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.
Symbiosis
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Symbiosis is any type of a close and long-term biological interaction between two different species, be it mutualistic, commensalistic, or parasitic. In 1879, Heinrich Anton de Bary defined it as the living together of unlike organisms, Symbiosis can be obligatory, which means that one or both of the symbionts entirely depend on each other for survival, or facultative when they can generally live independently. When one organism lives on another such as mistletoe, it is called ectosymbiosis, or endosymbiosis when one partner lives inside the tissues of another, as in Symbiodinium in corals. In 1877, Albert Bernhard Frank used the term symbiosis which previously had used to depict people living together in community to describe the mutualistic relationship in lichens. In 1879, the German mycologist Heinrich Anton de Bary defined it as the living together of unlike organisms, symbiotic relationships can be obligate, meaning that one or both of the symbionts entirely depend on each other for survival. For example, in lichens, which consist of fungal and photosynthetic symbionts, the algal or cyanobacterial symbionts in lichens, such as Trentepohlia, can generally live independently, and their symbiosis is, therefore, facultative. Endosymbiosis is any relationship in which one symbiont lives within the tissues of the other, either within the cells or extracellularly. Mutualism or interspecies reciprocal altruism is a relationship between individuals of different species where both individuals benefit, in general, only lifelong interactions involving close physical and biochemical contact can properly be considered symbiotic. Mutualistic relationships may be either obligate for both species, obligate for one but facultative for the other, or facultative for both, a large percentage of herbivores have mutualistic gut flora to help them digest plant matter, which is more difficult to digest than animal prey. This gut flora is made up of cellulose-digesting protozoans or bacteria living in the herbivores intestines, coral reefs are the result of mutualisms between coral organisms and various types of algae which live inside them. Most land plants and land ecosystems rely on mutualisms between the plants, which fix carbon from the air, and mycorrhyzal fungi, which help in extracting water, an example of mutual symbiosis is the relationship between the ocellaris clownfish that dwell among the tentacles of Ritteri sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protect the clownfish from its predators, a special mucus on the clownfish protects it from the stinging tentacles. A further example is the fish, which sometimes lives together with a shrimp. The shrimp digs and cleans up a burrow in the sand in which both the shrimp and the fish live. The shrimp is almost blind, leaving it vulnerable to predators when outside its burrow, in case of danger the goby fish touches the shrimp with its tail to warn it. When that happens both the shrimp and goby fish quickly retreat into the burrow, different species of gobies also exhibit mutualistic behavior through cleaning up ectoparasites in other fish. Another non-obligate symbiosis is known from encrusting bryozoans and hermit crabs, the bryozoan colony develops a cirumrotatory growth and offers the crab a helicospiral-tubular extension of its living chamber that initially was situated within a gastropod shell. A spectacular examples of mutualism is between the siboglinid tube worms and symbiotic bacteria that live at hydrothermal vents and cold seeps
4.
