1.
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
2.
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
3.
Proteobacteria
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The Proteobacteria are a major phylum of Gram-negative bacteria. The name of the phylum has never been published as no type genus has been proposed. They include a variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia. Others are free-living, and include many of the responsible for nitrogen fixation. Carl Woese established this grouping in 1987, calling it informally the purple bacteria, the Alphaproteobacteria grow at very low levels of nutrients and have unusual morphology such as stalks and buds. They include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants, the type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter. The Betaproteobacteria are highly diverse and contain chemolithoautotrophs, photoautotrophs. The type order is the Burkholderiales, comprising a range of metabolic diversity. The Gammaproteobacteria are the largest class in terms of species with validly published names, the type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter. The Deltaproteobacteria include bacteria that are predators on other bacteria and are important contributors to the side of the sulfur cycle. The type order is the Myxococcales, which includes organisms with self-organising abilities such as Myxococcus spp, the Epsilonproteobacteria are often slender, Gram-negative rods that are helical or curved. The type order is the Campylobacterales, which includes important food pathogens such as Campylobacter spp, the type order is the Oligoflexales, which contains the genus Oligoflexus. The Acidithiobacillia contain only sulfur-oxidising autotrophs, the type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp. All Proteobacteria are Gram-negative, though some may stain Gram-positive or Gram-variable in practice, many move about using flagella, but some are nonmotile or rely on bacterial gliding. The last include the Myxobacteriales, an order of bacteria that can aggregate to form fruiting bodies. Also, a variety in the types of metabolism exists. Most members are facultatively or obligately anaerobic, Chemolithoautotrophic, and heterotrophic, a variety of genera, which are not closely related to each other, convert energy from light through photosynthesis. Proteobacteria are associated with the imbalance of microbiota of the reproductive tract of women
4.
Gammaproteobacteria
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Gammaproteobacteria are a class of several medically, ecologically, and scientifically important groups of bacteria. An exceeding number of important pathogens belong to this class, like all Proteobacteria, the Gammaproteobacteria are Gram-negative. The Gammaproteobacteria comprise several medically and scientifically important groups of bacteria, such as the Enterobacteriaceae, Vibrionaceae, a number of important pathogens belong to this class, e. g. Salmonella spp. Yersinia pestis, Vibrio cholerae, Pseudomonas aeruginosa, and Escherichia coli, important plant pathogens such as Xanthomonas axonopodis pv. citri and Pseudomonas syringae pv. actinidiae are also Gammaproteobacteria. Members of Chromatium are photosynthetic and oxidize hydrogen sulfide instead of water, some Gammaproteobacteria are methane oxidizers, and many are symbiotic with geothermic ocean vent-dwelling animals. Due to a genus, Acidithiobacillus, the Gammaproteobacteria class is paraphyletic to Betaproteobacteria. A number of bacteria have been described as members of Gammaproteobacteria, Betaproteobacteria Proteobacteria Gammaproteobacteria at the US National Library of Medicine Medical Subject Headings
5.
Enterobacteriaceae
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Other disease-causing bacteria in this family include Proteus, Enterobacter, Serratia, and Citrobacter. This family is the representative in the order Enterobacteriales of the class Gammaproteobacteria in the phylum Proteobacteria. Members of the Enterobacteriaceae can be referred to as enterobacteria or enteric bacteria. In fact, the etymology of the family is enterobacterium with the suffix to designate a family —not after the genus Enterobacter —and the type genus is Escherichia, members of the Enterobacteriaceae are rod-shaped, and are typically 1–5 μm in length. They appear as small colonies on blood agar. Like other proteobacteria, enterobacteria have Gram-negative stains, and they are anaerobes, fermenting sugars to produce lactic acid. Most also reduce nitrate to nitrite, although exceptions exist, unlike most similar bacteria, enterobacteria generally lack cytochrome C oxidase, although there are exceptions. Most have many flagella used to move about, but a few genera are nonmotile, Escherichia coli is one of the most important model organisms, and its genetics and biochemistry have been closely studied. Most members of Enterobacteriaceae have peritrichous, type I fimbriae involved in the adhesion of the cells to their hosts. Endotoxins reside in the wall and are released when the cell dies. Some members of the Enterobacteriaceae produce endotoxins that, when released into the following cell lysis. The most severe form of this is known as endotoxic shock, to identify different genera of Enterobacteriaceae, a microbiologist may run a series of tests in the lab. The methyl red tests for acid endproducts, the Voges Proskauer tests for the production of acetylmethylcarbinol. Catalase test on nutrient agar tests for the production of catalase enzyme, oxidase test on nutrient agar tests for the production of the enzyme oxidase, which reacts with an aromatic amine to produce a purple color. Nutrient gelatin tests to detect activity of the enzyme gelatinase, in a clinical setting, three species make up 80 to 95% of all isolates identified. These are Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis, for instance, some Klebsiella pneumoniae strains are carbapenem resistant. E. Bensons microbiological applications, laboratory manual in general microbiology
6.
Salmonella enterica
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Salmonella enterica is a rod-shaped, flagellated, facultative anaerobic, Gram-negative bacterium and a member of the genus Salmonella. A number of its serovars are serious human pathogens, raw chicken eggs and goose eggs can harbor S. enterica, initially in the egg whites, although most eggs are not infected. As the egg ages at room temperature, the yolk membrane begins to break down, refrigeration and freezing do not kill all the bacteria, but substantially slow or halt their growth. Pasteurizing and food irradiation are used to kill Salmonella for commercially produced foodstuffs containing raw eggs such as ice cream, foods prepared in the home from raw eggs such as mayonnaise, cakes, and cookies can spread salmonella if not properly cooked before consumption. Secreted proteins are of importance for the pathogenesis of infectious diseases caused by Salmonella enterica. A remarkable large number of fimbrial and non-fimbrial adhesins are present in Salmonella, secreted proteins are also involved in host cell invasion and intracellular proliferation, two hallmarks of Salmonella pathogenesis. Small non-protein coding RNAs are able to perform specific functions without being translated into proteins,97 bacterial sRNAs from Salmonella Typhi were discovered by Chinni et al. Salmonella enterica has 7 subspecies, and each subspecies has associated serovars that differ by antigenic specificity, there are over 2500 serovars for S. enterica. Salmonella bongori was previously considered a subspecies of S. enterica, most of the human pathogenic Salmonella serovars belong to the S. enterica subsp. These serogroups include Salmonella Typhi, Salmonella Enteritidis, Salmonella Paratyphi, Salmonella Typhimurium, the serovars can be designated as written in the previous sentence, or as follows, S. enterica subsp. Type strain of Salmonella enterica at BacDive - the Bacterial Diversity Metadatabase
7.
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
8.
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
9.
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
10.
