1.
Science
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Science is a systematic enterprise that builds and organizes knowledge in the form of testable explanations and predictions about the universe. The formal sciences are often excluded as they do not depend on empirical observations, disciplines which use science, like engineering and medicine, may also be considered to be applied sciences. However, during the Islamic Golden Age foundations for the method were laid by Ibn al-Haytham in his Book of Optics. In the 17th and 18th centuries, scientists increasingly sought to formulate knowledge in terms of physical laws, over the course of the 19th century, the word science became increasingly associated with the scientific method itself as a disciplined way to study the natural world. It was during this time that scientific disciplines such as biology, chemistry, Science in a broad sense existed before the modern era and in many historical civilizations. Modern science is distinct in its approach and successful in its results, Science in its original sense was a word for a type of knowledge rather than a specialized word for the pursuit of such knowledge. In particular, it was the type of knowledge which people can communicate to each other, for example, knowledge about the working of natural things was gathered long before recorded history and led to the development of complex abstract thought. This is shown by the construction of calendars, techniques for making poisonous plants edible. For this reason, it is claimed these men were the first philosophers in the strict sense and they were mainly speculators or theorists, particularly interested in astronomy. In contrast, trying to use knowledge of nature to imitate nature was seen by scientists as a more appropriate interest for lower class artisans. A clear-cut distinction between formal and empirical science was made by the pre-Socratic philosopher Parmenides, although his work Peri Physeos is a poem, it may be viewed as an epistemological essay on method in natural science. Parmenides ἐὸν may refer to a system or calculus which can describe nature more precisely than natural languages. Physis may be identical to ἐὸν and he criticized the older type of study of physics as too purely speculative and lacking in self-criticism. He was particularly concerned that some of the early physicists treated nature as if it could be assumed that it had no intelligent order, explaining things merely in terms of motion and matter. The study of things had been the realm of mythology and tradition, however. Aristotle later created a less controversial systematic programme of Socratic philosophy which was teleological and he rejected many of the conclusions of earlier scientists. For example, in his physics, the sun goes around the earth, each thing has a formal cause and final cause and a role in the rational cosmic order. Motion and change is described as the actualization of potentials already in things, while the Socratics insisted that philosophy should be used to consider the practical question of the best way to live for a human being, they did not argue for any other types of applied science
2.
Genome
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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
3.
Organism
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In biology, an organism is any contiguous living system, such as an animal, plant, fungus, protist, archaeon, or bacterium. All known types of organisms are capable of some degree of response to stimuli, reproduction, growth and development and homeostasis. An organism consists of one or more cells, when it has one cell it is known as an organism. Most unicellular organisms are of microscopic scale and are thus described as microorganisms. Humans are multicellular organisms composed of trillions of cells grouped into specialized tissues. An organism may be either a prokaryote or a eukaryote, prokaryotes are represented by two separate domains—bacteria and archaea. Eukaryotic organisms are characterized by the presence of a cell nucleus. Fungi, animals and plants are examples of kingdoms of organisms within the eukaryotes, estimates on the number of Earths current species range from 10 million to 14 million, of which only about 1.2 million have been documented. More than 99% of all species, amounting to five billion species. In 2016, a set of 355 genes from the last universal ancestor of all living organisms living was identified. The term organism first appeared in the English language in 1703 and it is directly related to the term organization. There is a tradition of defining organisms as self-organizing beings. An organism may be defined as an assembly of molecules functioning as a more or less stable whole that exhibits the properties of life. Dictionary definitions can be broad, using such as any living structure, such as a plant, animal, fungus or bacterium, capable of growth. Many definitions exclude viruses and possible man-made non-organic life forms, as viruses are dependent on the machinery of a host cell for reproduction. A superorganism is an organism consisting of individuals working together as a single functional or social unit. There has been controversy about the best way to define the organism, several contributions are responses to the suggestion that the category of organism may well not be adequate in biology. Viruses are not typically considered to be organisms because they are incapable of autonomous reproduction and this controversy is problematic because some cellular organisms are also incapable of independent survival and live as obligatory intracellular parasites
4.
Animal
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Animals are multicellular, eukaryotic organisms of the kingdom Animalia. The animal kingdom emerged as a clade within Apoikozoa as the group to the choanoflagellates. Animals are motile, meaning they can move spontaneously and independently at some point in their lives and their body plan eventually becomes fixed as they develop, although some undergo a process of metamorphosis later in their lives. All animals are heterotrophs, they must ingest other organisms or their products for sustenance, most known animal phyla appeared in the fossil record as marine species during the Cambrian explosion, about 542 million years ago. Animals can be divided broadly into vertebrates and invertebrates, vertebrates have a backbone or spine, and amount to less than five percent of all described animal species. They include fish, amphibians, reptiles, birds and mammals, the remaining animals are the invertebrates, which lack a backbone. These include molluscs, arthropods, annelids, nematodes, flatworms, cnidarians, ctenophores, the study of animals is called zoology. The word animal comes from the Latin animalis, meaning having breath, the biological definition of the word refers to all members of the kingdom Animalia, encompassing creatures as diverse as sponges, jellyfish, insects, and humans. Aristotle divided the world between animals and plants, and this was followed by Carl Linnaeus, in the first hierarchical classification. In Linnaeuss original scheme, the animals were one of three kingdoms, divided into the classes of Vermes, Insecta, Pisces, Amphibia, Aves, and Mammalia. Since then the last four have all been subsumed into a single phylum, in 1874, Ernst Haeckel divided the animal kingdom into two subkingdoms, Metazoa and Protozoa. The protozoa were later moved to the kingdom Protista, leaving only the metazoa, thus Metazoa is now considered a synonym of Animalia. Animals have several characteristics that set apart from other living things. Animals are eukaryotic and multicellular, which separates them from bacteria and they are heterotrophic, generally digesting food in an internal chamber, which separates them from plants and algae. They are also distinguished from plants, algae, and fungi by lacking cell walls. All animals are motile, if only at life stages. In most animals, embryos pass through a stage, which is a characteristic exclusive to animals. With a few exceptions, most notably the sponges and Placozoa and these include muscles, which are able to contract and control locomotion, and nerve tissues, which send and process signals
5.
Plant
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Plants are mainly multicellular, predominantly photosynthetic eukaryotes of the kingdom Plantae. The term is generally limited to the green plants, which form an unranked clade Viridiplantae. This includes the plants, conifers and other gymnosperms, ferns, clubmosses, hornworts, liverworts, mosses and the green algae. Green plants have cell walls containing cellulose and obtain most of their energy from sunlight via photosynthesis by primary chloroplasts and their chloroplasts contain chlorophylls a and b, which gives them their green color. Some plants are parasitic and have lost the ability to produce amounts of chlorophyll or to photosynthesize. Plants are characterized by sexual reproduction and alternation of generations, although reproduction is also common. There are about 300–315 thousand species of plants, of which the great majority, green plants provide most of the worlds molecular oxygen and are the basis of most of Earths ecologies, especially on land. Plants that produce grains, fruits and vegetables form humankinds basic foodstuffs, Plants play many roles in culture. They are used as ornaments and, until recently and in variety, they have served as the source of most medicines. The scientific study of plants is known as botany, a branch of biology, Plants are one of the two groups into which all living things were traditionally divided, the other is animals. The division goes back at least as far as Aristotle, who distinguished between plants, which generally do not move, and animals, which often are mobile to catch their food. Much later, when Linnaeus created the basis of the system of scientific classification. Since then, it has become clear that the plant kingdom as originally defined included several unrelated groups, however, these organisms are still often considered plants, particularly in popular contexts. When the name Plantae or plant is applied to a group of organisms or taxon. The evolutionary history of plants is not yet settled. Those which have been called plants are in bold, the way in which the groups of green algae are combined and named varies considerably between authors. Algae comprise several different groups of organisms which produce energy through photosynthesis, most conspicuous among the algae are the seaweeds, multicellular algae that may roughly resemble land plants, but are classified among the brown, red and green algae. Each of these groups also includes various microscopic and single-celled organisms
6.
Fungus
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A fungus is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as a kingdom, Fungi, which is separate from the other eukaryotic life kingdoms of plants, a characteristic that places fungi in a different kingdom from plants, bacteria and some protists, is chitin in their cell walls. Similar to animals, fungi are heterotrophs, they acquire their food by absorbing dissolved molecules, growth is their means of mobility, except for spores, which may travel through the air or water. Fungi are the principal decomposers in ecological systems and this fungal group is distinct from the structurally similar myxomycetes and oomycetes. The discipline of biology devoted to the study of fungi is known as mycology, in the past, mycology was regarded as a branch of botany, although it is now known fungi are genetically more closely related to animals than to plants. Abundant worldwide, most fungi are inconspicuous because of the size of their structures. Fungi include symbionts of plants, animals, or other fungi and they may become noticeable when fruiting, either as mushrooms or as molds. Fungi perform a role in the decomposition of organic matter and have fundamental roles in nutrient cycling. Since the 1940s, fungi have been used for the production of antibiotics, Fungi are also used as biological pesticides to control weeds, plant diseases and insect pests. Many species produce bioactive compounds called mycotoxins, such as alkaloids and polyketides, the fruiting structures of a few species contain psychotropic compounds and are consumed recreationally or in traditional spiritual ceremonies. Fungi can break down manufactured materials and buildings, and become significant pathogens of humans, losses of crops due to fungal diseases or food spoilage can have a large impact on human food supplies and local economies. The fungus kingdom encompasses a diversity of taxa with varied ecologies, life cycle strategies. However, little is known of the biodiversity of Kingdom Fungi. Advances in molecular genetics have opened the way for DNA analysis to be incorporated into taxonomy, phylogenetic studies published in the last decade have helped reshape the classification within Kingdom Fungi, which is divided into one subkingdom, seven phyla, and ten subphyla. The English word fungus is directly adopted from the Latin fungus, used in the writings of Horace, a group of all the fungi present in a particular area or geographic region is known as mycobiota, e. g. the mycobiota of Ireland. Like plants, fungi grow in soil and, in the case of mushrooms, form conspicuous fruit bodies. The fungi are now considered a kingdom, distinct from both plants and animals, from which they appear to have diverged around one billion years ago. Fungi have membrane-bound cytoplasmic organelles such as mitochondria, sterol-containing membranes and they have a characteristic range of soluble carbohydrates and storage compounds, including sugar alcohols, disaccharides, and polysaccharides
7.
Bacterium
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
8.
