the consumers of primary and secondary production in aquatic ecosystems - consuming bacteria. They were sometimes grouped with Sarcodina in Sarcomastigophora, presently, these groups are known to be highly polyphyletic. Another term used is monadoid, from monad. as in Monas, flagellata at the US National Library of Medicine Medical Subject Headings Leadbeater, B. S. C
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Genetic engineering
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Genetic engineering, also called genetic modification, is the direct manipulation of an organisms genome using biotechnology. It is a set of used to change the genetic makeup of cells, including the transfer of genes within. Genes may be removed, or knocked out, using a nuclease, gene targeting is a different technique that uses homologous recombination to change an endogenous gene, and can be used to delete a gene, remove exons, add a gene, or introduce point mutations. An organism that is generated through genetic engineering is considered to be a modified organism. The first GMOs were bacteria generated in 1973 and GM mice in 1974, insulin-producing bacteria were commercialized in 1982 and genetically modified food has been sold since 1994. GloFish, the first GMO designed as a pet, was first sold in the United States in December 2003, Genetic engineering techniques have been applied in numerous fields including research, agriculture, industrial biotechnology, and medicine. However the European Commission has also defined genetic engineering broadly as including selective breeding, cloning and stem cell research, although not considered genetic engineering, are closely related and genetic engineering can be used within them. Synthetic biology is a discipline that takes genetic engineering a step further by introducing artificially synthesized material from raw materials into an organism. If genetic material from another species is added to the host, if genetic material from the same species or a species that can naturally breed with the host is used the resulting organism is called cisgenic. Genetic engineering can also be used to remove material from the target organism. In Europe genetic modification is synonymous with genetic engineering while within the United States of America it can refer to conventional breeding methods. The Canadian regulatory system is based on whether a product has novel features regardless of method of origin, within the scientific community, the term genetic engineering is not commonly used, more specific terms such as transgenic are preferred. Plants, animals or micro organisms that have changed through genetic engineering are termed genetically modified organisms or GMOs, bacteria were the first organisms to be genetically modified. Plasmid DNA containing new genes can be inserted into the bacterial cell and these genes can code for medicines or enzymes that process food and other substrates. Plants have been modified for insect protection, herbicide resistance, virus resistance, enhanced nutrition, tolerance to environmental pressures, most commercialised GMOs are insect resistant and/or herbicide tolerant crop plants. Genetically modified animals have used for research, model animals. The genetically modified animals include animals with genes knocked out, increased susceptibility to disease, hormones for extra growth, humans have altered the genomes of species for thousands of years through selective breeding, or artificial selection as contrasted with natural selection, and more recently through mutagenesis. Genetic engineering as the manipulation of DNA by humans outside breeding
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Spore
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In biology, a spore is a unit of sexual or asexual reproduction that may be adapted for dispersal and for survival, often for extended periods of time, in unfavorable conditions. Spores form part of the cycles of many plants, algae, fungi. Bacterial spores are not part of a sexual cycle but are resistant structures used for survival under unfavourable conditions, spores are usually haploid and unicellular and are produced by meiosis in the sporangium of a diploid sporophyte. Under favourable conditions the spore can develop into a new organism using mitotic division, producing a multicellular gametophyte, two gametes fuse to form a zygote which develops into a new sporophyte. This cycle is known as alternation of generations, the term spore derives from the ancient Greek word σπορά spora, meaning seed, sowing, related to σπόρος sporos, sowing, and σπείρειν speirein, to sow. Spores germinate to give rise to haploid gametophytes, while seeds germinate to give rise to diploid sporophytes, vascular plant spores are always haploid. Vascular plants are either homosporous or heterosporous, plants that are homosporous produce spores of the same size and type. Spores can be classified in several ways, In fungi and fungus-like organisms, spores are often classified by the structure in which meiosis, since fungi are often classified according to their spore-producing structures, these spores are often characteristic of a particular taxon of the fungi. Sporangiospores, spores produced by a sporangium in many such as zygomycetes. Zygospores, spores produced by a zygosporangium, characteristic of zygomycetes, ascospores, spores produced by an ascus, characteristic of ascomycetes. Basidiospores, spores produced by a basidium, characteristic of basidiomycetes, aeciospores, spores produced by an aecium in some fungi such as rusts or smuts. Urediniospores, spores produced by a uredinium in some such as rusts or smuts. Teliospores, spores produced by a telium in some such as rusts or smuts. Oospores, spores produced by an oogonium, characteristic of oomycetes, carpospores, spores produced by a carposporophyte, characteristic of red algae. Tetraspores, spores produced by a tetrasporophyte, characteristic of red algae, chlamydospores, thick-walled resting spores of fungi produced to survive unfavorable conditions. Parasitic fungal spores may be classified into internal spores, which germinate within the host, meiospores, spores produced by meiosis, they are thus haploid, and give rise to a haploid daughter cell or a haploid individual. Examples are the cells of gametophytes of seed plants found in flowers or cones. Microspores, meiospores that give rise to a male gametophyte, megaspores, meiospores that give rise to a female gametophyte
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Cellular differentiation