Subspecies
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In biological classification, subspecies is either a taxonomic rank subordinate to species, or a taxonomic unit in that rank. A subspecies cannot be recognized independently, a species will either be recognized as having no subspecies at all or at least two, in zoology, under the International Code of Zoological Nomenclature, the subspecies is the only taxonomic rank below that of species that can receive a name. In botany and mycology, under the International Code of Nomenclature for algae, fungi, in bacteriology and virology, under standard bacterial nomenclature and virus nomenclature, there are recommendations but not strict requirements for recognizing other important infraspecific ranks. A taxonomist decides whether to recognize a subspecies or not, the differences between subspecies are usually less distinct than the differences between species. In zoology, the International Code of Zoological Nomenclature accepts only one rank below that of species, other groupings, infrasubspecific entities do not have names regulated by the ICZN. Such forms have no official ICZN status, though they may be useful in describing altitudinal or geographical clines, pet breeds, transgenic animals, etc. While the scientific name of a species is a binomen, the name of a subspecies is a trinomen - a binomen followed by a subspecific name. A tigers binomen is Panthera tigris, so for a Sumatran tiger the trinomen is, for example, names published before 1992 in the rank of variety are taken to be names of subspecies. In botany, subspecies is one of many ranks below that of species, such as variety, subvariety, form, the subspecific name is preceded by subsp. or ssp. as Schoenoplectus californicus ssp. tatora. A botanical name consists of at most three parts, an infraspecific name includes the species binomial, and one infraspecific epithet, such as subspecies or variety. For example, Motacilla alba alba is the subspecies of the white wagtail. The subspecies name that repeats the name is referred to in botanical nomenclature as the subspecies autonym. When zoologists disagree over whether a population is a subspecies or a full species. A subspecies is a rank below species – the only recognized rank in the zoological code. Botanists and mycologists have the choice of ranks lower than subspecies, such as variety or form, in biological terms, rather than in relation to nomenclature, a polytypic species has two or more subspecies, races, or more generally speaking, populations that need a separate description. These are separate groups that are distinct from one another and do not generally interbreed. These subspecies, races, or populations, can be named as subspecies by zoologists, a monotypic species has no distinct population or races, or rather one race comprising the whole species. A taxonomist would not name a subspecies within such a species, monotypic species can occur in several ways, All members of the species are very similar and cannot be sensibly divided into biologically significant subcategories
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Serotype
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A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified based on their cell surface antigens. A group of serovars with common antigens is called a serogroup or sometimes serocomplex, serotyping often plays an essential role in determining species and subspecies. Vibrio cholerae, the species of bacteria that causes cholera, has over 200 serotypes, only two of them have been observed to produce the potent enterotoxin that results in cholera,0,1 and 0,139. Serotypes were discovered by the American microbiologist Rebecca Lancefield in 1933, the immune system is capable of discerning a cell as being self or non-self according to that cells serotype. In humans, that serotype is determined by human leukocyte antigen. Cells determined to be non-self are usually recognized by the system as foreign, causing an immune response. For this reason, transplants between genetically non-identical humans often induce an immune response in the recipient, leading to transplant rejection. In some situations this effect can be reduced by serotyping both recipient and potential donors to determine the closest HLA match, the Kauffman–White classification scheme is the basis for naming the manifold serovars of Salmonella. To date, more than 2600 different serotypes have been identified, a Salmonella serotype is determined by the unique combination of reactions of cell surface antigens. The O antigen is determined by the outermost portion of the Lipopolysaccharide, there are two species of Salmonella, Salmonella bongori and Salmonella enterica. Salmonella enterica can be subdivided into six subspecies, the process to identify the serovar of the bacterium consists of finding the formula of cell antigens which represent the variations of the bacteria. First of all, the use of the method on slides is required in order to get the antigen formula. The agglutination between the antigen and the antibody is made with a specific antisera, which reacts with the antigen to produce a mass. The antigen O is tested with a suspension from an agar plate whereas the antigen H is tested with a bacterial suspension from a broth culture. The scheme is used to classify the serovar depending on its antigen formula obtained with the reaction of the agglutination, biovar Morphovar HLA Allele and Haplotype Frequency Database
12.
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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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
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Flagellum
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A flagellum is a lash-like appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells. The word flagellum in Latin means whip, the primary role of the flagellum is locomotion, but it also often has function as a sensory organelle, being sensitive to chemicals and temperatures outside the cell. Flagella are organelles defined by function rather than structure, large differences occur between different types of flagella, the prokaryotic and eukaryotic flagella differ greatly in protein composition, structure, and mechanism of propulsion. However, both can be used for swimming, an example of a flagellated bacterium is the ulcer-causing Helicobacter pylori, which uses multiple flagella to propel itself through the mucus lining to reach the stomach epithelium. An example of a eukaryotic cell is the mammalian sperm cell. Eukaryotic flagella are structurally identical to eukaryotic cilia, although distinctions are made according to function and/or length. Fimbriae and pili are also thin appendages, but have different functions and are usually smaller, three types of flagella have so far been distinguished, bacterial, archaeal, and eukaryotic. The main differences among these three types are, Bacterial flagella are helical filaments, each with a motor at its base which can turn clockwise or counterclockwise. They provide two of several kinds of bacterial motility, archaeal flagella are superficially similar to bacterial flagella, but are different in many details and considered non-homologous. Eukaryotic flagella—those of animal, plant, and protist cells—are complex cellular projections that lash back, eukaryotic flagella are classed along with eukaryotic motile cilia as undulipodia to emphasize their distinctive wavy appendage role in cellular function or motility. Primary cilia are immotile, and are not undulipodia, they have a structurally different 9+0 axoneme rather than the 9+2 axoneme found in both flagella and motile cilia undulipodia, the bacterial flagellum is made up of the protein flagellin. Its shape is a 20-nanometer-thick hollow tube and it is helical and has a sharp bend just outside the outer membrane, this hook allows the axis of the helix to point directly away from the cell. A shaft runs between the hook and the body, passing through protein rings in the cells membrane that act as bearings. Gram-positive organisms have two of these basal body rings, one in the layer and one in the plasma membrane. The filament ends with a capping protein, the flagellar filament is the long, helical screw that propels the bacterium when rotated by the motor, through the hook. Each protofilament is a series of protein chains. However, Campylobacter jejuni has seven protofilaments, the basal body has several traits in common with some types of secretory pores, such as the hollow, rod-like plug in their centers extending out through the plasma membrane. The bacterial flagellum is driven by an engine made up of protein
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Chemotrophs
