1.
Taxonomy (biology)
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Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. The exact definition of taxonomy varies from source to source, but the core of the remains, the conception, naming. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, the broadest meaning of taxonomy is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique, the term alpha taxonomy is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, ideals can, it may be said, never be completely realized. They have, however, a value of acting as permanent stimulants. Some of us please ourselves by thinking we are now groping in a beta taxonomy, turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy, thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. This activity is what the term denotes, it is also referred to as beta taxonomy. How species should be defined in a group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy, by extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in scientific thinking. Early taxonomy was based on criteria, the so-called artificial systems. Later came systems based on a complete consideration of the characteristics of taxa, referred to as natural systems, such as those of de Jussieu, de Candolle and Bentham. The publication of Charles Darwins Origin of Species led to new ways of thinking about classification based on evolutionary relationships and this was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler and Engler, the advent of molecular genetics and statistical methodology allowed the creation of the modern era of phylogenetic systems based on cladistics, rather than morphology alone. Taxonomy has been called the worlds oldest profession, and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate
2.
Bacteria
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
3.
Firmicutes
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The Firmicutes are a phylum of bacteria, most of which have Gram-positive cell wall structure. A few, however, such as Megasphaera, Pectinatus, Selenomonas and they have round cells, called cocci, or rod-like forms. Many Firmicutes produce endospores, which are resistant to desiccation and can survive extreme conditions and they are found in various environments, and the group includes some notable pathogens. Those in one family, the heliobacteria, produce energy through photosynthesis, Firmicutes play an important role in beer, wine, and cider spoilage. The group is divided into the Clostridia, which are anaerobic, the Bacilli, which are obligate or facultative aerobes. On phylogenetic trees, the first two show up as paraphyletic or polyphyletic, as do their main genera, Clostridium. The division Firmicutes as part of the gut flora has been shown to be involved in energy resorption, presence of Christensenella, in class Clostridia and also isolated from human faeces, has been found to correlate with lower body mass index. The presence of Firmicutes can be detected with polymerase chain reaction techniques. Phylum Firmicutes - J. P. Euzéby, List of Prokaryotic names with Standing in Nomenclature
4.
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
5.
Lactobacillales
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These bacteria, usually found in decomposing plants and milk products, produce lactic acid as the major metabolic end product of carbohydrate fermentation. This trait has, throughout history, linked LAB with food fermentations, proteinaceous bacteriocins are produced by several LAB strains and provide an additional hurdle for spoilage and pathogenic microorganisms. Furthermore, lactic acid and other products contribute to the organoleptic. The lactic acid bacteria are either rod-shaped, or spherical, and are characterized by a tolerance to acidity. This aspect helps LAB to outcompete other bacteria in a natural fermentation, laboratory media used for LAB typically include a carbohydrate source, as most species are incapable of respiration. They consist of the organelles of a simple bacterial structure, LAB are amongst the most important groups of microorganisms used in the food industry. Two main hexose fermentation pathways are used to classify LAB genera, under conditions of excess glucose and limited oxygen, homolactic LAB catabolize one mole of glucose in the Embden-Meyerhof-Parnas pathway to yield two moles of pyruvate. Intracellular redox balance is maintained through the oxidation of NADH, concomitant with reduction to lactic acid. This process yields two moles of ATP per mole of glucose consumed, representative homolactic LAB genera include Lactococcus, Enterococcus, Streptococcus, Pediococcus, and group I lactobacilli. Heterofermentative LAB use the pentose phosphate pathway, alternatively referred to as the pentose phosphoketolase pathway, one mole of glucose-6-phosphate is initially dehydrogenated to 6-phosphogluconate and subsequently decarboxylated to yield one mole of CO2. The resulting pentose-5-phosphate is cleaved into one mole glyceraldehyde phosphate and one mole acetyl phosphate, GAP is further metabolized to lactate as in homofermentation, with the acetyl phosphate reduced to ethanol via acetyl-CoA and acetaldehyde intermediates. In theory, end products are produced in quantities from the catabolism of one mole of glucose. Obligate heterofermentative LAB include Leuconostoc, Oenococcus, Weissella, and group III lactobacilli, formerly, streptococci were segregated primarily based on serology, which has proven to correlate well with the current taxonomic definitions. Lactococci are used extensively as fermentation starters in dairy production, with humans estimated to consume 1018 lactococci annually, partly due to their industrial relevance, both L. lactis subspecies are widely used as generic LAB models for research. L. lactis ssp. cremoris, used in the production of cheeses, is represented by the laboratory strains LM0230. In similar manner, L. lactis ssp. lactis is employed in soft cheese fermentations, in 2001, Bolotin et al. sequenced the genome of IL1403, which coincided with a significant shift of resources to understanding LAB genomics and related applications. The relationship between bacteriophages and their hosts is very important in the context of the food fermentation industry. Sources of phage contamination, measures to control their propagation and dissemination, the first contact between an infecting phage and its bacterial host is the attachment of the phage to the host cell
6.