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In developmental biology, cellular differentiation is the process where a cell changes from one cell type to another. Most commonly the cell changes to a specialized type. Differentiation occurs numerous times during the development of an organism as it changes from a simple zygote to a complex system of tissues. Differentiation continues in adulthood as adult stem cells divide and create fully differentiated daughter cells during tissue repair, some differentiation occurs in response to antigen exposure. Differentiation dramatically changes a cells size, shape, membrane potential, metabolic activity and these changes are largely due to highly controlled modifications in gene expression and are the study of epigenetics. With a few exceptions, cellular differentiation almost never involves a change in the DNA sequence itself, thus, different cells can have very different physical characteristics despite having the same genome. There are multiple levels of potency, the cells ability to differentiate into other cell types. A greater potency indicates a number of cells that can be derived. A cell that can differentiate into all types, including the placental tissue, is known as totipotent. In mammals, only the zygote and subsequent blastomeres are totipotent, a cell that can differentiate into all cell types of the adult organism is known as pluripotent. Such cells are called meristematic cells in plants and embryonic stem cells in animals. Virally induced expression of four transcription factors Oct4, Sox2, c-Myc, a multipotent cell is one that can differentiate into multiple different, but closely related cell types. Oligopotent cells are more restricted than multipotent, but can still differentiate into a few closely related cell types, finally, unipotent cells can differentiate into only one cell type, but are capable of self-renewal. In cytopathology, the level of differentiation is used as a measure of cancer progression. Grade is a marker of how differentiated a cell in a tumor is, three basic categories of cells make up the mammalian body, germ cells, somatic cells, and stem cells. Most cells are diploid, they have two copies of each chromosome, such cells, called somatic cells, make up most of the human body, such as skin and muscle cells. Cells differentiate to specialize for different functions, germ line cells are any line of cells that give rise to gametes—eggs and sperm—and thus are continuous through the generations. Stem cells, on the hand, have the ability to divide for indefinite periods
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Escherichia coli
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Escherichia coli is a gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes can cause food poisoning in their hosts. The harmless strains are part of the flora of the gut, and can benefit their hosts by producing vitamin K2. E. coli is expelled into the environment within fecal matter, the bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards. E. coli and other facultative anaerobes constitute about 0. 1% of gut flora, cells are able to survive outside the body for a limited amount of time, which makes them potential indicator organisms to test environmental samples for fecal contamination. A growing body of research, though, has examined environmentally persistent E. coli which can survive for extended periods outside of a host, the bacterium can be grown and cultured easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is a chemoheterotroph whose chemically defined medium must include a source of carbon, under favorable conditions, it takes only 20 minutes to reproduce. E. coli is a Gram-negative, facultative anaerobic and nonsporulating bacterium, cells are typically rod-shaped, and are about 2.0 μm long and 0. 25–1.0 μm in diameter, with a cell volume of 0. 6–0.7 μm3. E. coli stains Gram-negative because its cell wall is composed of a peptidoglycan layer. During the staining process, E. coli picks up the color of the counterstain safranin, the outer membrane surrounding the cell wall provides a barrier to certain antibiotics such that E. coli is not damaged by penicillin. Strains that possess flagella are motile, the flagella have a peritrichous arrangement. E. coli can live on a variety of substrates and uses mixed-acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate. Optimum growth of E. coli occurs at 37 °C, and it uses oxygen when it is present and available. It can, however, continue to grow in the absence of oxygen using fermentation or anaerobic respiration, the ability to continue growing in the absence of oxygen is an advantage to bacteria because their survival is increased in environments where water predominates. The bacterial cell cycle is divided into three stages, the B period occurs between the completion of cell division and the beginning of DNA replication. The C period encompasses the time it takes to replicate the chromosomal DNA, the D period refers to the stage between the conclusion of DNA replication and the end of cell division. The doubling rate of E. coli is higher when more nutrients are available, However, the length of the C and D periods do not change, even when the doubling time becomes less than the sum of the C and D periods. At the fastest growth rates, replication begins before the round of replication has completed, resulting in multiple replication forks along the DNA
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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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Gut flora
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Gut flora is the complex community of microorganisms that live in the digestive tracts of humans and other animals, including insects. The gut metagenome is the aggregate of all the genomes of gut microbiota, the gut is one niche that human microbiota inhabit. In humans, the gut microbiota has the largest numbers of bacteria, the relationship between some gut flora and humans is not merely commensal, but rather a mutualistic relationship. Some human gut microorganisms benefit the host by fermenting dietary fiber into short-chain fatty acids, such as acid and butyric acid. Intestinal bacteria also play a role in synthesizing vitamin B and vitamin K as well as metabolizing bile acids, sterols, the composition of human gut flora changes over time, when the diet changes, and as overall health changes. The microbial composition of the gut flora varies across the digestive tract, in the stomach and small intestine, relatively few species of bacteria are generally present. The colon, in contrast, contains a densely-populated microbial ecosystem with up to 1012 cells per gram of intestinal content and these bacteria represent between 300 and 1000 different species. However, 99% of the come from about 30 or 40 species. As a consequence of their abundance in the intestine, bacteria also make up to 60% of the dry mass of feces, fungi, archaea, and viruses are also present in the gut flora, but less is known about their activities. Over 99% of the bacteria in the gut are anaerobes, but in the cecum and it is estimated that these gut flora have around a hundred times as many genes in total as there are in the human genome. Many species in the gut have not been studied outside of their hosts because most cannot be cultured, while there are a small number of core species of microbes shared by most individuals, populations of microbes can vary widely among different individuals. Within an individual, microbe populations stay fairly constant over time, even though some alterations may occur with changes in lifestyle, diet, the Human Microbiome Project has set out to better describe the microflora of the human gut and other body locations. The four dominant bacterial phyla in the gut are Firmicutes, Bacteroidetes, Actinobacteria. Most bacteria belong to the genera Bacteroides, Clostridium, Faecalibacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, other genera, such as Escherichia and Lactobacillus, are present to a lesser extent. Species from the genus Bacteroides alone constitute about 30% of all bacteria in the gut, fungal genera that have been detected in the gut include Candida, Saccharomyces, Aspergillus, Penicillium, Rhodotorula, Trametes, Pleospora, Sclerotinia, Bullera, and Galactomyces, among others. Rhodotorula is most frequently found in individuals with inflammatory bowel disease while Candida is most frequently found in individuals with hepatitis B cirrhosis, archaea constitute another large class of gut flora which are important in the metabolism of the bacterial products of fermentation. An enterotype is a classification of living based on its bacteriological ecosystem in the human gut microbiome not dictated by age, gender, body weight. There are indications that long-term diet influences enterotype, three human enterotypes have been proposed, but these claims remain highly controversial