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Chemotrophs are organisms that obtain energy by the oxidation of electron donors in their environments. These molecules can be organic or inorganic, the chemotroph designation is in contrast to phototrophs, which utilize solar energy. Chemotrophs can be either autotrophic or heterotrophic, chemotrophs are commonly found in ocean floors where sunlight cannot reach them because they are not dependent on solar energy. Ocean floors often contain underwater volcanos that can provide heat to substitute sunlight for warmth, originally used with a different meaning, the term took its current definition after Lwoff and collaborators. Chemoautotrophs, in addition to deriving energy from chemical reactions, synthesize all necessary organic compounds from carbon dioxide, chemoautotrophs use inorganic energy sources, such as hydrogen sulfide, elemental sulfur, ferrous iron, and also molecular hydrogen, and ammonia. Most are bacteria or archaea that live in environments such as deep sea vents and are the primary producers in such ecosystems. Chemoautotrophs generally fall into groups, methanogens, halophiles, sulfur oxidizers and reducers, nitrifiers, anammox bacteria. An example of one of these prokaryotes would be Sulfolobus, chemolithotrophic growth can be dramatically fast, such as Thiomicrospira crunogena with a doubling time around one hour. Later, the term would also the chemoorganoautotrophy, that is. Chemoheterotrophs are unable to fix carbon to form their own organic compounds, in the deep oceans, iron-oxidizing bacteria derive their energy needs by oxidizing iron to iron. The extra electron obtained from this powers the cells, replacing or augmenting traditional phototrophism. In general, iron-oxidizing bacteria can exist only in areas with high iron concentrations, most of the ocean is devoid of iron, due to both the oxidative effect of dissolved oxygen in the water and the tendency of prokaryotes to take up the iron. Lava beds supply bacteria with iron straight from the Earths mantle, in addition, because oxygen is necessary for the reaction, these bacteria are much more common in the upper ocean, where oxygen is more abundant. What is still unknown is how exactly iron bacteria extract iron from rock and it is accepted that some mechanism exists that eats away at the rock, perhaps through specialized enzymes or compounds that bring more FeO to the surface. It has been debated about how much of the weathering of the rock is due to biotic components. Hydrothermal vents also release large quantities of dissolved iron into the deep ocean, in addition, the high thermal gradient around vent systems means a wide variety of bacteria can coexist, each with its own specialized temperature niche. Manganese-oxidizing bacteria also use of igneous lava rocks in much the same way. Manganese is much rarer than iron in oceanic crust, but is easier for bacteria to extract from igneous glass
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Redox
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Redox is a chemical reaction in which the oxidation states of atoms are changed. Any such reaction involves both a process and a complementary oxidation process, two key concepts involved with electron transfer processes. Redox reactions include all chemical reactions in which atoms have their oxidation state changed, in general, the chemical species from which the electron is stripped is said to have been oxidized, while the chemical species to which the electron is added is said to have been reduced. It can be explained in terms, Oxidation is the loss of electrons or an increase in oxidation state by a molecule, atom. Reduction is the gain of electrons or a decrease in state by a molecule, atom. As an example, during the combustion of wood, oxygen from the air is reduced, the reaction can occur relatively slowly, as in the case of rust, or more quickly, as in the case of fire. Redox is a portmanteau of reduction and oxidation, the word oxidation originally implied reaction with oxygen to form an oxide, since dioxygen was historically the first recognized oxidizing agent. Later, the term was expanded to encompass oxygen-like substances that accomplished parallel chemical reactions, ultimately, the meaning was generalized to include all processes involving loss of electrons. The word reduction originally referred to the loss in weight upon heating a metallic ore such as an oxide to extract the metal. In other words, ore was reduced to metal, antoine Lavoisier showed that this loss of weight was due to the loss of oxygen as a gas. Later, scientists realized that the atom gains electrons in this process. The meaning of reduction then became generalized to all processes involving gain of electrons. Even though reduction seems counter-intuitive when speaking of the gain of electrons, it help to think of reduction as the loss of oxygen. Since electrons are charged, it is also helpful to think of this as reduction in electrical charge. The electrochemist John Bockris has used the words electronation and deelectronation to describe reduction and oxidation processes respectively when they occur at electrodes and these words are analogous to protonation and deprotonation, but they have not been widely adopted by chemists. The term hydrogenation could be used instead of reduction, since hydrogen is the agent in a large number of reactions. But, unlike oxidation, which has been generalized beyond its root element, the word redox was first used in 1928. The processes of oxidation and reduction occur simultaneously and cannot happen independently of one another, the oxidation alone and the reduction alone are each called a half-reaction, because two half-reactions always occur together to form a whole reaction
17.
Adenosine triphosphate
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Adenosine triphosphate is a nucleotide, also called a nucleoside triphosphate, is a small molecule used in cells as a coenzyme. It is often referred to as the unit of currency of intracellular energy transfer. ATP transports chemical energy within cells for metabolism, most cellular functions need energy in order to be carried out, synthesis of proteins, synthesis of membranes, movement of the cell, cellular division, transport of various solutes etc. The ATP is the molecule that carries energy to the place where the energy is needed, when ATP breaks into ADP and Pi, the breakdown of the last covalent link of phosphate liberates energy that is used in reactions where it is needed. Substrate-level phosphorylation, oxidative phosphorylation in cellular respiration, and photophosphorylation in photosynthesis are three mechanisms of ATP biosynthesis. Metabolic processes that use ATP as an energy source convert it back into its precursors, ATP is therefore continuously recycled in organisms, the human body, which on average contains only 250 grams of ATP, turns over its own body weight equivalent in ATP each day. ATP is used as a substrate in signal transduction pathways by kinases that phosphorylate proteins and it is also used by adenylate cyclase, which uses ATP to produce the second messenger molecule cyclic AMP. The ratio between ATP and AMP is used as a way for a cell to sense how much energy is available and control the metabolic pathways that produce and consume ATP. Apart from its roles in signaling and energy metabolism, ATP is also incorporated into nucleic acids by polymerases in the process of transcription, ATP is the neurotransmitter believed to signal the sense of taste. The structure of this consists of a purine base attached by the 9′ nitrogen atom to the 1′ carbon atom of a pentose sugar. Three phosphate groups are attached at the 5′ carbon atom of the pentose sugar and it is the addition and removal of these phosphate groups that inter-convert ATP, ADP and AMP. When ATP is used in DNA synthesis, the sugar is first converted to deoxyribose by ribonucleotide reductase. ATP was discovered in 1929 by Karl Lohmann, and independently by Cyrus Fiske and Yellapragada Subbarow of Harvard Medical School and it was proposed to be the intermediary molecule between energy-yielding and energy-requiring reactions in cells by Fritz Albert Lipmann in 1941. It was first artificially synthesized by Alexander Todd in 1948, ATP consists of adenosine – composed of an adenine ring and a ribose sugar – and three phosphate groups. The phosphoryl groups, starting with the group closest to the ribose, are referred to as the alpha, beta, consequently, it is closely related to the adenosine nucleotide, a monomer of RNA. ATP is highly soluble in water and is stable in solutions between pH6.8 and 7.4, but is rapidly hydrolysed at extreme pH. Consequently, ATP is best stored as an anhydrous salt, ATP is an unstable molecule in unbuffered water, in which it hydrolyses to ADP and phosphate. This is because the strength of the bonds between the groups in ATP is less than the strength of the hydrogen bonds, between its products, and water
18.