Streptococcus
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Streptococcus is a genus of coccus Gram-positive bacteria belonging to the phylum Firmicutes and the order Lactobacillales. Cell division in this genus occurs along an axis in these bacteria, thus they grow in chains or pairs, hence the name—from Greek στρεπτός streptos, meaning easily bent or twisted. Most are oxidase-negative and catalase-negative, and many are facultative anaerobes, in 1984, many bacteria formerly considered Streptococcus were separated out into the genera Enterococcus and Lactococcus. Currently, over 50 species are recognised in this genus, however, many streptococcal species are not pathogenic, and form part of the commensal human microbiota of the mouth, skin, intestine, and upper respiratory tract. Furthermore, streptococci are an ingredient in producing Emmentaler cheese. Species of Streptococcus are classified based on their hemolytic properties, alpha-hemolytic species cause oxidization of iron in hemoglobin molecules within red blood cells, giving it a greenish color on blood agar. Beta-hemolytic species cause complete rupture of red blood cells, on blood agar, this appears as wide areas clear of blood cells surrounding bacterial colonies. Beta-hemolytic streptococci are further classified by Lancefield grouping, a serotype classification, the 20 described serotypes are named Lancefield groups A to V. In the medical setting, the most important groups are the alpha-hemolytic streptococci S. pneumoniae and Streptococcus viridans group, table, Medically relevant streptococci When alpha hemolysis is present, the agar under the colony is dark and greenish. Streptococcus pneumoniae and a group of oral streptococci display alpha hemolysis and this is sometimes called green hemolysis because of the color change in the agar. Other synonymous terms are incomplete hemolysis and partial hemolysis, alpha hemolysis is caused by hydrogen peroxide produced by the bacterium, oxidizing hemoglobin to green methemoglobin. S. pneumoniae, is a cause of bacterial pneumonia and occasional etiology of otitis media, sinusitis, meningitis. Inflammation is thought to be the cause of how pneumococci cause disease. The viridans streptococci are a group of commensal bacteria, that are either α-hemolytic, producing a green coloration on blood agar plates. Beta hemolysis, sometimes called complete hemolysis, is a complete lysis of red cells in the media around and under the colonies, streptolysin, an exotoxin, is the enzyme produced by the bacteria which causes the complete lysis of red blood cells. SLS affects immune cells, including polymorphonuclear leukocytes and lymphocytes, and is thought to prevent the host immune system from clearing infection, Streptococcus pyogenes, or group A Streptococcus, displays beta hemolysis. Some weakly beta-hemolytic species cause intense beta hemolysis when grown together with a strain of Staphylococcus and this is called the CAMP test. Clostridium perfringens can be identified presumptively with this test, Listeria monocytogenes is also positive on sheeps blood agar
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
8.