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Cell division
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Cell division is the process by which a parent cell divides into two or more daughter cells. Cell division usually occurs as part of a cell cycle. Meiosis results in four daughter cells by undergoing one round of DNA replication followed by two divisions. Homologous chromosomes are separated in the first division, and sister chromatids are separated in the second division, both of these cell division cycles are used in the process of sexual reproduction at some point in their life cycle. Both are believed to be present in the last eukaryotic common ancestor, prokaryotes undergo a vegetative cell division known as binary fission, where their genetic material is segregated equally into two daughter cells. All cell divisions, regardless of organism, are preceded by a round of DNA replication. For simple unicellular organisms such as the amoeba, one cell division is equivalent to reproduction – an entire new organism is created, on a larger scale, mitotic cell division can create progeny from multicellular organisms, such as plants that grow from cuttings. Mitotic cell division enables sexually reproducing organisms to develop from the one-celled zygote, after growth, cell division by mitosis allows for continual construction and repair of the organism. The human body experiences about 10 quadrillion cell divisions in a lifetime, the primary concern of cell division is the maintenance of the original cells genome. Before division can occur, the information that is stored in chromosomes must be replicated. A great deal of infrastructure is involved in keeping genomic information consistent between generations. Interphase is the process a cell must go through mitosis, meiosis. Interphase consists of four stages, G1, S, G2. If the cell does not progress through G1, the cell enters a stage called G0. In G0, cells are living but they are put on hold. The cells may later be called back into interphase if needed at a later time, there are checkpoints during interphase that allow the cell to be either progressed or denied further development. In S phase, the chromosomes are replicated in order for the content to be maintained. During G2, the cell undergoes the final stages of growth before it enters the M phase, the M phase, can be either mitosis or meiosis depending on the type of cell
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Drought
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A drought is a period of below-average precipitation in a given region, resulting in prolonged shortages in its water supply, whether atmospheric, surface water or ground water. A drought can last for months or years, or may be declared after as few as 15 days and it can have a substantial impact on the ecosystem and agriculture of the affected region and harm to the local economy. Annual dry seasons in the tropics significantly increase the chances of a drought developing, periods of heat can significantly worsen drought conditions by hastening evaporation of water vapour. Many plant species, such as those in the family Cactaceae, have drought tolerance adaptations like reduced leaf area, some others survive dry periods as buried seeds. Semi-permanent drought produces arid biomes such as deserts and grasslands, prolonged droughts have caused mass migrations and humanitarian crises. Most arid ecosystems have inherently low productivity, the most prolonged drought ever in the world in recorded history occurred in the Atacama Desert in Chile. Mechanisms of producing precipitation include convective, stratiform, and orographic rainfall, precipitation can be divided into three categories, based on whether it falls as liquid water, liquid water that freezes on contact with the surface, or ice. Drought are mainly course by in low rain areas, if these factors do not support precipitation volumes sufficient to reach the surface over a sufficient time, the result is a drought. Once a region is within drought, feedback mechanisms such as local arid air, hot conditions which can promote warm core ridging, within the tropics, distinct, wet and dry seasons emerge due to the movement of the Intertropical Convergence Zone or Monsoon trough. The dry season greatly increases drought occurrence, and is characterized by its low humidity, with watering holes, because of the lack of these watering holes, many grazing animals are forced to migrate due to the lack of water and feed to more fertile spots. Examples of such animals are zebras, elephants, and wildebeest, because of the lack of water in the plants, bushfires are common. Since water vapor becomes more energetic with increasing temperature, more water vapor is required to increase relative humidity values to 100% at higher temperatures, periods of warmth quicken the pace of fruit and vegetable production, increase evaporation and transpiration from plants, and worsen drought conditions. Drier and hotter weather occurs in parts of the Amazon River Basin, Colombia, winters during the El Niño are warmer and drier than average conditions in the Northwest, northern Midwest, and northern Mideast United States, so those regions experience reduced snowfalls. Conditions are also drier than normal from December to February in south-central Africa, mainly in Zambia, Zimbabwe, Mozambique, and Botswana. Direct effects of El Niño resulting in drier conditions occur in parts of Southeast Asia and Northern Australia, increasing bush fires, worsening haze, drier-than-normal conditions are also in general observed in Queensland, inland Victoria, inland New South Wales, and eastern Tasmania from June to August. As warm water spreads from the west Pacific and the Indian Ocean to the east Pacific, it causes extensive drought in the western Pacific. Singapore experienced the driest February in 2014 since records began in 1869, with only 6.3 mm of rain falling in the month, the years 1968 and 2005 had the next driest Februaries, when 8.4 mm of rain fell. Human activity can directly trigger exacerbating factors such as farming, excessive irrigation, deforestation
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Salinity