Oxygen
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Oxygen is a chemical element with symbol O and atomic number 8. It is a member of the group on the periodic table and is a highly reactive nonmetal. By mass, oxygen is the third-most abundant element in the universe, after hydrogen, at standard temperature and pressure, two atoms of the element bind to form dioxygen, a colorless and odorless diatomic gas with the formula O2. This is an important part of the atmosphere and diatomic oxygen gas constitutes 20. 8% of the Earths atmosphere, additionally, as oxides the element makes up almost half of the Earths crust. Most of the mass of living organisms is oxygen as a component of water, conversely, oxygen is continuously replenished by photosynthesis, which uses the energy of sunlight to produce oxygen from water and carbon dioxide. Oxygen is too reactive to remain a free element in air without being continuously replenished by the photosynthetic action of living organisms. Another form of oxygen, ozone, strongly absorbs ultraviolet UVB radiation, but ozone is a pollutant near the surface where it is a by-product of smog. At low earth orbit altitudes, sufficient atomic oxygen is present to cause corrosion of spacecraft, the name oxygen was coined in 1777 by Antoine Lavoisier, whose experiments with oxygen helped to discredit the then-popular phlogiston theory of combustion and corrosion. One of the first known experiments on the relationship between combustion and air was conducted by the 2nd century BCE Greek writer on mechanics, Philo of Byzantium. In his work Pneumatica, Philo observed that inverting a vessel over a burning candle, Philo incorrectly surmised that parts of the air in the vessel were converted into the classical element fire and thus were able to escape through pores in the glass. Many centuries later Leonardo da Vinci built on Philos work by observing that a portion of air is consumed during combustion and respiration, Oxygen was discovered by the Polish alchemist Sendivogius, who considered it the philosophers stone. In the late 17th century, Robert Boyle proved that air is necessary for combustion, English chemist John Mayow refined this work by showing that fire requires only a part of air that he called spiritus nitroaereus. From this he surmised that nitroaereus is consumed in both respiration and combustion, Mayow observed that antimony increased in weight when heated, and inferred that the nitroaereus must have combined with it. Accounts of these and other experiments and ideas were published in 1668 in his work Tractatus duo in the tract De respiratione. Robert Hooke, Ole Borch, Mikhail Lomonosov, and Pierre Bayen all produced oxygen in experiments in the 17th and the 18th century but none of them recognized it as a chemical element. This may have been in part due to the prevalence of the philosophy of combustion and corrosion called the phlogiston theory, which was then the favored explanation of those processes. Established in 1667 by the German alchemist J. J. Becher, one part, called phlogiston, was given off when the substance containing it was burned, while the dephlogisticated part was thought to be its true form, or calx. The fact that a substance like wood gains overall weight in burning was hidden by the buoyancy of the combustion products
19.
Warm-blooded
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Warm-blooded animal species can maintain a body temperature higher than their environment. In particular, homeothermic species maintain a body temperature by regulating metabolic processes. The only known homeotherms are birds and mammals, other species have various degrees of thermoregulation. In general, warm-bloodedness refers to three categories of thermoregulation. Endothermy is the ability of creatures to control their body temperatures through internal means such as muscle shivering or increasing their metabolism. Some writers restrict the meaning of endothermy to mechanisms that raise the animals metabolic rate to produce heat. The opposite of endothermy is ectothermy, homeothermy maintains a stable internal body temperature regardless of external influence and temperatures. The stable internal temperature is higher than the immediate environment. Tachymetabolism maintains a high resting metabolism, in essence, tachymetabolic creatures are on all the time. Though their resting metabolism is still many times slower than their active metabolism, tachymetabolic creatures have greater difficulty dealing with a scarcity of food. A large proportion of the creatures traditionally called warm-blooded, like birds and mammals, however, over the past 30 years, studies in the field of animal thermophysiology have revealed many species belonging to these two groups that do not fit all these criteria. For example, many bats and small birds are poikilothermic and bradymetabolic when they sleep for the night, for these creatures, the term heterothermy was coined. Some fish have warm-blooded characteristics, such as the opah, swordfish and some sharks have circulatory mechanisms that keep their brains and eyes above ambient temperatures and thus increase their ability to detect and react to prey. Tunas and some sharks have similar mechanisms in their muscles, improving their stamina when swimming at high speed, body heat is generated by metabolism. This refers to the chemical reactions cells use to break down glucose into water and carbon dioxide and, in so doing, generate ATP, a high-energy compound used to power other cellular processes. Muscle contraction is a type of process that generates heat energy. All organisms metabolize food and other inputs, but some make use of the output than others. Like all energy conversions, metabolism is rather inefficient, and around 60% of the energy is converted to heat rather than to ATP
20.
Ectotherm
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An ectotherm, is an organism in which internal physiological sources of heat are of relatively small or quite negligible importance in controlling body temperature. Such organisms rely on environmental heat sources, which permit them to operate at very economical metabolic rates, colloquially, some refer to these organisms as cold blooded though such a term is not technically correct, as the blood temperature of the organism varies with ambient environmental temperature. Some of these live in environments where temperatures are practically constant. In contrast to ectotherms, endotherms rely largely, even predominantly, in ectotherms, fluctuating ambient temperatures may affect the body temperature. Such variation in temperature is called poikilothermy, though the concept is not widely satisfactory. Ectotherms can also display the features of homeothermy, especially within aquatic organisms, various patterns of behavior enable certain ectotherms to regulate body temperature to a useful extent. To warm up, reptiles and many insects find sunny places and adopt positions that maximise their exposure, in cold weather, honey bees huddle together to retain heat. Butterflies and moths may orient their wings to maximize exposure to radiation in order to build up heat before take-off. Gregarious caterpillars, such as the Forest Tent caterpillar, benefit from basking in groups for thermoregulation. Many flying insects, such as bees and bumble bees, also raise their internal temperatures endothermally prior to flight. Such endothermal activity is an example of the difficulty of consistent application of such as poikilothermy and homiothermy. In addition to adaptations, physiological adaptations help ectotherms regulate temperature. The skin of bullfrogs secretes more mucus when it is hot, during periods of cold, some ectotherms enter a state of torpor, in which their metabolism slows or, in some cases, such as the wood frog, effectively stops. The torpor might last overnight or last for a season, or even for years, ectotherms rely largely on external heat sources such as sunlight to achieve their optimal body temperature for various bodily activities. Accordingly, they depend on ambient conditions to reach operational body temperatures, also, as a rule, ectotherms have lower metabolic rates than endotherms at a given body mass. As a consequence, endotherms generally rely on food consumption. Such requirements may limit the capacity of a given environment for endotherms as compared to its carrying capacity for ectotherms. Because ectotherms depend on conditions for body temperature regulation, as a rule, they are more sluggish at night
21.
Reptile
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Reptiles are tetrapod animals in the class Reptilia, comprising todays turtles, crocodilians, snakes, amphisbaenians, lizards, tuatara, and their extinct relatives. The study of these traditional reptile orders, historically combined with that of amphibians, is called herpetology. Because some reptiles are more related to birds than they are to other reptiles. For this reason, many scientists prefer to consider the birds part of Reptilia as well. Some early examples include the lizard-like Hylonomus and Casineria, in addition to the living reptiles, there are many diverse groups that are now extinct, in some cases due to mass extinction events. In particular, the K–Pg extinction wiped out the pterosaurs, plesiosaurs, ornithischians, and sauropods, as well as species of theropods, crocodyliforms. Modern non-avian reptiles inhabit every continent with the exception of Antarctica, several living subgroups are recognized, Testudines, approximately 400 species, Sphenodontia,1 species, Squamata, over 9,600 species, Crocodilia,25 species, and Aves,10,000 species. Reptiles are tetrapod vertebrates, creatures that either have four limbs or, unlike amphibians, reptiles do not have an aquatic larval stage. As amniotes, reptile eggs are surrounded by membranes for protection and transport, many of the viviparous species feed their fetuses through various forms of placenta analogous to those of mammals, with some providing initial care for their hatchlings. In the 18th century, the reptiles were, from the outset of classification, the terms reptile and amphibian were largely interchangeable, reptile being preferred by the French. Josephus Nicolaus Laurenti was the first to use the term Reptilia for an expanded selection of reptiles. Today, the two groups are commonly treated under the same heading as herptiles. He subsequently proposed the names of Sauropsida and Ichthyopsida for the two groups. In 1866, Haeckel demonstrated that vertebrates could be divided based on their strategies, and that reptiles, birds. The terms Sauropsida and Theropsida were used again in 1916 by E. S, Goodrich to distinguish between lizards, birds, and their relatives on the one hand and mammals and their extinct relatives on the other. Goodrich supported this division by the nature of the hearts and blood vessels in each group, according to Goodrich, both lineages evolved from an earlier stem group, Protosauria in which he included some animals today considered reptile-like amphibians, as well as early reptiles. Watson observed that the first two groups diverged very early in history, so he divided Goodrichs Protosauria between them. He also reinterpreted Sauropsida and Theropsida to exclude birds and mammals, thus his Sauropsida included Procolophonia, Eosuchia, Millerosauria, Chelonia, Squamata, Rhynchocephalia, Crocodilia, thecodonts, non-avian dinosaurs, pterosaurs, ichthyosaurs, and sauropterygians
22.