Gram-positive bacteria
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Gram-positive bacteria are bacteria that give a positive result in the Gram stain test. Gram-positive bacteria take up the crystal violet stain used in the test and this is because the thick peptidoglycan layer in the bacterial cell wall retains the stain after it is washed away from the rest of the sample, in the decolorization stage of the test. Their peptidoglycan layer is thinner and sandwiched between an inner cell membrane and a bacterial outer membrane, causing them to take up the counterstain. Despite their thicker peptidoglycan layer, gram-positive bacteria are more receptive to antibiotics than gram-negative, peptidoglycan chains are cross-linked to form rigid cell walls by a bacterial enzyme DD-transpeptidase. A much smaller volume of periplasm than that in gram-negative bacteria, only some species have a capsule usually consisting of polysaccharides. Also only some species are flagellates, and when they do have flagella they only have two basal body rings to support them, both gram-positive and gram-negative bacteria commonly have a surface layer called an S-layer. In gram-positive bacteria, the S-layer is attached to the peptidoglycan layer, specific to gram-positive bacteria is the presence of teichoic acids in the cell wall. Some of these are lipoteichoic acids, which have a component in the cell membrane that can assist in anchoring the peptidoglycan. Along with cell shape, Gram staining is a method used to differentiate bacterial species. Historically, the kingdom Monera was divided into four divisions based primarily on Gram staining, based on molecular studies of the 16S sequences, Woese recognised twelve bacterial phyla. Two of these were both gram-positive and were divided on the proportion of the guanine and cytosine content in their DNA, the high G + C phylum was made up of the Actinobacteria and the low G + C phylum contained the Firmicutes. The Actinobacteria include the Corynebacterium, Mycobacterium, Nocardia and Streptomyces genera, the Firmicutes, have a 45–60% GC content, but this is lower than that of the Actinobacteria. The gram-positive and gram-negative staining response is not a reliable characteristic as these two kinds of bacteria do not form phylogenetic coherent groups. All gram-positive bacteria are bounded by a lipid membrane, and, in general. For the bacterial cells bounded by a cell membrane, the term monoderm bacteria or monoderm prokaryotes has been proposed. The presence of inner and outer cell membranes defines a new compartment in these cells and these bacteria have been designated as diderm bacteria. The distinction between the monoderm and diderm bacteria is supported by conserved signature indels in a number of important proteins, of these two structurally distinct groups of bacteria, monoderms are indicated to be ancestral. In general, gram-positive bacteria are monoderms and have a lipid bilayer whereas gram-negative bacteria are diderms and have two bilayers
9.
Hemolysis (microbiology)
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Hemolysis is the breakdown of red blood cells. The ability of bacterial colonies to induce hemolysis when grown on blood agar is used to classify certain microorganisms and this is particularly useful in classifying streptococcal species. A substance that causes hemolysis is a hemolysin, when alpha hemolysis is present, the agar under the colony is dark and greenish. Streptococcus pneumoniae and a group of oral streptococci display alpha hemolysis and this is sometimes called green hemolysis because of the color change in the agar. Other synonymous terms are incomplete hemolysis and partial hemolysis, alpha hemolysis is caused by hydrogen peroxide produced by the bacterium, reducing hemoglobin producing the green oxidized derivative methemoglobin. Beta hemolysis, sometimes called complete hemolysis, is a complete lysis of red cells in the media around and under the colonies, streptolysin, an exotoxin, is the enzyme produced by the bacteria which causes the complete lysis of red blood cells. SLS affects immune cells, including polymorphonuclear leukocytes and lymphocytes, and is thought to prevent the host immune system from clearing infection, streptococcus pyogenes, or Group A beta-hemolytic Strep, displays beta hemolysis. Some weakly beta-hemolytic species cause intense beta hemolysis when grown together with a strain of Staphylococcus and this is called the CAMP test. Clostridium perfringens can be identified presumptively with this test, listeria monocytogenes is also positive on sheeps blood agar. If an organism does not induce hemolysis, the agar under and around the colony is unchanged, enterococcus faecalis, Staphylococcus saprophyticus, and Staphylococcus epidermidis display gamma hemolysis. This is the killing of blood cells by metabolic by-products of bacteria. This can be seen on an agar plate, when the blood surrounding the confluent part of your streak turns green. Hemedigestion is seen with the bacteria, Vibrio cholerae. George, Ryan, Kenneth J. Kenneth, Ryan, sherris Medical Microbiology, An Introduction to Infectious Diseases
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Genus
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A genus is a taxonomic rank used in the biological classification of living and fossil organisms in biology. In the hierarchy of classification, genus comes above species. In binomial nomenclature, the name forms the first part of the binomial species name for each species within the genus. Felis catus and Felis silvestris are two species within the genus Felis, Felis is a genus within the family Felidae. The composition of a genus is determined by a taxonomist, the standards for genus classification are not strictly codified, so different authorities often produce different classifications for genera. Moreover, genera should be composed of units of the same kind as other genera. The term comes from the Latin genus, a noun form cognate with gignere, linnaeus popularized its use in his 1753 Species Plantarum, but the French botanist Joseph Pitton de Tournefort is considered the founder of the modern concept of genera. The scientific name of a genus may be called the name or generic epithet. It plays a role in binomial nomenclature, the system of naming organisms. The rules for the names of organisms are laid down in the Nomenclature Codes. The standard way of scientifically describing species and other lower-ranked taxa is by binomial nomenclature, the generic name forms its first half. For example, the gray wolfs binomial name is Canis lupus, with Canis being the name shared by the wolfs close relatives. The specific name is written in lower-case and may be followed by names in zoology or a variety of infraspecific names in botany. Especially with these names, when the generic name is known from context. Because animals are typically only grouped within subspecies, it is written as a trinomen with a third name. Dog breeds, meanwhile, are not scientifically distinguished, there are several divisions of plant species and therefore their infraspecific names generally include contractions explaining the relation. For example, the genus Hibiscus includes hundreds of other species apart from the Rose of Sharon or common garden hibiscus, Rose of Sharon doesnt have subspecies but has cultivars that carry desired traits, such as the bright white H. syriaca Diana. Hawaiian hibiscus, meanwhile, includes several separate species, since not all botanists agree on the divisions or names between species, it is common to specify the source of the name using author abbreviations
11.