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Salinity is the saltiness or amount of salt dissolved in a body of water. This is usually measured in g salt k g sea water, a contour line of constant salinity is called an isohaline – or sometimes isohale. Salinity in rivers, lakes, and the ocean is conceptually simple, conceptually the salinity is the quantity of dissolved salt content of the water. Salts are compounds like sodium chloride, magnesium sulfate, potassium nitrate, the concentration of dissolved chloride ions is sometimes referred to as chlorinity. Operationally, dissolved matter is defined as that which can pass through a fine filter. Salinity can be expressed in the form of a mass fraction, Seawater typically has a mass salinity of around 35 g/kg, although lower values are typical near coasts where rivers enter the ocean. Rivers and lakes can have a range of salinities, from less than 0.01 g/kg to a few g/kg. The Dead Sea has a salinity of more than 200 g/kg, whatever pore size is used in the definition, the resulting salinity value of a given sample of natural water will not vary by more than a few percent. A bottled seawater product known as IAPSO Standard Seawater is used by oceanographers to standardize their measurements with enough precision to meet this requirement, measurement and definition difficulties arise because natural waters contain a complex mixture of many different elements from different sources in different molecular forms. The chemical properties of some of these depend on temperature and pressure. Many of these forms are difficult to measure with high accuracy, different practical definitions of salinity result from different attempts to account for these problems, to different levels of precision, while still remaining reasonably easy to use. For many purposes this sum can be limited to a set of eight major ions in natural waters, the major ions dominate the inorganic composition of most natural waters. Exceptions include some pit lakes and waters from some hydrothermal springs, the concentrations of dissolved gases like oxygen and nitrogen are not usually included in descriptions of salinity. However, carbon dioxide gas, which when dissolved is partially converted into carbonates and bicarbonates, is often included. Silicon in the form of acid, which usually appears as a neutral molecule in the pH range of most natural waters. The term salinity is, for oceanographers, usually associated with one of a set of measurement techniques. As the dominant techniques evolve, so do different descriptions of salinity, the distinctions between these different descriptions are important to physical oceanographers but are obscure and confusing to nonspecialists. Salinities were largely measured using titration-based techniques before the 1980s, titration with silver nitrate could be used to determine the concentration of halide ions to give a chlorinity
32.
Radiation
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In physics, radiation is the emission or transmission of energy in the form of waves or particles through space or through a material medium. Radiation is often categorized as either ionizing or non-ionizing depending on the energy of the radiated particles, Ionizing radiation carries more than 10 eV, which is enough to ionize atoms and molecules, and break chemical bonds. This is an important distinction due to the difference in harmfulness to living organisms. A common source of ionizing radiation is radioactive materials that emit α, β, or γ radiation, consisting of helium nuclei, electrons or positrons, gamma rays, X-rays and the higher energy range of ultraviolet light constitute the ionizing part of the electromagnetic spectrum. The lower-energy, longer-wavelength part of the spectrum including visible light, infrared light, microwaves and this type of radiation only damages cells if the intensity is high enough to cause excessive heating. Ultraviolet radiation has some features of both ionizing and non-ionizing radiation and these properties derive from ultraviolets power to alter chemical bonds, even without having quite enough energy to ionize atoms. The word radiation arises from the phenomenon of waves radiating from a source and this aspect leads to a system of measurements and physical units that are applicable to all types of radiation. This law does not apply close to a source of radiation or for focused beams. Radiation with sufficiently high energy can ionize atoms, that is to say it can knock electrons off atoms, ionization occurs when an electron is stripped from an electron shell of the atom, which leaves the atom with a net positive charge. Because living cells and, more importantly, the DNA in those cells can be damaged by this ionization, thus ionizing radiation is somewhat artificially separated from particle radiation and electromagnetic radiation, simply due to its great potential for biological damage. While an individual cell is made of trillions of atoms, only a fraction of those will be ionized at low to moderate radiation powers. If the source of the radiation is a radioactive material or a nuclear process such as fission or fusion. Particle radiation is subatomic particles accelerated to relativistic speeds by nuclear reactions, because of their momenta they are quite capable of knocking out electrons and ionizing materials, but since most have an electrical charge, they dont have the penetrating power of ionizing radiation. The exception is neutron particles, see below, there are several different kinds of these particles, but the majority are alpha particles, beta particles, neutrons, and protons. Roughly speaking, photons and particles with energies above about 10 electron volts are ionizing, particle radiation from radioactive material or cosmic rays almost invariably carries enough energy to be ionizing. The radiation is invisible and not directly detectable by human senses, as a result, in some cases, it may lead to secondary emission of visible light upon its interaction with matter, as in the case of Cherenkov radiation and radio-luminescence. Ionizing radiation has many uses in medicine, research and construction. Ultraviolet, of wavelengths from 10 nm to 125 nm, ionizes air molecules, causing it to be absorbed by air
33.
Motility
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In biology, motility is the ability to move spontaneously and actively, consuming energy in the process. It is not to be confused with mobility, which describes the ability of an object to be moved, motility is genetically determined but may be affected by environmental factors. For instance, muscles give animals motility but the consumption of hydrogen cyanide would adversely affect muscle physiology causing them to stiffen leading to rigor mortis. Most animals are motile but the term applies to unicellular and simple multicellular organisms, as well as to some mechanisms of fluid flow in multicellular organs, motile marine animals are commonly called free-swimming. Motility may also refer to an ability to move food through its digestive tract. An example of intestinal motility is the contraction of muscles in the gastrointestinal tract. The nervous system and musculoskeletal system control the majority of mammalian motility
34.
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
35.