Archaea
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The Archaea constitute a domain and kingdom of single-celled microorganisms. These microbes are prokaryotes, meaning that they have no cell nucleus or any other membrane-bound organelles in their cells, Archaea were initially classified as bacteria, receiving the name archaebacteria, but this classification is outdated. Archaeal cells have unique properties separating them from the two domains of life, Bacteria and Eukaryota. The Archaea are further divided into multiple recognized phyla, classification is difficult because the majority have not been isolated in the laboratory and have only been detected by analysis of their nucleic acids in samples from their environment. Archaea and bacteria are generally similar in size and shape, although a few archaea have very strange shapes, such as the flat, other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more energy sources than eukaryotes, these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea use sunlight as a source, and other species of archaea fix carbon, however, unlike plants and cyanobacteria. Archaea reproduce asexually by fission, fragmentation, or budding, unlike bacteria and eukaryotes. They are also found in the colon, oral cavity. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet, Archaea are a major part of Earths life and may play roles in both the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, one example is the methanogens that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in production and sewage treatment, and enzymes from extremophile archaea that can endure high temperatures. For much of the 20th century, prokaryotes were regarded as a group of organisms and classified based on their biochemistry, morphology. For example, microbiologists tried to classify based on the structures of their cell walls, their shapes. In 1965, Emile Zuckerkandl and Linus Pauling proposed instead using the sequences of the genes in different prokaryotes to work out how they are related to each other and this approach, known as phylogenetics, is the main method used today. Archaea were first classified as a group of prokaryotes in 1977 by Carl Woese. These two groups were named the Archaebacteria and Eubacteria and treated as kingdoms or subkingdoms, which Woese. Woese argued that group of prokaryotes is a fundamentally different sort of life
9.
Protist
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Protist is an informal term for any eukaryotic organism that is not an animal, plant or fungus. The protists do not form a group, or clade. Besides their relatively simple levels of organization, protists do not necessarily have much in common, others use the term protist more broadly, to encompass both microbial eukaryotes and macroscopic organisms that do not fit into the other traditional kingdoms. In cladistic systems, there are no equivalents to the taxa Protista or Protoctista, in cladistic classification, the contents of Protista are distributed among various supergroups and Protista, Protoctista and Protozoa are considered obsolete. However, the term protist continues to be used informally as a term for eukaryotic microorganisms. For example, the phrase protist pathogen may be used to denote any disease-causing microbe which is not bacteria, virus, the term protista was first used by Ernst Haeckel in 1866. Some protists, sometimes called ambiregnal protists, have considered to be both protozoa and algae or fungi, and names for these have been published under either or both of the ICN and the ICZN. Conflicts, such as these – for example the dual-classification of Euglenids and Dinobryons and these traditional subdivisions, largely based on superficial commonalities, have been replaced by classifications based on phylogenetics. Molecular analyses in modern taxonomy have been used to redistribute former members of this group into diverse, however, the older terms are still used as informal names to describe the morphology and ecology of various protists. For example, the term protozoa is used to refer to species of protists that do not form filaments. Among the pioneers in the study of the protists, which were almost ignored by Linnaeus except for some genera were Leeuwenhoek, O. F. Müller, C. G. Ehrenberg, the first groups used to classify microscopic organism were the Animalcules and the Infusoria. In 1817, the German naturalist Georg August Goldfuss introduced the word Protozoa to refer to such as ciliates. After the cell theory of Schwann and Schleiden, this group was modified in 1848 by Carl von Siebold to include only animal-like unicellular organisms, such as foraminifera and amoebae. He defined the Protoctista as a kingdom of nature, in addition to the then-traditional kingdoms of plants. The kingdom of minerals was later removed from taxonomy in 1866 by Ernst Haeckel, leaving plants, animals, in 1938, Herbert Copeland resurrected Hoggs label, arguing that Haeckels term Protista included anucleated microbes such as bacteria, which the term Protoctista did not. In contrast, Copelands term included nucleated eukaryotes such as diatoms, green algae and this classification was the basis for Whittakers later definition of Fungi, Animalia, Plantae and Protista as the four kingdoms of life. The kingdom Protista was later modified to separate prokaryotes into the kingdom of Monera. Many systematists today do not treat Protista as a formal taxon, some systematists judge paraphyletic taxa acceptable, and use Protista in this sense as a formal taxon
10.
Gene
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A gene is a locus of DNA which is made up of nucleotides and is the molecular unit of heredity. The transmission of genes to an offspring is the basis of the inheritance of phenotypic traits. These genes make up different DNA sequences called genotypes, genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions, genes can acquire mutations in their sequence, leading to different variants, known as alleles, in the population. These alleles encode slightly different versions of a protein, which cause different phenotypical traits, usage of the term having a gene typically refers to containing a different allele of the same, shared gene. Genes evolve due to natural selection or survival of the fittest of the alleles, the concept of a gene continues to be refined as new phenomena are discovered. For example, regulatory regions of a gene can be far removed from its coding regions, some viruses store their genome in RNA instead of DNA and some gene products are functional non-coding RNAs. The existence of discrete inheritable units was first suggested by Gregor Mendel, from 1857 to 1864, in Brno, he studied inheritance patterns in 8000 common edible pea plants, tracking distinct traits from parent to offspring. He described these mathematically as 2n combinations where n is the number of differing characteristics in the original peas, although he did not use the term gene, he explained his results in terms of discrete inherited units that give rise to observable physical characteristics. This description prefigured the distinction between genotype and phenotype, charles Darwin developed a theory of inheritance he termed pangenesis, from Greek pan and genesis / genos. Darwin used the term gemmule to describe hypothetical particles that would mix during reproduction, de Vries called these units pangenes, after Darwins 1868 pangenesis theory. In 1909 the Danish botanist Wilhelm Johannsen shortened the name to gene, advances in understanding genes and inheritance continued throughout the 20th century. Deoxyribonucleic acid was shown to be the repository of genetic information by experiments in the 1940s to 1950s. In the early 1950s the prevailing view was that the genes in a chromosome acted like discrete entities, indivisible by recombination, collectively, this body of research established the central dogma of molecular biology, which states that proteins are translated from RNA, which is transcribed from DNA. This dogma has since shown to have exceptions, such as reverse transcription in retroviruses. The modern study of genetics at the level of DNA is known as molecular genetics, in 1972, Walter Fiers and his team at the University of Ghent were the first to determine the sequence of a gene, the gene for Bacteriophage MS2 coat protein. The subsequent development of chain-termination DNA sequencing in 1977 by Frederick Sanger improved the efficiency of sequencing, an automated version of the Sanger method was used in early phases of the Human Genome Project. The theories developed in the 1930s and 1940s to integrate molecular genetics with Darwinian evolution are called the evolutionary synthesis
11.
DNA
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Deoxyribonucleic acid is a molecule that carries the genetic instructions used in the growth, development, functioning and reproduction of all known living organisms and many viruses. DNA and RNA are nucleic acids, alongside proteins, lipids and complex carbohydrates, most DNA molecules consist of two biopolymer strands coiled around each other to form a double helix. The two DNA strands are termed polynucleotides since they are composed of simpler units called nucleotides. Each nucleotide is composed of one of four nitrogen-containing nucleobases—cytosine, guanine, adenine, or thymine —a sugar called deoxyribose, and a phosphate group. The nucleotides are joined to one another in a chain by covalent bonds between the sugar of one nucleotide and the phosphate of the next, resulting in an alternating sugar-phosphate backbone. The nitrogenous bases of the two polynucleotide strands are bound together, according to base pairing rules, with hydrogen bonds to make double-stranded DNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison the total mass of the biosphere has been estimated to be as much as 4 trillion tons of carbon. The DNA backbone is resistant to cleavage, and both strands of the double-stranded structure store the same biological information and this information is replicated as and when the two strands separate. A large part of DNA is non-coding, meaning that these sections do not serve as patterns for protein sequences, the two strands of DNA run in opposite directions to each other and are thus antiparallel. Attached to each sugar is one of four types of nucleobases and it is the sequence of these four nucleobases along the backbone that encodes biological information. RNA strands are created using DNA strands as a template in a process called transcription, under the genetic code, these RNA strands are translated to specify the sequence of amino acids within proteins in a process called translation. Within eukaryotic cells DNA is organized into structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, eukaryotic organisms store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast prokaryotes store their DNA only in the cytoplasm, within the eukaryotic chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed, DNA was first isolated by Friedrich Miescher in 1869. DNA is used by researchers as a tool to explore physical laws and theories, such as the ergodic theorem. The unique material properties of DNA have made it an attractive molecule for material scientists and engineers interested in micro-, among notable advances in this field are DNA origami and DNA-based hybrid materials. DNA is a polymer made from repeating units called nucleotides
12.
Chromosome
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A chromosome is a DNA molecule with part or all of the genetic material of an organism. Prokaryotes usually have one single circular chromosome, whereas most eukaryotes are diploid, chromosomes in eukaryotes are composed of chromatin fiber. Chromatin fiber is made of nucleosomes, a nucleosome is a histone octamer with part of a longer DNA strand attached to and wrapped around it. Chromatin fiber, together with associated proteins is known as chromatin, chromatin is present in most cells, with a few exceptions, for example, red blood cells. Occurring only in the nucleus of cells, chromatin contains the vast majority of DNA, except for a small amount inherited maternally. Chromosomes are normally visible under a microscope only when the cell is undergoing the metaphase of cell division. Before this happens every chromosome is copied once, and the copy is joined to the original by a centromere resulting in an X-shaped structure, the original chromosome and the copy are now called sister chromatids. During metaphase, when a chromosome is in its most condensed state, in this highly condensed form chromosomes are easiest to distinguish and study. In prokaryotic cells, chromatin occurs free-floating in cytoplasm, as these cells lack organelles, the main information-carrying macromolecule is a single piece of coiled double-helix DNA, containing many genes, regulatory elements and other noncoding DNA. The DNA-bound macromolecules are proteins that serve to package the DNA, chromosomes vary widely between different organisms. Some species such as certain bacteria also contain plasmids or other extrachromosomal DNA and these are circular structures in the cytoplasm that contain cellular DNA and play a role in horizontal gene transfer. Chromosomal recombination during meiosis and subsequent sexual reproduction plays a significant role in genetic diversity. In prokaryotes and viruses, the DNA is often densely packed and organized, in the case of archaea, by homologs to eukaryotic histones, small circular genomes called plasmids are often found in bacteria and also in mitochondria and chloroplasts, reflecting their bacterial origins. Some use the term chromosome in a sense, to refer to the individualized portions of chromatin in cells. However, others use the concept in a sense, to refer to the individualized portions of chromatin during cell division. The word chromosome comes from the Greek χρῶμα and σῶμα, describing their strong staining by particular dyes, schleiden, Virchow and Bütschli were among the first scientists who recognized the structures now so familiar to everyone as chromosomes. The term was coined by von Waldeyer-Hartz, referring to the term chromatin, in a series of experiments beginning in the mid-1880s, Theodor Boveri gave the definitive demonstration that chromosomes are the vectors of heredity. His two principles were the continuity of chromosomes and the individuality of chromosomes and it is the second of these principles that was so original
13.
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
14.