Flagellum
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A flagellum is a lash-like appendage that protrudes from the cell body of certain prokaryotic and eukaryotic cells. The word flagellum in Latin means whip, the primary role of the flagellum is locomotion, but it also often has function as a sensory organelle, being sensitive to chemicals and temperatures outside the cell. Flagella are organelles defined by function rather than structure, large differences occur between different types of flagella, the prokaryotic and eukaryotic flagella differ greatly in protein composition, structure, and mechanism of propulsion. However, both can be used for swimming, an example of a flagellated bacterium is the ulcer-causing Helicobacter pylori, which uses multiple flagella to propel itself through the mucus lining to reach the stomach epithelium. An example of a eukaryotic cell is the mammalian sperm cell. Eukaryotic flagella are structurally identical to eukaryotic cilia, although distinctions are made according to function and/or length. Fimbriae and pili are also thin appendages, but have different functions and are usually smaller, three types of flagella have so far been distinguished, bacterial, archaeal, and eukaryotic. The main differences among these three types are, Bacterial flagella are helical filaments, each with a motor at its base which can turn clockwise or counterclockwise. They provide two of several kinds of bacterial motility, archaeal flagella are superficially similar to bacterial flagella, but are different in many details and considered non-homologous. Eukaryotic flagella—those of animal, plant, and protist cells—are complex cellular projections that lash back, eukaryotic flagella are classed along with eukaryotic motile cilia as undulipodia to emphasize their distinctive wavy appendage role in cellular function or motility. Primary cilia are immotile, and are not undulipodia, they have a structurally different 9+0 axoneme rather than the 9+2 axoneme found in both flagella and motile cilia undulipodia, the bacterial flagellum is made up of the protein flagellin. Its shape is a 20-nanometer-thick hollow tube and it is helical and has a sharp bend just outside the outer membrane, this hook allows the axis of the helix to point directly away from the cell. A shaft runs between the hook and the body, passing through protein rings in the cells membrane that act as bearings. Gram-positive organisms have two of these basal body rings, one in the layer and one in the plasma membrane. The filament ends with a capping protein, the flagellar filament is the long, helical screw that propels the bacterium when rotated by the motor, through the hook. Each protofilament is a series of protein chains. However, Campylobacter jejuni has seven protofilaments, the basal body has several traits in common with some types of secretory pores, such as the hollow, rod-like plug in their centers extending out through the plasma membrane. The bacterial flagellum is driven by an engine made up of protein
5.
Parasitism
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In biology/ecology, parasitism is a non-mutual relationship between species, where one species, the parasite, benefits at the expense of the other, the host. Traditionally parasite referred primarily to organisms visible to the naked eye, Parasites can be microparasites, which are typically smaller, such as protozoa, viruses, and bacteria. Examples of parasites include the plants mistletoe and cuscuta, and animals such as hookworms, unlike predators, parasites typically do not kill their host, are generally much smaller than their host, and will often live in or on their host for an extended period. Both are special cases of consumer-resource interactions, Parasites show a high degree of specialization, and reproduce at a faster rate than their hosts. Classic examples of parasitism include interactions between vertebrate hosts and tapeworms, flukes, the Plasmodium species, and fleas, parasitism differs from the parasitoid relationship in that parasitoids generally kill their hosts. Parasites reduce host biological fitness by general or specialized pathology, such as parasitic castration and impairment of secondary sex characteristics, Parasites increase their own fitness by exploiting hosts for resources necessary for their survival, e. g. food, water, heat, habitat, and transmission. Although parasitism applies unambiguously to many cases, it is part of a continuum of types of interactions between species, rather than an exclusive category, in many cases, it is difficult to demonstrate harm to the host. In others, there may be no apparent specialization on the part of the parasite, coined in English in 1611, the word parasitism comes from the Greek παρά + σιτισμός feeding, fattening. Parasites are classified based on their interactions with their hosts and on their life cycles, an obligate parasite is totally dependent on the host to complete its life cycle, while a facultative parasite is not. A direct parasite has one host while an indirect parasite has multiple hosts. For indirect parasites, there always be a definitive host. Parasites that live on the outside of the host, either on the skin or the outgrowths of the skin, are called ectoparasites and those that live inside the host are called endoparasites. Endoparasites can exist in one of two forms, intercellular parasites or intracellular parasites, intracellular parasites, such as protozoa, bacteria or viruses, tend to rely on a third organism, which is generally known as the carrier or vector. The vector does the job of transmitting them to the host, an example of this interaction is the transmission of malaria, caused by a protozoan of the genus Plasmodium, to humans by the bite of an anopheline mosquito. Those parasites living in a position, being half-ectoparasites and half-endoparasites, are called mesoparasites. An epiparasite is one that feeds on another parasite and this relationship is also sometimes referred to as hyperparasitism, exemplified by a protozoan living in the digestive tract of a flea living on a dog. Social parasites take advantage of interactions between members of social organisms such as ants, termites, and bumblebees, an extreme example of social parasitism is the ant species of Tetramorium inquilinum of the Alps, which spend their whole lives on the back of Tetramorium host ants. With tiny and deprecated bodies they have evolved for one single task, if they fall off, they most likely would not have the strength to climb back on top of another ant, and eventually they will die
6.