Antibiotic
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Antibiotics, also called antibacterials, are a type of antimicrobial drug used in the treatment and prevention of bacterial infections. They may either kill or inhibit the growth of bacteria, a limited number of antibiotics also possess antiprotozoal activity. Antibiotics are not effective against viruses such as the cold or influenza. Drugs which inhibit viruses are termed antiviral drugs or antivirals rather than antibiotics, sometimes the term antibiotic is used to refer to any substance used against microbes, synonymous with antimicrobial. Some sources distinguish between antibacterial and antibiotic, antibacterials are used in soaps and disinfectants, while antibiotics are used as medicine, Antibiotics revolutionized medicine in the 20th century, and have together with vaccination led to the near eradication of diseases such as tuberculosis in the developed world. However, their effectiveness and easy access led to overuse, especially in raising, prompting bacteria to develop resistance. All classes of antibiotics in use today were first discovered prior to the mid 1980s, substances with antibiotic properties had been used for various purposes since ancient times. Before the early 20th century, treatments for infections were based primarily on medicinal folklore, mixtures with antimicrobial properties that were used in treatments of infections were described over 2000 years ago. Many ancient cultures, including the ancient Egyptians and ancient Greeks, used specially selected mold and plant materials, more recent observations made in the laboratory of antibiosis between microorganisms led to the discovery of natural antibacterials produced by microorganisms. Louis Pasteur observed, if we could intervene in the antagonism observed between some bacteria, it would offer perhaps the greatest hopes for therapeutics. In 1874, physician Sir William Roberts noted that cultures of the mold Penicillium glaucum that is used in the making of types of blue cheese did not display bacterial contamination. In 1876, physicist John Tyndall also contributed to this field, Louis Pasteur conducted research showing that Bacillus anthracis would not grow in the presence of the related mold Penicillium notatum. In his thesis, Duchesne proposed that bacteria and molds engage in a battle for survival. Duchesne observed that E. coli was eliminated by the fungus Penicillium glaucum when they were grown in the same culture. He also observed that when he inoculated animals with lethal doses of typhoid bacilli together with Penicillium glaucum. Unfortunately Duchesnes army service after getting his degree prevented him from doing any further research, Duchesne died of tuberculosis, a disease now treated by antibiotics. In 1928, Sir Alexander Fleming identified penicillin, a molecule produced by molds that kills or stops the growth of certain kinds of bacteria. Fleming was working on a culture of disease-causing bacteria when he noticed the spores of a mold, Penicillium chrysogenum
36.
Sporulation in Bacillus subtilis
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The endospore is formed at times of nutritional stress, allowing the organism to persist in the environment until conditions become favourable. Although sporulation in B. subtilis is induced by starvation, the developmental program is not initiated immediately when growth slows due to nutrient limitation. Sporulation is the response to starvation and is suppressed until alternative responses prove inadequate. Even then, certain conditions must be met such as integrity, the state of chromosomal replication. In short, initiation of sporulation is a tightly regulated network with numerous checkpoints for efficient control. Two transcriptional regulators, σH and Spo0A, play key roles in initiation of sporulation, several additional proteins participate, mainly by controlling the accumulated concentration of Spo0A~P. Spo0A lies at the end of a series of inter-protein phosphotransfer reactions, Kin–Spo0F–Spo0B–Spo0A, spores form a part of the life cycles of a diverse range of organisms such as many bacteria, plants, algae, fungi and some protozoa. In Saccharomyces cerevisiae, the set of early genes activating sporulation is induced by Ime1, Bacillus Sporophyte Bacillus subtilis SubtiList - GenoList - Institut Pasteur SubtilisWiki Bacillus subtilis - Parts Registry Video - Sporulation in Bacillus subtilis
37.
Circular bacterial chromosome
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A circular bacterial chromosome is a bacterial chromosome in the form of a molecule of circular DNA. Unlike the linear DNA of most eukaryotes, typical bacterial chromosomes are circular, most bacterial chromosomes contain a circular DNA molecule – there are no free ends to the DNA. Free ends would otherwise create significant challenges to cells with respect to DNA replication, cells that do contain chromosomes with DNA ends, or telomeres, have acquired elaborate mechanisms to overcome these challenges. However, a chromosome can provide other challenges for cells. Bacterial chromosome replication is best understood in the well-studied bacteria Escherichia coli, chromosome replication proceeds in three major stages, initiation, elongation and termination. The initiation stage starts with the assembly of initiator proteins at the origin region of the chromosome. These assembly stages are regulated to ensure that chromosome replication occurs only once in each cell cycle and this process is known as bidirectional replication. The entire assembly of molecules involved in DNA replication on each arm is called a replisome, at the forefront of the replisome is a DNA helicase that unwinds the two strands of DNA, creating a moving replication fork. The two unwound single strands of DNA serve as templates for DNA polymerase, which moves with the helicase to synthesise a complementary copy of each strand, in this way, two identical copies of the original DNA are created. Eventually, the two replication forks moving around the circular chromosome meet in a zone of the chromosome, approximately opposite oriC. The elongation enzymes then disassemble, and the two daughter chromosomes are resolved before cell division is completed, the E. coli bacterial replication origin, called oriC consists of DNA sequences that are recognised by the DnaA protein, which is highly conserved amongst different bacterial species. DnaA binding to the origin initiates the recruitment of other enzymes. DnaA protein plays a role in the initiation of chromosomal DNA replication. This region also contains four “GATC” sequences that are recognized by DNA adenine methylase, the methylation of adenines is important as it alters the conformation of DNA to promote strand separation, and it appears that this region of oriC has a natural tendency to unwind. DnaA then recruits the replicative helicase, DnaB, from the DnaB-DnaC complex to the region to form the pre-priming complex. After DnaB translocates to the apex of each replication fork, the helicase both unwinds the parental DNA and interacts momentarily with primase. In order for DNA replication to continue, single stranded binding proteins are needed to prevent the single strands of DNA from forming secondary structures, in addition, DNA gyrase is needed to relieve the topological stress created by the action of DnaB helicase. When the replication fork moves around the circle, a structure shaped like the Greek letter theta Ө is formed, john Cairns demonstrated the theta structure of E. coli chromosomal replication in 1963, using an innovative method to visualize DNA replication
38.