Intracellular pathogen
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Intracellular parasites are parasitic microorganisms - microparasites that are capable of growing and reproducing inside the cells of a host. Facultative intracellular parasites are capable of living and reproducing either inside or outside cells, cryptococcus neoformans Obligate intracellular parasites cannot reproduce outside their host cell, meaning that the parasites reproduction is entirely reliant on intracellular resources. Obligate intracellular parasites of humans include, Viruses Certain bacteria, including, Chlamydia, study of obligate pathogens is difficult because they cannot usually be reproduced outside the host. However, in 2009 scientists reported a technique allowing the Q-fever pathogen Coxiella burnetii to grow in an axenic culture, the majority of intracellular parasites must keep host cells alive as long as possible while they are reproducing and growing. In order to grow they need nutrients that might be scarce in their form in the cell. To study the mechanism that intracellular parasites use to obtain nutrients Legionella pneumophila and it is known that Legionella pneumophila obtains nutrients by promoting host proteasomal degradation. Self-degradation of host proteins into amino acids provides the parasite with its primary carbon, people with T cell deficiencies are particularly susceptible to intracellular pathogens
23.
Foodborne illness
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Symptoms vary depending on the cause, and are described below in this article. A few broad generalizations can be made, e. g, the incubation period ranges from hours to days, depending on the cause and on how much was consumed. The incubation period tends to cause sufferers to not associate the symptoms with the item consumed, symptoms often include vomiting, fever, and aches, and may include diarrhea. Some types of microbes stay in the intestine, some produce a toxin that is absorbed into the bloodstream, Foodborne illness usually arises from improper handling, preparation, or food storage. Good hygiene practices before, during, and after food preparation can reduce the chances of contracting an illness, there is a consensus in the public health community that regular hand-washing is one of the most effective defenses against the spread of foodborne illness. The action of monitoring food to ensure that it will not cause illness is known as food safety. Foodborne disease can also be caused by a variety of toxins that affect the environment. Foodborne illness can also be caused by pesticides or medicines in food, bacteria are a common cause of foodborne illness. In the United Kingdom during 2000, the bacteria involved were the following, Campylobacter jejuni 77. 3%, Salmonella 20. 9%, Escherichia coli O157, H71. 4%. In the past, bacterial infections were thought to be prevalent because few places had the capability to test for norovirus. Toxins from bacterial infections are delayed because the bacteria need time to multiply, as a result, symptoms associated with intoxication are usually not seen until 12–72 hours or more after eating contaminated food. However, in cases, such as Staphylococcal food poisoning. Most common bacterial foodborne pathogens are, Campylobacter jejuni which can lead to secondary Guillain–Barré syndrome and periodontitis Clostridium perfringens, enterotoxins can produce illness even when the microbes that produced them have been killed. Symptom appearance varies with the toxin but may be rapid in onset and this causes intense vomiting including or not including diarrhea, and staphylococcal enterotoxins are the most commonly reported enterotoxins although cases of poisoning are likely underestimated. The CDC has estimated about 240,000 cases per year in the United States, many foodborne illnesses remain poorly understood. In August 2006, the United States Food and Drug Administration approved Phage therapy which involves spraying meat with viruses that infect bacteria and this has raised concerns, because without mandatory labelling consumers would not be aware that meat and poultry products have been treated with the spray. At home, prevention mainly consists of food safety practices. Many forms of bacterial poisoning can be prevented by cooking it sufficiently, many toxins, however, are not destroyed by heat treatment
24.
Sub-Saharan Africa
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Sub-Saharan Africa is, geographically, the area of the continent of Africa that lies south of the Sahara. According to the UN, it consists of all African countries that are fully or partially located south of the Sahara and it contrasts with North Africa, whose territories are part of the League of Arab states within the Arab world. Somalia, Djibouti, Comoros and Mauritania are geographically in Sub-Saharan Africa, the Sahel is the transitional zone between the Sahara and the tropical savanna and forest-savanna mosaic to the south. The Sahara pump theory explains how flora and fauna left Africa to penetrate the Middle East, African pluvial periods are associated with a wet Sahara phase during which larger lakes and more rivers existed. Geographers historically divided the region into several distinct ethnographic sections based on each areas respective inhabitants, commentators in Arabic in the medieval period used the general term bilâd as-sûdân for the vast Sudan region, or sometimes extending from the coast of West Africa to Western Sudan. Its equivalent in Southeast Africa was Zanj, which was situated in the vicinity of the Great Lakes region. The geographers drew an explicit distinction between the Sudan region and its analogue Zanj, from the area to their extreme east on the Red Sea coast in the Horn of Africa. In modern-day Ethiopia and Eritrea was Al-Habash or Abyssinia, which was inhabited by the Habash or Abyssinians, Sub-Saharan Africa has a wide variety of climate zones or biomes. South Africa and the Democratic Republic of the Congo in particular are considered Megadiverse countries, the Sahel shoots across all of Africa at a latitude of about 10° to 15° N. Countries that include parts of the Sahara Desert proper in their territories and parts of the Sahel in their southern region include Mauritania, Mali, Niger, Chad. The Sahel has a hot semi-arid climate, South of the Sahel, there is a belt of savanna, widening to include most of South Sudan and Ethiopia in the east. The Serengeti ecosystem is located in northwestern Tanzania and extends to southwestern Kenya, the Kalahari Basin includes the Kalahari Desert surrounded by a belt of semi-desert. The Bushveld is a tropical ecoregion of Southern Africa. The Karoo is a semi-desert in western South Africa and this occurred 10 million to 5 million years ago. By 3 million years ago several australopithecine hominid species had developed throughout southern, eastern and they were tool users rather than tool manufacturers. The tools were classed as Oldowan, roughly 1.8 million years ago, Homo ergaster first appeared in the fossil record in Africa. From Homo ergaster, Homo erectus evolved 1.5 million years ago, some of the earlier representatives of this species were small-brained and used primitive stone tools, much like H. habilis. The brain later grew in size, and H. erectus eventually developed a complex stone tool technology called the Acheulean
25.
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
26.