Humoral immunity
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Humoral immunity is so named because it involves substances found in the humors, or body fluids. Its aspects involving antibodies are often called antibody-mediated immunity, the study of the molecular and cellular components that form the immune system, including their function and interaction, is the central science of immunology. The immune system is divided into a more primitive innate immune system, the concept of humoral immunity developed based on analysis of antibacterial activity of the serum components. Hans Buchner is credited with the development of the humoral theory, in 1890 he described alexins, or “protective substances”, which exist in the blood serum and other bodily fluid and are capable of killing microorganisms. Following the 1888 discovery of the bacteria that cause diphtheria and tetanus, Emil von Behring and they discovered that cell-free filtrates were sufficient to cause disease. In 1897, Paul Ehrlich showed that antibodies form against the plant toxins ricin and abrin, Ehrlich, with his friend Emil von Behring, went on to develop the diphtheria antitoxin, which became the first major success of modern immunotherapy. The presence and specificity of compatibility antibodies became the tool for standardizing the state of immunity. The complement system is a cascade of the innate immune system that helps clear pathogens from an organism. It is derived from many small blood plasma proteins that together to disrupt the target cells plasma membrane leading to cytolysis of the cell. The complement system consists of more than 35 soluble and cell-bound proteins,12 of which are involved in the complement pathways. The complement system is involved in the activities of both innate immunity and acquired immunity, activation of this system leads to cytolysis, chemotaxis, opsonization, immune clearance, and inflammation, as well as the marking of pathogens for phagocytosis. The proteins account for 5% of the globulin fraction. Most of these proteins circulate as zymogens, which are inactive until proteolytic cleavage, three biochemical pathways activate the complement system, the classical complement pathway, the alternate complement pathway, and the mannose-binding lectin pathway. Antibodies, in particular the IgG1 class, can also fix complement, the principal function of B cells is to make antibodies against soluble antigens. B cell recognition of antigen is not the only element necessary for B cell activation, naïve B cells can be activated in a T-cell dependent or independent manner, but two signals are always required to initiate activation. B cell activation depends on one of three mechanisms, Type 1 T cell-independent activation, Type 2 T cell-independent activation, and T cell-dependent activation, during T cell-dependent activation, an antigen presenting cell presents a processed antigen to a T helper cell, priming it. When a B cell processes and presents the antigen to the primed Th cell. Immunoglobulins are glycoproteins in the superfamily that function as antibodies
12.
