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Prophage
A PROPHAGE is a bacteriophage (often shortened to "phage") 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 viral 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. CONTENTS * 1 Prophage
Prophage
induction * 2 Zygotic induction * 3 References * 4 See also PROPHAGE INDUCTIONUpon detection of host cell damage, such as UV light or certain chemicals, the prophage is excised from the bacterial chromosome in a process called prophage induction. After induction, viral replication begins via the Lytic Cycle . In the lytic cycle, the virus commandeers the cell's 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 gene transfer , and are considered part of the mobilome
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Bacteriophage
A BACTERIOPHAGE /ˈbækˈtɪər.i.oʊˌfeɪdʒ/ , also known informally as a _PHAGE_ /ˈfeɪdʒ/ , is a virus that infects and replicates within a bacterium . The term is derived from "bacteria" and the Greek : φαγεῖν (_phagein_), "to devour". 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 . Bacteriophages are ubiquitous viruses, found wherever bacteria exist. It’s estimated there are more than 1031 bacteriophages on the planet, more than every other organism on Earth, including bacteria, combined. Phages are widely distributed in locations populated by bacterial hosts, such as soil or the intestines of animals. One of the densest natural sources for phages and other viruses is sea water, where up to 9×108 virions per milliliter have been found in microbial mats at the surface, and up to 70% of marine bacteria may be infected by phages. They have been used for over 90 years as an alternative to antibiotics in the former Soviet Union and Central Europe, as well as in France
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Genome
In modern molecular biology and genetics , a GENOME is the GENETIC MATERIAL of an organism. It consists of DNA (or RNA in RNA viruses ). The genome includes both the genes (the coding regions ), the noncoding DNA and the genetic material of the mitochondria and chloroplasts . CONTENTS * 1 Origin of term * 2 Overview * 3 Sequencing and mapping * 4 Genome compositions * 4.1 Genome size * 4.2 Proportion of non-repetitive DNA * 4.3 Proportion of repetitive DNA * 4.3.1 Tandem repeats * 4.3.2 Interspersed repeats * 4.3.2.1 Retrotransposons * 4.3.2.2 DNA transposons * 5 Genome evolution * 6 See also * 7 References * 8 Further reading * 9 External links ORIGIN OF TERMThe term _genome_ was created in 1920 by Hans Winkler , professor of botany at the University of Hamburg , Germany . The Oxford Dictionary suggests the name is a blend of the words _gene _ and _chromosome _. However, see omics for a more thorough discussion. A few related _-ome_ words already existed—such as _biome _, _rhizome _, forming a vocabulary into which _genome_ fits systematically. OVERVIEWSome organisms have multiple copies of chromosomes : diploid , triploid , tetraploid and so on
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Circular Bacterial Chromosome
A CIRCULAR BACTERIAL CHROMOSOME is a bacterial chromosome in the form of a molecule of circular DNA. Unlike the linear DNA
DNA
of most eukaryotes , typical bacterial chromosomes are circular. Most bacterial chromosomes contain a circular DNA
DNA
molecule – there are no free ends to the DNA
DNA
. Free ends would otherwise create significant challenges to cells with respect to DNA
DNA
replication and stability. Cells that do contain chromosomes with DNA
DNA
ends, or telomeres (most eukaryotes), have acquired elaborate mechanisms to overcome these challenges. However, a circular chromosome can provide other challenges for cells. After replication, the two progeny circular chromosomes can sometimes remain interlinked or tangled, and they must be resolved so that each cell inherits one complete copy of the chromosome during cell division . CONTENTS * 1 Replication of a circular bacterial chromosome * 2 Initiation * 3 Elongation * 4 Termination * 5 Acknowledgments * 6 See also * 7 References REPLICATION OF A CIRCULAR BACTERIAL CHROMOSOME Bacterial chromosome replication is best understood in the well-studied bacteria Escherichia coli and Bacillus subtilis . Chromosome replication proceeds in three major stages: initiation, elongation and termination
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Plasmid