Model organism
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Model organisms are in vivo models and are widely used to research human disease when human experimentation would be unfeasible or unethical. This strategy is made possible by the descent of all living organisms. Studying model organisms can be informative, but care must be taken when extrapolating from one organism to another, in researching human disease, model organisms allow for better understanding the disease process without the added risk of harming an actual human. The species chosen will usually meet a determined taxonomic equivalency to humans, although biological activity in a model organism does not ensure an effect in humans, many drugs, treatments and cures for human diseases are developed in part with the guidance of animal models. There are three types of disease models, homologous, isomorphic and predictive. Homologous animals have the same causes, symptoms and treatment options as would humans who have the same disease, isomorphic animals share the same symptoms and treatments. Predictive models are similar to a human disease in only a couple of aspects. The use of animals in research dates back to ancient Greece, with Aristotle, research using animal models has been central to most of the achievements of modern medicine. It has contributed most of the knowledge in fields such as human physiology and biochemistry. For example, the results have included the near-eradication of polio and the development of organ transplantation, from 1910 to 1927, Thomas Hunt Morgans work with the fruit fly Drosophila melanogaster identified chromosomes as the vector of inheritance for genes. Drosophila became one of the first, and for some time the most widely used, model organisms, D. melanogaster remains one of the most widely used eukaryotic model organisms. The mouse has since been used extensively as an organism and is associated with many important biological discoveries of the 20th. In the late 19th century, Emil von Behring isolated the diphtheria toxin and he went on to develop an antitoxin against diphtheria in animals and then in humans, which resulted in the modern methods of immunization and largely ended diphtheria as a threatening disease. The diphtheria antitoxin is famously commemorated in the Iditarod race, which is modeled after the delivery of antitoxin in the 1925 serum run to Nome. The success of animal studies in producing the diphtheria antitoxin has also attributed as a cause for the decline of the early 20th-century opposition to animal research in the United States. This led to the 1922 discovery of insulin and its use in treating diabetes, modern general anaesthetics, such as halothane and related compounds, were also developed through studies on model organisms, and are necessary for modern, complex surgical operations. In the 1940s, Jonas Salk used rhesus monkey studies to isolate the most virulent forms of the polio virus, the vaccine, which was made publicly available in 1955, reduced the incidence of polio 15-fold in the United States over the following five years. It has been estimated that developing and producing the vaccines required the use of 100,000 rhesus monkeys, models are those organisms with a wealth of biological data that make them attractive to study as examples for other species and/or natural phenomena that are more difficult to study directly
7.
Biochemistry
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Biochemistry, sometimes called biological chemistry, is the study of chemical processes within and relating to living organisms. By controlling information flow through biochemical signaling and the flow of energy through metabolism. Biochemistry is closely related to biology, the study of the molecular mechanisms by which genetic information encoded in DNA is able to result in the processes of life. Depending on the definition of the terms used, molecular biology can be thought of as a branch of biochemistry, or biochemistry as a tool with which to investigate. The chemistry of the cell depends on the reactions of smaller molecules. These can be inorganic, for water and metal ions, or organic, for example the amino acids. The mechanisms by which cells harness energy from their environment via chemical reactions are known as metabolism, the findings of biochemistry are applied primarily in medicine, nutrition, and agriculture. In medicine, biochemists investigate the causes and cures of diseases, in nutrition, they study how to maintain health and study the effects of nutritional deficiencies. In agriculture, biochemists investigate soil and fertilizers, and try to discover ways to improve crop cultivation, crop storage and pest control. However, biochemistry as a scientific discipline has its beginning sometime in the 19th century, or a little earlier. Gowland Hopkins on enzymes and the nature of biochemistry. The term biochemistry itself is derived from a combination of biology, the German chemist Carl Neuberg however is often cited to have coined the word in 1903, while some credited it to Franz Hofmeister. Then, in 1828, Friedrich Wöhler published a paper on the synthesis of urea and these techniques allowed for the discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as glycolysis and the Krebs cycle. Another significant historic event in biochemistry is the discovery of the gene and this part of biochemistry is often called molecular biology. In the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, in 1958, George Beadle and Edward Tatum received the Nobel Prize for work in fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first person convicted of murder with DNA evidence, mello received the 2006 Nobel Prize for discovering the role of RNA interference, in the silencing of gene expression. Around two dozen of the 92 naturally occurring elements are essential to various kinds of biological life. Most rare elements on Earth are not needed by life, while a few common ones are not used, most organisms share element needs, but there are a few differences between plants and animals
8.
