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
Taxonomy (biology)
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Title page of
Systema Naturae, Leiden, 1735
Taxonomy (biology)
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Evolution of the
vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are typical for
Evolutionary taxonomy
Taxonomy (biology)
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The same relationship, expressed as a
cladogram typical for
cladistics
Taxonomy (biology)
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Type specimen for
Nepenthes smilesii, a tropical
pitcher plant.
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
Bacteria
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Had'n
Bacteria
Bacteria
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A
biofilm of thermophilic bacteria in the outflow of
Mickey Hot Springs,
Oregon, approximately 20 mm thick.
Bacteria
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Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface
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
Proteobacteria
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Proteobacteria
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
Gammaproteobacteria
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Gammaproteobacteria
5.
Pseudomonadales
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The Pseudomonadales are an order of Proteobacteria. A few members are opportunistic pathogens, such as species of Pseudomonas, Moraxella, and Acinetobacter, P. aeruginosa can cause chronic opportunistic infections that have become increasingly apparent in immunocompromised patients and the ageing population of industrialised societies. The genome sequences of several pseudomonads have become available in recent years and researchers are beginning to use the data to new discoveries about this bacterium. The genus Acinetobacter is a group of Gram-negative, nonmotile and nonfermentative bacteria belonging to the family Moraxellaceae and they are important soil organisms where they contribute to the mineralisation of, for example, aromatic compounds. Acinetobacter species are able to survive on surfaces in the hospital environment. These bacteria are resistant to many classes of antibiotics. In addition, Acinetobacter is uniquely suited to exploitation for biotechnological purposes
Pseudomonadales
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Pseudomonadales
6.
Moraxellaceae
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The Moraxellaceae are a family of Gammaproteobacteria, including a few pathogenic species. Others are harmless parasites of mammals and humans or occur in water or soil, the species are mesophilic or psychrotrophic. Moraxella catarrhalis is a pathogen, and Moraxella bovis is the cause of pinkeye of cattle. J. P. Euzéby, List of Prokaryotic names with Standing in Nomenclature Pink-eye in Beef Cattle - Department of Primary Industries
Moraxellaceae
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Moraxellaceae
7.
Binomial nomenclature
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Such a name is called a binomial name, a binomen, binominal name or a scientific name, more informally it is also called a Latin name. The first part of the name identifies the genus to which the species belongs, for example, humans belong to the genus Homo and within this genus to the species Homo sapiens. The formal introduction of system of naming species is credited to Carl Linnaeus. But Gaspard Bauhin, in as early as 1623, had introduced in his book Pinax theatri botanici many names of genera that were adopted by Linnaeus. Although the general principles underlying binomial nomenclature are common to these two codes, there are differences, both in the terminology they use and in their precise rules. Similarly, both parts are italicized when a binomial name occurs in normal text, thus the binomial name of the annual phlox is now written as Phlox drummondii. In scientific works, the authority for a name is usually given, at least when it is first mentioned. In zoology Patella vulgata Linnaeus,1758, the original name given by Linnaeus was Fringilla domestica, the parentheses indicate that the species is now considered to belong in a different genus. The ICZN does not require that the name of the person who changed the genus be given, nor the date on which the change was made, in botany Amaranthus retroflexus L. – L. is the standard abbreviation used in botany for Linnaeus. – Linnaeus first named this bluebell species Scilla italica, Rothmaler transferred it to the genus Hyacinthoides, the ICN does not require that the dates of either publication be specified. Prior to the adoption of the binomial system of naming species. Together they formed a system of polynomial nomenclature and these names had two separate functions. First, to designate or label the species, and second, to be a diagnosis or description, such polynomial names may sometimes look like binomials, but are significantly different. For example, Gerards herbal describes various kinds of spiderwort, The first is called Phalangium ramosum, Branched Spiderwort, is aptly termed Phalangium Ephemerum Virginianum, Soon-Fading Spiderwort of Virginia. The Latin phrases are short descriptions, rather than identifying labels, the Bauhins, in particular Caspar Bauhin, took some important steps towards the binomial system, by pruning the Latin descriptions, in many cases to two words. The adoption by biologists of a system of binomial nomenclature is due to Swedish botanist and physician Carl von Linné. It was in his 1753 Species Plantarum that he first began using a one-word trivial name together with a generic name in a system of binomial nomenclature. This trivial name is what is now known as an epithet or specific name
Binomial nomenclature
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Carl Linnaeus (1707–1778), a Swedish botanist, invented the modern system of binomial nomenclature.
8.
Gram-negative
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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
Gram-negative
–
Microscopic image of gram-negative
Pseudomonas aeruginosa bacteria (pink-red rods)
9.
Aerobic organism
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An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. In contrast, an organism is any organism that does not require oxygen for growth. Some anaerobes react negatively or even die if oxygen is present, obligate aerobes need oxygen to grow. In a process known as respiration, these organisms use oxygen to oxidize substrates. Facultative anaerobes use oxygen if it is available, but also have anaerobic methods of energy production, microaerophiles require oxygen for energy production, but are harmed by atmospheric concentrations of oxygen. Aerotolerant anaerobes do not use oxygen but are not harmed by it, a good example is the oxidation of glucose in aerobic respiration. C6H12O6 +6 O2 +38 ADP +38 phosphate →6 CO2 +6 H2O +38 ATP Oxygen is used during the oxidation of glucose and water is produced. This equation is a summary of what happens in three series of reactions, glycolysis, the Krebs cycle, and oxidative phosphorylation. Aerobic digestion Anaerobic digestion Fermentation Aerobic vaginitis Oxygenation
Aerobic organism
10.
Oxidase test
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The oxidase test is a test used in microbiology to determine if a bacterium produces certain cytochrome c oxidases. It uses disks impregnated with a reagent such as N, N, N′, N′-tetramethyl-p-phenylenediamine or N, N-dimethyl-p-phenylenediamine, the reagent is a dark-blue to maroon color when oxidized, and colorless when reduced. Oxidase-positive bacteria possess cytochrome oxidase or indophenol oxidase and these both catalyze the transport of electrons from donor compounds to electron acceptors. The test reagent, TMPD dihydrochloride acts as an electron donor for the enzyme oxidase. The oxidized reagent forms the colored compound indophenol blue, the cytochrome system is usually only present in aerobic organisms that are capable of using oxygen as the terminal electron acceptor. The end-product of this metabolism is either water or hydrogen peroxide, strains may be either oxidase-positive or oxidase-negative. OX+ normally means the bacterium contains cytochrome c oxidase and can use oxygen for energy production by converting O2 to H2O2 or H2O with an electron transfer chain. The Pseudomonadaceae are typically OX+ The Gram-negative diplococci Neisseria and Moraxella are oxidase-positive, many Gram-negative, spiral curved rods are also oxidase-positive, which includes Helicobacter pylori, Vibrio cholerae, and Campylobacter jejuni. Wet each disk with about four inoculating loops of deionized water, use a loop to aseptically transfer a large mass of pure bacteria to the disk. Observe the disk for up to three minutes, if the area of inoculation turns dark-blue to maroon to almost black, then the result is positive. If a color change does not occur within three minutes, the result is negative, in alternative manner, live bacteria cultivated on trypticase soy agar plates may be prepared using sterile technique with a single-line streak inoculation. The inoculated plates are incubated at 37 °C for 24–48 hours to establish colonies, fresh bacterial preparations should be used. After colonies have grown on the medium, 2-3 drops of the reagent DMPD are added to the surface of each organism to be tested, a positive test will result in a color change violet to purple, within 10–30 seconds. A negative test will result in a light-pink or absence of coloration, Oxidase test video Oxidase Test Procedure
Oxidase test
–
DMPD
11.
Respiratory system
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The respiratory system is a biological system consisting of specific organs and structures used for the process of respiration in an organism. The respiratory system is involved in the intake and exchange of oxygen, in air-breathing vertebrates like human beings, respiration takes place in the respiratory organs called lungs. In humans and other mammals, the features of the respiratory system include trachea, bronchi, bronchioles, lungs. Molecules of oxygen and carbon dioxide are exchanged, by diffusion. This exchange process occurs in the alveoli in the lungs, in fish and many invertebrates, respiration takes place through the gills. Other animals, such as insects, have respiratory systems with very simple anatomical features, plants also have respiratory systems but the directionality of gas exchange can be opposite to that in animals. The respiratory system in plants also includes features such as holes on the undersides of leaves known as stomata. The elephant is the animal known to have no pleural space. Rather, the parietal and visceral pleura are both composed of connective tissue and joined to each other via loose connective tissue. The respiratory system of birds differs significantly from that found in mammals, the lungs of birds also do not have the capacity to inflate as birds lack a diaphragm and a pleural cavity. Gas exchange in birds occurs between air capillaries and blood capillaries, rather than in alveoli, the anatomical structure of the lungs is less complex in reptiles than in mammals, with reptiles lacking the very extensive airway tree structure found in mammalian lungs. Gas exchange in reptiles still occurs in alveoli however, reptiles do not possess a diaphragm, thus, breathing occurs via a change in the volume of the body cavity which is controlled by contraction of intercostal muscles in all reptiles except turtles. In turtles, contraction of specific pairs of flank muscles governs inspiration or expiration, both the lungs and the skin serve as respiratory organs in amphibians. The ventilation of the lungs in amphibians uses positive pressure ventilation, muscles lower the floor of the oral cavity, enlarging it and drawing in air through the nostrils. While the lungs are of importance to breathing control, the skins unique properties aid rapid gas exchange when amphibians are submerged in oxygen-rich water. In most fish, respiration takes place through gills, lungfish, however, do possess one or two lungs. The labyrinth fish have developed an organ that allows them to take advantage of the oxygen of the air. Some species of crab use an organ called a branchiostegal lung
Respiratory system
–
A complete, schematic view of the human respiratory system with their parts and functions.
12.
Joint
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A joint or articulation is the connection made between bones in the body which link the skeletal system into a functional whole. They are constructed to allow for different degrees and types of movement, other joints such as sutures between the bones of the skull permit very little movement in order to protect the brain and the sense organs. The connection between a tooth and the jawbone is also called a joint, and is described as a fibrous joint known as a gomphosis, joints are classified both structurally and functionally. Joints are mainly classified structurally and functionally, structural classification is determined by how the bones connect to each other, while functional classification is determined by the degree of movement between the articulating bones. In practice, there is significant overlap between the two types of classifications, a facet joint is the joint between two articular processes between two vertebrae. Structural classification names and divides joints according to the type of binding tissue that connects the bones to each other, joints can also be classified functionally according to the type and degree of movement they allow, Joint movements are described with reference to the basic anatomical planes. Synarthrosis – permits little or no mobility, most synarthrosis joints are fibrous joints. Most amphiarthrosis joints are cartilaginous joints, Synovial joints can in turn be classified into six groups according to the type of movement they allow, plane joint, ball and socket joint, hinge joint, pivot joint, condyloid joint and saddle joint. Joints can also be classified, according to the number of axes of movement they allow, another classification is according to the degrees of freedom allowed, and distinguished between joints with one, two or three degrees of freedom. A further classification is according to the number and shapes of the surfaces, flat, concave. Types of articular surfaces include trochlear surfaces, joints can also be classified based on their anatomy or on their biomechanical properties. Swimming is a way to exercise the joints with minimal damage. A joint disorder is termed arthropathy, and when involving inflammation of one or more joints the disorder is called arthritis, most joint disorders involve arthritis, but joint damage by external physical trauma is typically not termed arthritis. Arthropathies are called polyarticular when involving many joints and monoarticular when involving only a single joint, arthritis is the leading cause of disability in people over the age of 55. There are many different forms of arthritis, each of which has a different cause, furthermore, there is emerging evidence that abnormal anatomy may contribute to early development of osteoarthritis. Other forms of arthritis are rheumatoid arthritis and psoriatic arthritis, which are diseases in which the body is attacking itself. Septic arthritis is caused by joint infection, gouty arthritis is caused by deposition of uric acid crystals in the joint that results in subsequent inflammation. Additionally, there is a common form of gout that is caused by the formation of rhomboidal-shaped crystals of calcium pyrophosphate
Joint
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Diagram of a typical synovial (diarthrosis) joint
13.