Lipopolysaccharide
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The term lipooligosaccharide is used to refer to a low-molecular-weight form of bacterial lipopolysaccharides. LPS also increases the charge of the cell membrane and helps stabilize the overall membrane structure. It is of importance to Gram-negative bacteria, which die if it is mutated or removed. LPS induces a response from normal animal immune systems. It has also implicated in non-pathogenic aspects of bacterial ecology, including surface adhesion, bacteriophage sensitivity. LPS is required for the conformation of Omptin activity, however. The O antigen is attached to the core oligosaccharide, and comprises the outermost domain of the LPS molecule, the composition of the O chain varies from strain to strain. For example, there are over 160 different O antigen structures produced by different E. coli strains, the presence or absence of O chains determines whether the LPS is considered rough or smooth. Full-length O-chains would render the LPS smooth, whereas the absence or reduction of O-chains would make the LPS rough, bacteria with rough LPS usually have more penetrable cell membranes to hydrophobic antibiotics, since a rough LPS is more hydrophobic. O antigen is exposed on the outer surface of the bacterial cell. The Core domain always contains a component that attaches directly to lipid A and commonly contains sugars such as heptose. The LPS Cores of many bacteria also contain non-carbohydrate components, such as phosphate, amino acids, Lipid A is, in normal circumstances, a phosphorylated glucosamine disaccharide decorated with multiple fatty acids. These hydrophobic fatty acid chains anchor the LPS into the membrane. The lipid A domain is responsible for much of the toxicity of Gram-negative bacteria, when bacterial cells are lysed by the immune system, fragments of membrane containing lipid A are released into the circulation, causing fever, diarrhea, and possible fatal endotoxic shock. The Lipid A moiety is a very conserved component of the LPS, lipooligosaccharides are glycolipids found in the outer membrane of some types of Gram-negative bacteria, such as Neisseria spp. and Haemophilus spp. The term is synonymous with the low molecular weight form of bacterial LPS, LOS plays a central role in maintaining the integrity and functionality of the outer membrane of the Gram negative cell envelope. Lipooligosaccharides play an important role in the pathogenesis of bacterial infections because they are capable of acting as immunostimulators and immunomodulators. Chemically, lipooligosaccharides lack O-antigens and possess only the a lipid A-based outer membrane-anchoring moiety, in the case of Neisseria meningitidis, the lipid A portion of the molecule has a symmetrical structure and the inner core is composed of 3-deoxy-D-manno-2-octulosonic acid and heptose moieties
27.
Epidemiology
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Epidemiology is the study and analysis of the patterns, causes, and effects of health and disease conditions in defined populations. It is the cornerstone of public health, and shapes policy decisions and evidence-based practice by identifying risk factors for disease, epidemiologists help with study design, collection, and statistical analysis of data, amend interpretation and dissemination of results. Epidemiology has helped develop methodology used in research, public health studies. However, the term is used in studies of zoological populations, although the term epizoology is available. The distinction between epidemic and endemic was first drawn by Hippocrates, to distinguish between diseases that are visited upon a population from those that reside within a population. The term epidemiology appears to have first been used to describe the study of epidemics in 1802 by the Spanish physician Villalba in Epidemiología Española, epidemiologists also study the interaction of diseases in a population, a condition known as a syndemic. Therefore, this epidemiology is based upon how the pattern of the disease cause changes in the function of everyone, Hippocrates believed sickness of the human body to be caused by an imbalance of the four humors. The cure to the sickness was to remove or add the humor in question to balance the body and this belief led to the application of bloodletting and dieting in medicine. He coined the terms endemic and epidemic, in the middle of the 16th century, a doctor from Verona named Girolamo Fracastoro was the first to propose a theory that these very small, unseeable, particles that cause disease were alive. They were considered to be able to spread by air, multiply by themselves, in this way he refuted Galens miasma theory. In 1543 he wrote a book De contagione et contagiosis morbis, the development of a sufficiently powerful microscope by Antonie van Leeuwenhoek in 1675 provided visual evidence of living particles consistent with a germ theory of disease. Wu Youke developed the concept that some diseases were caused by transmissible agents and his book Wenyi Lun can be regarded as the main etiological work that brought forward the concept, ultimately attributed to Westerners, of germs as a cause of epidemic diseases. His concepts are considered in current scientific research in relation to Traditional Chinese Medicine studies. Another pioneer, Thomas Sydenham, was the first to distinguish the fevers of Londoners in the later 1600s and his theories on cures of fevers met with much resistance from traditional physicians at the time. He was not able to find the cause of the smallpox fever he researched and treated. John Graunt, a haberdasher and amateur statistician, published Natural and Political Observations, upon the Bills of Mortality in 1662. In it, he analysed the mortality rolls in London before the Great Plague, presented one of the first life tables and he provided statistical evidence for many theories on disease, and also refuted some widespread ideas on them. John Snow is famous for his investigations into the causes of the 19th century cholera epidemics and he began with noticing the significantly higher death rates in two areas supplied by Southwark Company
28.
Antibiotic sensitivity
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Antibiotic sensitivity or antibiotic susceptibility is the susceptibility of bacteria to antibiotics. Testing for antibiotic sensitivity is often done by the Kirby-Bauer method, small wafers containing antibiotics are placed onto a plate upon which bacteria are growing. If the bacteria are sensitive to the antibiotic, a clear ring, other methods to test antimicrobial susceptibility include the Stokes method, Etest, Agar and Broth dilution methods for minimum inhibitory concentration determination. The results of the test are reported on the antibiogram, ideal antibiotic therapy is based on determination of the aetiological agent and its relevant antibiotic sensitivity. Empiric treatment is started before laboratory microbiological reports are available when treatment should not be delayed due to the seriousness of the disease. Some antibiotics actually kill the bacteria, whereas others merely prevent the bacteria from multiplying so that the immune system can overcome them. Müeller-Hinton agar is most frequently used in this antibiotic susceptibility test, an antibiogram is the result of an antibiotic sensitivity test. It is by definition an in vitro sensitivity, but the correlation of in vitro to in vivo sensitivity is high enough for the test to be clinically useful. This is because Escherichia coli is the most likely causative pathogen, however, many bacteria are known to be resistant to several classes of antibiotics, and treatment is not so straightforward. This is especially the case in vulnerable patients, such as patients in the intensive care unit, when these patients develop a hospital-acquired pneumonia, more hardy bacteria like Pseudomonas aeruginosa are potentially involved. Treatment is then started on the basis of surveillance data about the local pathogens probably involved. This first treatment, based on information about former patients. These samples are transferred to the lab, which looks at the sample under the microscope. This can help in the diagnosis, the antibiotic will diffuse in the area surrounding each tablet, and a disc of bacterial lysis will become visible. Since the concentration of the antibiotic was the highest at the centre, and the lowest at the edge of this zone, a quantitative way based on dilution, a dilution series of antibiotics is established. The last vial in which no bacteria grow contains the antibiotic at the Minimal Inhibiting Concentration. Once the MIC is calculated, it can be compared to values for a given bacterium and antibiotic. Such information may be useful to the clinician, who can change the empirical treatment, often clinical specimens are sent to the clinical laboratory for culture and sensitivity, which is culture and antibiotic sensitivity testing offered as one combined service
29.