Community-acquired pneumonia
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Community-acquired pneumonia refers to pneumonia contracted by a person with little contact with the healthcare system. The chief difference between hospital-acquired pneumonia and CAP is that patients with HAP live in long-term care facilities or have recently visited a hospital, CAP is common, affecting people of all ages, and its symptoms occur as a result of oxygen-absorbing areas of the lung filling with fluid. This inhibits lung function, causing dyspnea, fever, chest pains, CAP, the most common type of pneumonia, is a leading cause of illness and death worldwide. Its causes include bacteria, viruses, fungi and parasites, CAP is diagnosed by assessing symptoms, making a physical examination and on x-ray. Other tests, such as sputum examination, supplement chest x-rays, Patients with CAP sometimes require hospitalization, and it is treated primarily with antibiotics, antipyretics and cough medicine. Some forms of CAP can be prevented by vaccination and by abstaining from tobacco products, a definitive cause is identified in only half the cases. Infants can acquire lung infections before birth by breathing infected amniotic fluid or through an infection which crossed the placenta. Infants can also inhale contaminated fluid from the vagina at birth, the most prevalent pathogen causing CAP in newborns is Streptococcus agalactiae, also known as group-B streptococcus. GBS causes more than half of CAP in the first week after birth, other bacterial causes of neonatal CAP include Listeria monocytogenes and a variety of mycobacteria. CAP-causing viruses may also be transferred from mother to child, herpes simplex virus is life-threatening, maternally-derived syphilis is also a cause of CAP in this age group. CAP caused by fungi or parasites is not usually seen in otherwise-healthy infants, in contrast, older children and teenagers are more likely to acquire Mycoplasma pneumoniae and Chlamydophila pneumoniae than adults. A full spectrum of microorganisms is responsible for CAP in adults, identifying people at risk for infection by these organisms aids in appropriate treatment. Many less-common organisms can cause CAP in adults, and are identified from specific risk factors or treatment failure for common causes, some patients have an underlying problem which increases their risk of infection. Some risk factors are, Obstruction, When part of the leading to the alveoli is obstructed, the lung cannot eliminate fluid. One cause of obstruction, especially in children, is inhalation of a foreign object such as a marble or toy. The object lodges in an airway, and pneumonia develops in the obstructed area of the lung. Another cause of obstruction is lung cancer, which can block the flow of air, lung disease, Patients with underlying lung disease are more likely to develop pneumonia. Diseases such as emphysema and habits such as smoking result in more-frequent, in children, recurrent pneumonia may indicate cystic fibrosis or pulmonary sequestration
13.
Viridans streptococci
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The viridans streptococci are a large group of commensal streptococcal bacteria species that are either α-hemolytic, producing a green coloration on blood agar plates, or nonhemolytic. These species possess no Lancefield antigens, pneumoniae or the Lancefield antigens of the pyogenic members of the genus. The organisms are most abundant in the mouth, and one member of the group, S. mutans, is the cause of dental caries in most cases, S. sanguinis is also another potential cause. Others may be involved in other mouth or gingival infections as pericoronitis, if they are introduced into the bloodstream, they have the potential of causing endocarditis, in particular in individuals with damaged heart valves. They are the most common causes of bacterial endocarditis. Viridans streptococci have the ability to synthesize dextrans from glucose. This mechanism underlies their ability to cause subacute valvular heart disease following their introduction into the bloodstream, identification of VGS to the species level can be difficult, and phenotypic identification is not always accurate. The name “viridans” is somewhat of a misnomer, as many species do not produce any hemolysis on blood agar. Lack of alpha hemolysis does not seem to correlate with the outcome or severity of disease. The VGS are a group of catalase-negative, Gram-positive cocci with a chaining morphology on microscopic examination and they are leucine aminopeptidase positive, pyrrolidonylarylamidase negative, and do not grow in 6. 5% NaCl, and almost all species are negative for growth on bile esculin agar. They differ from pneumococci in that they are resistant and are not bile soluble. The S. anginosus group of organisms can be beta-, alpha- or nonhemolytic, the isolates lacking beta-hemolysis are generally those grouped with the VGS. S. constellatus is the most likely of this group to be beta-hemolytic. There is some evidence implicating beta-hemolytic S. constellatus subsp, pharyngis as a cause of pharyngitis. S. intermedius is the species in this group most commonly isolated from brain, the S. anginosus group can possess Lancefield group antigens A, C, G, and F, although S. intermedius almost never possesses Lancefield group antigens. Isolates of the S. anginosus group have a characteristic “butterscotch” odor, members of the group are universally positive for three biochemical reactions, acetoin production from glucose, arginine, and sorbitol. These are very useful for the differentiation of this group from other VGS. S. mitis group, the S. mitis group of organisms contains several species and is biochemically very inert, which can make species level identification very challenging. The use of species names has also been a particular problem with the S. mitis group. Isolates in this group are negative for acetoin production, arginine, esculin, S. pneumoniae is a recently characterized member of the S. mitis group
14.