Host (biology)
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In biology, a host is an organism that harbors a parasitic, a mutual, or a commensal symbiont, typically providing nourishment and shelter. Examples include animals playing host to parasitic worms, cells harbouring a parasitic virus, more specifically in botany, a host plant supplies food resources and acts as a substrate for commensalist insects or other fauna. Guest is the term used for parasites, mutualists and commensals. The host range of a parasite is the collection of hosts that an organism can utilize as a partner, in the case of human parasites, the host range influences the epidemiology of the parasitism or disease. For instance, the production of antigenic shifts in Influenza A virus can result from pigs being infected with the virus from different hosts. This co-infection provides an opportunity for mixing of the viral genes between existing strains, thereby producing a new viral strain
Host (biology)
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The
roof rat (Rattus rattus) is a reservoir host for
bubonic plague: the
oriental rat fleas that infest these rats are a prime
source for the disease.
14.
Cell (biology)
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The cell is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life that can replicate independently, the study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many such as proteins. Organisms can be classified as unicellular or multicellular, while the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion cells. Most plant and animal cells are only under a microscope. The cell was discovered by Robert Hooke in 1665, who named the unit for its resemblance to cells inhabited by Christian monks in a monastery. Cells emerged on Earth at least 3.5 billion years ago, Cells are of two types, eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular, prokaryotic cells were the first form of life on Earth, characterised by having vital biological processes including cell signaling and being self-sustaining. They are simpler and smaller than eukaryotic cells, and lack membrane-bound organelles such as the nucleus, prokaryotes include two of the domains of life, bacteria and archaea. The DNA of a prokaryotic cell consists of a chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid, most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 µm in diameter. Though most prokaryotes have both a cell membrane and a wall, there are exceptions such as Mycoplasma and Thermoplasma which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, the cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting from osmotic pressure due to a hypotonic environment, some eukaryotic cells also have a cell wall. Inside the cell is the region that contains the genome, ribosomes. The genetic material is found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular, linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a nucleoid, plasmids encode additional genes, such as antibiotic resistance genes
Cell (biology)
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Onion (
Allium) cells in different phases of the cell cycle
Cell (biology)
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Structure of an animal cell
Cell (biology)
–
A fluorescent image of an endothelial cell. Nuclei are stained blue,
mitochondria are stained red, and microfilaments are stained green.
Cell (biology)
–
Human cancer cells with nuclei (specifically the DNA) stained blue. The central and rightmost cell are in
interphase, so the entire nuclei are labeled. The cell on the left is going through
mitosis and its DNA has condensed.
15.
Trimeric autotransporter adhesin
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In molecular biology, trimeric autotransporter adhesins, are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion, TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful, TAAs are just one of many methods bacteria use to infect their hosts, infection resulting in diseases such as pneumonia, sepsis, and meningitis. Most bacteria infect their host through a method named the secretion pathway, TAAs are part of the secretion pathway, to be more specific the type Vc secretion system. Trimeric autotransporter adhesins have a unique structure, the structure they hold is crucial to their function. They all appear to have a head-stalk-anchor structure, each TAA is made up of three identical proteins, hence the name trimeric. The head domain, once assembled, then adheres to an element of the host extracellular matrix, for example, collagen, fibronectin, most TAAs have a similar protein structure. When observed with microscopy, the structure has been described as a lollipop shape consisting of an N-terminal head domain, a stalk domain. Often, the literature refers to these as Passenger domain, containing the N-terminal, head, neck, and coiled-coil stalk, although all TAAs carry a membrane anchor in common, they may not all contain both a stalk and a head as well. In addition, all membrane anchor domains are of the left-handed parallel beta-roll type, the Extended Signal Peptide Region is found in the N-terminus of the signal peptides of proteins belonging to the Type V secretion systems. The function of the ESPR is to aid inner membrane translocation by acting as a temporary tether and this prevents the accumulation of misfolded proteins. The ESPR can be divided into regions, they are as follows, N1, H1, N2, H2. N1 and H1 form the ESPR and have strong conservation, function, There are several roles that the Extended Signal Peptide Region is thought to hold. First, biogenesis of proteins in the Type V Secretion System, second, it is thought to target the protein to the inner membrane to be translocated either by the signal recognition particle pathway or by twin arginine translocated. Third, it has observed and believed to regulate the rate of protein migration into the periplasm. Structure, This particular domain is a trimer of single-stranded, left-handed beta-helices and these associate to form a nine-coiled left-handed beta-roll. It contains sequence motifs, of which there is a similarity with other TAA heads. This indicates that there is a lot of similarity when comparing protein structure, the head domain is connected to the stalk by a short, highly conserved sequence, which is often called the neck, or occasionally named the connector
Trimeric autotransporter adhesin
–
Figure 1
Trimeric autotransporter adhesin
–
Figure 3
Trimeric autotransporter adhesin
–
Figure 4
Trimeric autotransporter adhesin
–
The beta barrel structure found in the C-terminus of the bacterial adhesin anchor domain, YadA
16.
Bacilli
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Bacilli refers to a taxonomic class of bacteria. It includes two orders, Bacillales and Lactobacillales, which contain several well-known pathogens such as Bacillus anthracis, several related concepts make use of similar words, and the ambiguity can create considerable confusion. The term Bacillus is also the name of a genus that, among other genera. Also, bacillus can be a term to describe the morphology of any rod-shaped bacterium. This general term does not mean that the subject is a member of class Bacilli or genus Bacillus, thus, it does not necessarily imply a similar group of characteristics. Not all members of class Bacilli are rod-shaped, and many other rod-shaped bacteria that do not fall within that class exist, moreover, the general term bacillus does not necessarily indicate the Gram-positive staining common to class Bacilli. For example, E. coli is a bacterium that could, therefore, be described as a bacillus. Some microbiologists have forsaken the general term because of the confusion it can create
Bacilli
–
Bacillus
17.
16S ribosomal RNA
–
16S ribosomal RNA is the component of the 30S small subunit of a prokaryotic ribosome that binds to the Shine-Dalgarno sequence. The genes coding for it are referred to as 16S rRNA gene and are used in reconstructing phylogenies, carl Woese and George E. Fox were two of the people who pioneered the use of 16S rRNA in phylogenies. Multiple sequences of the 16S rRNA gene can exist within a single bacterium and it has several functions, Like the large ribosomal RNA, it has a structural role, acting as a scaffold defining the positions of the ribosomal proteins. The 3 end contains the sequence, which binds upstream to the AUG start codon on the mRNA. The 3-end of 16S RNA binds to the proteins S1 and S21 known to be involved in initiation of protein synthesis, carl Woese pioneered this use of 16S rRNA. Some thermophilic archaea contain 16S rRNA gene introns that are located in highly conserved regions, mitochondrial and chloroplastic rRNA are also amplified. The most common primer pair was devised by Weisburg et al, often 8F is used rather than 27F. The two primers are almost identical, but 27F has an M instead of a C, as a result, 16S rRNA gene sequencing has become prevalent in medical microbiology as a rapid and cheap alternative to phenotypic methods of bacterial identification. Although it was used to identify bacteria, 16S sequencing was subsequently found to be capable of reclassifying bacteria into completely new species. It has also used to describe new species that have never been successfully cultured. The bacterial 16S gene contains nine hypervariable regions ranging from about 30-100 base pairs long that are involved in the structure of the small ribosomal subunit. These studies commonly utilize the Illumina platform, which reads at rates 50-fold and 12, 000-fold less expensive than 454 pyrosequencing and Sanger sequencing. Full hypervariable regions can be assembled from a single Illumina run, however, while 16S hypervariable regions can vary dramatically between bacteria, the 16S gene as a whole maintains greater length homogeneity than its Eukaryotic counterpart, which can make alignments easier. Although no hypervariable region can accurately classify all bacteria from Domain to Species, many community studies select semi-conserved hypervariable regions like the V4 for this reason, as it can provide resolution at the phylum level as accurately as the full 16S gene. While lesser-conserved regions struggle to classify new species when higher order taxonomy is unknown, while 16S hypervariable region analysis is a powerful tool for bacterial taxonomic studies, it struggles to differentiate between closely related species. In the families Enterobacteriaceae, Clostridiaceae, and Peptostreptococcaceae, species can share up to 99% sequence similarity across the full 16S gene. As a result, the V4 sequences can differ by only a few nucleotides, furthermore, bacterial genomes can house multiple 16S genes, with the V1, V2, and V6 regions containing the greatest intraspecies diversity. While not the most precise method of classifying bacterial species, analysis of the hypervariable regions remains one of the most useful tools available to bacterial community studies
16S ribosomal RNA
16S ribosomal RNA
–
Atomic structure of the 30S Subunit from
Thermus thermophilus. Proteins are shown in blue and the single RNA strand in orange.
18.
Ribosomal RNA
–
Ribosomal ribonucleic acid is the RNA component of the ribosome, and is essential for protein synthesis in all living organisms. It constitutes the predominant material within the ribosome, which is approximately 60% rRNA and 40% protein by weight, ribosomes contain two major rRNAs and 50 or more proteins. The ribosomal RNAs form two subunits, the large subunit and small subunit, the LSU rRNA acts as a ribozyme, catalyzing peptide bond formation. RRNA sequences are used for working out evolutionary relationships among organisms. The ribosomal RNAs complex with proteins to form two subunits, the large subunit and small subunit. During translation, mRNA is sandwiched between the small and large subunits, and the ribosome catalyzes the formation of a bond between the two amino acids that are contained in the rRNA. A ribosome also has three binding sites called A, P, and E, the A site in the ribosome binds to an aminoacyl-tRNA. This reaction is catalyzed by peptidyl transferase, the tRNA that was holding onto the last amino acid is moved to the E site, and what used to be the aminoacyl-tRNA is the peptidyl-tRNA. A single mRNA can be translated simultaneously by multiple ribosomes, the sedimentation rate of each subunit is affected by its shape, as well as by its mass. Thent units can be added as these represent the number of units in the linear rRNA polymers. In prokaryotes a small 30S ribosomal subunit contains the 16S ribosomal RNA, the large 50S ribosomal subunit contains two rRNA species. Bacterial 16S ribosomal RNA, 23S ribosomal RNA, and 5S rRNA genes are organized as a co-transcribed operon. There may be one or more copies of the operon dispersed in the genome, archaea contains either a single rDNA operon or multiple copies of the operon. The 3 end of the 16S ribosomal RNA binds to a sequence on the 5 end of mRNA called the Shine-Dalgarno sequence, in contrast, eukaryotes generally have many copies of the rRNA genes organized in tandem repeats, in humans approximately 300–400 repeats are present in five clusters. Because of their structure and transcription behaviour, rRNA gene clusters are commonly called ribosomal DNA. The 18S rRNA in most eukaryotes is in the small subunit. Mammalian cells have 2 mitochondrial rRNA molecules and 4 types of cytoplasmic rRNA, the 28S,5. 8S, and 18S rRNAs are encoded by a single transcription unit separated by 2 internally transcribed spacers. The 45S rDNA is organized into 5 clusters on chromosomes 13,14,15,21 and these are transcribed by RNA polymerase I
Ribosomal RNA
–
Small subunit ribosomal RNA, 5' domain taken from the
Rfam database. This example is RF00177
Ribosomal RNA
–
Three-dimensional views of the ribosome, showing rRNA in dark blue (small subunit) and dark red (large subunit). Lighter colors represent ribosomal proteins.
19.