Origin of replication
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The origin of replication is a particular sequence in a genome at which replication is initiated. This can either involve the replication of DNA in living such as prokaryotes and eukaryotes, or that of DNA or RNA in viruses. DNA replication may proceed from this point bidirectionally or unidirectionally, the specific structure of the origin of replication varies somewhat from species to species, but all share some common characteristics such as high AT content. The origin of replication binds the pre-replication complex, a complex that recognizes, unwinds. The origin of replication are classified in two ways, Narrow or broad host range High- or low-copy number, most archaea have a single circular molecule of DNA, and several origins of replication along this circular chromosome. Eukaryotes often have multiple origins of replication on each chromosome that initiate at different times. Having many origins of replication helps to speed the duplication of their much larger store of genetic material, the segment of DNA that is copied starting from each unique replication origin is called a replicon. Origins of replication are typically assigned names containing ori, the genome of E. coli consists of a single circular DNA molecule of approximately 4.6 x 106 nucleotide pairs. DNA replication typically begins at an origin of replication. In E. coli, the origin of replication — oriC — consists of three A–T rich 13-mer repeats and four 9-mer repeats. Ten to 20 monomers of the initiator protein DnaA bind to the 9 mer repeats. This coiling stimulates the AT rich region in the 13 mer sequence to unwind, the helicase DnaB forms the basis of the primosome, a complex of enzymes to which DNA polymerase III is recruited before replication can occur. Many bacteria, including E. coli, contain plasmids that contain an origin of replication. These are separate from the origins of replication that are used by the bacteria to copy their genome, for example, the E. coli plasmid pBR322 uses a protein called Rop/Rom to regulate the number of plasmids that are within each bacterial cell. The most common origin of replication that is used in plasmids for genetic engineering is called pUC and this origin is derived from pBR322 but it contains two mutations. One single point mutation in the origin itself and another that deletes the Rop/Rom gene and this removes all the regulatory constraints on the plasmids replication and the bacteria then go from producing 30-40 plasmids per cell with pBR322 up to producing over 500 with pUC. This allows genetic engineers to large quantities of DNA for research purposes. Other origins of replication include pSC101, 15A origin and Bacterial artificial chromosomes, each budding yeast origin consists of a short essential DNA sequence that recruits replication proteins
39.
DNA replication
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In molecular biology, DNA replication is the biological process of producing two identical replicas of DNA from one original DNA molecule. This process occurs in all living organisms and is the basis for biological inheritance, DNA is made up of a double helix of two complementary strands. During replication, these strands are separated, each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication, in a cell, DNA replication begins at specific locations, or origins of replication, in the genome. Unwinding of DNA at the origin and synthesis of new results in replication forks growing bi-directionally from the origin. A number of proteins are associated with the fork to help in the initiation and continuation of DNA synthesis. Most prominently, DNA polymerase synthesizes the new strands by adding nucleotides that complement each strand, DNA replication occurs during the S-stage of interphase. DNA replication can also be performed in vitro, DNA polymerases isolated from cells and artificial DNA primers can be used to initiate DNA synthesis at known sequences in a template DNA molecule. The polymerase chain reaction, a laboratory technique, cyclically applies such artificial synthesis to amplify a specific target DNA fragment from a pool of DNA. DNA usually exists as a structure, with both strands coiled together to form the characteristic double-helix. Each single strand of DNA is a chain of four types of nucleotides, nucleotides in DNA contain a deoxyribose sugar, a phosphate, and a nucleobase. These nucleotides form phosphodiester bonds, creating the phosphate-deoxyribose backbone of the DNA double helix with the bases pointing inward. Nucleotides are matched between strands through hydrogen bonds to form base pairs, adenine pairs with thymine, and guanine pairs with cytosine. DNA strands have a directionality, and the different ends of a single strand are called the 3 end and the 5 end. By convention, if the sequence of a single strand of DNA is given. The strands of the helix are anti-parallel with one being 5 to 3. These terms refer to the atom in deoxyribose to which the next phosphate in the chain attaches. Directionality has consequences in DNA synthesis, because DNA polymerase can synthesize DNA in only one direction by adding nucleotides to the 3 end of a DNA strand, the pairing of complementary bases in DNA means that the information contained within each strand is redundant
40.
Chromosome map
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A karyotype is the number and appearance of chromosomes in the nucleus of a eukaryotic cell. The term is used for the complete set of chromosomes in a species or in an individual organism. Karyotypes describe the chromosome count of an organism and what these chromosomes look like under a light microscope, attention is paid to their length, the position of the centromeres, banding pattern, any differences between the sex chromosomes, and any other physical characteristics. The preparation and study of karyotypes is part of cytogenetics, the study of whole sets of chromosomes is sometimes known as karyology. The chromosomes are depicted in a format known as a karyogram or idiogram, in pairs, ordered by size. The basic number of chromosomes in the cells of an individual or a species is called the somatic number and is designated 2n. In the germ-line the chromosome number is n. p28 Thus, so, in normal diploid organisms, autosomal chromosomes are present in two copies. There may, or may not, be sex chromosomes, polyploid cells have multiple copies of chromosomes and haploid cells have single copies. The study of karyotypes is important for cell biology and genetics, Karyotypes can be used for many purposes, such as to study chromosomal aberrations, cellular function, taxonomic relationships, and to gather information about past evolutionary events. Chromosomes were first observed in plant cells by Carl Wilhelm von Nägeli in 1842 and their behavior in animal cells was described by Walther Flemming, the discoverer of mitosis, in 1882. The name was coined by another German anatomist, Heinrich von Waldeyer in 1888 and it is New Latin from Ancient Greek κάρυον karyon, kernel, seed, or nucleus, and τύπος typos, general form). The next stage took place after the development of genetics in the early 20th century, lev Delaunay seems to have been the first person to define the karyotype as the phenotypic appearance of the somatic chromosomes, in contrast to their genic contents. The subsequent history of the concept can be followed in the works of C. D. Darlington, investigation into the human karyotype took many years to settle the most basic question, how many chromosomes does a normal diploid human cell contain. In 1912, Hans von Winiwarter reported 47 chromosomes in spermatogonia and 48 in oogonia, concluding an XX/XO sex determination mechanism. Painter in 1922 was not certain whether the diploid of humans was 46 or 48, at first favouring 46, but revised his opinion from 46 to 48, considering the techniques of the time, these results were remarkable. In textbooks, the number of human chromosomes remained at 48 for over thirty years, New techniques were needed to correct this error. The work took place in 1955, and was published in 1956, the karyotype of humans includes only 46 chromosomes. Rather interestingly, the apes have 48 chromosomes
41.