Lysis
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Lysis refers to the breaking down of the membrane of a cell, often by viral, enzymic, or osmotic mechanisms that compromise its integrity. A fluid containing the contents of lysed cells is called a lysate, many species of bacteria are subject to lysis by the enzyme lysozyme, found in animal saliva, egg white, and other secretions. Phage lytic enzymes produced during infection are responsible for the ability of these viruses to lyse bacterial cells. Penicillin and related β-lactam antibiotics cause the death of bacteria through enzyme-mediated lysis that occurs after the causes the bacterium to form a defective cell wall. If cell wall is completely lost, the bacterium is referred as a protoplast if penicillin was used on gram-positive bacteria, cytolysis occurs when a cell bursts due to an osmotic imbalance that has caused excess water to move into the cell. Cytolysis can be prevented by several different mechanisms, including the contractile vacuole that exists in some paramecia, oncolysis refers to the destruction of neoplastic cells or of a tumour. Its also used to refer to the reduction of any swelling, plasmolysis is the contraction of cells within plants due to the loss of water through osmosis. In a hypertonic environment, the cell membrane peels off of the cell wall and these cells will eventually wilt and die unless the flow of water caused by osmosis can stop the contraction of the cell membrane. Erythrocytes hemoglobin release free radicals in response to pathogens when lysed by them, cell lysis is used in laboratories to break open cells and purify or further study their contents. Lysis in the laboratory may be affected by enzymes or detergents or other chaotropic agents, mechanical disruption of cell membranes, as by repeated freezing and thawing, sonication, pressure, or filtration may also be referred to as lysis. The unprocessed solution immediately after lysis but before any further extraction steps is referred to as a crude lysate. For example, lysis is used in western and Southern blotting to analyze the composition of proteins, lipids. Depending on the detergent used, either all or some membranes are lysed, for example, if only the cell membrane is lysed then gradient centrifugation can be used to collect certain organelles. Lysis is also used for purification, DNA extraction. Cell disruption Crenation Hemolysis Lysogenic Pitted keratolysis
15.
Bile
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Bile or gall is a dark green to yellowish brown fluid, produced by the liver of most vertebrates, that aids the digestion of lipids in the small intestine. In humans, bile is produced continuously by the liver, after eating, this stored bile is discharged into the duodenum. The composition of gallbladder bile is 97% water,0. 7% bile salts,0. 2% bilirubin,0. 51% fats, and 200 meq/l inorganic salts. Bile was the yellow bile in the four humor system of medicine, about 400 to 800 ml of bile is produced per day in adult humans. Bile acts to some extent as a surfactant, helping to emulsify the lipids in food, the hydrophilic sides are negatively charged, and this charge prevents fat droplets coated with bile from re-aggregating into larger fat particles. Ordinarily, the micelles in the duodenum have a diameter around 14–33 μm, a triglyceride is broken down into two fatty acids and a monoglyceride, which are absorbed by the villi on the intestine walls. After being transferred across the membrane, the fatty acids reform into triglycerides. Without bile salts, most of the lipids in food would be excreted in faeces, since bile increases the absorption of fats, it is an important part of the absorption of the fat-soluble substances, such as the vitamins A, D, E, and K. Besides its digestive function, bile serves also as the route of excretion for bilirubin, bilirubin derives from hemoglobin by glucuronidation. Bile tends to be alkali on average, the pH of common duct bile is higher than that of the corresponding gallbladder bile. It becomes more acidic in the gallbladder the longer you go without eating, as an alkali, it also has the function of neutralizing any excess stomach acid before it enters the duodenum, the first section of the small intestine. Bile salts also act as bactericides, destroying many of the microbes that may be present in the food, in the absence of bile, fats become indigestible and are instead excreted in feces, a condition called steatorrhea. Feces lack their characteristic color and instead are white or gray. Steatorrhea can lead to deficiencies in essential fatty acids and fat-soluble vitamins, in addition, past the small intestine the gastrointestinal tract and gut flora are not adapted to processing fats, leading to problems in the large intestine. The cholesterol contained in bile will occasionally accrete into lumps in the gallbladder, cholesterol gallstones are generally treated through surgical removal of the gallbladder. However, they can sometimes be dissolved by increasing the concentration of naturally occurring bile acids, such as chenodeoxycholic acid. On an empty stomach – after repeated vomiting, for example – a persons vomit may be green or dark yellow, the bitter and greenish component may be bile or normal digestive juices originating in the stomach. The color of bile is often likened to fresh-cut grass, unlike components in the stomach that look greenish yellow or dark yellow