Greek language
–
Greek is an independent branch of the Indo-European family of languages, native to Greece and other parts of the Eastern Mediterranean. It has the longest documented history of any living language, spanning 34 centuries of written records and its writing system has been the Greek alphabet for the major part of its history, other systems, such as Linear B and the Cypriot syllabary, were used previously. The alphabet arose from the Phoenician script and was in turn the basis of the Latin, Cyrillic, Armenian, Coptic, Gothic and many other writing systems. Together with the Latin texts and traditions of the Roman world, during antiquity, Greek was a widely spoken lingua franca in the Mediterranean world and many places beyond. It would eventually become the official parlance of the Byzantine Empire, the language is spoken by at least 13.2 million people today in Greece, Cyprus, Italy, Albania, Turkey, and the Greek diaspora. Greek roots are used to coin new words for other languages, Greek. Greek has been spoken in the Balkan peninsula since around the 3rd millennium BC, the earliest written evidence is a Linear B clay tablet found in Messenia that dates to between 1450 and 1350 BC, making Greek the worlds oldest recorded living language. Among the Indo-European languages, its date of earliest written attestation is matched only by the now extinct Anatolian languages, the Greek language is conventionally divided into the following periods, Proto-Greek, the unrecorded but assumed last ancestor of all known varieties of Greek. The unity of Proto-Greek would have ended as Hellenic migrants entered the Greek peninsula sometime in the Neolithic era or the Bronze Age, Mycenaean Greek, the language of the Mycenaean civilisation. It is recorded in the Linear B script on tablets dating from the 15th century BC onwards, Ancient Greek, in its various dialects, the language of the Archaic and Classical periods of the ancient Greek civilisation. It was widely known throughout the Roman Empire, after the Roman conquest of Greece, an unofficial bilingualism of Greek and Latin was established in the city of Rome and Koine Greek became a first or second language in the Roman Empire. The origin of Christianity can also be traced through Koine Greek, Medieval Greek, also known as Byzantine Greek, the continuation of Koine Greek in Byzantine Greece, up to the demise of the Byzantine Empire in the 15th century. Much of the written Greek that was used as the language of the Byzantine Empire was an eclectic middle-ground variety based on the tradition of written Koine. Modern Greek, Stemming from Medieval Greek, Modern Greek usages can be traced in the Byzantine period and it is the language used by the modern Greeks, and, apart from Standard Modern Greek, there are several dialects of it. In the modern era, the Greek language entered a state of diglossia, the historical unity and continuing identity between the various stages of the Greek language is often emphasised. Greek speakers today still tend to regard literary works of ancient Greek as part of their own rather than a foreign language and it is also often stated that the historical changes have been relatively slight compared with some other languages. According to one estimation, Homeric Greek is probably closer to demotic than 12-century Middle English is to modern spoken English, Greek is spoken by about 13 million people, mainly in Greece, Albania and Cyprus, but also worldwide by the large Greek diaspora. Greek is the language of Greece, where it is spoken by almost the entire population
Greek language
–
Idealized portrayal of
Homer
Greek language
–
regions where Greek is the official language
Greek language
–
Greek language road sign, A27 Motorway, Greece
20.
Genome
–
In modern molecular biology and genetics, a genome is the genetic material of an organism. The genome includes both the genes, the noncoding DNA and the material of the mitochondria and chloroplasts. The term genome was created in 1920 by Hans Winkler, professor of botany at the University of Hamburg, the Oxford Dictionary suggests the name is a blend of the words gene and chromosome. However, see omics for a thorough discussion. A few related -ome words already existed—such as biome, rhizome, Some organisms have multiple copies of chromosomes, diploid, triploid, tetraploid and so on. In classical genetics, in a sexually reproducing organism the gamete has half the number of chromosomes of the somatic cell, the halving of the genetic material in gametes is accomplished by the segregation of homologous chromosomes during meiosis. Additionally, the genome can comprise non-chromosomal genetic elements such as viruses, plasmids, even in species that exist in only one sex, what is described as a genome sequence may be a composite read from the chromosomes of various individuals. Colloquially, the genetic makeup is sometimes used to signify the genome of a particular individual or organism. Both the number of pairs and the number of genes vary widely from one species to another. The only exception in humans is found in red blood cells which become enucleated during development. In 1976, Walter Fiers at the University of Ghent was the first to establish the complete sequence of a viral RNA-genome. The next year Fred Sanger completed the first DNA-genome sequence, Phage Φ-X174, the first genome sequence for an archaeon, Methanococcus jannaschii, was completed in 1996, again by The Institute for Genomic Research. The development of new technologies has made it easier and cheaper to do sequencing. The US National Institutes of Health maintains one of several databases of genomic information. Among the thousands of completed genome sequencing projects include those for rice, a mouse, the plant Arabidopsis thaliana, the fish. In December 2013, scientists first sequenced the genome of a Neanderthal. The genome was extracted from the toe bone of a 130, new sequencing technologies, such as massive parallel sequencing have also opened up the prospect of personal genome sequencing as a diagnostic tool, as pioneered by Manteia Predictive Medicine. A major step toward that goal was the completion in 2007 of the genome of James D. Watson
Genome
–
An image of the 46 chromosomes making up the diploid genome of a human male. (The
mitochondrial chromosome is not shown.)
21.
DNA Data Bank of Japan
–
The DNA Data Bank of Japan is a biological database that collects DNA sequences. It is located at the National Institute of Genetics in the Shizuoka prefecture of Japan and it is also a member of the International Nucleotide Sequence Database Collaboration or INSDC. It exchanges its data with European Molecular Biology Laboratory at the European Bioinformatics Institute, thus these three databanks contain the same data at any given time. DDBJ began data bank activities in 1986 at NIG and remains the only nucleotide sequence data bank in Asia, although DDBJ mainly receives its data from Japanese researchers, it can accept data from contributors from any other country. DDBJ is primarily funded by the Japanese Ministry of Education, Culture, Sports, Science, DDBJ has an international advisory committee which consists of nine members,3 members each from Europe, US, and Japan. This committee advises DDBJ about its maintenance, management and future plans once a year, apart from this DDBJ also has an international collaborative committee which advises on various technical issues related to international collaboration and consists of working-level participants. National Center for Biotechnology Information European Bioinformatics Institute Official site DDBJ entry in MetaBase
DNA Data Bank of Japan
–
DNA Data Bank of
Japan
22.
European Nucleotide Archive
–
The European Nucleotide Archive is a repository providing free and unrestricted access to annotated DNA and RNA sequences. It also stores information such as experimental procedures, details of sequence assembly. The archive is composed of three databases, the Sequence Read Archive, the Trace Archive and the EMBL Nucleotide Sequence Database. The ENA has grown out of the EMBL Data Library which was released in 1982 as the first internationally supported resource for nucleotide sequence data. As of early 2012, the ENA and other INSDC member databases each contained complete genomes of 5,682 organisms, moreover, the volume of data is increasing exponentially with a doubling time of approximately 10 months. The first release of this database was made in April 1982, despite the primary distribution method at the time being via magnetic tape, by 1987, the EMBL Data Library was being used by an estimated 10,000 scientists internationally. The same year, the EMBL File Server was introduced to serve database records over BITNET, EARN, during the 1990s the EMBL Data Library was renamed the EMBL Nucleotide Sequence Database and was formally relocated to the European Bioinformatics Institute from Heidelberg. In 2003, the Nucleotide Sequence Database was extended with the addition of the Sequence Version Archive, a year later in June 2004, limits on the maximum sequence length for each record were removed, allowing entire genome sequences to be stored as a single database entry. Following the uptake of Sanger sequencing, the Wellcome Trust Sanger Institute had begun cataloguing sequence reads along with quality information in a database called The Trace Archive, the Trace Archive grew substantially with the commercialisation of high-throughput parallel sequencing technologies by companies such as Roche and Illumina. As a member of the International Nucleotide Sequence Database Collaboration, the ENA exchanges data submissions each day with both the DNA Data Bank of Japan and GenBank. The EMBL Nucleotide Sequence Database is the section of the ENA which contains high-level genome assembly details, as well as assembled sequences, EMBL-Bank is contributed to by direct submission from genome consortia and smaller research groups as well as by the retrieval of sequence data associated with patent applications. As of release 114, the EMBL Nucleotide Sequence Database contains approximately 5×1011 nucleotides with an uncompressed filesize of 1.6 terabytes. The EMBL Nucleotide Sequence Database supports a variety of data derived from different sources including, Nucleotide sequence being generated from whole genome sequencing projects at varying stages of assembly, including complete contigs and annotated, fully assembled sequence. Data relating to transcriptomics, such as complementary DNA, with optional annotation, novel or extended annotations of existing coding sequences, for example new sequence versions with corrected start or stop codons. The EMBL Nucleotide Sequence Database uses a flat file plaintext format to represent, EMBL-Bank format uses a different syntax to the records in DDBJ and GenBank, though each format uses certain standardised nomenclature, such as taxonomies as defined by the NCBI Taxon database. Each line of an EMBL-format file beings with a code, such as AC to label the accession number and KW for a list of keywords relevant to the record. The ENA operates an instance of the Sequence Read Archive, a repository of sequence reads. Originally called the Short Read Archive, the name was changed in anticipation of future sequencing technologies being able to produce longer sequence reads, the SRA operates under the guidance of the International Nucleotide Sequence Database Collaboration and is the fastest-growing repository in the ENA
European Nucleotide Archive
–
Nucleotide sequence data in book form.
European Nucleotide Archive
–
The EBI at the
Wellcome Trust Genome Campus in
Hinxton,
UK which hosts the European Nucleotide Archive.
23.
GenBank
–
The GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations. This database is produced and maintained by the National Center for Biotechnology Information as part of the International Nucleotide Sequence Database Collaboration, the National Center for Biotechnology Information is a part of the National Institutes of Health in the United States. GenBank and its collaborators receive sequences produced in laboratories throughout the world more than 100,000 distinct organisms. GenBank continues to grow at a rate, doubling every 18 months. Release 194, produced in February 2013, contained over 150 billion nucleotide bases in more than 162 million sequences, GenBank is built by direct submissions from individual laboratories, as well as from bulk submissions from large-scale sequencing centers. Only original sequences can be submitted to GenBank, direct submissions are made to GenBank using BankIt, which is a Web-based form, or the stand-alone submission program, Sequin. Upon receipt of a submission, the GenBank staff examines the originality of the data and assigns an accession number to the sequence. The submissions are then released to the database, where the entries are retrievable by Entrez or downloadable by FTP. Bulk submissions of Expressed Sequence Tag, Sequence-tagged site, Genome Survey Sequence, the GenBank direct submissions group also processes complete microbial genome sequences. Funding was provided by the National Institutes of Health, the National Science Foundation, the Department of Energy, LANL collaborated on GenBank with the firm Bolt, Beranek, and Newman, and by the end of 1983 more than 2,000 sequences were stored in it. In the mid 1980s, the Intelligenetics bioinformatics company at Stanford University managed the GenBank project in collaboration with LANL, as one of the earliest bioinformatics community projects on the Internet, the GenBank project started BIOSCI/Bionet news groups for promoting open access communications among bioscientists. During 1989 to 1992, the GenBank project transitioned to the newly created National Center for Biotechnology Information, the GenBank release notes for release 162.0 state that from 1982 to the present, the number of bases in GenBank has doubled approximately every 18 months. As of 15 June 2016, GenBank release 214.0 has 194,463,572 loci,213,200,907,819 bases, from 194,463,572 reported sequences. The GenBank database includes data sets that are constructed mechanically from the main sequence data collection. On the other hand, while commercial databases potentially contain high-quality filtered sequence data, the results showed that analyses performed using GenBank combined with EzTaxon-e were more discriminative than using GenBank or other databases alone. GenBank Example sequence record, for hemoglobin beta BankIt Sequin — a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank sequence database. EMBOSS — free, open source software for molecular biology GenBank, RefSeq, TPA and UniProt, Whats in a Name
GenBank
–
Genbank and EMBL: NucleotideSequences 1986/1987 Volumes I to VII.
GenBank
–
CDRom of Genbank v100
24.
Immune system
–
The immune system is a host defense system comprising many biological structures and processes within an organism that protects against disease. To function properly, a system must detect a wide variety of agents, known as pathogens, from viruses to parasitic worms. In many species, the system can be classified into subsystems, such as the innate immune system versus the adaptive immune system. In humans, the barrier, blood–cerebrospinal fluid barrier, and similar fluid–brain barriers separate the peripheral immune system from the neuroimmune system. Even simple unicellular organisms such as bacteria possess a rudimentary immune system in the form of enzymes that protect against bacteriophage infections, other basic immune mechanisms evolved in ancient eukaryotes and remain in their modern descendants, such as plants and invertebrates. These mechanisms include phagocytosis, antimicrobial peptides called defensins, and the complement system, jawed vertebrates, including humans, have even more sophisticated defense mechanisms, including the ability to adapt over time to recognize specific pathogens more efficiently. Adaptive immunity creates immunological memory after a response to a specific pathogen. This process of acquired immunity is the basis of vaccination, disorders of the immune system can result in autoimmune diseases, inflammatory diseases and cancer. Immunodeficiency occurs when the system is less active than normal. In humans, immunodeficiency can either be the result of a disease such as severe combined immunodeficiency, acquired conditions such as HIV/AIDS. In contrast, autoimmunity results from an immune system attacking normal tissues as if they were foreign organisms. Common autoimmune diseases include Hashimotos thyroiditis, rheumatoid arthritis, diabetes mellitus type 1, immunology covers the study of all aspects of the immune system. Immunology is a science that examines the structure and function of the immune system and it originates from medicine and early studies on the causes of immunity to disease. The earliest known reference to immunity was during the plague of Athens in 430 BC, thucydides noted that people who had recovered from a previous bout of the disease could nurse the sick without contracting the illness a second time. In the 18th century, Pierre-Louis Moreau de Maupertuis made experiments with scorpion venom and observed that certain dogs and this and other observations of acquired immunity were later exploited by Louis Pasteur in his development of vaccination and his proposed germ theory of disease. Pasteurs theory was in opposition to contemporary theories of disease. It was not until Robert Kochs 1891 proofs, for which he was awarded a Nobel Prize in 1905, viruses were confirmed as human pathogens in 1901, with the discovery of the yellow fever virus by Walter Reed. Immunology made an advance towards the end of the 19th century, through rapid developments, in the study of humoral immunity
Immune system
–
A
scanning electron microscope image of a single
neutrophil (yellow), engulfing
anthrax bacteria (orange)
Immune system
–
A
scanning electron microscope image of normal circulating human
blood. One can see
red blood cells, several knobby white blood cells including
lymphocytes, a
monocyte, a
neutrophil, and many small disc-shaped
platelets.