Escherichia coli
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Escherichia coli is a gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes can cause food poisoning in their hosts. The harmless strains are part of the flora of the gut, and can benefit their hosts by producing vitamin K2. E. coli is expelled into the environment within fecal matter, the bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards. E. coli and other facultative anaerobes constitute about 0. 1% of gut flora, cells are able to survive outside the body for a limited amount of time, which makes them potential indicator organisms to test environmental samples for fecal contamination. A growing body of research, though, has examined environmentally persistent E. coli which can survive for extended periods outside of a host, the bacterium can be grown and cultured easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is a chemoheterotroph whose chemically defined medium must include a source of carbon, under favorable conditions, it takes only 20 minutes to reproduce. E. coli is a Gram-negative, facultative anaerobic and nonsporulating bacterium, cells are typically rod-shaped, and are about 2.0 μm long and 0. 25–1.0 μm in diameter, with a cell volume of 0. 6–0.7 μm3. E. coli stains Gram-negative because its cell wall is composed of a peptidoglycan layer. During the staining process, E. coli picks up the color of the counterstain safranin, the outer membrane surrounding the cell wall provides a barrier to certain antibiotics such that E. coli is not damaged by penicillin. Strains that possess flagella are motile, the flagella have a peritrichous arrangement. E. coli can live on a variety of substrates and uses mixed-acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate. Optimum growth of E. coli occurs at 37 °C, and it uses oxygen when it is present and available. It can, however, continue to grow in the absence of oxygen using fermentation or anaerobic respiration, the ability to continue growing in the absence of oxygen is an advantage to bacteria because their survival is increased in environments where water predominates. The bacterial cell cycle is divided into three stages, the B period occurs between the completion of cell division and the beginning of DNA replication. The C period encompasses the time it takes to replicate the chromosomal DNA, the D period refers to the stage between the conclusion of DNA replication and the end of cell division. The doubling rate of E. coli is higher when more nutrients are available, However, the length of the C and D periods do not change, even when the doubling time becomes less than the sum of the C and D periods. At the fastest growth rates, replication begins before the round of replication has completed, resulting in multiple replication forks along the DNA
9.