Autosome
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An autosome is a chromosome that is not an allosome. Autosomes appear in pairs whose members have the form but differ from other pairs in a diploid cell, whereas members of an allosome pair may differ from one another. The DNA in autosomes is collectively known as atDNA or auDNA, for example, humans have a diploid genome that usually contains 22 pairs of autosomes and one allosome pair. The autosome pairs are labeled with numbers roughly in order of their sizes in base pairs, by contrast, the allosome pair consists of two X chromosomes in females or one X and one Y chromosome in males. Autosomes still contain sexual determination genes even though they are not sex chromosomes, for example, the SRY gene on the Y chromosome encodes the transcription factor TDF and is vital for male sex determination during development. TDF functions by activating the SOX9 gene on chromosome 17, so mutations of the SOX9 gene can cause humans with a Y chromosome to develop as females. All human autosomes have been identified and mapped by extracting the chromosomes from a cell arrested in metaphase or prometaphase and these chromosomes are typically viewed as karyograms for easy comparison. Clinical geneticists can compare the karyogram of an individual to a reference karyogram to discover the basis of certain phenotypes. For example, the karyogram of someone with Patau Syndrome would show that they possess three copies of chromosome 13, karyograms and staining techniques can only detect large-scale disruptions to chromosomes—chromosomal aberrations smaller than a few million base pairs generally cannot be seen on a karyogram. Autosomal genetic disorders can arise due to a number of causes, Autosomal genetic disorders which exhibit Mendelian inheritance can be inherited either in an autosomal dominant or recessive fashion. These disorders manifest in and are passed on by sex with equal frequency. Autosomal dominant disorders are present in both parent and child, as the child needs to inherit only one copy of the deleterious allele to manifest the disease. Autosomal recessive diseases, however, require two copies of the allele for the disease to manifest. Autosomal aneuploidy can also result in disease conditions, aneuploidy of autosomes is not well tolerated and usually results in miscarriage of the developing fetus. Possessing a single copy of an autosome is nearly always incompatible with life, having three copies of an autosome is far more compatible with life, however. A common example is Down syndrome, which is caused by possessing three copies of chromosome 21 instead of the usual two, partial aneuploidy can also occur as a result of unbalanced translocations during meiosis. Deletions of part of a chromosome cause partial monosomies, while duplications can cause partial trisomies, if the duplication or deletion is large enough, it can be discovered by analyzing a karyogram of the individual. Autosomal translocations can be responsible for a number of diseases, ranging from cancer to schizophrenia, unlike single gene disorders, diseases caused by aneuploidy are the result of improper gene dosage, not nonfunctional gene product
15.
Human Genome Project
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It remains the worlds largest collaborative biological project. After the idea was picked up in 1984 by the US government when the planning started, funding came from the US government through the National Institutes of Health as well as numerous other groups from around the world. A parallel project was conducted outside of government by the Celera Corporation, or Celera Genomics, most of the government-sponsored sequencing was performed in twenty universities and research centers in the United States, the United Kingdom, Japan, France, Germany, Canada, and China. The Human Genome Project originally aimed to map the nucleotides contained in a human haploid reference genome, the finished human genome is thus a mosaic, not representing any one individual. The Human Genome Project was a 13-year-long, publicly funded project initiated in 1990 with the objective of determining the DNA sequence of the euchromatic human genome within 15 years. In May 1985, Robert Sinsheimer organized a workshop to discuss sequencing the human genome, the following March, the Santa Fe Workshop was organized by Charles DeLisi and David Smith of the Department of Energys Office of Health and Environmental Research. At the same time Renato Dulbecco proposed whole genome sequencing in an essay in Science, James Watson followed two months later with a workshop held at the Cold Spring Harbor Laboratory. The fact that the Santa Fe workshop was motivated and supported by a Federal Agency opened a path, albeit a difficult and tortuous one, for converting the idea into public policy. In a memo to the Assistant Secretary for Energy Research, Charles DeLisi, of particular importance in Congressional approval was the advocacy of Senator Peter Domenici, whom DeLisi had befriended. Domenici chaired the Senate Committee on Energy and Natural Resources, as well as the Budget Committee, Congress added a comparable amount to the NIH budget, thereby beginning official funding by both agencies. Alvin Trivelpiece sought and obtained the approval of DeLisis proposal by Deputy Secretary William Flynn Martin and this reprogramming was followed by a line item budget of $16 million in the Reagan Administration’s 1987 budget submission to Congress. The Project was planned for 15 years, candidate technologies were already being considered for the proposed undertaking at least as early as 1985. In 1990, the two major funding agencies, DOE and NIH, developed a memorandum of understanding in order to coordinate plans, a working draft of the genome was announced in 2000 and the papers describing it were published in February 2001. A more complete draft was published in 2003, and genome finishing work continued for more than a decade, the $3-billion project was formally founded in 1990 by the US Department of Energy and the National Institutes of Health, and was expected to take 15 years. In addition to the United States, the consortium comprised geneticists in the United Kingdom, France, Australia, China. Due to widespread international cooperation and advances in the field of genomics, as well as advances in computing technology. This first available rough draft assembly of the genome was completed by the Genome Bioinformatics Group at the University of California, Santa Cruz, ongoing sequencing led to the announcement of the essentially complete genome on April 14,2003, two years earlier than planned. In May 2006, another milestone was passed on the way to completion of the project, the project was not able to sequence all the DNA found in human cells
16.
Sequence assembly
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In bioinformatics, sequence assembly refers to aligning and merging fragments from a longer DNA sequence in order to reconstruct the original sequence. This is needed as DNA sequencing technology cannot read whole genomes in one go, typically the short fragments, called reads, result from shotgun sequencing genomic DNA, or gene transcript. Besides the obvious difficulty of this task, there are some practical issues, the original may have many repeated paragraphs. Excerpts from another book may also be added in, and some shreds may be completely unrecognizable, expressed Sequence Tag or EST assembly differs from genome assembly in several ways. The sequences for EST assembly are the transcribed mRNA of a cell, at a first glance, underlying algorithmical problems differ between genome and EST assembly. For instance, genomes often have large amounts of repetitive sequences, since ESTs represent gene transcripts, they will not contain these repeats. Furthermore, genes sometimes overlap in the genome, and should still be assembled separately. EST assembly is also complicated by features like alternative splicing, trans-splicing, single-nucleotide polymorphism and this is mostly due to the fact that the assembly algorithm needs to compare every read with every other read. Also, every shred would be compared with every other shred, the complexity of sequence assembly is driven by two major factors, the number of fragments and their lengths. And while shorter sequences are faster to align, they complicate the layout phase of an assembly as shorter reads are more difficult to use with repeats or near identical repeats. In the earliest days of DNA sequencing, scientists could only gain a few sequences of short length after weeks of work in laboratories. Hence, these sequences could be aligned in a few minutes by hand.5 and 10% With the Sanger technology, larger projects, like the human genome with approximately 35 million reads, needed large computing farms and distributed computing. By 2004 /2005, pyrosequencing had been brought to commercial viability by 454 Life Sciences and this new sequencing method generated reads much shorter than those of Sanger sequencing, initially about 100 bases, now 400-500 bases. The sheer amount of data coupled with technology-specific error patterns in the delayed development of assemblers. Assembling sequences from different sequencing technologies was subsequently coined hybrid assembly, from 2006, the Illumina technology has been available and can generate about 100 million reads per run on a single sequencing machine. Compare this to the 35 million reads of the human genome project which needed several years to be produced on hundreds of sequencing machines. Announced at the end of 2007, the SHARCGS assembler by Dohm et al. was the first published assembler that was used for an assembly with Solexa reads and it was quickly followed by a number of others. Later, new technologies like SOLiD from Applied Biosystems, Ion Torrent and SMRT were released, given a set of sequence fragments the object is to find the shortest common supersequence
17.
Nucleic acid sequence
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A nucleic acid sequence is a succession of letters that indicate the order of nucleotides within a DNA or RNA molecule. By convention, sequences are presented from the 5 end to the 3 end. For DNA, the strand is used. Because nucleic acids are linear polymers, specifying the sequence is equivalent to defining the covalent structure of the entire molecule. For this reason, the nucleic acid sequence is also termed the primary structure, the sequence has capacity to represent information. Biological deoxyribonucleic acid represents the information which directs the functions of a living thing, nucleic acids also have a secondary structure and tertiary structure. Primary structure is sometimes referred to as primary sequence. Conversely, there is no concept of secondary or tertiary sequence. Nucleic acids consist of a chain of linked units called nucleotides, each nucleotide consists of three subunits, a phosphate group and a sugar make up the backbone of the nucleic acid strand, and attached to the sugar is one of a set of nucleobases. The nucleobases are important in base pairing of strands to form secondary and tertiary structure such as the famed double helix. The possible letters are A, C, G, and T, in the typical case, the sequences are printed abutting one another without gaps, as in the sequence AAAGTCTGAC, read left to right in the 5 to 3 direction. With regards to transcription, a sequence is on the strand if it has the same order as the transcribed RNA. One sequence can be complementary to sequence, meaning that they have the base on each position in the complementary. For example, the sequence to TTAC is GTAA. If one strand of the double-stranded DNA is considered the sense strand, then the other strand, considered the antisense strand, will have the complementary sequence to the sense strand. Apart from adenine, cytosine, guanine, thymine and uracil, in DNA, the most common modified base is 5-methylcytidine. In RNA, there are many modified bases, including pseudouridine, dihydrouridine, inosine, ribothymidine and 7-methylguanosine, hypoxanthine and xanthine are two of the many bases created through mutagen presence, both of them through deamination. Hypoxanthine is produced from adenine, xanthine from guanine, similarly, deamination of cytosine results in uracil
18.
Shotgun sequencing
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In genetics, shotgun sequencing is a method used for sequencing long DNA strands. It is named by analogy with the rapidly expanding, quasi-random firing pattern of a shotgun, the chain termination method of DNA sequencing can only be used for fairly short strands of 100 to 1000 base pairs. Longer sequences are subdivided into smaller fragments that can be sequenced separately, in shotgun sequencing, DNA is broken up randomly into numerous small segments, which are sequenced using the chain termination method to obtain reads. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation, computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence. Shotgun sequencing was one of the technologies that was responsible for enabling full genome sequencing. In reality, this process uses enormous amounts of information that are rife with ambiguities, assembly of complex genomes is additionally complicated by the great abundance of repetitive sequences, meaning similar short reads could come from completely different parts of the sequence. Many overlapping reads for each segment of the original DNA are necessary to overcome these difficulties, even so, current methods have failed to isolate or assemble reliable sequence for approximately 1% of the human genome, as of 2004. The first genome sequenced by shotgun sequencing was that of cauliflower mosaic virus, however, whole genome shotgun sequencing for small genomes had been suggested already in 1979. Broader application benefited from pairwise end sequencing, known colloquially as double-barrel shotgun sequencing, the first theoretical description of a pure pairwise end sequencing strategy, assuming fragments of constant length, was in 1991. At the time, there was community consensus that the optimal fragment length for pairwise end sequencing would be three times the sequence read length. In 1995 Roach et al. introduced the innovation of using fragments of varying sizes, to apply the strategy, a high-molecular-weight DNA strand is sheared into random fragments, size-selected, and cloned into an appropriate vector. The clones are sequenced from both ends using the chain termination method yielding two short sequences. Each sequence is called an end-read or read and two reads from the clone are referred to as mate pairs. Since the chain termination method usually can only produce reads between 500 and 1000 bases long, in all but the smallest clones, mate pairs will rarely overlap, the original sequence is reconstructed from the reads using sequence assembly software. First, overlapping reads are collected into longer composite sequences known as contigs, contigs can be linked together into scaffolds by following connections between mate pairs. The distance between contigs can be inferred from the mate pair positions if the average fragment length of the library is known and has a window of deviation. Depending on the size of the gap between contigs, different techniques can be used to find the sequence in the gaps, if the gap is small then the use of PCR to amplify the region is required, followed by sequencing. If the gap is then the large fragment is cloned in special vectors such as BAC followed by sequencing of the vector
19.