Immune system
–
An antibody is made up of two heavy chains and two light chains. The unique variable region allows an antibody to recognize its matching antigen.
Immune system
–
The time-course of an immune response begins with the initial pathogen encounter, (or initial vaccination) and leads to the formation and maintenance of active immunological memory.
25.
Microbiological
–
Microbiology is the study of microscopic organisms, those being unicellular, multicellular, or acellular. Microbiology encompasses numerous sub-disciplines including virology, mycology, parasitology, microbiologists traditionally relied on culture, staining, and microscopy. However, less than 1% of the present in common environments can be cultured in isolation using current means. Microbiologists often rely on extraction or detection of nucleic acid, either DNA or RNA sequences, viruses have been variably classified as organisms, as they have been considered either as very simple microorganisms or very complex molecules. As an application of microbiology, medical microbiology is often introduced with medical principles of immunology as microbiology and immunology, otherwise, microbiology, virology, and immunology as basic sciences have greatly exceeded the medical variants, applied sciences. The existence of microorganisms was hypothesized for many centuries before their actual discovery, the existence of unseen microbiological life was postulated by Jainism which is based on Mahavira’s teachings as early as 6th century BCE. Paul Dundas notes that Mahavira asserted existence of unseen microbiological creatures living in earth, water, air, in 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or vehicle transmission. However, early claims about the existence of microorganisms were speculative, actual observation and discovery of microbes had to await the invention of the microscope in the 17th century. In 1676, Anton van Leeuwenhoek, who lived most of his life in Delft, Holland, observed bacteria and other microorganisms using a single-lens microscope of his own design. While Van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke made the first recorded microscopic observation, of the bodies of moulds. It has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe micro-organisms and he was among the first to design magic lanterns for projection purposes, so he must have been well acquainted with the properties of lenses. One of his books contains a chapter in Latin, which reads in translation – Concerning the wonderful structure of things in nature, here, he wrote who would believe that vinegar and milk abound with an innumerable multitude of worms. He also noted that material is full of innumerable creeping animalcule. These observations antedate Robert Hookes Micrographia by nearly 20 years and were published some 29 years before van Leeuwenhoek saw protozoa and 37 years before he described having seen bacteria. Joseph Lister was the first person who said infectious diseases are caused by micro-organism and was first person who used phenol as disinfectant on the wounds of patients. Cohn was also the first to formulate a scheme for the classification of bacteria. Louis Pasteur and Robert Koch were contemporaries of Cohn’s and are considered to be the father of microbiology and medical microbiology. Pasteur is most famous for his series of experiments designed to disprove the widely held theory of spontaneous generation
Microbiological
–
An
agar plate streaked with
microorganisms
Microbiological
–
Fermenting tanks with
yeast being used to
brew beer
Microbiological
–
Antonie van Leeuwenhoek, is considered to be the one of the first to observe microorganisms using a microscope.
Microbiological
–
Innovative
laboratory glassware and experimental methods developed by
Louis Pasteur and other biologists contributed to the young field of bacteriology in the late 19th century.
26.
Neisseria
–
Neisseria is a large genus of bacteria that colonize the mucosal surfaces of many animals. Of the 11 species that humans, only two are pathogens, N. meningitidis and N. gonorrhoeae. Most gonoccocal infections are asymptomatic and self-resolving, and epidemic strains of the meningococcus may be carried in >95% of a population where systemic disease occurs at <1% prevalence, Neisseria species are Gram-negative bacteria included among the proteobacteria, a large group of Gram-negative forms. Neisseria diplococci resemble coffee beans when viewed microscopically and this genus of parasitic bacteria grow in pairs and occasionally tetrads, and thrive best at 98.6 °F in the animal body or serum media. The genus includes, N. gonorrhoeae, which causes gonorrhea, N. meningitidis, one of the most common causes of bacterial meningitis and the causative agent of meningococcal septicaemia. These two species have the ability of breaching the barrier, local cytokines of the area become secreted to initiate an immune response. Neisseria species are able to alter their antigens to avoid being engulfed by a process called antigenic variation. The pathogenic species along with some species, have type IV pili which serve multiple functions for this organism. Neisseria bacteria have also shown to be an important factor in the early stages of canine plaque development. Fa that is exhibited in N. meningitidis and some species is the main inhibitor of the alternative complement pathway. FHbp protects meningococci from complement-mediated death in human experiments, but has also been shown to protect meningococci from antimicrobial peptides in vitro. Factor H binding protein is key to the pathogenesis of N. meningitidis, porins are also an important factor for complement inhibition for both pathogenic and commensal species. Porins are important for nutrient acquisition, porins are also recognized by TLR2, they bind complement factors. Cooperation with pili for CR3-mediated internalization is another function of porins, ability to translocate into host cells and modulate reactive oxygen species production and apoptosis is made possible by porins, as well. Strains of the species can express different porins. The genus Neisseria is named after the German bacteriologist Albert Neisser, who in 1879 discovered its first example, Neisseria gonorrheae, Neisser also codiscovered the pathogen that causes leprosy, Mycobacterium leprae. These discoveries were made possible by the development of new staining techniques which he helped to develop, all the medically significant species of Neisseria are positive for both catalase and oxidase. Different Neisseria species can be identified by the sets of sugars from which they will produce acid, for example, N. gonorrheae makes acid from only glucose, but N. meningitidis produces acid from both glucose and maltose
Neisseria
–
Neisseria
27.
Mortality rate
–
Mortality rate, or death rate, is a measure of the number of deaths in a particular population, scaled to the size of that population, per unit of time. It is distinct from morbidity, a used to refer to either the prevalence or incidence of a disease. Other specific measures of mortality include, Crude death rate – the total number of deaths per year per 1,000 people, as of 2014 the crude death rate for the whole world is 7.89 per 1,000 according to the current CIA World Factbook. Note that the death rate can be misleading. The crude death rate depends on the age specific mortality rates, the number of deaths per 1,000 people can be higher in developed nations than in less-developed countries, despite a higher life expectancy in developed countries due to better standards of health. This happens because developed countries typically have a higher proportion of older people. A more complete picture of mortality is given by a life table, a life table is necessary to give a good estimate of life expectancy. Perinatal mortality rate – the sum of neonatal deaths and fetal deaths per 1,000 births, maternal mortality ratio – the number of maternal deaths per 100,000 live births in same time period. Maternal mortality rate – the number of deaths per 1,000 women of reproductive age in the population. Infant mortality rate – the number of deaths of less than 1 year old per 1,000 live births. Child mortality rate, the number of deaths of less than 5 years old per 1,000 live births. Standardized mortality ratio – a proportional comparison to the numbers of deaths that would have expected if the population had been of a standard composition in terms of age, gender. Age-specific mortality rate – the total number of deaths per year per 1,000 people of a given age, cause-specific mortality rate – the mortality rate for a specified cause of death. Cumulative death rate, a measure of the proportion of a group that die over a specified period, case fatality rate – the proportion of cases of a particular medical condition that lead to death. Late mortality rate – the total number of deaths in the stages of an ongoing treatment. Mortality may also be expressed in terms of survival, thus, the survival rate is equivalent to 1 minus the cumulative death rate. The ten countries with the highest crude death rate, according to the 2014 CIA World Factbook estimates, are, See list of causes of death by rate for worldwide statistics. According to Jean Ziegler, mortality due to malnutrition accounted for 58% of the mortality in 2006, In the world, approximately 62 millions people, all causes of death combined
Mortality rate
–
Scatter plot of the
natural logarithm of the crude death rate against the natural log of per capita real GDP. The slope of the trend line is the elasticity of the crude death rate with respect to per capita real income. It indicates that a 10% increase in per capita real income is associated with a 1.5% decrease in the crude death rate. Source: World Development Indicators.
Mortality rate
–
Crude death rate by country (2006).
28.
Epithelium
–
Epithelial is one of the four basic types of animal tissue, along with connective tissue, muscle tissue and nervous tissue. Epithelial tissues line the cavities and surfaces of blood vessels and organs throughout the body, there are three principal shapes of epithelial cell, squamous, columnar, and cuboidal. All glands are made up of epithelial cells, functions of epithelial cells include secretion, selective absorption, protection, transcellular transport, and sensing. Epithelial layers contain no blood vessels, so they must receive nourishment via diffusion of substances from the connective tissue. Cell junctions are well-employed in epithelial tissues, in general, epithelial tissues are classified by the number of their layers and by the shape and function of the cells. The three principal shapes associated with epithelial cells are—squamous, cuboidal and columnar, squamous epithelium has cells that are wider than their height. Cuboidal epithelium has cells whose height and width are approximately the same, columnar epithelium has cells taller than they are wide. However, when taller simple columnar epithelial cells are viewed in cross section showing several nuclei appearing at different heights and this kind of epithelium is therefore described as pseudostratified columnar epithelium. Transitional epithelium has cells that can change from squamous to cuboidal, Simple epithelium is a single layer of cells with every cell in direct contact with the basement membrane that separates it from the underlying connective tissue. In general, it is found where absorption and filtration occur, the thinness of the epithelial barrier facilitates these processes. In general, simple epithelial tissues are classified by the shape of their cells, the four major classes of simple epithelium are, simple squamous, simple cuboidal, simple columnar, pseudostratified. Simple squamous, which is found lining areas where passive diffusion of gases occur, E. g. skin, walls of capillaries, linings of the pericardial, pleural, and peritoneal cavities, as well as the linings of the alveoli of the lungs. Simple cuboidal, these cells may have secretory, absorptive, or excretory functions, examples include small collecting ducts of kidney, pancreas and salivary gland. Simple columnar, cells can be secretory, absorptive, or excretory, Simple columnar epithelium can be ciliated or non-ciliated, ciliated columnar is found in the reproductive tract. Non-ciliated epithelium can also possess microvilli, pseudostratified columnar epithelium, can be ciliated or non-ciliated. The ciliated type is called respiratory epithelium as it is almost exclusively confined to the larger respiratory airways of the nasal cavity, trachea. Stratified epithelium differs from simple epithelium in that it is multilayered and it is therefore found where body linings have to withstand mechanical or chemical insult such that layers can be abraded and lost without exposing subepithelial layers. Cells flatten as the layers become more apical, though in their most basal layers the cells can be squamous, stratified epithelia can have the following specializations, The basic cell types are squamous, cuboidal, and columnar classed by their shape
Epithelium
–
Types of epithelium
Epithelium
–
Different forms of secretion are possible in epithelial tissue or in glands.
Epithelium
–
Summary showing different epithelial cells/tissues and their characteristics.
Epithelium
–
Different characteristics of glands of the body.
29.