Molecular biology
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Writing in Nature in 1961, William Astbury described molecular biology as. It is concerned particularly with the forms of biological molecules and is predominantly three-dimensional and structural—which does not mean, however and it must at the same time inquire into genesis and function. Researchers in molecular biology use specific techniques native to molecular biology but increasingly combine these techniques and ideas from genetics. There is not a line between these disciplines. Biochemists focus heavily on the role, function, and structure of biomolecules, the study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry. Genetics is the study of the effect of differences on organisms. This can often be inferred by the absence of a normal component, the study of mutants – organisms which lack one or more functional components with respect to the so-called wild type or normal phenotype. Genetic interactions can often confound simple interpretations of such knockout studies, molecular biology is the study of molecular underpinnings of the processes of replication, transcription, translation, and cell function. This picture, however, is undergoing revision in light of emerging novel roles for RNA, much of molecular biology is quantitative, and recently much work has been done at its interface with computer science in bioinformatics and computational biology. In the early 2000s, the study of structure and function. There is also a tradition of studying biomolecules from the ground up in biophysics. One of the most basic techniques of molecular biology to study protein function is molecular cloning, in this technique, DNA coding for a protein of interest is cloned using PCR and/or restriction enzymes into a plasmid. A vector has 3 distinctive features, an origin of replication, a multiple cloning site, the origin of replication will have promoter regions upstream from the replication/transcription start site. This plasmid can be inserted into either bacterial or animal cells, introducing DNA into bacterial cells can be done by transformation via uptake of naked DNA, conjugation via cell-cell contact or by transduction via viral vector. Introducing DNA into eukaryotic cells, such as cells, by physical or chemical means is called transfection. Several different transfection techniques are available, such as calcium phosphate transfection, electroporation, microinjection, the plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection. DNA coding for a protein of interest is now inside a cell, a variety of systems, such as inducible promoters and specific cell-signaling factors, are available to help express the protein of interest at high levels. Large quantities of a protein can then be extracted from the bacterial or eukaryotic cell, polymerase chain reaction is an extremely versatile technique for copying DNA
30.
Pulsed-field gel electrophoresis
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Pulsed field gel electrophoresis is a technique used for the separation of large deoxyribonucleic acid molecules by applying to a gel matrix an electric field that periodically changes direction. Standard gel electrophoresis techniques for separation of DNA molecules provided huge advantages for molecular biology research, however, it was unable to separate very large molecules of DNA effectively. DNA molecules larger than 15–20 kb migrating through a gel will essentially move together in a size-independent manner and this technique became known as pulsed-field gel electrophoresis. The development of PFGE expanded the range of resolution for DNA fragments by as much as two orders of magnitude, the pulse times are equal for each direction resulting in a net forward migration of the DNA. This procedure takes longer than normal gel electrophoresis due to the size of the fragments being resolved, however, with periodic changing of field direction, the various lengths of DNA react to the change at differing rates. That is, larger pieces of DNA will be slower to realign their charge when field direction is changed, over the course of time with the consistent changing of directions, each band will begin to separate more and more even at very large lengths. Thus separation of very large DNA pieces using PFGE is made possible, PFGE may be used for genotyping or genetic fingerprinting. It is commonly considered a standard in epidemiological studies of pathogenic organisms. Subtyping has made it easier to discriminate among strains of Listeria monocytogenes, pulse field method Applied Maths BioNumerics PFGE typing
31.
Whole genome sequencing
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Whole genome sequencing is the process of determining the complete DNA sequence of an organisms genome at a single time. This entails sequencing all of an organisms chromosomal DNA as well as DNA contained in the mitochondria and, for plants, whole genome sequencing has largely been used as a research tool, but is currently being introduced to clinics. In the future of personalized medicine, whole genome sequence data will be an important tool to guide therapeutic intervention, in addition, whole genome sequencing should not be confused with methods that sequence specific subsets of the genome - such methods include whole exome sequencing or SNP genotyping. Almost all truly complete genomes are of microbes, the full genome is thus sometimes used loosely to mean greater than 95%. The remainder of this focuses on nearly complete human genomes. The DNA sequencing methods used in the 1970s and 1980s were manual, for example Maxam-Gilbert sequencing, the shift to more rapid, automated sequencing methods in the 1990s finally allowed the sequence of whole genomes. The first organism to have its genome sequenced was Haemophilus influenzae in 1995. After it, the genomes of bacteria and some archaea were first sequenced. H. influenzae has a genome of 1,830,140 base pairs of DNA, in contrast, eukaryotes, both unicellular and multicellular such as Amoeba dubia and humans respectively, have much larger genomes. Amoeba dubia has a genome of 700 billion nucleotide pairs spread across thousands of chromosomes, humans contain fewer nucleotide pairs than A. dubia however their genome size far outweighs the genome size of individual bacteria. The first bacterial and archaeal genomes, including that of H. influenzae, were sequenced by Shotgun sequencing, in 1996 the first eukaryotic genome was sequenced. S. cerevisiae, an organism in biology has a genome of only around 12 million nucleotide pairs. The first multicellular eukaryote, and animal, to have its genome sequenced was the nematode worm. In 1999, the entire DNA sequence of human chromosome 22, by the year 2000, the second animal and second invertebrate genome was sequenced - that of the fruit fly Drosophila melanogaster - a popular choice of model organism in experimental research. The first plant genome - that of the model organism Arabidopsis thaliana - was also fully sequenced by 2000, by 2001, a draft of the entire human genome sequence was published. The genome of the laboratory mouse Mus musculus was completed in 2002, in 2004, the Human Genome Project published the human genome. Currently, thousands of genomes have been sequenced, almost any biological sample containing a full copy of the DNA—even a very small amount of DNA or ancient DNA—can provide the genetic material necessary for full genome sequencing. Such samples may include saliva, epithelial cells, bone marrow, hair, seeds, plant leaves, the genome sequence of a single cell selected from a mixed population of cells can be determined using techniques of single cell genome sequencing
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Karl Joseph Eberth
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Karl Joseph Eberth was a German pathologist and bacteriologist who was a native of Würzburg. In 1859 he earned his doctorate at the University of Würzburg, in 1869 he became a full professor of pathological anatomy at the University of Zurich, and from 1881 until his retirement in 1911, he was a professor at the University of Halle. In 1880 Eberth described a bacillus that he suspected was the cause of typhoid, in 1884 pathologist Georg Theodor August Gaffky confirmed Eberths findings, and the organism was given names such as Eberthella typhi, Eberths bacillus and Gaffky-Eberth bacillus. Today the bacillus that causes typhoid fever goes by the name of Salmonella enterica subspecies enterica serovar Typhi. Eberths lines, Microscopic lines that appear between the cells of the myocardium when stained with silver nitrate, Eberths perithelium, an incomplete layer of connective tissue cells encasing the blood capillaries. Zur kenntniss der blutplättchen bei den niederen wirbelthieren, die Thrombose nach Versuchen und Leichenbefunden, with Curt Schimmelbusch. Pathology List of pathologists Parts of this article are based on a translation of an article from the German Wikipedia
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Peyer's patch
