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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
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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
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Cell (biology)
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The cell is the basic structural, functional, and biological unit of all known living organisms. A cell is the smallest unit of life that can replicate independently, the study of cells is called cell biology. Cells consist of cytoplasm enclosed within a membrane, which contains many such as proteins. Organisms can be classified as unicellular or multicellular, while the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion cells. Most plant and animal cells are only under a microscope. The cell was discovered by Robert Hooke in 1665, who named the unit for its resemblance to cells inhabited by Christian monks in a monastery. Cells emerged on Earth at least 3.5 billion years ago, Cells are of two types, eukaryotic, which contain a nucleus, and prokaryotic, which do not. Prokaryotes are single-celled organisms, while eukaryotes can be either single-celled or multicellular, prokaryotic cells were the first form of life on Earth, characterised by having vital biological processes including cell signaling and being self-sustaining. They are simpler and smaller than eukaryotic cells, and lack membrane-bound organelles such as the nucleus, prokaryotes include two of the domains of life, bacteria and archaea. The DNA of a prokaryotic cell consists of a chromosome that is in direct contact with the cytoplasm. The nuclear region in the cytoplasm is called the nucleoid, most prokaryotes are the smallest of all organisms ranging from 0.5 to 2.0 µm in diameter. Though most prokaryotes have both a cell membrane and a wall, there are exceptions such as Mycoplasma and Thermoplasma which only possess the cell membrane layer. The envelope gives rigidity to the cell and separates the interior of the cell from its environment, the cell wall consists of peptidoglycan in bacteria, and acts as an additional barrier against exterior forces. It also prevents the cell from expanding and bursting from osmotic pressure due to a hypotonic environment, some eukaryotic cells also have a cell wall. Inside the cell is the region that contains the genome, ribosomes. The genetic material is found in the cytoplasm. Prokaryotes can carry extrachromosomal DNA elements called plasmids, which are usually circular, linear bacterial plasmids have been identified in several species of spirochete bacteria, including members of the genus Borrelia notably Borrelia burgdorferi, which causes Lyme disease. Though not forming a nucleus, the DNA is condensed in a nucleoid, plasmids encode additional genes, such as antibiotic resistance genes
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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
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Bacteriophage
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A bacteriophage /ˈbækˈtɪər. i. oʊˌfeɪdʒ/ is a virus that infects and replicates within a bacterium. The term is derived from bacteria and the Greek, φαγεῖν, bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have relatively simple or elaborate structures. Their genomes may encode as few as four genes, and as many as hundreds of genes, phages replicate within the bacterium following the injection of their genome into its cytoplasm. Bacteriophages are among the most common and diverse entities in the biosphere, phages are widely distributed in locations populated by bacterial hosts, such as soil or the intestines of animals. They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Central Europe and they are seen as a possible therapy against multi-drug-resistant strains of many bacteria. Bacteriophages occur abundantly in the biosphere, with different virions, genomes, phages are classified by the International Committee on Taxonomy of Viruses according to morphology and nucleic acid. Nineteen families are recognized by the ICTV that infect bacteria. Of these, only two families have RNA genomes, and only five families are enveloped, of the viral families with DNA genomes, only two have single-stranded genomes. Eight of the families with DNA genomes have circular genomes while nine have linear genomes. Nine families infect bacteria only, nine infect archaea only, in 1915, British bacteriologist Frederick Twort, superintendent of the Brown Institution of London, discovered a small agent that infected and killed bacteria. He believed the agent must be one of the following, a stage in the cycle of the bacteria. Tworts work was interrupted by the onset of World War I, for d’Hérelle, there was no question as to the nature of his discovery, In a flash I had understood, what caused my clear spots was in fact an invisible microbe … a virus parasitic on bacteria. DHérelle called the virus a bacteriophage or bacteria-eater and he also recorded a dramatic account of a man suffering from dysentery who was restored to good health by the bacteriophages. It was DHerelle who conducted research into bacteriophages and introduced the concept of phage therapy. In 1969, Max Delbrück, Alfred Hershey and Salvador Luria were awarded the Nobel Prize in Physiology and Medicine for their discoveries of the replication of viruses and their genetic structure. Phages were discovered to be agents and were used in the former Soviet Republic of Georgia. They had widespread use, including treatment of soldiers in the Red Army, however, they were abandoned for general use in the West for several reasons, Medical trials were carried out, but a basic lack of understanding of phages made these invalid. Antibiotics were discovered and marketed widely and they were easier to make, store and to prescribe
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Prophage
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A prophage is a bacteriophage genome inserted and integrated into the circular bacterial DNA chromosome or existing as an extrachromosomal plasmid. This is a latent form of a phage, in which the genes are present in the bacterium without causing disruption of the bacterial cell. Pro means before, so, prophage means the stage of a virus in the form of genome inserted into host DNA before attaining its real form inside host. Upon detection of host cell damage, such as UV light or certain chemicals, after induction, viral replication begins via the Lytic Cycle. In the lytic cycle, the virus commandeers the cells reproductive machinery, the cell may fill with new viruses until it lyses or bursts, or it may release the new viruses one at a time in a reverse endocytotic process. The period from infection to lysis is termed the latent period, a virus following a lytic cycle is called a virulent virus. Prophages are important agents of horizontal transfer, and are considered part of the mobilome. All families of viruses with circular DNA genomes or replicating their genomes through a circular intermediate have temperate members. If a target cell doesnt have the same prophage, upon infection by a phage the lytic pathway is immediately activated and this phenomenon is called Zygotic induction