Antibiotic resistance
–
Antimicrobial resistance is the ability of a microbe to resist the effects of medication previously used to treat them. This broader term also covers antibiotic resistance, which applies to bacteria, resistance arises through one of three ways, natural resistance in certain types of bacteria, genetic mutation, or by one species acquiring resistance from another. Resistance can appear spontaneously because of mutations, or more commonly following gradual buildup over time. Resistant microbes are increasingly difficult to treat, requiring alternative medications or higher doses, microbes resistant to multiple antimicrobials are called multidrug resistant, or sometimes superbugs. Antimicrobial resistance is on the rise with millions of deaths every year, Antibiotics should only be used when needed as prescribed by health professionals. The prescriber should closely adhere to the five rights of administration, the right patient, the right drug, the right dose, the right route. Narrow-spectrum antibiotics are preferred over broad-spectrum antibiotics when possible, as effectively and accurately targeting specific organisms is less likely to cause resistance, cultures should be taken before treatment when indicated and treatment potentially changed based on the susceptibility report. For people who take these medications at home, education about proper use is essential, rising drug resistance is caused mainly by improper use of antimicrobials in humans as well as in animals, and spread of resistant strains between the two. Antibiotics increase selective pressure in bacterial populations, causing vulnerable bacteria to die, with resistance to antibiotics becoming more common there is greater need for alternative treatments. Calls for new antibiotic therapies have been issued, but new development is becoming rarer. Antibiotic resistance—when bacteria change so antibiotics no longer work in people who need them to treat infections—is now a threat to public health. Increasing public calls for collective action to address the threat include proposals for international treaties on antimicrobial resistance. Worldwide antibiotic resistance is not fully mapped, but poorer countries with weak healthcare systems are more affected, the WHO defines antimicrobial resistance as a microorganisms resistance to an antimicrobial drug that was once able to treat an infection by that microorganism. A person cannot become resistant to antibiotics, resistance is a property of the microbe, not a person or other organism infected by a microbe. Bacteria with resistance to antibiotics predate medical use of antibiotics by humans, however and this may result in emergence of resistance in any remaining bacteria. Antibiotic use in feed at low doses for growth promotion is an accepted practice in many industrialized countries and is known to lead to increased levels of resistance. It is uncertain whether antibacterials in soaps and other products contribute to antibiotic resistance, increasing bacterial resistance is linked with the volume of antibiotic prescribed, as well as missing doses when taking antibiotics. Up to half of antibiotics used in humans are unnecessary and inappropriate, a single regimen of antibiotics even in compliant individuals leads to a greater risk of resistant organisms to that antibiotic in the person for a month to possibly a year
Antibiotic resistance
–
Antibiotic resistance tests: Bacteria are streaked on the dish on which antibiotic impregnated white disks are placed. Bacteria in the culture on the left are susceptible to the antibiotic in each disk, as shown by the dark, clear rings where bacteria have not grown. Those on the right are fully susceptible to only three of the seven antibiotics tested.
Antibiotic resistance
–
Deaths attributable to antimicrobial resistance every year compared to other major causes of death.
Antibiotic resistance
–
All animals carry bacteria in their intestines. Antibiotics are given to animals. Antibiotics kill most bacteria. But resistant bacteria survive and multiply.
Antibiotic resistance
–
A number of mechanisms used by common antibiotics to deal with bacteria and ways by which bacteria become resistant to them.
30.
Penicillin
–
Penicillin is a group of antibiotics which include penicillin G, penicillin V, procaine penicillin, and benzathine penicillin. Penicillin antibiotics were among the first medications to be effective against many bacterial infections caused by staphylococci and streptococci, penicillins are still widely used today, though many types of bacteria have developed resistance following extensive use. About 10% of people report that they are allergic to penicillin, however, serious allergies only occur in about 0. 03%. Penicillin was discovered in 1928 by Scottish scientist Alexander Fleming, people began using it to treat infections in 1942. There are several enhanced penicillin families which are effective against additional bacteria, these include the penicillins, aminopenicillins. They are derived from Penicillium fungi, the term penicillin is often used generically to refer to benzylpenicillin, procaine benzylpenicillin, benzathine benzylpenicillin, and phenoxymethylpenicillin. Procaine penicillin and benzathine penicillin have the same activity as benzylpenicillin. Phenoxymethylpenicillin is less active against gram-negative bacteria than benzylpenicillin, infrequent adverse effects include fever, vomiting, erythema, dermatitis, angioedema, seizures, and pseudomembranous colitis. About 10% of people report that they are allergic to penicillin, however, serious allergies only occur in about 0. 03%. Penicillin can also induce serum sickness or a serum sickness-like reaction in some individuals, serum sickness is a type III hypersensitivity reaction that occurs one to three weeks after exposure to drugs including penicillin. It is not a drug allergy, because allergies are type I hypersensitivity reactions. Pain and inflammation at the site is also common for parenterally administered benzathine benzylpenicillin, benzylpenicillin. Significantly, there is a reaction to Streptolysin S, a toxin released by certain killed bacteria and associated with Penicillin injection. Allergic reactions to any β-lactam antibiotic may occur in up to 1% of patients receiving that agent, the allergic reaction is a Type I hypersensitivity reaction. Anaphylaxis will occur in approximately 0. 01% of patients and it has previously been accepted that there was up to a 10% cross-sensitivity between penicillin-derivatives, cephalosporins, and carbapenems, due to the sharing of the β-lactam ring. Assessments in 2006 found no risk for cross-allergy for second-generation or later cephalosporins than the first generation. However, as a risk, research shows that all beta lactams have the intrinsic hazard of very serious hazardous reactions in susceptible patients. Only the frequency of these reactions vary, based on the structure, bacteria constantly remodel their peptidoglycan cell walls, simultaneously building and breaking down portions of the cell wall as they grow and divide
Penicillin
–
Alexander Fleming, who is credited with discovering penicillin in 1928.
Penicillin
–
Penicillin core structure, where "R" is the variable group.
Penicillin
–
Sample of penicillium mould presented by Alexander Fleming to Douglas Macleod, 1935
Penicillin
–
Florey (pictured), Fleming and Chain shared a Nobel Prize in 1945 for their work on penicillin.
31.
Vaccine
–
A vaccine is a biological preparation that provides active acquired immunity to a particular disease. A vaccine typically contains an agent that resembles a disease-causing microorganism and is made from weakened or killed forms of the microbe. Vaccines can be prophylactic, or therapeutic, the administration of vaccines is called vaccination. The effectiveness of vaccination has been studied and verified, for example, the influenza vaccine, the HPV vaccine. The World Health Organization reports that licensed vaccines are available to prevent or contribute to the prevention. The terms vaccine and vaccination are derived from Variolae vaccinae, the term devised by Edward Jenner to denote cowpox. He used it in 1798 in the title of his Inquiry into the. Variolae vaccinae. known. the Cow Pox. In 1881, to honor Jenner, Louis Pasteur proposed that the terms should be extended to cover the new protective inoculations then being developed, vaccines have historically been the most effective means to fight and eradicate infectious diseases. Limitations to their effectiveness, nevertheless, exist, sometimes, protection fails because the hosts immune system simply does not respond adequately or at all. Lack of response commonly results from factors such as diabetes, steroid use. Adjuvants commonly are used to boost immune response, particularly for older people, the efficacy or performance of the vaccine is dependent on a number of factors, the disease itself the strain of vaccine whether the vaccination schedule has been properly observed. Idiosyncratic response to vaccination, some individuals are non-responders to certain vaccines, assorted factors such as ethnicity, age, or genetic predisposition. If a vaccinated individual does develop the disease vaccinated against, the disease is likely to be less virulent than in unvaccinated victims, in 1958, there were 763,094 cases of measles in the United States,552 deaths resulted. After the introduction of new vaccines, the number of cases dropped to fewer than 150 per year, in early 2008, there were 64 suspected cases of measles. Vaccines have contributed to the eradication of smallpox, one of the most contagious, other diseases such as rubella, polio, measles, mumps, chickenpox, and typhoid are nowhere near as common as they were a hundred years ago. As long as the vast majority of people are vaccinated, it is more difficult for an outbreak of disease to occur. This effect is called herd immunity, polio, which is transmitted only between humans, is targeted by an extensive eradication campaign that has seen endemic polio restricted to only parts of three countries. However, the difficulty of reaching all children as well as cultural misunderstandings have caused the anticipated eradication date to be missed several times, vaccination given during childhood is generally safe
Vaccine
–
Jonas Salk in 1955 holds two bottles of a culture used to grow
polio vaccines.
Vaccine
–
Maurice Hilleman 's measles vaccine is estimated to prevent 1 million deaths every year.
Vaccine
–
Electroporation System for experimental "DNA vaccine" delivery
Vaccine
–
Edward Jenner
32.
Complement (biology)
–
It is part of the innate immune system, which is not adaptable and does not change over the course of an individuals lifetime. It can be recruited and brought into action by the immune system. The complement system consists of a number of proteins found in the blood, in general synthesized by the liver. When stimulated by one of several triggers, proteases in the system cleave specific proteins to release cytokines, over 30 proteins and protein fragments make up the complement system, including serum proteins, serosal proteins, and cell membrane receptors. They account for about 10% of the fraction of blood serum. Three biochemical pathways activate the complement system, the complement pathway, the alternative complement pathway. In 1888, George Nuttall found that blood serum had mild killing activity against the bacterium that causes anthrax. The killing activity disappeared when he heated the blood, in 1891, Hans Ernst August Buchner, noting the same property of blood in his experiments, named the killing property alexin, which means to ward off in Greek. By 1884, several laboratories had demonstrated that serum from guinea pigs that had recovered from cholera killed the cholera bacterium in vitro, heating the serum destroyed its killing activity. Nevertheless, the serum, when injected into guinea pigs exposed to the cholera bacteria. In 1899, Paul Ehrlich renamed the heat-sensitive component complement, Ehrlich introduced the term complement as part of his larger theory of the immune system. According to this theory, the system consists of cells that have specific receptors on their surface to recognize antigens. Upon immunisation with an antigen, more of these receptors are formed, Ehrlich, therefore, named this heat-labile component complement, because it is something in the blood that complements the cells of the immune system. Ehrlich believed that each antigen-specific amboceptor has its own specific complement, in the early 20th century, this controversy was resolved when it became understood that complement can act in combination with specific antibodies, or on its own in a non-specific way. Complement triggers the immune functions, Phagocytosis – by opsonizing antigens. But significant amounts are produced by tissue macrophages, blood monocytes. The three pathways of activation all generate homologous variants of the protease C3-convertase, the mannose-binding lectin pathway can be activated by C3 hydrolysis or antigens without the presence of antibodies. In all three pathways, C3-convertase cleaves and activates component C3, creating C3a and C3b, and causes a cascade of further cleavage, C3b binds to the surface of pathogens, leading to greater internalization by phagocytic cells by opsonization
Complement (biology)
–
Membrane attack complex causing cell lysis
33.
Lipooligosaccharide
–
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
Lipooligosaccharide
–
Toll-like receptors of the
innate immune system recognize LPS and trigger an
immune response.
Lipooligosaccharide
–
Structure of a lipopolysaccharide
34.
Cotrimoxazole
–
Trimethoprim/sulfamethoxazole, also known as co-trimoxazole among other names, is an antibiotic used to treat a variety of bacterial infections. It consists of one part trimethoprim to five parts sulfamethoxazole and it is used for urinary tract infections, MRSA skin infections, travelers diarrhea, respiratory tract infections, and cholera, among others. It may be used both to treat and prevent pneumocystis pneumonia in people with HIV/AIDS and it can be given by mouth or intravenously. Common side effects include nausea, vomiting, rash, and diarrhea, severe allergic reactions and Clostridium difficile diarrhea may occasionally occur. Its use near the end of pregnancy is not recommended and it appears to be safe for use during breastfeeding as long as the baby is healthy. TMP/SMX generally results in bacterial death and it works by blocking the making of folate by the bacteria. TMP/SMX was first sold in 1974 and it is on the World Health Organizations List of Essential Medicines, the most effective and safe medicines needed in a health system. It is available as a medication and is not very expensive. In the United States it is about 0.40 USD per dose, co-trimoxazole was claimed to be more effective than either of its components individually in treating bacterial infections, although this was later disputed. Co-trimoxazole in retinochoroiditis shows a reduction in the risk of recurrent retinochoroiditis, the global problem of advancing antimicrobial resistance has led to a renewed interest in the use of co-trimoxazole more recently. Organisms against which co-trimoxazole can be effective include, The only notable nonsusceptible organisms are the mycoplasmae and its use during pregnancy is contraindicated, although it has been placed in Australian and American pregnancy category C. Its use later on during pregnancy increases the risk of preterm labour. Animal studies have yielded similarly discouraging results and it is also excreted in breast milk and hence nursing during treatment with co-trimoxazole is generally advised against. A significant risk of megaloblastic anaemia exists with doses of pyrimethamine in excess of 25 mg/wk, antivirals, more specifically, lamivudine, zalcitabine and zidovudine Procainamide and/or amantadine may have their plasma concentrations increased bilaterally or unilaterally. Spironolactone — concurrent use can increase the likelihood of hyperkalemia, especially in the elderly, the trimethoprim portion acts to prevent potassium excretion in the distal tubule of the nephron. Potassium aminobenzoate — effects of sulfonamides inhibited, the synergy between trimethoprim and sulfamethoxazole was first described in the late 1960s. Trimethoprim and sulfamethoxazole have an effect when given together than when given separately. Sulfamethoxazole, a sulfonamide, induces its effects by interfering with the de novo synthesis of folate inside microbial organisms such as protozoa, fungi
Cotrimoxazole
–
Trimethoprim (top) and sulfamethoxazole (bottom)
35.