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Bacterial capsule
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The cell capsule is a very large structure of some prokaryotic cells, such as bacterial cells. It is a layer that lies outside the cell envelope of bacteria. It is a layer, not easily washed off. When the amorphous viscid secretion diffuses into the medium and remains as a loose undemarcated secretion. It usually consists of polysaccharides, but can be composed of materials, also peptidoglycan. Because most capsules are so packed, they are difficult to stain using standard stains because most stains cannot adhere to the capsule. For examination under the microscope, the bacteria and their background are stained darker than the capsule, which doesnt stain. When viewed, bacterial cells as well as the surface they are on, are stained dark, while the capsule remains pale or colorless and appears as a ring, or halo, the capsule is considered a virulence factor because it enhances the ability of bacteria to cause disease. The capsule can protect cells from engulfment by eukaryotic cells, such as macrophages, a capsule-specific antibody may be required for phagocytosis to occur. Capsules also contain water which protects the bacteria against desiccation and they also exclude bacterial viruses and most hydrophobic toxic materials such as detergents. Immunity to one type does not result in immunity to the other types. Capsules also help cells adhere to surfaces, Streptococcus pyogenes synthesizes a hyaluronic acid capsule. Streptococcus pneumoniae has at least 91 different capsular serotypes and these serotypes are the basis for the pneumococcal vaccines. Streptococcus agalactiae produces a capsule of nine antigenic types that all contain sialic acid. Staphylococcus epidermidis The yeast Cryptococcus neoformans, though not a bacterium, has a similar capsule, capsules too small to be seen with an ordinary microscope, such as the M protein of Streptococcus pyogenes, are called microcapsules. India ink staining, the capsule appears as a halo around the bacterium as the ink cant penetrate the capsule. Manevals capsule stain, the capsule appears as a clear halo between the bacterium and the bluish-grey stained background. The background stain is the acidic stain Congo red, and the stain is acid fuschin
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Coccus
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A coccus is any bacterium that has a spherical, ovoid, or generally round shape. It is one of the three distinct shapes, the other two being bacillus and spiral-shaped cells. Cocci is an English loanword of a modern or neo-Latin noun, cocci may occur as single cells or remain attached following cell division. Those that remain attached can be classified based on cellular arrangement, staphylococci are irregular clusters of cocci. Tetrads are clusters of four cocci arranged within the same plane, sarcina is a genus of bacteria that are found in cuboidal arrangements of eight cocci
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Scalpel
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A scalpel, or lancet, is a small and extremely sharp bladed instrument used for surgery, anatomical dissection, and various arts and crafts. Scalpels may be disposable or re-usable. Re-usable scalpels can have permanently attached blades that can be sharpened or, more commonly, disposable scalpels usually have a plastic handle with an extensible blade and are used once, then the entire instrument is discarded. Scalpel blades are usually packed in sterile pouches but are also offered non-sterile. Double-edged scalpels are referred to as lancets, scalpel blades are usually made of hardened and tempered steel, stainless steel, or high carbon steel, in addition, titanium, ceramic, diamond and even obsidian knives are not uncommon. For example, when performing surgery under MRI guidance, steel blades are unusable, historically, the preferred material for surgical scalpels was silver, on account of its antimicrobial properties. Scalpel blades are also offered by manufacturers with a zirconium nitride-coated edge to improve sharpness. Others manufacture blades that are coated to enhance lubricity during a cut. Alternatives to scalpels in surgical applications include electrocautery and lasers, Surgical scalpels consist of two parts, a blade and a handle. The handles are often reusable, with the blades being replaceable, in medical applications, each blade is only used once. The handle is known as a B. P. handle, named after Charles Russell Bard and Morgan Parker. The handle of medical scalpels come in two basic types, the first is a flat handle used in the #3 and #4 handles. The #7 handle is more like a writing pen, rounded at the front. A #4 handle is larger than a #3, blades are manufactured with a corresponding fitment size so that they fit on only one size handle. The following table of blades is incomplete and some blades listed may work with handles not specified here, also called the dinner knife grip. This grip is best for initial incisions and larger cuts, best used for more accurate cuts with smaller blades and the #7 handle. The scalpel is held with the tips of the first and second fingers, care should be taken not to allow the handle to rest too far along the index finger as this promotes an unstable grip and cramped fingers. Graphical and model-making scalpels tend to have handles, with textured grips