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Lysogenic cycle
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Lysogeny, or the lysogenic cycle, is one of two cycles of viral reproduction. Lysogeny is characterized by integration of the nucleic acid into the host bacteriums genome or formations of a circular replicon in the bacterial cytoplasm. In this condition the bacterium continues to live and reproduce normally, lysogenic cycles can also occur in eukaryotes, although the method of DNA incorporation is not fully understood. The key difference between the cycle and the lysogenic cycle is that the lysogenic cycle does not lyse the host cell. Phages that replicate only via the cycle are known as virulent phages while phages that replicate using both lytic and lysogenic cycles are known as temperate phages. In the lysogenic cycle, the phage DNA first integrates into the chromosome to produce the prophage. When the bacterium reproduces, the prophage is also copied and is present in each of the daughter cells, the daughter cells can continue to replicate with the prophage present or the prophage can exit the bacterial chromosome to initiate the lytic cycle. Bacteriophages are viruses that infect and replicate within a bacterium, temperate phages can reproduce using both the lytic and the lysogenic cycle. Via the lysogenic cycle, the genome is not expressed and is instead integrated into the bacterias genome to form the prophage. In this scenario, the daughter bacteria cells contain prophage and are known as lysogens, lysogens can remain in the lysogenic cycle for many generations but can switch to the lytic cycle at any time via a process known as induction. During induction, prophage DNA is excised from the genome and is transcribed and translated to make coat proteins for the virus. The model organism for studying lysogeny is lambda phage, prophage integration, maintenance of lysogeny, induction, and control of phage genome excision in induction is described in detail in the lambda phage article. Bacteriophages are parasitic because they infect their hosts, use bacterial machinery to replicate, temperate phages can lead to both advantages and disadvantages for their hosts via the lysogenic cycle. During the lysogenic cycle, the genome is incorporated as prophage. Nonetheless, a temperate phage can escape repression to replicate, produce viral particles, the temperate phage escaping repression would be a disadvantage for the bacteria. On the other hand, the prophage may transfer genes that enhance host virulence and resistance to the immune system, also, the repressor produced by the prophage that prevents prophage genes from being expressed confers an immunity for the host bacteria from lytic infection by related viruses. In some interactions between lysogenic phages and bacteria, lysogenic conversion may occur, which can also be called phage conversion and it is when a temperate phage induces a change in the phenotype of the infected bacteria that is not part of a usual phage cycle. Changes can often involve the external membrane of the cell by making it impervious to other phages or even by increasing the capability of the bacteria for a host
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Endogenous retrovirus
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Endogenous retroviruses are endogenous viral elements in the genome that closely resemble and can be derived from retroviruses. They are abundant in the genomes of jawed vertebrates, and they comprise up to 5–8% of the human genome. ERVs are a subclass of a type of gene called a transposon and they are distinguished as retrotransposons, which are Class I elements. This means that not all ERVs may have originated as an insertion by a retrovirus, when integration of viral DNA occurs in the germ-line, it can give rise to an ERV, which can later become fixed in the gene pool of the host population. The replication cycle of a retrovirus entails the insertion of a DNA copy of the genome into the nuclear genome of the host cell. Most retroviruses infect somatic cells, but occasional infection of cells can also occur. Rarely, retroviral integration may occur in a cell that goes on to develop into a viable organism. This organism will carry the inserted retroviral genome as an part of its own genome—an endogenous retrovirus that may be inherited by its offspring as a novel allele. Many ERVs have persisted in the genome of their hosts for millions of years, however, most of these have acquired inactivating mutations during host DNA replication and are no longer capable of producing virus. The general retrovirus genome consists of three genes vital for the invasion, replication, escape, and spreading of its viral genome and these three genes are gag, pol, and env. These viral proteins are encoded as polyproteins, in order to carry out their life cycle, the retrovirus relies heavily on the host cells machinery. Protease degrades peptide bonds of the viral polyproteins, making the separate proteins functional, reverse transcriptase functions to synthesize viral DNA from the viral RNA in the host cells cytoplasm before it entering the nucleus. Integrase guides the integration of viral DNA into the host genome, endogenous retroviruses can play an active role in shaping genomes. Most studies in this area have focused on the genomes of humans and higher primates, the long terminal repeat sequences that flank ERV genomes frequently act as alternate promoters and enhancers, often contributing to the transcriptome by producing tissue-specific variants. In addition, the proteins themselves have been co-opted to serve novel host functions, particularly in reproduction. Recombination between homologous retroviral sequences has contributed to gene shuffling and the generation of genetic variation. Furthermore, in the instance of potentially antagonistic effects of retroviral sequences, solo LTRs and LTRs associated with complete retroviral sequences have been shown to act as transcriptional elements on host genes. Their range of action is mainly by insertion into the 5’ UTRs of protein coding genes, however, in a few cases, the LTR functions as the major promoter for the gene
. PMID 15044706.