Sulfadimidine
–
Sulfadimidine or sulfamethazine is a sulfonamide antibacterial. There are non-standardizeda abbreviations for it as sulfadimidine and as sulfamethazine, other names include sulfadimerazine, sulfadimezine, and sulphadimethylpyrimidine. In Pakistan, it is available with the name of Sanadine-33.3 % as potential treatment of E-coli enteritis in veterinary medicine. ^a Abbreviations are not found in the databases, but often seen in the published literature, sulfamethazine, ChemDB, National Institute of Allergy and Infectious Diseases, National Institutes of Health Sulfadimidine in the ChemIDplus database PubChem. Sulfamethazine - Substance Summary, PubChem, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health
Sulfadimidine
–
Sulfamethazine
36.
Beta-lactamase
–
Beta-lactamase provides antibiotic resistance by breaking the antibiotics structure. These antibiotics all have an element in their molecular structure. Through hydrolysis, the lactamase enzyme breaks the β-lactam ring open, beta-lactam antibiotics are typically used to treat a broad spectrum of Gram-positive and Gram-negative bacteria. Beta-lactamases produced by Gram-negative organisms are usually secreted, especially when antibiotics are present in the environment, the structure of a Streptomyces β-lactamase is given by 1BSG. Penicillinase is a type of β-lactamase, showing specificity for penicillins. Molecular weights of the various penicillinases tend to cluster near 50 kiloDaltons, penicillinase-resistant beta-lactams such as methicillin were developed, but there is now widespread resistance to even these. Additionally, many class A TEM β-lactamases are inhibited by β-lactamase inhibitor protein, because of the increasing number of TEM- and SHV-derived β-lactamases, they were divided into two subclasses, 2a and 2b. GROUP 2a PENICILLINASE, Molecular Class A The 2a subgroup contains just penicillinases, GROUP 2b BROAD-SPECTRUM, Molecular Class A 2b Opposite to 2a, 2b are broad-spectrum β-lactamases, meaning that they are capable of inactivating penicillins and cephalosporins at the same rate. GROUP 2c CARBENICILLINASE, Molecular Class A Latersubgroup 2c was segregated from group 2 because these enzymes inactivate carbenicillin more than benzylpenicillin and these enzymes are able to inactivate the oxazolylpenicillins like oxacillin, cloxacillin, dicloxacillin. The enzymes belong to the molecular class D not molecular class A. Metallo B-lactamases are able to hydrolyse penicillins, cephalosporins and this group has been omitted from the current scheme, as when it was described originally it included enzymes not classifiable into other groups. The molecular classification of β-lactamases is based on the nucleotide and amino acid sequences in these enzymes, to date, four classes are recognised, correlating with the functional classification. Among Gram-negative bacteria, the emergence of resistance to expanded-spectrum cephalosporins has been a major concern and it appeared initially in a limited number of bacterial species that could mutate to hyperproduce their chromosomal class C β-lactamase. A few years later, resistance appeared in bacterial species not naturally producing AmpC enzymes due to the production of TEM- or SHV-type ESBLs, members of the family commonly express plasmid-encoded β-lactamases. Which confer resistance to penicillins but not to expanded-spectrum cephalosporins, in the mid-1980s, a new group of enzymes, the extended-spectrum β-lactamases, was detected. The prevalence of ESBL-producing bacteria have been increasing in acute care hospitals. ESBLs are beta-lactamases that hydrolyze extended-spectrum cephalosporins with a side chain. These cephalosporins include cefotaxime, ceftriaxone, and ceftazidime, as well as the oxyimino-monobactam aztreonam, thus ESBLs confer multi-resistance to these antibiotics and related oxyimino-beta lactams. In typical circumstances, they derive from genes for TEM-1, TEM-2, a broader set of β-lactam antibiotics are susceptible to hydrolysis by these enzymes
Beta-lactamase
–
Structure of a
Streptomyces albus beta-lactamase
Beta-lactamase
–
Escherichia coli bacteria on the right are sensitive to two beta-lactam antibiotics, and do not grow in the semi-circular regions surrounding the antibiotics. E. coli bacteria on the left are resistant to beta-lactam antibiotics, and grow next to one antibiotic (bottom) and are less inhibited by another antibiotic (top).
37.
Protein
–
Proteins are large biomolecules, or macromolecules, consisting of one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, a linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide, short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides, or sometimes oligopeptides. The individual amino acid residues are bonded together by peptide bonds, the sequence of amino acid residues in a protein is defined by the sequence of a gene, which is encoded in the genetic code. In general, the code specifies 20 standard amino acids, however. Sometimes proteins have non-peptide groups attached, which can be called prosthetic groups or cofactors, proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes. Once formed, proteins only exist for a period of time and are then degraded and recycled by the cells machinery through the process of protein turnover. A proteins lifespan is measured in terms of its half-life and covers a wide range and they can exist for minutes or years with an average lifespan of 1–2 days in mammalian cells. Abnormal and or misfolded proteins are degraded more rapidly due to being targeted for destruction or due to being unstable. Like other biological macromolecules such as polysaccharides and nucleic acids, proteins are essential parts of organisms, many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism. Proteins also have structural or mechanical functions, such as actin and myosin in muscle and the proteins in the cytoskeleton, other proteins are important in cell signaling, immune responses, cell adhesion, and the cell cycle. In animals, proteins are needed in the diet to provide the essential amino acids that cannot be synthesized, digestion breaks the proteins down for use in the metabolism. Methods commonly used to study structure and function include immunohistochemistry, site-directed mutagenesis, X-ray crystallography, nuclear magnetic resonance. Most proteins consist of linear polymers built from series of up to 20 different L-α-amino acids, all proteinogenic amino acids possess common structural features, including an α-carbon to which an amino group, a carboxyl group, and a variable side chain are bonded. Only proline differs from this structure as it contains an unusual ring to the N-end amine group. The amino acids in a chain are linked by peptide bonds. Once linked in the chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen. The peptide bond has two forms that contribute some double-bond character and inhibit rotation around its axis, so that the alpha carbons are roughly coplanar
Protein
–
Proteins in different
cellular compartments and structures tagged with
green fluorescent protein (here, white)
Protein
–
A representation of the 3D structure of the protein
myoglobin showing turquoise
alpha helices. This protein was the first to have its structure solved by
X-ray crystallography. Towards the right-center among the coils, a
prosthetic group called a
heme group (shown in gray) with a bound oxygen molecule (red).
Protein
–
Constituent amino-acids can be analyzed to predict secondary, tertiary and quaternary protein structure, in this case hemoglobin containing
heme units
Protein
–
John Kendrew with model of myoglobin in progress
38.
Antigen
–
In immunology, an antigen is a molecule capable of inducing an immune response on the part of the host organism, though sometimes antigens can be part of the host itself. In other words, an antigen is any substance that causes a system to produce antibodies against it. In most cases, an antibody can bind one specific antigen, in some instances, however. An antigen is a molecule that binds to Ag-specific receptors, Antigens are usually peptides, polysaccharides or lipids. In general, molecules other than peptides qualify as antigens but not as immunogens since they cannot elicit a response on their own. Furthermore, for a peptide to induce a response it must be a large enough size. The term antigen originally described a structural molecule that specifically to an antibody. It expanded to refer to any molecule or a molecular fragment that can be recognized by highly variable antigen receptors of the adaptive immune system. The antigen may originate from within the body or from the external environment, antigen presenting cells present antigens in the form of peptides on histocompatibility molecules. The T cells of the immune system recognize the antigens. Depending on the antigen and the type of the histocompatibility molecule, for T-Cell Receptor recognition, the peptide must be processed into small fragments inside the cell and presented by a major histocompatibility complex. The antigen cannot elicit the immune response without the help of an immunologic adjuvant, similarly, the adjuvant component of vaccines plays an essential role in the activation of the innate immune system. An immunogen is a substance that is able to trigger a humoral and/or cell-mediated immune response and it first initiates an innate immune response, which then causes the activation of the adaptive immune response. An antigen binds the highly variable immunoreceptor products once these have been generated, all immunogen molecules are also antigens, although the reverse is not true. At the molecular level, an antigen can be characterized by its ability to bind to an antibodys variable Fab region, different antibodies have the potential to discriminate among specific epitopes present on the antigen surface. A hapten is a molecule that changes the structure of an antigenic epitope. In order to induce a response, it needs to be attached to a large carrier molecule such as a protein. Antigens are usually proteins and polysaccharides, and less frequently, lipids and this includes parts of bacteria, viruses, and other microorganisms
Antigen
–
Contents
39.
Antibody
–
An antibody, also known as an immunoglobulin, is a large, Y-shaped protein produced mainly by plasma cells that is used by the immune system to neutralize pathogens such as bacteria and viruses. The antibody recognizes a molecule of the harmful agent, called an antigen. Each tip of the Y of an antibody contains a paratope that is specific for one particular epitope on an antigen, allowing these two structures to bind together with precision. Using this binding mechanism, an antibody can tag a microbe or a cell for attack by other parts of the immune system. Depending on the antigen, the binding may impede the process causing the disease or may activate macrophages to destroy the foreign substance. The ability of an antibody to communicate with the components of the immune system is mediated via its Fc region. The production of antibodies is the function of the humoral immune system. Antibodies are secreted by B cells of the immune system. In most cases, interaction of the B cell with a T helper cell is necessary to produce full activation of the B cell and, therefore, soluble antibodies are released into the blood and tissue fluids, as well as many secretions to continue to survey for invading microorganisms. Antibodies are glycoproteins belonging to the immunoglobulin superfamily and they constitute most of the gamma globulin fraction of the blood proteins. They are typically made of basic structural units—each with two heavy chains and two small light chains. There are several different types of heavy chains that define the five different types of crystallisable fragments that may be attached to the antigen-binding fragments. The five different types of Fc regions allow antibodies to be grouped into five isotypes, each Fc region of a particular antibody isotype is able to bind to its specific Fc Receptor, thus allowing the antigen-antibody complex to mediate different roles depending on which FcR it binds. The ability of an antibody to bind to its corresponding FcR is further modulated by the structure of the present at conserved sites within its Fc region. The ability of antibodies to bind to FcRs helps to direct the immune response for each different type of foreign object they encounter. For example, IgE is responsible for an allergic response consisting of mast cell degranulation, igEs Fab paratope binds to allergic antigen, for example house dust mite particles, while its Fc region binds to Fc receptor ε. The allergen-IgE-FcRε interaction mediates allergic signal transduction to induce conditions such as asthma and this region is known as the hypervariable region. Each of these variants can bind to a different antigen and this enormous diversity of antibody paratopes on the antigen-binding fragments allows the immune system to recognize an equally wide variety of antigens
Antibody
–
Immunofluorescence image of the eukaryotic
cytoskeleton.
Actin filaments are shown in red,
microtubules in green, and the
nuclei in blue.
Antibody
–
Each antibody binds to a specific
antigen; an interaction similar to a lock and key.
Antibody
–
Example of tissue cross-reactivity on human
tissue microarray
Antibody
–
Angel of the West (2008) by
Julian Voss-Andreae is a sculpture based on the antibody structure published by E. Padlan. Created for the Florida campus of
the Scripps Research Institute, the antibody is placed into a ring referencing
Leonardo da Vinci's Vitruvian Man thus highlighting the similarity of the antibody and the human body.
40.