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Polysaccharide
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They range in structure from linear to highly branched. Examples include storage polysaccharides such as starch and glycogen, and structural polysaccharides such as cellulose, polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure, these macromolecules can have distinct properties from their building blocks. They may be amorphous or even insoluble in water, natural saccharides are generally of simple carbohydrates called monosaccharides with general formula n where n is three or more. Examples of monosaccharides are glucose, fructose, and glyceraldehyde, polysaccharides, meanwhile, have a general formula of Cxy where x is usually a large number between 200 and 2500. When the repeating units in the backbone are six-carbon monosaccharides, as is often the case, the general formula simplifies to n. Polysaccharides are an important class of biological polymers and their function in living organisms is usually either structure- or storage-related. Starch is used as a polysaccharide in plants, being found in the form of both amylose and the branched amylopectin. In animals, the structurally similar glucose polymer is the more densely branched glycogen, glycogens properties allow it to be metabolized more quickly, which suits the active lives of moving animals. Cellulose and chitin are examples of structural polysaccharides, cellulose is used in the cell walls of plants and other organisms, and is said to be the most abundant organic molecule on Earth. It has many such as a significant role in the paper and textile industries, and is used as a feedstock for the production of rayon, cellulose acetate, celluloid. Chitin has a structure, but has nitrogen-containing side branches. It is found in arthropod exoskeletons and in the walls of some fungi. It also has multiple uses, including surgical threads, polysaccharides also include callose or laminarin, chrysolaminarin, xylan, arabinoxylan, mannan, fucoidan and galactomannan. Nutrition polysaccharides are common sources of energy, many organisms can easily break down starches into glucose, however, most organisms cannot metabolize cellulose or other polysaccharides like chitin and arabinoxylans. These carbohydrate types can be metabolized by bacteria and protists. Ruminants and termites, for example, use microorganisms to process cellulose, even though these complex carbohydrates are not very digestible, they provide important dietary elements for humans. Called dietary fiber, these carbohydrates enhance digestion among other benefits, the main action of dietary fiber is to change the nature of the contents of the gastrointestinal tract, and to change how other nutrients and chemicals are absorbed
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Serotype
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A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified based on their cell surface antigens. A group of serovars with common antigens is called a serogroup or sometimes serocomplex, serotyping often plays an essential role in determining species and subspecies. Vibrio cholerae, the species of bacteria that causes cholera, has over 200 serotypes, only two of them have been observed to produce the potent enterotoxin that results in cholera,0,1 and 0,139. Serotypes were discovered by the American microbiologist Rebecca Lancefield in 1933, the immune system is capable of discerning a cell as being self or non-self according to that cells serotype. In humans, that serotype is determined by human leukocyte antigen. Cells determined to be non-self are usually recognized by the system as foreign, causing an immune response. For this reason, transplants between genetically non-identical humans often induce an immune response in the recipient, leading to transplant rejection. In some situations this effect can be reduced by serotyping both recipient and potential donors to determine the closest HLA match, the Kauffman–White classification scheme is the basis for naming the manifold serovars of Salmonella. To date, more than 2600 different serotypes have been identified, a Salmonella serotype is determined by the unique combination of reactions of cell surface antigens. The O antigen is determined by the outermost portion of the Lipopolysaccharide, there are two species of Salmonella, Salmonella bongori and Salmonella enterica. Salmonella enterica can be subdivided into six subspecies, the process to identify the serovar of the bacterium consists of finding the formula of cell antigens which represent the variations of the bacteria. First of all, the use of the method on slides is required in order to get the antigen formula. The agglutination between the antigen and the antibody is made with a specific antisera, which reacts with the antigen to produce a mass. The antigen O is tested with a suspension from an agar plate whereas the antigen H is tested with a bacterial suspension from a broth culture. The scheme is used to classify the serovar depending on its antigen formula obtained with the reaction of the agglutination, biovar Morphovar HLA Allele and Haplotype Frequency Database
. PMID 22078162.