Mammal
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Mammals are any vertebrates within the class Mammalia, a clade of endothermic amniotes distinguished from reptiles by the possession of a neocortex, hair, three middle ear bones and mammary glands. All female mammals nurse their young with milk, secreted from the mammary glands, Mammals include the largest animals on the planet, the great whales. The basic body type is a quadruped, but some mammals are adapted for life at sea, in the air, in trees. The largest group of mammals, the placentals, have a placenta, Mammals range in size from the 30–40 mm bumblebee bat to the 30-meter blue whale. With the exception of the five species of monotreme, all modern mammals give birth to live young, most mammals, including the six most species-rich orders, belong to the placental group. The largest orders are the rodents, bats and Soricomorpha, the next three biggest orders, depending on the biological classification scheme used, are the Primates, the Cetartiodactyla, and the Carnivora. Living mammals are divided into the Yinotheria and Theriiformes There are around 5450 species of mammal, in some classifications, extant mammals are divided into two subclasses, the Prototheria, that is, the order Monotremata, and the Theria, or the infraclasses Metatheria and Eutheria. The marsupials constitute the group of the Metatheria, and include all living metatherians as well as many extinct ones. Much of the changes reflect the advances of cladistic analysis and molecular genetics, findings from molecular genetics, for example, have prompted adopting new groups, such as the Afrotheria, and abandoning traditional groups, such as the Insectivora. The mammals represent the only living Synapsida, which together with the Sauropsida form the Amniota clade, the early synapsid mammalian ancestors were sphenacodont pelycosaurs, a group that produced the non-mammalian Dimetrodon. At the end of the Carboniferous period, this group diverged from the line that led to todays reptiles. Some mammals are intelligent, with some possessing large brains, self-awareness, Mammals can communicate and vocalize in several different ways, including the production of ultrasound, scent-marking, alarm signals, singing, and echolocation. Mammals can organize themselves into fission-fusion societies, harems, and hierarchies, most mammals are polygynous, but some can be monogamous or polyandrous. They provided, and continue to provide, power for transport and agriculture, as well as commodities such as meat, dairy products, wool. Mammals are hunted or raced for sport, and are used as model organisms in science, Mammals have been depicted in art since Palaeolithic times, and appear in literature, film, mythology, and religion. Defaunation of mammals is primarily driven by anthropogenic factors, such as poaching and habitat destruction, Mammal classification has been through several iterations since Carl Linnaeus initially defined the class. No classification system is accepted, McKenna & Bell and Wilson & Reader provide useful recent compendiums. Though field work gradually made Simpsons classification outdated, it remains the closest thing to a classification of mammals
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Nucleotide
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Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers DNA and RNA, both of which are essential biomolecules in all life-forms on Earth. Nucleotides are the blocks of nucleic acids, they are composed of three subunit molecules, a nitrogenous base, a five-carbon sugar, and at least one phosphate group. They are also known as phosphate nucleotides, a nucleoside is a nitrogenuous base and a 5-carbon sugar. Thus a nucleoside plus a group yields a nucleotide. Nucleotides also play a role in life-form metabolism at the fundamental. In addition, nucleotides participate in signaling, and are incorporated into important cofactors of enzymatic reactions. In experimental biochemistry, nucleotides can be radiolabeled with radionuclides to yield radionucleotides, a nucleotide is composed of three distinctive chemical sub-units, a five-carbon sugar molecule, a nitrogenous base—which two together are called a nucleoside—and one phosphate group. With all three joined, a nucleotide is also termed a nucleoside monophosphate, thus, the terms nucleoside diphosphate or nucleoside triphosphate may also indicate nucleotides. Nucleotides contain either a purine or a pyrimidine base—i. e, the nitrogenous base molecule, also known as a nucleobase—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. These chain-joins of sugar and phosphate molecules create a backbone strand for a single- or double helix, in any one strand, the chemical orientation of the chain-joins runs from the 5-end to the 3-end —referring to the five carbon sites on sugar molecules in adjacent nucleotides. Unlike in nucleic acid nucleotides, singular cyclic nucleotides are formed when the group is bound twice to the same sugar molecule. These individual nucleotides function in cell metabolism rather than the nucleic acid structures of long-chain molecules, nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units of nucleic acids. The purine bases adenine and guanine and pyrimidine base cytosine occur in both DNA and RNA, while the pyrimidine bases thymine and uracil in just one, adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds. Nucleotides can be synthesized by a variety of both in vitro and in vivo. In vivo, nucleotides can be synthesized de novo or recycled through salvage pathways, the components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate and amino acid metabolism, and from ammonia and carbon dioxide. The liver is the organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways, purines, however, are first synthesized from the sugar template onto which the ring synthesis occurs. For reference, the syntheses of the purine and pyrimidine nucleotides are carried out by several enzymes in the cytoplasm of the cell, nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides
21.
Adenine
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It also has functions in protein synthesis and as a chemical component of DNA and RNA. The shape of adenine is complementary to either thymine in DNA or uracil in RNA, the image on the right shows pure adenine, as an independent molecule. When connected into DNA, a covalent bond is formed between deoxyribose sugar and the bottom left nitrogen, so removing the hydrogen, the remaining structure is called an adenine residue, as part of a larger molecule. Adenosine is adenine reacted with ribose as used in RNA and ATP, deoxyadenosine adenine attached to deoxyribose, adenine forms several tautomers, compounds that can be rapidly interconverted and are often considered equivalent. However, in isolated conditions, i. e. in an inert gas matrix and in the gas phase, purine metabolism involves the formation of adenine and guanine. Adenine is one of the two purine nucleobases used in forming nucleotides of the nucleic acids, in DNA, adenine binds to thymine via two hydrogen bonds to assist in stabilizing the nucleic acid structures. In RNA, which is used for synthesis, adenine binds to uracil. Adenine forms adenosine, a nucleoside, when attached to ribose and it forms adenosine triphosphate, a nucleoside triphosphate, when three phosphate groups are added to adenosine. Adenosine triphosphate is used in cellular metabolism as one of the methods of transferring chemical energy between chemical reactions. In older literature, adenine was sometimes called Vitamin B4 and it is no longer considered a true vitamin or part of the Vitamin B complex. However, two B vitamins, niacin and riboflavin, bind with adenine to form the essential cofactors nicotinamide adenine dinucleotide and flavin adenine dinucleotide, hermann Emil Fischer was one of the early scientists to study adenine. It was named in 1885 by Albrecht Kossel, in reference to the pancreas from which Kossels sample had been extracted. On August 8,2011, a report, based on NASA studies with meteorites found on Earth, was published suggesting building blocks of DNA and RNA may have been formed extraterrestrially in outer space
22.
Guanine
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Guanine is one of the four main nucleobases found in the nucleic acids DNA and RNA, the others being adenine, cytosine, and thymine. In DNA, guanine is paired with cytosine, the guanine nucleoside is called guanosine. With the formula C5H5N5O, guanine is a derivative of purine, being unsaturated, the bicyclic molecule is planar. Guanine, along with adenine and cytosine, is present in both DNA and RNA, whereas thymine is usually only in DNA, and uracil only in RNA. Guanine has two forms, the major keto form and rare enol form. It binds to cytosine through three hydrogen bonds, in cytosine, the amino group acts as the hydrogen bond donor and the C-2 carbonyl and the N-3 amine as the hydrogen-bond acceptors. Guanine has the C-6 carbonyl group that acts as the hydrogen acceptor, while a group at N-1. Guanine can be hydrolyzed with strong acid to glycine, ammonia, carbon dioxide, first, guanine gets deaminated to become xanthine. Guanine oxidizes more readily than adenine, the other purine-derivative base in DNA and its high melting point of 350 °C reflects the intermolecular hydrogen bonding between the oxo and amino groups in the molecules in the crystal. Because of this bonding, guanine is relatively insoluble in water. Between 1882 and 1906, Fischer determined the structure and also showed that uric acid can be converted to guanine, trace amounts of guanine form by the polymerization of ammonium cyanide. These results indicate guanine could arise in frozen regions of the primitive earth. In 1984, Yuasa reported a 0. 00017% yield of guanine after the discharge of NH3, CH4, C 2H6. However, it is whether the presence of guanine was not simply a resultant contaminant of the reaction. 10NH3 + 2CH4 + 4C2H6 + 2H2O → 2C5H8N5O + 25H2 A Fischer-Tropsch synthesis can also be used to form guanine, along with adenine, uracil, traubes synthesis involves heating 2,4, 5-triamino-1, 6-dihydro-6-oxypyrimidine with formic acid for several hours. The word guanine derives from the Spanish loanword guano, which itself is from the Quechua word wanu, as the Oxford English Dictionary notes, guanine is A white amorphous substance obtained abundantly from guano, forming a constituent of the excrement of birds. In 1656 in Paris, a Mr. Jaquin extracted from the scales of the fish Alburnus alburnus so-called pearl essence, in the cosmetics industry, crystalline guanine is used as an additive to various products, where it provides a pearly iridescent effect. It is also used in paints and simulated pearls and plastics
23.