Conserved sequence
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Conservation across species indicates that a sequence has been maintained by evolution despite speciation. A highly conserved sequence is one that has remained unchanged far back up the phylogenetic tree, parts of the 16S and 23S ribosomal RNA genes have been identified as the most conserved DNA sequences across the domains of life. Highly conserved regions typically indicates that selection has continually eliminated forms with mutations in that sequence. Highly conserved DNA sequences are thought to have functional value, the role for many of these highly conserved non-coding DNA sequences is not understood. Ultra-conserved elements or sequences that share 100% identity among human, mouse and rat were first described by Bejerano, many regions of the DNA, including highly conserved DNA sequences, consist of repeated sequence elements. Although most of the conserved sequences biological function is still unknown, a common notation to denote the level of sequence conservation is used by the clustal alignment programs. Below a set of aligned sequences, residue columns are indicated as fully conserved, containing only conservative mutations, semi-conservative mutations, cytosine-guanine dinucleotides are present at high frequency in CpG islands within the promoter regions of about 70% of human genes. CpG sites are subject to methylation on their cytosine, if a substantial proportion of CpG sites in a CpG island within a promoter of a gene are methylated, this silences expression of that gene. In the mammalian germ line DNA, demethylation occurs immediately following fertilization in the zygote, the mutation frequency of CpG sites within CpG islands of gene promoters was compared to the mutation frequency of CpG sites in non-coding regions of genes. The mutation frequencies were determined by comparing gene sequences in homologous genes in chimpanzees and it was found that the CpG sites in CpG islands in promoters were mutated at a substantially lower rate than CpG sites in the non-coding regions of genes. Thus CpG sites within gene promoters tend to be conserved in evolution, a GERP score measures evolutionary conservation of genetic sequences across species. There is a relationship between a sequences GERP score and the proportion of variant alleles within that sequence, as the GERP score of a sequence increases, variation within that sequence becomes more rare. A higher GERP signifies a highly conserved sequence, where alteration is harmful, so adverse variants would reduce the fitness of the organism, sequences are only likely to be highly conserved through geological time if they are required for basic cellular functions, stability, embryonic development, reproduction. Sequence similarity is used as evidence of structural and functional conservation, consequently, functional elements are frequently identified by searching for conserved sequences in a genome. Conservation of protein-coding sequences leads to the presence of amino acid residues at analogous regions of the protein structure. Conservative mutations alter amino acids to similar chemically residues and so may not affect the proteins function. Among the most highly conserved sequences are the sites of enzymes. Conserved non-coding sequences do not encode protein, but often harbour cis-regulatory elements, some deletions of highly conserved sequences in humans and other organisms have been suggested to be a potential cause of the anatomical and behavioural differences between humans and other mammals
42.
Transformation (genetics)
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Transformation is one of three processes for horizontal gene transfer, in which exogenous genetic material passes from bacterium to another, the other two being conjugation and transduction. In transformation, the material passes through the intervening medium. Transformation in bacteria was first demonstrated in 1928 by British bacteriologist Frederick Griffith, Griffith discovered that a strain of Streptococcus pneumoniae could be made virulent after being exposed to heat-killed virulent strains. Griffith hypothesized that some transforming principle from the strain was responsible for making the harmless strain virulent. In 1944 this transforming principle was identified as being genetic by Oswald Avery, Colin MacLeod and they isolated DNA from a virulent strain of S. pneumoniae and using just this DNA were able to make a harmless strain virulent. They called this uptake and incorporation of DNA by bacteria transformation, the results of Avery et al. It was originally thought that Escherichia coli, a used laboratory organism, was refractory to transformation. However, in 1970, Morton Mandel and Akiko Higa showed that E. coli may be induced to take up DNA from bacteriophage λ without the use of helper phage after treatment with calcium chloride solution. Two years later in 1972, Stanley Norman Cohen, Annie Chang, the method of transformation by Mandel and Higa was later improved upon by Douglas Hanahan. Transformation of animal and plant cells was also investigated with the first transgenic mouse being created by injecting a gene for a rat growth hormone into an embryo in 1982. In 1907 a bacterium that caused plant tumors, Agrobacterium tumefaciens, was discovered, not all plant cells are susceptible to infection by A. tumefaciens, so other methods were developed, including electroporation and micro-injection. Particle bombardment was possible with the invention of the Biolistic Particle Delivery System by John Sanford in the 1980s. In transformation, the material passes through the intervening medium. Competence refers to a state of being able to take up exogenous DNA from the environment. Natural genetic transformation appears to be an adaptation for repair of DNA damage that also generates genetic diversity and it has also been reported in at least 30 species of Proteobacteria distributed in the classes alpha, beta, gamma and epsilon. Naturally competent bacteria carry sets of genes that provide the protein machinery to bring DNA across the cell membrane, the DNA first binds to the surface of the competent cells on a DNA receptor, and passes through the cytoplasmic membrane via DNA translocase. Only single-stranded DNA may pass through, the other strand being degraded by nucleases in the process, the translocated single-stranded DNA may then be integrated into the bacterial chromosomes by a RecA-dependent process. In Gram-negative cells, due to the presence of an extra membrane, pilin may be required for competence, but its role is uncertain
43.