A PLASMID is a small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently. They are most commonly found in bacteria as small circular, double-stranded DNA molecules; however, plasmids are sometimes present in archaea and eukaryotic organisms . In nature, plasmids often carry genes that may benefit the survival of the organism, for example antibiotic resistance . While the chromosomes are big and contain all the essential genetic information for living under normal conditions, plasmids usually are very small and contain only additional genes that may be useful to the organism under certain situations or particular conditions. Artificial plasmids are widely used as vectors in molecular cloning , serving to drive the replication of recombinant DNA sequences within host organisms. Plasmids are considered _replicons _, a unit of DNA capable of replicating autonomously within a suitable host. However, plasmids, like viruses , are not generally classified as life . Plasmids can be transmitted from one bacterium to another (even of another species) via three main mechanisms: transformation , transduction , and conjugation . This host-to-host transfer of genetic material is called horizontal gene transfer , and plasmids can be considered part of the mobilome
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Viral Latency
INFLUENZA VIRUS LIFE CYCLE * Entry * Replication * Latency * Shedding VIRUS LATENCY (or VIRAL LATENCY) is the ability of a pathogenic virus to lie dormant (latent) within a cell, denoted as the lysogenic part of the viral life cycle. A latent viral infection is a type of persistent viral infection which is distinguished from a chronic viral infection. Latency is the phase in certain viruses' life cycles in which, after initial infection, proliferation of virus particles ceases. However, the viral genome is not fully eradicated. The result of this is that the virus can reactivate and begin producing large amounts of viral progeny without the host being infected by new outside virus, denoted as the lytic part of the viral life cycle, and stays within the host indefinitely. Virus
Virus
latency is not to be confused with clinical latency during the incubation period when a virus is not dormant. CONTENTS* 1 Mechanisms * 1.1 Episomal latency * 1.2 Proviral latency * 1.3 Maintaining latency * 2 Ramifications * 3 See also * 4 References MECHANISMSEPISOMAL LATENCYEpisomal latency refers to the use of genetic episomes during latency. In this type, viral genes are stabilized floating in the cytoplasm or nucleus as distinct objects, both as linear or lariat structures. Episomal latency is more vulnerable to ribozymes or host foreign gene degradation than provirus latency
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Bacteria
Actinobacteria (high-G+C ) Firmicutes (low-G+C ) Tenericutes (no wall ) * GRAM NEGATIVE / OUTER MEMBRANE PRESENT Aquificae Bacteroidetes / Fibrobacteres Chlorobi ( FCB group ) Chlamydiae Deinococcus-Thermus Fusobacteria Gemmatimonadetes Nitrospirae Planctomycetes Verrucomicrobia / Chlamydiae ( PVC group ) Proteobacteria Spirochaetes Synergistetes * UNKNOWN / UNGROUPED Acidobacteria Chloroflexi Chrysiogenetes Cyanobacteria Deferribacteres Dictyoglomi Thermodesulfobacteria Thermotogae SYNONYMS Eubacteria Woese common noun BACTERIA, singular BACTERIUM) constitute a large domain of prokaryotic microorganisms . Typically a few micrometres in length, bacteria have a number of shapes , ranging from spheres to rods and spirals . 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 , and the deep portions of Earth\'s crust . Bacteria also live in symbiotic and parasitic relationships with plants and animals
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Cell (biology)
The CELL (from Latin
Latin
cella, meaning "small room" ) 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, and cells are often called the "building blocks of life". The study of cells is called cell biology . Cells consist of cytoplasm enclosed within a membrane , which contains many biomolecules such as proteins and nucleic acids . Organisms can be classified as unicellular (consisting of a single cell; including bacteria ) or multicellular (including plants and animals ). While the number of cells in plants and animals varies from species to species, humans contain more than 10 trillion (1012) cells. Most plant and animal cells are visible only under a microscope , with dimensions between 1 and 100 micrometres . The cell was discovered by Robert Hooke in 1665, who named the biological units for their resemblance to cells inhabited by Christian monks in a monastery
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Lytic Cycle