Vaccination
–
Vaccination is the administration of antigenic material to stimulate an individuals immune system to develop adaptive immunity to a pathogen. Vaccines can prevent or ameliorate morbidity from infection, when a sufficiently large percentage of a population has been vaccinated, this results in herd immunity. The effectiveness of vaccination has been studied and verified, for example, the influenza vaccine, the HPV vaccine. The World Health Organization reports that licensed vaccines are available to prevent or contribute to the prevention. The active agent of a vaccine may be intact but inactivated or attenuated forms of the causative pathogens, toxoids are produced for immunization against toxin-based diseases, such as the modification of tetanospasmin toxin of tetanus to remove its toxic effect but retain its immunogenic effect. Smallpox was most likely the first disease people tried to prevent by inoculating themselves and was the first disease for which a vaccine was produced, Louis Pasteur furthered the concept through his work in microbiology. The immunization was called vaccination because it was derived from a virus affecting cows, smallpox was a contagious and deadly disease, causing the deaths of 20–60% of infected adults and over 80% of infected children. When smallpox was finally eradicated in 1979, it had killed an estimated 300–500 million people in the 20th century. In common speech, vaccination and immunization have a similar meaning and this distinguishes it from inoculation, which uses unweakened live pathogens, although in common usage either can refer to an immunization. Vaccination efforts have met with some controversy on scientific, ethical, political, medical safety. In rare cases, vaccinations can injure people and, in the United States, early success and compulsion brought widespread acceptance, and mass vaccination campaigns have greatly reduced the incidence of many diseases in numerous geographic regions. Generically, the process of induction of immunity, in an effort to protect against infectious disease. Stimulating immune responses with an agent is known as immunization. Vaccination includes various ways of administering immunogens, some vaccines are administered after the patient already has contracted a disease. The first rabies immunization was given by Louis Pasteur to a child after he was bitten by a rabid dog, other examples include experimental AIDS, cancer and Alzheimers disease vaccines. Such immunizations aim to trigger a response more rapidly and with less harm than natural infection. Most vaccines are given by injection as they are not absorbed reliably through the intestines. Live attenuated polio, some typhoid, and some cholera vaccines are given orally to produce immunity in the bowel, while vaccination provides a lasting effect, it usually takes several weeks to develop, while passive immunity has immediate effect
Vaccination
–
Child receiving an
oral polio vaccine
Vaccination
–
Polio vaccination started in Sweden in 1957.
Vaccination
–
Jenner's handwritten draft of the first vaccination
Vaccination
–
A doctor performing a
typhoid vaccination in
Texas, 1943
41.
Macromolecule
–
A macromolecule is a very large molecule, such as protein, commonly created by polymerization of smaller subunits. They are typically composed of thousands of atoms or more, the most common macromolecules in biochemistry are biopolymers and large non-polymeric molecules. Synthetic macromolecules include common plastics and synthetic fibres as well as materials such as carbon nanotubes. The term macromolecule was coined by Nobel laureate Hermann Staudinger in the 1920s, usage of the term to describe large molecules varies among the disciplines. According to the standard IUPAC definition, the term macromolecule as used in science refers only to a single molecule. For example, a polymeric molecule is appropriately described as a macromolecule or polymer molecule rather than a polymer. Because of their size, macromolecules are not conveniently described in terms of stoichiometry alone, the structure of simple macromolecules, such as homopolymers, may be described in terms of the individual monomer subunit and total molecular mass. Complicated biomacromolecules, on the hand, require multi-faceted structural description such as the hierarchy of structures used to describe proteins. In British English. Macromolecules often have physical properties that do not occur for smaller molecules. For example, DNA in a solution can be simply by sucking the solution through an ordinary straw because the physical forces on the molecule can overcome the strength of its covalent bonds. The 1964 edition of Linus Paulings College Chemistry asserted that DNA in nature is never longer than about 5,000 base pairs and this error arose because biochemists were inadvertently breaking their samples into fragments. In fact, the DNA of chromosomes can be hundreds of millions of base pairs long, another common macromolecular property that does not characterize smaller molecules is their relative insolubility in water and similar solvents, instead forming colloids. Many require salts or particular ions to dissolve in water, similarly, many proteins will denature if the solute concentration of their solution is too high or too low. High concentrations of macromolecules in a solution can alter the rates and equilibrium constants of the reactions of other macromolecules and this comes from macromolecules excluding other molecules from a large part of the volume of the solution, thereby increasing the effective concentrations of these molecules. All living organisms are dependent on three essential biopolymers for their functions, DNA, RNA and Proteins. Each of these molecules is required for life since each plays a distinct, the simple summary is that DNA makes RNA, and then RNA makes proteins. DNA, RNA and proteins all consist of a structure of related building blocks. In general, they are all unbranched polymers, and so can be represented in the form of a string
Macromolecule
–
Chemical structure of a
polypeptide macromolecule
Macromolecule
–
Structure of a polyphenylene
dendrimer macromolecule reported by Müllen, et al.
42.
Neisseria gonorrhoeae
–
Neisseria gonorrhoeae, also known as gonococci, or gonococcus, is a species of Gram-negative coffee bean-shaped diplococci bacteria responsible for the sexually transmitted infection gonorrhea. N. gonorrhoeae was first described by Albert Neisser in 1879, Neisseria species are fastidious Gram-negative cocci that require nutrient supplementation to grow in laboratory cultures. To be specific, they grow on agar with carbon dioxide. These cocci are facultatively intracellular and typically appear in pairs, in the shape of coffee beans, of the 11 species of Neisseria that colonize humans, only two are pathogens. N. gonorrhoeae is the agent of gonorrhea and is transmitted via sexual contact. Further testing to differentiate the species includes testing for oxidase and the carbohydrates maltose, sucrose, N. gonorrhoeae possess many dynamic polymeric protein filaments called type IV pili, which allow the bacteria to adhere and move along surfaces. The bacterial movement is mediated by twitching motility powered by the extension and retraction of the type IV pilus, pili extend and attach to a substrate that signals the pilus to retract, dragging the cell forward. N. gonorrhoeae is able to pull 100,000 times its own weight, the pulling of type IV pilus is powered by a set of ATPases proteins, Pil F and Pil T. The type IV pilus in N. gonorrhoeae adhesive properties also play a role in microcolony aggregation, N. gonorrhoeae is naturally competent for DNA exchange, which is also dependent on type IV pilus dynamics, specifically proteins Pil Q and Pil T. These processes allow for the DNA of N. gonorrhoeae to acquire or spread new genes, especially dangerous from the aspect of healthcare is the ability to conjugate, since this can lead to antibiotic resistance. N. gonorrhoeae has surface proteins called Opa proteins, which bind to receptors on immune cells, in so doing, N. gonorrhoeae is able to prevent an immune response. The host is unable to develop an immunological memory against N. gonorrhoeae – which means that future reinfection is possible. The many permutations of proteins make it more difficult for immune cells to recognize N. gonorrhoeae. The genomes of several strains of N. gonorrhoeae have been sequenced, most of them are about 2.1 Mb in size and encode 2,100 to 2,600 proteins. For instance, strain NCCP11945 consists of one circular chromosome encoding 2,662 predicted ORFs, the estimated coding density over the entire genome is 87%, and the average G+C content is 52. 4%, values that are similar to those of strain FA1090. The NCCP11945 genome encodes 54 tRNAs and four copies of 16S-23S-5S rRNA operons, N. gonorrhoeae is transmitted from person to person during sexual relations. Traditionally, the bacteria was thought to move attached to spermatozoon, a recent study suggests that rather than “surf” on wiggling sperm, N. gonorrhoeae bacteria uses hairlike structures called pili to anchor onto proteins in the sperm and move through coital liquid. It can also be transmitted to the fetus in utero and afterward become apparent as a neonatal infection, symptoms of infection with N. gonorrhoeae differ, depending on the site of infection
Neisseria gonorrhoeae
–
The growth of Neisseria gonorrhoeae colonies on New York City medium agar, a specialised and selective media for Gonococci
Neisseria gonorrhoeae
–
Neisseria gonorrhoeae
43.
Outer membrane protein
–
Virulence-related outer membrane proteins are expressed in Gram-negative bacteria and are essential to bacterial survival within macrophages and for eukaryotic cell invasion. This family consists of bacterial and phage Ail/Lom-like proteins. The Yersinia enterocolitica Ail protein is a virulence factor. Proteins in this family are predicted to consist of eight transmembrane beta-sheets and it is thought that Ail directly promotes invasion and loop 2 contains an active site, perhaps a receptor-binding domain. The phage protein Lom is expressed during lysogeny, and encode host-cell envelope proteins, Lom is found in the bacterial outer membrane, and is homologous to virulence proteins of two other enterobacterial genera. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, Borrelia burgdorferi outer surface proteins play role in persistence within ticks, mammalian host transmission, host cell adhesion, and in evasion of the host immune system. OspC trigger innate immune system via signaling through TLR1, TLR2, members of this group include, PagC, required by Salmonella typhimurium for survival in macrophages and for virulence in mice Rck outer membrane protein of the S. typhimurium and S. It also has a role in the resistance against attack by the complement system a Bacteriophage lambda outer membrane protein. OspA OspC is a major surface lipoprotein produced by Borrelia burgdorferi when infected ticks feed, OspC is necessary for tick salivary gland invasion. OspC-deficient B. burgdorferi have a reduced capacity for successful transmission to mice. Its synthesis decreases after transmission to a mammalian host and this protein disappears from the bacterial surface around 2 weeks after infection. The crystal structure of OmpX from E. coli reveals that OmpX consists of an eight-stranded antiparallel all-next-neighbour beta barrel, the structure shows two girdles of aromatic amino acid residues and a ribbon of nonpolar residues that attach to the membrane interior. The core of the consists of an extended hydrogen bonding network of highly conserved residues. OmpX thus resembles an inverse micelle, the OmpX structure shows that the membrane-spanning part of the protein is much better conserved than the extracellular loops. Moreover, these form a protruding beta sheet, the edge of which presumably binds to external proteins. It is suggested that type of binding promotes cell adhesion and invasion. OspA from Borrelia burgdorferi is an outer surface protein, it has two globular domains which are connected with a single-layer β-sheet. This protein is soluble, contains a large number of Lys
Outer membrane protein
–
Virulence-related OMP
44.
Polypeptide chain
–
Peptides are biologically occurring short chains of amino acid monomers linked by peptide bonds. The covalent chemical bonds are formed when the group of one amino acid reacts with the amine group of another. The shortest peptides are dipeptides, consisting of 2 amino acids joined by a peptide bond, followed by tripeptides, tetrapeptides. A polypeptide is a long, continuous, and unbranched peptide chain, hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides and polysaccharides, etc. Peptides are distinguished from proteins on the basis of size, all peptides except cyclic peptides have an N-terminal and C-terminal residue at the end of the peptide. Ribosomal peptides Ribosomal peptides are synthesized by translation of mRNA and they are often subjected to proteolysis to generate the mature form. These function, typically in higher organisms, as hormones and signaling molecules, some organisms produce peptides as antibiotics, such as microcins. Since they are translated, the amino acid residues involved are restricted to those utilized by the ribosome, however, these peptides frequently have posttranslational modifications such as phosphorylation, hydroxylation, sulfonation, palmitoylation, glycosylation and disulfide formation. In general, they are linear, although lariat structures have been observed, more exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom. Nonribosomal peptides Nonribosomal peptides are assembled by enzymes that are specific to each peptide, the most common non-ribosomal peptide is glutathione, which is a component of the antioxidant defenses of most aerobic organisms. Other nonribosomal peptides are most common in organisms, plants. These complexes are often out in a similar fashion. These peptides are often cyclic and can have highly complex cyclic structures, since the system is closely related to the machinery for building fatty acids and polyketides, hybrid compounds are often found. The presence of oxazoles or thiazoles often indicates that the compound was synthesized in this fashion, Peptones See also Tryptone Peptones are derived from animal milk or meat digested by proteolysis. In addition to containing small peptides, the material includes fats, metals, salts, vitamins. Peptones are used in nutrient media for growing bacteria and fungi, Peptide fragments Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein. Peptides received prominence in molecular biology for several reasons, the first is that peptides allow the creation of peptide antibodies in animals without the need of purifying the protein of interest. This involves synthesizing antigenic peptides of sections of the protein of interest and these will then be used to make antibodies in a rabbit or mouse against the protein
Polypeptide chain
–
A tetrapeptide (example
Val -
Gly -
Ser -
Ala) with green marked
amino end (
L-Valine) and blue marked
carboxyl end (
L-Alanine).
45.