Natural competence
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In microbiology, genetics, cell biology, and molecular biology, competence is the ability of a cell to take up extracellular DNA from its environment in the process called transformation. This article primarily deals with natural competence in bacteria, although information about artificial competence is also provided, in 1944 Oswald Avery, Colin MacLeod, and Maclyn McCarty demonstrated that this transforming factor was pure DNA. This was the first compelling evidence that DNA carries the information of the cell. Since then, natural competence has been studied in a number of different bacteria, particularly Bacillus subtilis, Streptococcus pneumoniae, Neisseria gonorrhoeae, areas of active research include the mechanisms of DNA transport, the regulation of competence in different bacteria, and the evolutionary function of competence. In the natural world DNA usually becomes available by death and lysis of other cells, during uptake, DNA is transported across the cell membrane, and the cell wall if one is present. Once the DNA is inside the cell it may be degraded to nucleotides, alternatively it may be recombined into the cell’s genome by its DNA repair enzymes. If this recombination changes the cell’s genotype the cell is said to have been transformed, artificial competence and transformation are used as research tools in many organisms. In almost all naturally competent bacteria components of extracellular filaments called type 4 pili bind extracellular double stranded DNA, the DNA is then translocated across the membrane through multi-component protein complexes driven by the degradation of one strand of the DNA. Single stranded DNA in the cell is bound by a protein, DprA, which loads the DNA onto RecA. In laboratory cultures, natural competence is usually tightly regulated and often triggered by nutritional shortages or adverse conditions, transcription factors have been discovered which regulate competence, an example is sxy which has been found to be regulated in turn by a 5 non-coding RNA element. In bacteria capable of forming spores, conditions inducing sporulation often overlap with those inducing competence, thus cultures or colonies containing sporulating cells often also contain competent cells. Recent research by Süel et al. has identified a core module of genes which can explain entry into. Neisserial genomes contain thousands of copies of the preferred sequence GCCGTCTGAA, a secondary suggestion has also been made, noting the occasional advantage of horizontal gene transfer. Arguments to support genetic diversity as the evolutionary function of sex are given by Barton and Charleworth. and by Otto. However, the difficulties associated with the evolution of sex suggest that sex for genetic diversity is problematic. However, since bacteria tend to grow in clones, the DNA available for transformation would generally have the same genotype as that of the recipient cells, thus, there is always a high cost in protein expression without, in general, an increase in diversity. Some naturally competent bacteria also secrete nucleases into their surroundings, the energetics of DNA uptake are not understood in any system, so it is difficult to compare the efficiency of nuclease secretion to that of DNA uptake and internal degradation. In principle the cost of production and the uncertainty of nucleotide recovery must be balanced against the energy needed to synthesize the uptake machinery
44.
Antibiotics
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Antibiotics, also called antibacterials, are a type of antimicrobial drug used in the treatment and prevention of bacterial infections. They may either kill or inhibit the growth of bacteria, a limited number of antibiotics also possess antiprotozoal activity. Antibiotics are not effective against viruses such as the cold or influenza. Drugs which inhibit viruses are termed antiviral drugs or antivirals rather than antibiotics, sometimes the term antibiotic is used to refer to any substance used against microbes, synonymous with antimicrobial. Some sources distinguish between antibacterial and antibiotic, antibacterials are used in soaps and disinfectants, while antibiotics are used as medicine, Antibiotics revolutionized medicine in the 20th century, and have together with vaccination led to the near eradication of diseases such as tuberculosis in the developed world. However, their effectiveness and easy access led to overuse, especially in raising, prompting bacteria to develop resistance. All classes of antibiotics in use today were first discovered prior to the mid 1980s, substances with antibiotic properties had been used for various purposes since ancient times. Before the early 20th century, treatments for infections were based primarily on medicinal folklore, mixtures with antimicrobial properties that were used in treatments of infections were described over 2000 years ago. Many ancient cultures, including the ancient Egyptians and ancient Greeks, used specially selected mold and plant materials, more recent observations made in the laboratory of antibiosis between microorganisms led to the discovery of natural antibacterials produced by microorganisms. Louis Pasteur observed, if we could intervene in the antagonism observed between some bacteria, it would offer perhaps the greatest hopes for therapeutics. In 1874, physician Sir William Roberts noted that cultures of the mold Penicillium glaucum that is used in the making of types of blue cheese did not display bacterial contamination. In 1876, physicist John Tyndall also contributed to this field, Louis Pasteur conducted research showing that Bacillus anthracis would not grow in the presence of the related mold Penicillium notatum. In his thesis, Duchesne proposed that bacteria and molds engage in a battle for survival. Duchesne observed that E. coli was eliminated by the fungus Penicillium glaucum when they were grown in the same culture. He also observed that when he inoculated animals with lethal doses of typhoid bacilli together with Penicillium glaucum. Unfortunately Duchesnes army service after getting his degree prevented him from doing any further research, Duchesne died of tuberculosis, a disease now treated by antibiotics. In 1928, Sir Alexander Fleming identified penicillin, a molecule produced by molds that kills or stops the growth of certain kinds of bacteria. Fleming was working on a culture of disease-causing bacteria when he noticed the spores of a mold, Penicillium chrysogenum
. PMID 12682299.
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