Algorithm
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In mathematics and computer science, an algorithm is a self-contained sequence of actions to be performed. Algorithms can perform calculation, data processing and automated reasoning tasks, an algorithm is an effective method that can be expressed within a finite amount of space and time and in a well-defined formal language for calculating a function. The transition from one state to the next is not necessarily deterministic, some algorithms, known as randomized algorithms, giving a formal definition of algorithms, corresponding to the intuitive notion, remains a challenging problem. In English, it was first used in about 1230 and then by Chaucer in 1391, English adopted the French term, but it wasnt until the late 19th century that algorithm took on the meaning that it has in modern English. Another early use of the word is from 1240, in a manual titled Carmen de Algorismo composed by Alexandre de Villedieu and it begins thus, Haec algorismus ars praesens dicitur, in qua / Talibus Indorum fruimur bis quinque figuris. Which translates as, Algorism is the art by which at present we use those Indian figures, the poem is a few hundred lines long and summarizes the art of calculating with the new style of Indian dice, or Talibus Indorum, or Hindu numerals. An informal definition could be a set of rules that precisely defines a sequence of operations, which would include all computer programs, including programs that do not perform numeric calculations. Generally, a program is only an algorithm if it stops eventually, but humans can do something equally useful, in the case of certain enumerably infinite sets, They can give explicit instructions for determining the nth member of the set, for arbitrary finite n. An enumerably infinite set is one whose elements can be put into one-to-one correspondence with the integers, the concept of algorithm is also used to define the notion of decidability. That notion is central for explaining how formal systems come into being starting from a set of axioms. In logic, the time that an algorithm requires to complete cannot be measured, from such uncertainties, that characterize ongoing work, stems the unavailability of a definition of algorithm that suits both concrete and abstract usage of the term. Algorithms are essential to the way computers process data, thus, an algorithm can be considered to be any sequence of operations that can be simulated by a Turing-complete system. Although this may seem extreme, the arguments, in its favor are hard to refute. Gurevich. Turings informal argument in favor of his thesis justifies a stronger thesis, according to Savage, an algorithm is a computational process defined by a Turing machine. Typically, when an algorithm is associated with processing information, data can be read from a source, written to an output device. Stored data are regarded as part of the state of the entity performing the algorithm. In practice, the state is stored in one or more data structures, for some such computational process, the algorithm must be rigorously defined, specified in the way it applies in all possible circumstances that could arise. That is, any conditional steps must be dealt with, case-by-case
24.
Computational biology
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Computational Biology, sometimes referred to as bioinformatics, is the science of using biological data to develop algorithms and relations among various biological systems. Prior to the advent of computational biology, biologists did not have access to large amounts of data, researchers were able to develop analytical methods for interpreting biological information, but were unable to share them quickly among colleagues. Bioinformatics began to develop in the early 1970s and it was considered the science of analyzing informatics processes of various biological systems. At this time, research in intelligence was using network models of the human brain in order to generate new algorithms. This use of data to develop other fields pushed biological researchers to revisit the idea of using computers to evaluate. By 1982, information was being shared amongst researchers through the use of punch cards, the amount of data being shared began to grow exponentially by the end of the 1980s. This required the development of new methods in order to quickly analyze. Since the late 1990s, computational biology has become an important part of developing emerging technologies for the field of biology, the terms computational biology and evolutionary computation have a similar name, but are not to be confused. Unlike computational biology, evolutionary computation is not concerned with modeling and analyzing biological data and it instead creates algorithms based on the ideas of evolution across species. Sometimes referred to as genetic algorithms, the research of this field can be applied to computational biology, while evolutionary computation is not inherently a part of computational biology, Computational evolutionary biology is a subfield of it. Computational biology has been used to sequence the human genome, create accurate models of the human brain. Computational anatomy is a discipline focusing on the study of anatomical shape and it involves the development and application of computational, mathematical and data-analytical methods for modeling and simulation of biological structures. It focuses on the structures being imaged, rather than the medical imaging devices. It is similar in spirit to the history of Computational linguistics, at Computational anatomys heart is the comparison of shape by recognizing in one shape the other. This connects it to DArcy Wentworth Thompsons developments On Growth and Form which has led to scientific explanations of morphogenesis, the original formulation of Computational anatomy is as a generative model of shape and form from exemplars acted upon via transformations. It is a branch of the analysis and pattern theory school at Brown University pioneered by Ulf Grenander. The models of metric pattern theory, in group action on the orbit of shapes. Computational biomodeling is a field concerned with building computer models of biological systems, Computational biomodeling aims to develop and use visual simulations in order to assess the complexity of biological systems
25.
Contig
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A contig is a set of overlapping DNA segments that together represent a consensus region of DNA. Contigs can thus refer both to overlapping DNA sequence and to overlapping physical segments contained in clones depending on the context, a sequence contig is a continuous sequence resulting from the reassembly of the small DNA fragments generated by bottom-up sequencing strategies. This meaning of contig is consistent with the definition by Rodger Staden. The bottom-up DNA sequencing strategy involves shearing genomic DNA into many fragments, sequencing these fragments, reassembling them back into contigs. Because current technology allows for the sequencing of only relatively short DNA fragments. In bottom-up sequencing projects, amplified DNA is sheared randomly into fragments appropriately sized for sequencing, the subsequent sequence reads, which are the data that contain the sequences of the small fragments, are put into a database. The assembly software then searches this database for pairs of overlapping reads, assembling the reads from such a pair produces a longer contiguous read of sequenced DNA. Today, it is common to use paired-end sequencing technology where both ends of consistently sized longer DNA fragments are sequenced, here, a contig still refers to any contiguous stretch of sequence data created by read overlap. Because the fragments are of length, the distance between the two end reads from each fragment is known. This gives additional information about the orientation of contigs constructed from these reads, scaffolds consist of overlapping contigs separated by gaps of known length. The new constraints placed on the orientation of the contigs allows for the placement of highly repeated sequences in the genome, if one end read has a repetitive sequence, as long as its mate pair is located within a contig, its placement is known. Contig can also refer to the clones that form a physical map of a chromosome when the top-down or hierarchical sequencing strategy is used. In this sequencing method, a map is made prior to sequencing in order to provide a framework to guide the later assembly of the sequence reads of the genome. This map identifies the relative positions and overlap of the used for sequencing. Once a tiling path has been selected, its component BACs are sheared into smaller fragments, contigs therefore provide the framework for hierarchical sequencing. The assembly of a contig map involves several steps, first, DNA is sheared into larger pieces, which are cloned into BACs or PACs to form a BAC library. Since these clones should cover the entire genome/chromosome, it is possible to assemble a contig of BACs that covers the entire chromosome. Reality, however, is not always ideal, gaps often remain, and a scaffold—consisting of contigs and gaps—that covers the map region is often the first result
26.
Gene mapping
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Gene mapping describes the methods used to identify the locus of a gene and the distances between genes. The essence of all genome mapping is to place a collection of molecular markers onto their positions on the genome. Molecular markers come in all forms, genes can be viewed as one special type of genetic markers in the construction of genome maps, and mapped the same way as any other markers. There are two types of Maps used in the field of genome mapping, genetic maps and physical maps. While the physical map could be an accurate representation of the genome, genetic maps often offer insights into the nature of different regions of the chromosome. Researchers begin a genetic map by collecting samples of blood or tissue from family members that carry a prominent disease or trait and these unique molecular patterns in the DNA are referred to as polymorphisms, or markers. The first steps of building a map are the development of genetic markers. The closer two markers are on the chromosome, the more likely they are to be passed on to the next generation together, therefore, the co-segregation patterns of all markers can be used to reconstruct their order. With this in mind, the genotypes of each genetic marker are recorded for both parents and each individual in the following generations. The quality of the maps is largely dependent upon these factors, the number of genetic markers on the map. The two factors are interlinked, as a mapping population could increase the resolution of the map. In gene mapping, any sequence feature that can be distinguished from the two parents can be used as a genetic marker. Genes, in regard, are represented by traits that can be faithfully distinguished between two parents. Their linkage with other markers are calculated same way as if they are common markers. The entire process is repeated by looking at more markers which target that region to map the gene neighbourhood to a higher resolution until a specific causative locus can be identified. This process is referred to as positional cloning, and it is used extensively in the study of plant species. Since actual base-pair distances are hard or impossible to directly measure. The fragmentation of the genome can be achieved by restriction enzyme cutting or by physically shattering the genome by processes like sonication, once cut, the DNA fragments are separated by electrophoresis
27.
Beijing Genomics Institute
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BGI, known as the Beijing Genomics Institute prior to 2008, is one of the worlds genome sequencing centers, headquartered in Shenzhen, Guangdong, China. After the project was completed, funding dried up, so BGI moved to Hangzhou in exchange for funding from the Hangzhou Municipal Government. In 2002, BGI sequenced the genome which was a cover story in the journal Science. In 2003 BGI decoded the SARS virus genome and created a kit for detection of the virus, in 2003, BGI Hangzhou and the Zhejiang University founded a new research institute, the James D. Watson Institute of Genome Sciences, Zhejiang University. The Watson Institute was intended to become a center for research. In 2007 BGI’s headquarters relocated to Shenzhen as the first citizen-managed, yu Jun left BGI at this time purportedly selling his stake to the other 3 founders for a nominal sum. In 2008, BGI-Shenzhen was officially recognized as a state agency, in 2008, BGI published the first human genome of an Asian individual. In 2010 it was reported that BGI would receive US$1.5 billion in “collaborative funds” over the next 10 years from the China Development Bank, in 2010, BGI Americas was established with its main office in Cambridge, Massachusetts and BGI Europe was established in Copenhagen. In 2011 BGI reported it employed 4,000 scientists and technicians, BGI did the genome sequencing for the deadly 2011 Germany E. coli O104, H4 outbreak in three days under open licence. That year it bought Complete Genomics of Mountain View, California, the institute has described itself as partly private and partly public, receiving funds both from private investors and the Chinese government. The laboratory was also the Bioinformatics Center of the Chinese Academy of Sciences, coli O104, H4 outbreak Sequenced 40 domesticated and wild silkworms, identifying 354 genes likely important in domestication. The mutation might be the reason why the panda prefers bamboo over meat. However, the panda also lacks genes expected for bamboo digestion, key player in the Sino-British Chicken Genome Project As of 2010, plant genomes sequenced include rice, cucumber, soybean, and Sorghum. Animal genomes sequenced include silkworm, honey bee, water flea, lizard, an additional 40 animal and plant species and over 1000 bacteria had also been sequenced. Nature in 2010 ranked BGI Shenzhen as the fourth among the ten top institutions in China with all the others being universities, the ranking was based on articles in Nature research journals. There were similar results for other tops journals, in 2014, BGI was reported to be producing 500 cloned pigs a year to test new medicines. The first genome data was published in October 2007, an anonymous Chinese billionaire donated $10 million RMB to the project and his genome was sequenced at the beginning of the project. Nine Danish universities and institutes will collaborate with BGI in this targeted resequencing project, the Cognitive Research Lab at BGI is working with Stephen Hsu on a project to discover the genetic basis of human intelligence
28.