Respiratory tract
–
In humans, the respiratory tract is the part of the anatomy involved with the process of respiration. The respiratory tract is divided into the airways and lower airways. The upper airways or upper respiratory tract includes the nose and nasal passages, paranasal sinuses, the pharynx, the lower airways or lower respiratory tract includes the portion of the larynx below the vocal folds, trachea, bronchi and bronchioles. The lungs can be included in the respiratory tract or as separate entity and include the respiratory bronchioles, alveolar ducts, alveolar sacs. The respiratory tract can also be divided into a conducting zone, from the bronchi, the dividing tubes become progressively smaller with an estimated 20 to 23 divisions before ending at an alveolus. The upper respiratory tract, can refer to the parts of the respiratory system lying above the angle, above the vocal folds. The larynx is sometimes included in both the upper and lower airways, the larynx is also called the voice box and has the associated cartilage that produces sound. The tract consists of the cavity and paranasal sinuses, the pharynx. The lower respiratory tract or lower airway is derived from the foregut and consists of the trachea, bronchi, bronchioles. It also sometimes includes the larynx, the respiratory tree or tracheobronchial tree is a term also used to refer to the branching structure of airways supplying air to the lungs and includes the trachea, bronchi and bronchioles. The human respiratory tree may consist on average of 23 generations, proximal divisions mainly function to transmit air to the lower airways. Later divisions including the respiratory bronchiole, alveolar ducts and alveoli, are specialized for gas exchange, the trachea is the largest tube in the respiratory tract and consists of tracheal rings of hyaline cartilage. It branches off into two tubes, a left and a right main bronchus. The bronchi branch off into smaller sections inside the lungs, called bronchioles and these bronchioles give rise to the air sacs in the lungs called the alveoli. The lungs are the largest organs in the respiratory tract. The lungs are suspended within the cavity of the thorax. The pleurae are two thin membranes, one layer thick, which surround the lungs. The inner covers the lungs and the lines the inner surface of the chest wall
Respiratory tract
–
1.
Trachea 2.
Mainstem bronchus 3.
Lobar bronchus 4.
Segmental bronchus 5. Bronchiole 6.
Alveolar duct 7.
Alveolus
Respiratory tract
–
Conducting passages
46.
Laboratory mice
–
The laboratory mouse is a small mammal of the order Rodentia which is bred and used for scientific research. Laboratory mice are usually of the species Mus musculus and they are the most commonly used mammalian research model and are used for research in genetics, psychology, medicine and other scientific disciplines. Mice belong to the Euarchontoglires clade, which includes humans, the laboratory mouse genome has been sequenced and many mouse genes have human homologues. Other mouse species sometimes used in research include the American white-footed mouse. During the 18th Century Joseph Priestley and Antoine Lavoisier both used mice to study respiration, in the early part of the 20th century Clarence Cook Little, a Harvard undergraduate was conducting studies on mouse genetics in the laboratory of William Ernest Castle. Together they generated the DBA inbred mouse strain and initiated the systematic generation of inbred strains, the mouse has since been used extensively as a model organism and is associated with many important biological discoveries of the 20th and 21st Centuries. The Jackson laboratory in Bar Harbor, Maine is currently one of the worlds largest suppliers of laboratory mice, the laboratory is also the worlds source for more than 8,000 strains of genetically defined mice and is home of the Mouse Genome Informatics database. Breeding onset occurs at about 50 days of age in females and males, although females may have their first estrus at 25–40 days. Mice are polyestrous and breed year round, ovulation is spontaneous, the duration of the estrous cycle is 4–5 days and lasts about 12 hours, occurring in the evening. Vaginal smears are useful in timed matings to determine the stage of the estrous cycle, mating can be confirmed by the presence of a copulatory plug in the vagina up to 24 hours post-copulation. The presence of sperm on a smear is also a reliable indicator of mating. The average gestation period is 20 days, a fertile postpartum estrus occurs 14–24 hours following parturition, and simultaneous lactation and gestation prolongs gestation by 3–10 days owing to delayed implantation. The average litter size is 10–12 during optimum production, but is highly strain-dependent, as a general rule, inbred mice tend to have longer gestation periods and smaller litters than outbred and hybrid mice. The young are called pups and weigh 0. 5–1.5 g at birth, are hairless, pups are weaned at 3 weeks of age when they weigh about 10–12 g. If the female does not mate during the postpartum estrus, she resumes cycling 2–5 days post-weaning, newborn males are distinguished from newborn females by noting the greater anogenital distance and larger genital papilla in the male. This is best accomplished by lifting the tails of littermates and comparing perineums, Mice are mammals of the Glires clade, which means they are amongst the closest relatives of humans along with lagomorphs, treeshrews, flying lemurs and other primates. Laboratory mice are the species as the house mouse, however, they are often very different in behaviour. There are hundreds of established inbred, outbred, and transgenic strains, a strain, in reference to rodents, is a group in which all members are as nearly as possible genetically identical
Laboratory mice
–
An albino
SCID laboratory mouse
Laboratory mice
–
A laboratory mouse with intermediate coat colour
Laboratory mice
–
1 day old pups
Laboratory mice
–
Two mice expressing enhanced green fluorescent protein under UV-illumination flanking one plain mouse from the non-transgenic parental line.
47.
Passive immunity
–
Passive immunity is the transfer of active humoral immunity in the form of ready-made antibodies. Passive immunization can be provided when people cannot synthesize antibodies, maternal passive immunity is a type of naturally acquired passive immunity, and refers to antibody-mediated immunity conveyed to a fetus or infant by its mother. Naturally acquired passive immunity can be provided during pregnancy, and through breast-feeding, in humans, maternal antibodies are passed through the placenta to the fetus by an FcRn receptor on placental cells. This occurs predominately during the third trimester of pregnancy, and thus is reduced in babies born prematurely. Immunoglobulin G is the only isotype that can pass through the human placenta. IgG antibodies protects against bacterial and viral infections in fetuses and this effect is usually overcome by secondary responses to booster immunization. Maternal antibodies protect against some diseases more than such as measles, rubella, and tetanus compared to the protection provided against polio. Maternal passive immunity offers immediate protection, though protection mediated by maternal IgG typically only lasting four to six months after birth, only a few other species besides humans transfer maternal antibodies before birth, including primates and lagomorphs. In some of these species IgM can be transferred across the placenta as well as IgG, all other mammalian species predominantly or solely transfer maternal antibodies after birth through milk. In these species, the gut is able to absorb IgG for hours to days after birth. However, after a period of time the neonate can no longer absorb maternal IgG through their gut, an event that is referred to as gut closure. If a neonatal animal does not receive adequate amounts of colostrum prior to gut closure, is does not have a sufficient amount of maternal IgG in its blood to fight off common diseases and this condition is referred to as failure of passive transfer. It can be diagnosed by measuring the amount of IgG in a newborns blood, if not treated, it can be fatal. Passive transfer is used to prevent disease or used prophylactically in the case of immunodeficiency diseases and it is also used in the treatment of several types of acute infection, and to treat poisoning. Immunity derived from passive immunization lasts for a few weeks to three to four months, there is also a potential risk for hypersensitivity reactions, and serum sickness, especially from gamma globulin of non-human origin. By 1896, the introduction of diphtheria antitoxin was hailed as the most important advance of the Century in the treatment of acute infective disease. Prior to the advent of vaccines and antibiotics, specific antitoxin was often the treatment available for infections such as diphtheria. Immunoglobulin therapy continued to be a first line therapy in the treatment of respiratory diseases until the 1930s
Passive immunity
–
A vial of diphtheria antitoxin, dated 1895
48.
Immunoglobulin domains
–
The backbone switches repeatedly between the two β-sheets. The cross-overs between sheets form an X, so that the N- and C-terminal hairpins are facing each other, members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin, and receptor tyrosine kinases, immunoglobulin-like domains may be involved in protein–protein and protein–ligand interactions
Immunoglobulin domains
–
Structure of an antigen binding fragment of an antibody.
49.
Fluoroquinolones
–
The quinolones are a family of synthetic broad-spectrum antibiotic drugs. Quinolones, and derivatives, have also been isolated from natural sources, Quinolones exert their antibacterial effect by preventing bacterial DNA from unwinding and duplicating. The majority of quinolones in clinical use are fluoroquinolones, which have a fluorine atom attached to the ring system. Most of them are named with the -oxacin suffix, for patients with these conditions, fluoroquinolones should be reserved for those who do not have alternative treatment options. Fluoroquinolones are featured prominently in The American Thoracic Society guidelines for the treatment of hospital-acquired pneumonia, the Society recommends fluoroquinolones not be used as a first-line agent for community-acquired pneumonia, instead recommending macrolide or doxycycline as first-line agents. Fluoroquinolones are often used for infections, and are widely used in the treatment of hospital-acquired infections associated with urinary catheters. In community-acquired infections, they are recommended only when risk factors for multidrug resistance are present or after other antibiotic regimens have failed, however, for serious acute cases of pyelonephritis or bacterial prostatitis where the patient may need to be hospitalised, fluoroquinolones are recommended as first-line therapy. The use of fluoroquinolones to treat infections in children is controversial, in the UK, the prescribing indications for fluoroquinolones for children are severely restricted. Only inhalant anthrax and pseudomonal infections in cystic fibrosis infections are licensed indications in the UK due to ongoing safety concerns, most of these were considered by the treating physician to be unrelated or doubtfully related to the study drug. Two deaths were observed in the group, neither of which was thought to be treatment-related. An estimated 130,000 pediatric prescriptions for levofloxacin were filled on behalf of 112,000 pediatric patients during that period, a number of recent meta-analyses have concluded that fluoroquinolones pose little or no additional risk to children compared to other antibiotic classes. While typical drug side effects reactions are mild to moderate, sometimes serious adverse effects occur, prominent among these are side effects that became the subject of a black box warning by the FDA in 2016. The FDA wrote, An FDA safety review has shown that fluoroquinolones when used systemically are associated with disabling and these side effects can involve the tendons, muscles, joints, nerves, and central nervous system. Quinolones are associated with a risk of tendinitis and tendon rupture. Some experts have advised avoidance of fluoroquinolones in athletes, if tendonitis occurs, it generally appears within one month, and the most common tendon that is injured appears to be the Achilles tendon. The cause is not well understood, nervous system effects include insomnia, restlessness, and rarely, seizure, convulsions, and psychosis. Other rare and serious events have been observed with varying degrees of evidence for causation. More generally, fluoroquinolones are tolerated, with typical side effects being mild to moderate
Fluoroquinolones
–
Essential structure of all quinolone antibiotics: the blue drawn remainder of R is usually
piperazine; if the connection contains fluorine (red), it is a fluoroquinolone.
50.
Porin (protein)
–
Porins are beta barrel proteins that cross a cellular membrane and act as a pore, through which molecules can diffuse. Unlike other membrane proteins, porins are large enough to allow passive diffusion. They are present in the membrane of gram-negative bacteria and some gram-positive bacteria of the group Mycolata, the mitochondria. Porins are composed of β strands, which are, in general, linked together by beta turns on the cytoplasmic side, the β strands lie in an antiparallel fashion and form a cylindrical tube, called a β barrel. The amino acid composition of the porin β strands are unique in that polar and nonpolar residues alternate along them, the porin channel is partially blocked by a loop, called the eyelet, which projects into the cavity. In general, it is found between strands 5 and 6 of each barrel, and it defines the size of solute that can traverse the channel. It is lined almost exclusively with charged amino acids arranged on opposite sides of the channel, to transport medium-sized or charged molecules across, the molecules move through a porin, a water-filled channel or pore. Porins typically control the diffusion of small metabolites like sugars, ions, porins are chemically selective – transporting only one group of molecules – or may be specific for one molecule. Beta-lactam and fluoroquinolone antibiotics must pass through porins to reach their targets in gram negative bacteria, bacteria can develop resistance to these antibiotics by mutating the gene that encodes the porin – the antibiotics are then excluded from passing through the outer membrane. The term nucleoporin refers to completely unrelated proteins facilitating transport through nuclear pores in the nuclear envelope, the discovery of porins has been attributed to Hiroshi Nikaido, nicknamed the porinologist. There are five evolutionarily independent superfamilies of porins, porin superfamily I includes 47 families of porins with a range of numbers of trans-membrane β-strands. These include the GBP, SP and RPP porin families, while PSF I includes 47 families, PSF II-V each contain only 2 families. While PSF I derives members from gram-negative bacteria primarily one family of eukaryotic mitochondrial porins, PSF II, PSF III and V are derived from eukaryotic organelle
Porin (protein)
–
A
sucrose specific porin from
Salmonella typhimurium, a
gram-negative bacterium.
PDB: 1A0S
. PMID 20667430. doi:10.1016/j.vetmic.2010.06.029. Retrieved 2 October 2013.