Fermentation
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Fermentation is a metabolic process that converts sugar to acids, gases, or alcohol. It occurs in yeast and bacteria, and also in oxygen-starved muscle cells, Fermentation is also used more broadly to refer to the bulk growth of microorganisms on a growth medium, often with the goal of producing a specific chemical product. French microbiologist Louis Pasteur is often remembered for his insights into fermentation, the science of fermentation is known as zymology. Fermentation takes place when the transport chain is unusable. In this case it becomes the primary means of ATP production. Fermentation turns NADH and pyruvate produced in glycolysis into NAD+. In the presence of O2, NADH and pyruvate are used to generate ATP in respiration and this is called oxidative phosphorylation, and it generates much more ATP than glycolysis alone. For that reason, cells generally benefit from avoiding fermentation when oxygen is available, the exception being obligate anaerobes which cannot tolerate oxygen. The first step, glycolysis, is common to all fermentation pathways, two ADP molecules and two Pi are converted to two ATP and two water molecules via substrate-level phosphorylation. Two molecules of NAD+ are also reduced to NADH, in oxidative phosphorylation the energy for ATP formation is derived from an electrochemical proton gradient generated across the inner mitochondrial membrane via the electron transport chain. Humans have used fermentation to produce drinks and beverages since the Neolithic age, Fermentation can even occur within the stomachs of animals, such as humans. To many people, fermentation simply means the production of alcohol, grains and fruits are fermented to produce beer, if a food soured, one might say it was off or fermented. Here are some definitions of fermentation and they range from informal, general usage to more scientific definitions. Preservation methods for food via microorganisms, any process that produces alcoholic beverages or acidic dairy products. Any large-scale microbial process occurring with or without air, any energy-releasing metabolic process that takes place only under anaerobic conditions. Fermentation does not necessarily have to be carried out in an anaerobic environment, for example, even in the presence of abundant oxygen, yeast cells greatly prefer fermentation to aerobic respiration, as long as sugars are readily available for consumption. The antibiotic activity of hops also inhibits aerobic metabolism in yeast, Fermentation reacts NADH with an endogenous, organic electron acceptor. Usually this is formed from the sugar during the glycolysis step. Sugars are the most common substrate of fermentation, and typical examples of products are ethanol, lactic acid, carbon dioxide
10.
Yersinia pestis
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Yersinia pestis is a Gram-negative, rod-shaped coccobacillus, a facultative anaerobic organism that can infect humans via the oriental rat flea. It causes the disease called bubonic plague. Human Y. pestis infection takes three forms, pneumonic, septicemic, and bubonic plagues. These plagues probably originated in China and were transmitted west via trade routes, Y. pestis was discovered in 1894 by Alexandre Yersin, a Swiss/French physician and bacteriologist from the Pasteur Institute, during an epidemic of the plague in Hong Kong. Yersin was a member of the Pasteur school of thought, kitasato Shibasaburō, a German-trained Japanese bacteriologist who practised Kochs methodology, was also engaged at the time in finding the causative agent of the plague. However, Yersin actually linked plague with Y. pestis, named Pasteurella pestis in the past, the organism was renamed Yersinia pestis in 1944. Every year, thousands of cases of the plague are still reported to the World Health Organization, although, with proper treatment, the prognosis for victims is now much better. A five- to six-fold increase in cases occurred in Asia during the time of the Vietnam War, possibly due to the disruption of ecosystems, the plague also has a detrimental effect on non-human mammals. In the United States, mammals such as the prairie dog. Y. pestis is a non-motile, stick-shaped, facultative anaerobic bacterium with bipolar staining that produces an anti-phagocytic slime layer, similar to other Yersinia species, it tests negative for urease, lactose fermentation, and indole. The closest relative is the gastrointestinal pathogen Yersinia pseudotuberculosis, and more distantly Yersinia enterocolitica, the complete genomic sequence is available for two of the three subspecies of Y. pestis, strain KIM, and strain CO92. As of 2006, the sequence of a strain of biovar Antiqua has been recently completed. Similar to the pathogenic strains, there are signs of loss of function mutations. The chromosome of strain KIM is 4,600,755 base pairs long, like Y. pseudotuberculosis and Y. enterocolitica, Y. pestis is host to the plasmid pCD1. In addition, it hosts two other plasmids, pPCP1 and pMT1 that are not carried by the other Yersinia species. PFra codes for a phospholipase D that is important for the ability of Y. pestis to be transmitted by fleas, pPla codes for a protease, Pla, that activates plasmin in human hosts and is a very important virulence factor for pneumonic plague. Together, these plasmids, and a pathogenicity island called HPI, encode proteins that cause the pathogenesis. Y. pestis is thought to be descendant from Y. pseudotuberculosis, a comprehensive and comparative proteomics analysis of Y. pestis strain KIM was performed in 2006