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Peyers patches are organized lymphoid follicles, named after the 17th-century Swiss anatomist Johann Conrad Peyer. Peyers patches are observable as elongated thickenings of the intestinal epithelium measuring a few centimeters in length, about 100 are found in humans. Microscopically, Peyers patches appear as oval or round lymphoid follicles located in the layer of the ileum. The number of Peyers patches peaks at age 15–25 and then declines during adulthood, in the distal ileum, they are numerous and they form a lymphoid ring. At least 46% of Peyers patches are concentrated in the distal 25 cm of ileum in humans and it is important to note that there are large variations in size, shape, and distribution of Peyers patches from one individual to another one. In adults, B lymphocytes are seen to dominate the follicles germinal centers, T lymphocytes are found in the zones between follicles. Among the mononuclear cells, CD4+/CD25+ cells and CD8+/CD25+ cells are more abundant in Peyers patches than in the peripheral blood, Peyers patches are characterized by the follicle-associated epithelium, which covers every lymphoid follicles. Moreover, basal lamina of follicle-associated epithelium is more porous compare to intestinal villus, finally, follicle-associated epithelium is less permeable for ions and macromolecules, basically due to higher expression of tight junction proteins. Because the lumen of the tract is exposed to the external environment. Peyers patches thus establish their importance in the surveillance of the intestinal lumen. Peyers patches thus act for the system much as the tonsils act for the respiratory system, trapping foreign particles, surveilling them. Dendritic cells and macrophages can also sample the lumen by extending dendrites through transcellular M cell-specific pores. At the same time the paracellular pathway of follicle-associated epithelium is closed tightly to prevent penetration of antigens, T cells, B-cells and memory cells are stimulated upon encountering antigen in Peyers patches. These cells then pass to the lymph nodes where the immune response is amplified. The hypertrophy of Peyers patches has also associated with susceptibility to transmissible spongiform encephalopathies. Salmonella typhi and poliovirus also target this section of the intestine
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Georg Theodor August Gaffky
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Georg Theodor August Gaffky was a Hanover born bacteriologist best known for identifying bacillus salmonella typhi as the cause of typhoid disease in 1884. Gaffkys parents were the shipping agent Georg Friedrich Wilhelm Gaffky, and his medical studies at the Friedrich Wilhelm University in Berlin were completed in 1873 after an interruption by the Franco-Prussian War in 1870. His dissertation postulated a relationship between lead poisoning and kidney disease and he worked as an assistant at the Berlin Charité hospital and passed the state medical exams in 1875. He then worked as an army surgeon, Gaffky worked as an assistant to Robert Koch in Berlin. Under Kochs leadership, Gaffky and others developed bacteriological protocols and achieved progress in identifying causes of infectious diseases and he was able to produce cultures in gelatin and other hosts. In 1884, Gaffky published results reporting that he had isolated the eberthella or Gaffky-Eberth bacillus in 26 of 28 cases of typhoid, Gaffky was later part of an expedition to Egypt in which Koch identified transmission methods of cholera. He became a government advisor during the 1892 cholera outbreak in Hamburg and he led an investigation of the 1897 outbreak of bubonic plague in India. Gaffky served as director of the Berlin Institute for Infectious Diseases from 1904–1913, gloria Robinson, Gaffky, Georg Theodor August. Charles Coulston Gillispie, Dictionary of Scientific Biographies, works by or about Georg Theodor August Gaffky at Internet Archive
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Theobald Smith
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Theobald Smith ForMemRS was a pioneering epidemiologist and pathologist and is widely considered to be Americas first internationally significant medical research scientist. Smith was born in Albany, New York, and received a Bachelor of Philosophy degree from Cornell University in 1881, after his graduation from medical school, Smith held a variety of temporary positions which might broadly be considered under the modern heading of medical laboratory technician. Smith became the Inspector of the newly created Bureau of Animal Industry in 1884, after two years of work studying the efficacy of bacterial vaccination in pigs, Smith erroneously believed he had found the causative agent of hog cholera. Smith turned his attention to Texas fever, a cattle disease. In 1889, he along with the veterinarian F. L, kilbourne discovered Babesia bigemina, the tick-borne protozoan parasite responsible for Texas fever. Smith also taught at Columbian University in Washington, D. C. from 1886–1895, in 1887, Smith began research on water sanitation in his spare time, investigating the level of fecal coliform contamination in the Potomac River. Over the next five years, Smith expanded his studies to include the Hudson River, while Smiths work at the BAI had been highly productive, he chafed against the federal government bureaucracy and the lack of leadership from his supervisor. Smith joined the Rockefeller Institute for Medical Research as Director of the Department of Animal Pathology in 1915, in 1933, Smith was awarded the Royal Societys prestigious Copley Medal For his original research and observation on diseases of animals and man. Observed differences between human and bovine tuberculosis, discussed the possibility of mosquitos as a malaria transmission vector. Brucellosis infections Smith used toxin/antitoxin as a vaccine for diphtheria, in the process of investigating an epidemic of infectious abortions of cattle in 1919, Smith described the bacteria responsible for fetal membrane disease in cows now known as Campylobacter fetus
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United States Department of Agriculture
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Approximately 80% of USDAs $140 billion budget goes to the Food and Nutrition Service program. The largest component of the FNS budget is the Supplemental Nutrition Assistance Program, after the resignation of Thomas Vilsack on January 13,2017 and the departure of President Barack Obama from office on January 20,2017, the acting Secretary of Agriculture is Michael Young. Activities in this include the Supplemental Nutrition Assistance Program, which provides healthy food to over 40 million low-income. The USDA also is concerned with assisting farmers and food producers with the sale of crops and it plays a role in overseas aid programs by providing surplus foods to developing countries. This aid can go through USAID, foreign governments, international bodies such as World Food Program, the Agricultural Act of 1949, section 416 and Agricultural Trade Development and Assistance Act of 1954, also known as Food for Peace, provides the legal basis of such actions. The USDA is a partner of the World Cocoa Foundation, early in its history, the economy of the United States was largely agrarian. Officials in the government had long sought new and improved varieties of seeds, plants. In 1837 Henry Leavitt Ellsworth, a Yale-educated attorney interested in improving agriculture, became Commissioner of Patents and he began collecting and distributing new varieties of seeds and plants through members of the Congress and agricultural societies. In 1839, Congress established the Agricultural Division within the Patent Office and allotted $1,000 for the collection of agricultural statistics, Ellsworth was called the Father of the Department of Agriculture. In 1849, the Patent Office was transferred to the newly created Department of the Interior, in the ensuing years, agitation for a separate bureau of agriculture within the department or a separate department devoted to agriculture kept recurring. Lincoln called it the peoples department, in the 1880s, varied advocacy groups were lobbying for Cabinet representation. Business interests sought a Department of Commerce and Industry, and farmers tried to raise the Department of Agriculture to Cabinet rank, finally, on February 9,1889, President Grover Cleveland signed a bill into law elevating the Department of Agriculture to Cabinet level. In 1887, the Hatch Act provided for the funding of agricultural experiment stations in each state. The Smith-Lever Act of 1914 then funded cooperative extension services in each state to teach agriculture, home economics, with these and similar provisions, the USDA reached out to every county of every state. During the Great Depression, farming remained a way of life for millions of Americans. The Department of Agricultures Bureau of Home Economics, established in 1923, published shopping advice and recipes to stretch family budgets and make food go farther. USDA helped ensure that continued to be produced and distributed to those who needed it, assisted with loans for small landowners. The Department of Agriculture was authorized a budget for Fiscal Year 2015 of $139.7 billion, the Washington Post reports that he said There are days when I have literally nothing to do, he recalled thinking as he weighed his decision to quit
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