Single-nucleotide polymorphism
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For example, at a specific base position in the human genome, the base C may appear in most individuals, but in a minority of individuals, the position is occupied by base A. There is a SNP at this base position, and the two possible nucleotide variations - C or A - are said to be alleles for this base position. SNPs underlie differences in our susceptibility to disease, a range of human diseases, e. g. sickle-cell anemia, β-thalassemia. The severity of illness and the way our body responds to treatments are also manifestations of genetic variations, for example, a single base mutation in the APOE gene is associated with a higher risk for Alzheimers disease. A single-nucleotide variant is a variation in a single nucleotide without any limitations of frequency, a somatic single nucleotide variation may also be called a single-nucleotide alteration. Single-nucleotide polymorphisms may fall within coding sequences of genes, non-coding regions of genes, SNPs within a coding sequence do not necessarily change the amino acid sequence of the protein that is produced, due to degeneracy of the genetic code. SNPs in the region are of two types, synonymous and nonsynonymous SNPs. Synonymous SNPs do not affect the sequence while nonsynonymous SNPs change the amino acid sequence of protein. The nonsynonymous SNPs are of two types, missense and nonsense, SNPs that are not in protein-coding regions may still affect gene splicing, transcription factor binding, messenger RNA degradation, or the sequence of non-coding RNA. Gene expression affected by type of SNP is referred to as an eSNP. Association studies can determine whether a variant is associated with a disease or trait. A tag SNP is a representative single-nucleotide polymorphism in a region of the genome with high linkage disequilibrium, tag SNPs are useful in whole-genome SNP association studies in which hundreds of thousands of SNPs across the entire genome are genotyped. Haplotype mapping, sets of alleles or DNA sequences can be clustered so that a single SNP can identify many linked SNPs, linkage Disequilibrium, a term used in population genetics, indicates non-random association of alleles at two or more loci, not necessarily on the same chromosome. It refers to the phenomenon that SNP allele or DNA sequence which are together in the genome tend to be inherited together. LD is affected by two parameters, 1) The distance between the SNPs, other factors, like genetic recombination and mutation rate, can also determine SNP density. There are variations between populations, so a SNP allele that is common in one geographical or ethnic group may be much rarer in another. Within a population, SNPs can be assigned a minor allele frequency — the lowest allele frequency at a locus that is observed in a particular population and this is simply the lesser of the two allele frequencies for single-nucleotide polymorphisms. Variations in the DNA sequences of humans can affect how humans develop diseases and respond to pathogens, chemicals, drugs, vaccines, SNPs are also critical for personalized medicine
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Molecular biology
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Writing in Nature in 1961, William Astbury described molecular biology as. It is concerned particularly with the forms of biological molecules and is predominantly three-dimensional and structural—which does not mean, however and it must at the same time inquire into genesis and function. Researchers in molecular biology use specific techniques native to molecular biology but increasingly combine these techniques and ideas from genetics. There is not a line between these disciplines. Biochemists focus heavily on the role, function, and structure of biomolecules, the study of the chemistry behind biological processes and the synthesis of biologically active molecules are examples of biochemistry. Genetics is the study of the effect of differences on organisms. This can often be inferred by the absence of a normal component, the study of mutants – organisms which lack one or more functional components with respect to the so-called wild type or normal phenotype. Genetic interactions can often confound simple interpretations of such knockout studies, molecular biology is the study of molecular underpinnings of the processes of replication, transcription, translation, and cell function. This picture, however, is undergoing revision in light of emerging novel roles for RNA, much of molecular biology is quantitative, and recently much work has been done at its interface with computer science in bioinformatics and computational biology. In the early 2000s, the study of structure and function. There is also a tradition of studying biomolecules from the ground up in biophysics. One of the most basic techniques of molecular biology to study protein function is molecular cloning, in this technique, DNA coding for a protein of interest is cloned using PCR and/or restriction enzymes into a plasmid. A vector has 3 distinctive features, an origin of replication, a multiple cloning site, the origin of replication will have promoter regions upstream from the replication/transcription start site. This plasmid can be inserted into either bacterial or animal cells, introducing DNA into bacterial cells can be done by transformation via uptake of naked DNA, conjugation via cell-cell contact or by transduction via viral vector. Introducing DNA into eukaryotic cells, such as cells, by physical or chemical means is called transfection. Several different transfection techniques are available, such as calcium phosphate transfection, electroporation, microinjection, the plasmid may be integrated into the genome, resulting in a stable transfection, or may remain independent of the genome, called transient transfection. DNA coding for a protein of interest is now inside a cell, a variety of systems, such as inducible promoters and specific cell-signaling factors, are available to help express the protein of interest at high levels. Large quantities of a protein can then be extracted from the bacterial or eukaryotic cell, polymerase chain reaction is an extremely versatile technique for copying DNA
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Bioinformatics
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Bioinformatics /ˌbaɪ. oʊˌɪnfərˈmætɪks/ is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines computer science, statistics, mathematics, Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques. Common uses of bioinformatics include the identification of genes and nucleotides. Often, such identification is made with the aim of understanding the genetic basis of disease, unique adaptations, desirable properties. In a less formal way, bioinformatics also tries to understand the principles within nucleic acid and protein sequences. Bioinformatics has become an important part of areas of biology. In experimental molecular biology, bioinformatics techniques such as image and signal processing allow extraction of useful results from large amounts of raw data, in the field of genetics and genomics, it aids in sequencing and annotating genomes and their observed mutations. It plays a role in the mining of biological literature. It also plays a role in the analysis of gene and protein expression and regulation, Bioinformatics tools aid in the comparison of genetic and genomic data and more generally in the understanding of evolutionary aspects of molecular biology. At a more level, it helps analyze and catalogue the biological pathways. In structural biology, it aids in the simulation and modeling of DNA, RNA, historically, the term bioinformatics did not mean what it means today. Paulien Hogeweg and Ben Hesper coined it in 1970 to refer to the study of processes in biotic systems. This definition placed bioinformatics as a parallel to biophysics or biochemistry. Computers became essential in molecular biology when protein sequences became available after Frederick Sanger determined the sequence of insulin in the early 1950s, comparing multiple sequences manually turned out to be impractical. A pioneer in the field was Margaret Oakley Dayhoff, who has been hailed by David Lipman, director of the National Center for Biotechnology Information, Dayhoff compiled one of the first protein sequence databases, initially published as books and pioneered methods of sequence alignment and molecular evolution. To study how normal cellular activities are altered in different disease states, therefore, the field of bioinformatics has evolved such that the most pressing task now involves the analysis and interpretation of various types of data. This includes nucleotide and amino acid sequences, protein domains, the actual process of analyzing and interpreting data is referred to as computational biology. For example, there are methods to locate a gene within a sequence, to predict protein structure and/or function, the primary goal of bioinformatics is to increase the understanding of biological processes
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Whole genome sequencing
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Whole genome sequencing is the process of determining the complete DNA sequence of an organisms genome at a single time. This entails sequencing all of an organisms chromosomal DNA as well as DNA contained in the mitochondria and, for plants, whole genome sequencing has largely been used as a research tool, but is currently being introduced to clinics. In the future of personalized medicine, whole genome sequence data will be an important tool to guide therapeutic intervention, in addition, whole genome sequencing should not be confused with methods that sequence specific subsets of the genome - such methods include whole exome sequencing or SNP genotyping. Almost all truly complete genomes are of microbes, the full genome is thus sometimes used loosely to mean greater than 95%. The remainder of this focuses on nearly complete human genomes. The DNA sequencing methods used in the 1970s and 1980s were manual, for example Maxam-Gilbert sequencing, the shift to more rapid, automated sequencing methods in the 1990s finally allowed the sequence of whole genomes. The first organism to have its genome sequenced was Haemophilus influenzae in 1995. After it, the genomes of bacteria and some archaea were first sequenced. H. influenzae has a genome of 1,830,140 base pairs of DNA, in contrast, eukaryotes, both unicellular and multicellular such as Amoeba dubia and humans respectively, have much larger genomes. Amoeba dubia has a genome of 700 billion nucleotide pairs spread across thousands of chromosomes, humans contain fewer nucleotide pairs than A. dubia however their genome size far outweighs the genome size of individual bacteria. The first bacterial and archaeal genomes, including that of H. influenzae, were sequenced by Shotgun sequencing, in 1996 the first eukaryotic genome was sequenced. S. cerevisiae, an organism in biology has a genome of only around 12 million nucleotide pairs. The first multicellular eukaryote, and animal, to have its genome sequenced was the nematode worm. In 1999, the entire DNA sequence of human chromosome 22, by the year 2000, the second animal and second invertebrate genome was sequenced - that of the fruit fly Drosophila melanogaster - a popular choice of model organism in experimental research. The first plant genome - that of the model organism Arabidopsis thaliana - was also fully sequenced by 2000, by 2001, a draft of the entire human genome sequence was published. The genome of the laboratory mouse Mus musculus was completed in 2002, in 2004, the Human Genome Project published the human genome. Currently, thousands of genomes have been sequenced, almost any biological sample containing a full copy of the DNA—even a very small amount of DNA or ancient DNA—can provide the genetic material necessary for full genome sequencing. Such samples may include saliva, epithelial cells, bone marrow, hair, seeds, plant leaves, the genome sequence of a single cell selected from a mixed population of cells can be determined using techniques of single cell genome sequencing
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Base pair
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A base pair is a unit consisting of two nucleobases bound to each other by hydrogen bonds. They form the blocks of the DNA double helix. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs allow the DNA helix to maintain a regular helical structure that is dependent on its nucleotide sequence. The complementary nature of this structure provides a backup copy of all genetic information encoded within double-stranded DNA. Many DNA-binding proteins can recognize specific base pairing patterns that identify particular regulatory regions of genes, intramolecular base pairs can occur within single-stranded nucleic acids. The size of a gene or an organisms entire genome is often measured in base pairs because DNA is usually double-stranded. Hence, the number of base pairs is equal to the number of nucleotides in one of the strands. The haploid human genome is estimated to be about 3.2 billion bases long and to contain 20, a kilobase is a unit of measurement in molecular biology equal to 1000 base pairs of DNA or RNA. The total amount of related DNA base pairs on Earth is estimated at 5.0 x 1037, in comparison, the total mass of the biosphere has been estimated to be as much as 4 TtC. Hydrogen bonding is the interaction that underlies the base-pairing rules described above. Appropriate geometrical correspondence of hydrogen donors and acceptors allows only the right pairs to form stably. Purine-pyrimidine base pairing of AT or GC or UA results in proper duplex structure, the only other purine-pyrimidine pairings would be AC and GT and UG, these pairings are mismatches because the patterns of hydrogen donors and acceptors do not correspond. The GU pairing, with two bonds, does occur fairly often in RNA. Higher GC content results in higher melting temperatures, it is, therefore, on the converse, regions of a genome that need to separate frequently — for example, the promoter regions for often-transcribed genes — are comparatively GC-poor. GC content and melting temperature must also be taken into account when designing primers for PCR reactions, the following DNA sequences illustrate pair double-stranded patterns. By convention, the top strand is written from the 5 end to the 3 end, thus and this is due to their isosteric chemistry. One common mutagenic base analog is 5-bromouracil, which resembles thymine, most intercalators are large polyaromatic compounds and are known or suspected carcinogens. Examples include ethidium bromide and acridine, an unnatural base pair is a designed subunit of DNA which is created in a laboratory and does not occur in nature
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Mitochondrion
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The mitochondrion is a double membrane-bound organelle found in all eukaryotic organisms. Some cells in multicellular organisms may however lack them. A number of organisms, such as microsporidia, parabasalids. To date, only one eukaryote, Monocercomonoides, is known to have completely lost its mitochondria, the word mitochondrion comes from the Greek μίτος, mitos, thread, and χονδρίον, chondrion, granule or grain-like. Mitochondria generate most of the supply of adenosine triphosphate, used as a source of chemical energy. Mitochondria are commonly between 0.75 and 3 μm in diameter but vary considerably in size and structure, unless specifically stained, they are not visible. Mitochondrial biogenesis is in turn temporally coordinated with these cellular processes, Mitochondria have been implicated in several human diseases, including mitochondrial disorders, cardiac dysfunction, heart failure and autism. The number of mitochondria in a cell can vary widely by organism, tissue, for instance, red blood cells have no mitochondria, whereas liver cells can have more than 2000, The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the space, the inner membrane. Although most of a cells DNA is contained in the cell nucleus, mitochondrial proteins vary depending on the tissue and the species. In humans,615 distinct types of protein have been identified from cardiac mitochondria, the mitochondrial proteome is thought to be dynamically regulated. The first observations of structures that probably represented mitochondria were published in the 1840s. Richard Altmann, in 1890, established them as cell organelles, the term mitochondria was coined by Carl Benda in 1898. Leonor Michaelis discovered that Janus green can be used as a stain for mitochondria in 1900. Benjamin F. Kingsbury, in 1912, first related them with cell respiration, in 1913, particles from extracts of guinea-pig liver were linked to respiration by Otto Heinrich Warburg, which he called grana. Warburg and Heinrich Otto Wieland, who had postulated a similar particle mechanism. It was not until 1925, when David Keilin discovered cytochromes, in the following years, the mechanism behind cellular respiration was further elaborated, although its link to the mitochondria was not known. The introduction of tissue fractionation by Albert Claude allowed mitochondria to be isolated from other cell fractions, in 1946, he concluded that cytochrome oxidase and other enzymes responsible for the respiratory chain were isolated to the mitchondria
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Chloroplast
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Chloroplasts /ˈklɔːrəˌplæsts, -plɑːsts/ are organelles, specialized subunits, in plant and algal cells. Their discovery inside plant cells is usually credited to Julius von Sachs and they then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of functions, including fatty acid synthesis, much amino acid synthesis. The number of chloroplasts per cell varies from one, in algae, up to 100 in plants like Arabidopsis. A chloroplast is a type of known as a plastid. Other plastid types, such as the leucoplast and the chromoplast, contain little chlorophyll, chloroplasts are highly dynamic—they circulate and are moved around within plant cells, and occasionally pinch in two to reproduce. Their behavior is influenced by environmental factors like light color. Chloroplasts, like mitochondria, contain their own DNA, which is thought to be inherited from their ancestor—a photosynthetic cyanobacterium that was engulfed by a eukaryotic cell. Chloroplasts cannot be made by the plant cell and must be inherited by each cell during cell division. With one exception, all chloroplasts can probably be traced back to a single endosymbiotic event, despite this, chloroplasts can be found in an extremely wide set of organisms, some not even directly related to each other—a consequence of many secondary and even tertiary endosymbiotic events. The word chloroplast is derived from the Greek words chloros, which means green, and plastes, the first definitive description of a chloroplast was given by Hugo von Mohl in 1837 as discrete bodies within the green plant cell. In 1883, A. F. W. Schimper would name these bodies as chloroplastids, in 1884, Eduard Strasburger adopted the term chloroplasts. Chloroplasts are one of many types of organelles in the plant cell and they are considered to have originated from cyanobacteria through endosymbiosis—when a eukaryotic cell engulfed a photosynthesizing cyanobacterium that became a permanent resident in the cell. Mitochondria are thought to have come from an event, where an aerobic prokaryote was engulfed. This origin of chloroplasts was first suggested by the Russian biologist Konstantin Mereschkowski in 1905 after Andreas Schimper observed in 1883 that chloroplasts closely resemble cyanobacteria, chloroplasts are only found in plants, algae, and the amoeboid Paulinella chromatophora. Cyanobacteria are considered the ancestors of chloroplasts and they are sometimes called blue-green algae even though they are prokaryotes. They are a phylum of bacteria capable of carrying out photosynthesis. Cyanobacteria also contain a cell wall, which is thicker than in other gram-negative bacteria
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Organelle
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In cell biology, an organelle is a specialized subunit within a cell that has a specific function. Individual organelles are usually enclosed within their own lipid bilayers. The name organelle comes from the idea that these structures are to cells what an organ is to the body, organelles are identified by microscopy, and can also be purified by cell fractionation. There are many types of organelles, particularly in eukaryotic cells, while prokaryotes do not possess organelles per se, some do contain protein-based bacterial microcompartments, which are thought to act as primitive organelles. In biology organs are defined as confined functional units within an organism, the analogy of bodily organs to microscopic cellular substructures is obvious, as from even early works, authors of respective textbooks rarely elaborate on the distinction between the two. In the 1830s, Félix Dujardin refuted Ehrenberg theory which said that microorganims have the organs of multicellular animals. Credited as the first to use a diminutive of organ for cellular structures was German zoologist Karl August Möbius, under this definition, there would only be two broad classes of organelles, mitochondria plastids. Other organelles are also suggested to have endosymbiotic origins, but do not contain their own DNA, under the more restricted definition of membrane-bound structures, some parts of the cell do not qualify as organelles. Nevertheless, the use of organelle to refer to non-membrane bound structures such as ribosomes is common and this has led some texts to delineate between membrane-bound and non-membrane bound organelles. The larger organelles, such as the nucleus and vacuoles, are visible with the light microscope. They were among the first biological discoveries made after the invention of the microscope, not all eukaryotic cells have each of the organelles listed below. Exceptional organisms have cells that do not include some organelles that might otherwise be considered universal to eukaryotes, there are also occasional exceptions to the number of membranes surrounding organelles, listed in the tables below. In addition, the number of organelles of each type found in a given cell varies depending upon the function of that cell. This idea is supported in the Endosymbiotic theory, in the past, they were often viewed as having little internal organization, but slowly, details are emerging about prokaryotic internal structures. However, more recent research has revealed that at least some prokaryotes have microcompartments such as carboxysomes and these subcellular compartments are 100–200 nm in diameter and are enclosed by a shell of proteins. The function of a protein is correlated with the organelle in which it resides. CoRR Hypothesis Ejectosome Endosymbiotic theory Organelle biogenesis Membrane vesicle trafficking Host-pathogen interface Tree of Life project, Eukaryotes
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Eukaryote
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A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota, the presence of a nucleus gives eukaryotes their name, which comes from the Greek εὖ and κάρυον. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular or multicellular, only eukaryotes form multicellular organisms consisting of many kinds of tissue made up of different cell types. Eukaryotes can reproduce asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two identical cells. In meiosis, DNA replication is followed by two rounds of division to produce four daughter cells each with half the number of chromosomes as the original parent cell. These act as sex cells resulting from genetic recombination during meiosis, the domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features, eukaryotes represent a tiny minority of all living things. However, due to their larger size, eukaryotes collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1. 6–2.1 billion years ago, in 1905 and 1910, the Russian biologist Konstantin Mereschkowsky argued three things about the origin of nucleated cells. Firstly, plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, secondly, the host had earlier in evolution formed by symbiosis between an amoeba-like host and a bacteria-like cell that formed the nucleus. Thirdly, plants inherited photosynthesis from cyanobacteria, the split between the prokaryotes and eukaryotes was introduced in the 1960s. The concept of the eukaryote has been attributed to the French biologist Edouard Chatton, the terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1938 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in one paragraph, and the idea was effectively ignored until Chattons statement was rediscovered by Stanier. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in cells in her paper. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA and this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts
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Noncoding DNA
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In genomics and related disciplines, noncoding DNA sequences are components of an organisms DNA that do not encode protein sequences. Some noncoding DNA is transcribed into functional non-coding RNA molecules, the amount of noncoding DNA varies greatly among species. Often, only a percentage of the genome is responsible for coding proteins. When there is much non-coding DNA, a large proportion appears to have no biological function, since that time, this non-functional portion has controversially been called junk DNA. The international Encyclopedia of DNA Elements project uncovered, by direct biochemical approaches, estimates for the biologically functional fraction of our genome based on comparative genomics range between 8 and 15%. However, others have argued against relying solely on estimates from comparative genomics due to its limited scope, non-coding DNA has been found to be involved in epigenetic activity and complex networks of genetic interactions, and is being explored in evolutionary developmental biology. The amount of total genomic DNA varies widely between organisms, and the proportion of coding and noncoding DNA within these genomes varies greatly as well, while overall genome size, and by extension the amount of noncoding DNA, are correlated to organism complexity, there are many exceptions. For example, the genome of the unicellular Polychaos dubium has been reported to contain more than 200 times the amount of DNA in humans, the extensive variation in nuclear genome size among eukaryotic species is known as the C-value enigma or C-value paradox. Most of the size difference appears to lie in the noncoding DNA. In 2013, a new record for the most efficient eukaryotic genome was discovered with Utricularia gibba, parts of the noncoding DNA were being deleted by the plant and this suggested that noncoding DNA may not be as critical for plants, even though noncoding DNA is useful for humans. Noncoding RNAs are functional RNA molecules that are not translated into protein, examples of noncoding RNA include ribosomal RNA, transfer RNA, Piwi-interacting RNA and microRNA. Cis-regulatory elements are sequences that control the transcription of a nearby gene, many such elements are involved in the evolution and control of development. Cis-elements may be located in 5 or 3 untranslated regions or within introns, trans-regulatory elements control the transcription of a distant gene. Promoters facilitate the transcription of a gene and are typically upstream of the coding region. Enhancer sequences may also exert very distant effects on the levels of genes. Introns are non-coding sections of a gene, transcribed into the precursor mRNA sequence, many introns appear to be mobile genetic elements. Pseudogenes are DNA sequences, related to genes, that have lost their protein-coding ability or are otherwise no longer expressed in the cell. Because pseudogenes are presumed to change without evolutionary constraint, they can serve as a model of the type
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Gene prediction
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In computational biology gene prediction or gene finding refers to the process of identifying the regions of genomic DNA that encode genes. This includes protein-coding genes as well as RNA genes, but may also include prediction of other elements such as regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced, in its earliest days, gene finding was based on painstaking experimentation on living cells and organisms. Today, with comprehensive genome sequence and powerful computational resources at the disposal of the research community, determining that a sequence is functional should be distinguished from determining the function of the gene or its product. Gene prediction is one of the key steps in genome annotation, following sequence assembly, gene prediction is closely related to the so-called target search problem investigating how DNA-binding proteins locate specific binding sites within the genome. Given an mRNA sequence, it is trivial to derive a unique genomic DNA sequence from which it had to have been transcribed, given a protein sequence, a family of possible coding DNA sequences can be derived by reverse translation of the genetic code. Once candidate DNA sequences have been determined, it is a relatively straightforward algorithmic problem to efficiently search a target genome for matches, complete or partial, and exact or inexact. Given a sequence, local alignment algorithms such as BLAST, FASTA, matches can be complete or partial, and exact or inexact. The success of this approach is limited by the contents and accuracy of the sequence database, a high degree of similarity to a known messenger RNA or protein product is strong evidence that a region of a target genome is a protein-coding gene. However, to apply this approach systemically requires extensive sequencing of mRNA, thus, to collect extrinsic evidence for most or all of the genes in a complex organism requires the study of many hundreds or thousands of cell types, which presents further difficulties. For example, some genes may be expressed only during development as an embryo or fetus. Despite these difficulties, extensive transcript and protein sequence databases have been generated for human as well as other important model organisms in biology, such as mice and yeast. For example, the RefSeq database contains transcript and protein sequence from different species. It is, however, likely that these databases are both incomplete and contain small but significant amounts of erroneous data, in prokaryotes its essential to consider horizontal gene transfer when searching for gene sequence homology. An additional important factor underused in current gene detection tools is existence of gene clusters—operons in both prokaryotes and eukaryotes, most popular gene detectors treat each gene in isolation, independent of others, which is not biologically accurate. Ab Initio gene prediction is a method based on gene content. These signs can be categorized as either signals, specific sequences that indicate the presence of a gene nearby, or content. Ab initio gene finding might be accurately characterized as gene prediction
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Messenger RNA
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Messenger RNA is a large family of RNA molecules that convey genetic information from DNA to the ribosome, where they specify the amino acid sequence of the protein products of gene expression. As in DNA, mRNA genetic information is in the sequence of nucleotides, each codon encodes for a specific amino acid, except the stop codons, which terminate protein synthesis. It should not be confused with mitochondrial DNA, the brief existence of an mRNA molecule begins with transcription, and ultimately ends in degradation. During its life, a molecule may also be processed, edited. Eukaryotic mRNA molecules often require extensive processing and transport, while prokaryotic mRNA molecules do not, a molecule of eukaryotic mRNA and the proteins surrounding it are together called a messenger RNP. Transcription is when RNA is made from DNA, during transcription, RNA polymerase makes a copy of a gene from the DNA to mRNA as needed. This process is similar in eukaryotes and prokaryotes, the short-lived, unprocessed or partially processed product is termed precursor mRNA, or pre-mRNA, once completely processed, it is termed mature mRNA. Processing of mRNA differs greatly among eukaryotes, bacteria, and archea, non-eukaryotic mRNA is, in essence, mature upon transcription and requires no processing, except in rare cases. Eukaryotic pre-mRNA, however, requires extensive processing, a 5 cap is a modified guanine nucleotide that has been added to the front or 5 end of a eukaryotic messenger RNA shortly after the start of transcription. The 5 cap consists of a terminal 7-methylguanosine residue that is linked through a 5-5-triphosphate bond to the first transcribed nucleotide and its presence is critical for recognition by the ribosome and protection from RNases. Cap addition is coupled to transcription, and occurs co-transcriptionally, such that each influences the other, shortly after the start of transcription, the 5 end of the mRNA being synthesized is bound by a cap-synthesizing complex associated with RNA polymerase. This enzymatic complex catalyzes the reactions that are required for mRNA capping. Synthesis proceeds as a biochemical reaction. In some instances, an mRNA will be edited, changing the composition of that mRNA. An example in humans is the apolipoprotein B mRNA, which is edited in some tissues, the editing creates an early stop codon, which, upon translation, produces a shorter protein. Polyadenylation is the covalent linkage of a moiety to a messenger RNA molecule. In eukaryotic organisms most messenger RNA molecules are polyadenylated at the 3 end, the poly tail and the protein bound to it aid in protecting mRNA from degradation by exonucleases. Polyadenylation is also important for transcription termination, export of the mRNA from the nucleus, MRNA can also be polyadenylated in prokaryotic organisms, where poly tails act to facilitate, rather than impede, exonucleolytic degradation
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Caenorhabditis elegans
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Caenorhabditis elegans is a free-living, transparent nematode, about 1 mm in length, that lives in temperate soil environments. The name is a blend of the Greek caeno-, rhabditis, in 1900, Maupas initially named it Rhabditides elegans, Osche placed it in the subgenus Caenorhabditis in 1952, and in 1955, Dougherty raised it to the status of genus. C. elegans is an unsegmented pseudocoelomate, and lacks a respiratory and it possesses gut granules which emit a brilliant blue fluorescence, a wave of which is seen at death in a death fluorescence. The majority of these nematodes are hermaphrodites, males have specialised tails for mating that include spicules. In 1963, Sydney Brenner proposed research into C. elegans primarily in the area of neuronal development, in 1974, he began research into the molecular and developmental biology of C. elegans, which has since been extensively used as a model organism. C. elegans was the first multicellular organism to have its genome sequenced, and as of 2012. It is the species of its genus. C. elegans is unsegmented, vermiform, and bilaterally symmetrical and it has a cuticle, four main epidermal cords, and a fluid-filled pseudocoelom. It also has some of the organ systems as larger animals. About one in an individuals is male and the rest are hermaphrodites. The basic anatomy of C. elegans includes a mouth, pharynx, intestine, gonad, like all nematodes, they have neither a circulatory nor a respiratory system. When a wave of dorsal/ventral muscle contractions proceeds from the back to the front of the animal, when wave of contractions is initiated at the front and proceeds posteriorly along the body, the animal is propelled forwards. Because of this bias in body bends, any normal living, moving individual tends to lie on either its left side or its right side when observed crossing a horizontal surface. A set of ridges on the sides of the body cuticle. The pharynx is a muscular food pump in the head of C. elegans and this grinds food and transports it directly to the intestine. A set of valve cells connects the pharynx to the intestine, after digestion, the contents of the intestine are released via the rectum, as is the case with all other nematodes. No direct connection exists between the pharynx and the canal, which functions in the release of liquid urine. Males have a single-lobed gonad, a vas deferens, and a tail specialized for mating, hermaphrodites have two ovaries, oviducts, spermatheca, and a single uterus
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DNA sequencing
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DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four bases—adenine, guanine, cytosine, the advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery. The first DNA sequences were obtained in the early 1970s by academic researchers using laborious methods based on two-dimensional chromatography, following the development of fluorescence-based sequencing methods with a DNA sequencer, DNA sequencing has become easier and orders of magnitude faster. DNA sequencing may be used to determine the sequence of genes, larger genetic regions, full chromosomes or entire genomes. DNA sequencing is also the most efficient way to sequence RNA or proteins, in fact, DNA sequencing has become a key technology in many areas of biology and other sciences such as medicine, forensics, or anthropology. Sequencing is used in biology to study genomes and the proteins they encode. Information obtained using sequencing allows researchers to identify changes in genes, associations with diseases and phenotypes, the field of metagenomics involves identification of organisms present in a body of water, sewage, dirt, debris filtered from the air, or swab samples from organisms. Knowing which organisms are present in an environment is critical to research in ecology, epidemiology, microbiology. Sequencing enables researchers to determine which types of microbes may be present in a microbiome, medical technicians may sequence genes from patients to determine if there is risk of genetic diseases. This is a form of testing, though some genetic tests may not involve DNA sequencing. DNA sequencing may be used along with DNA profiling methods for forensic identification, the canonical structure of DNA has four bases, thymine, adenine, cytosine, and guanine. DNA sequencing is the determination of the order of these bases in a molecule of DNA. However, there are other bases that may be present in a molecule. In some viruses, cytosine may be replaced by hydroxy methyl or hydroxy methyl glucose cytosine, in mammalian DNA, variant bases with methyl groups or phosphosulfate may be found. Depending on the technique, a particular modification, e. g. the 5mC common in humans. This situation changed after 1944 as a result of experiments by Oswald Avery, Colin MacLeod. This was the first time that DNA was shown capable of transforming the properties of cells, in 1953, James Watson and Francis Crick put forward their double-helix model of DNA, based on crystallized X-ray structures being studied by Rosalind Franklin. According to the model, DNA is composed of two strands of nucleotides coiled around each other, linked together by bonds and running in opposite directions
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Model organism
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Model organisms are in vivo models and are widely used to research human disease when human experimentation would be unfeasible or unethical. This strategy is made possible by the descent of all living organisms. Studying model organisms can be informative, but care must be taken when extrapolating from one organism to another, in researching human disease, model organisms allow for better understanding the disease process without the added risk of harming an actual human. The species chosen will usually meet a determined taxonomic equivalency to humans, although biological activity in a model organism does not ensure an effect in humans, many drugs, treatments and cures for human diseases are developed in part with the guidance of animal models. There are three types of disease models, homologous, isomorphic and predictive. Homologous animals have the same causes, symptoms and treatment options as would humans who have the same disease, isomorphic animals share the same symptoms and treatments. Predictive models are similar to a human disease in only a couple of aspects. The use of animals in research dates back to ancient Greece, with Aristotle, research using animal models has been central to most of the achievements of modern medicine. It has contributed most of the knowledge in fields such as human physiology and biochemistry. For example, the results have included the near-eradication of polio and the development of organ transplantation, from 1910 to 1927, Thomas Hunt Morgans work with the fruit fly Drosophila melanogaster identified chromosomes as the vector of inheritance for genes. Drosophila became one of the first, and for some time the most widely used, model organisms, D. melanogaster remains one of the most widely used eukaryotic model organisms. The mouse has since been used extensively as an organism and is associated with many important biological discoveries of the 20th. In the late 19th century, Emil von Behring isolated the diphtheria toxin and he went on to develop an antitoxin against diphtheria in animals and then in humans, which resulted in the modern methods of immunization and largely ended diphtheria as a threatening disease. The diphtheria antitoxin is famously commemorated in the Iditarod race, which is modeled after the delivery of antitoxin in the 1925 serum run to Nome. The success of animal studies in producing the diphtheria antitoxin has also attributed as a cause for the decline of the early 20th-century opposition to animal research in the United States. This led to the 1922 discovery of insulin and its use in treating diabetes, modern general anaesthetics, such as halothane and related compounds, were also developed through studies on model organisms, and are necessary for modern, complex surgical operations. In the 1940s, Jonas Salk used rhesus monkey studies to isolate the most virulent forms of the polio virus, the vaccine, which was made publicly available in 1955, reduced the incidence of polio 15-fold in the United States over the following five years. It has been estimated that developing and producing the vaccines required the use of 100,000 rhesus monkeys, models are those organisms with a wealth of biological data that make them attractive to study as examples for other species and/or natural phenomena that are more difficult to study directly
. PMID 20019144.