The LYTIC CYCLE (/ˈlɪtɪk/ LIT-ək ), is one of the two cycles of viral reproduction , the other being the lysogenic cycle . The lytic cycle results in the destruction of the infected cell and its membrane. A key difference between the lytic and lysogenic phage cycles is that in the lytic phage, the viral DNA
DNA
exists as a separate molecule within the bacterial cell, and replicates separately from the host bacterial DNA. The location of viral DNA
DNA
in the lysogenic phage cycle is within the host DNA, therefore in both cases the virus/phage replicates using the host DNA
DNA
machinery, but in the lytic phage cycle, the phage is a free floating separate molecule to the host DNA. CONTENTS* 1 Description * 1.1 Penetrating * 1.2 Gene regulation biochemistry * 1.3 Maturation and lysis * 1.3.1 Lytic cycle
Lytic cycle
without lysis * 2 References DESCRIPTIONViruses that only use lvytic cycle are called virulent viruses (in contrast to temperate viruses). The lytic cycle is a six-stage cycle. In the first stage, called "penetration", the virus injects its own nucleic acid into a host cell. In some viruses this genetic material is circular and mimics a bacterial plasmid . The virus hijacks the cell's replication and translation mechanisms, using them to make more viruses
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Virulent
VIRULENCE is a pathogen or microbe's ability to infect or damage a host. In the context of gene for gene systems, often in plants, virulence refers to a pathogen's ability to infect a resistant host. In most other contexts, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host . The pathogenicity of an organism - its ability to cause disease - is determined by its virulence factors . The noun virulence derives from the adjective virulent. Virulent can describe either disease severity or a pathogen's infectivity. The word virulent derives from the Latin word virulentus, meaning "a poisoned wound" or "full of poison." In an ecological context, virulence can be defined as the host's parasite-induced loss of fitness . Virulence can be understood in terms of proximate causes —those specific traits of the pathogen that help make the host ill—and ultimate causes —the evolutionary pressures that lead to virulent traits occurring in a pathogen strain. CONTENTS* 1 Virulent bacteria * 1.1 Methods by which bacteria cause disease * 2 Virulent viruses * 3 Evolution
Evolution
* 4 See also * 5 References VIRULENT BACTERIAThe ability of bacteria to cause disease is described in terms of the number of infecting bacteria, the route of entry into the body, the effects of host defense mechanisms, and intrinsic characteristics of the bacteria called virulence factors
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Horizontal Gene Transfer
HORIZONTAL GENE TRANSFER (HGT) or LATERAL GENE TRANSFER (LGT) is the movement of genetic material between unicellular and/or multicellular organisms other than by the ("vertical") transmission of DNA from parent to offspring. HGT is an important factor in the evolution of many organisms. Horizontal gene transfer is the primary mechanism for the spread of antibiotic resistance in bacteria, plays an important role in the evolution of bacteria that can degrade novel compounds such as human-created pesticides and in the evolution, maintenance, and transmission of virulence . It often involves temperate bacteriophages and plasmids . Genes responsible for antibiotic resistance in one species of bacteria can be transferred to another species of bacteria through various mechanisms such as F -pilus , subsequently arming the antibiotic resistant genes' recipient against antibiotics, which is becoming medically challengeing to deal with. Most thinking in genetics has focused upon vertical transfer, but horizontal gene transfer is important, and among single-celled organisms is perhaps the dominant form of genetic transfer. Artificial horizontal gene transfer is a form of genetic engineering
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Mobilome
The MOBILOME is the total of all mobile genetic elements in a genome . Elements that can move within the genome (transposable elements ) are the major constituents of the mobilome in eukaryotes . In prokaryotes , however, mobile genetic elements that can move between genomes, like prophages and plasmids , are also an important part of the mobilome. REFERENCES * Barkay, T. and Smets, B.F. 2005. Horizontal gene flow in microbial communities. ASM News 71: 412-419.(PDF) * Frost, L.S. et al., 2005. Mobile genetic elements: the agents of open source evolution. Nat. Rev. of Microbiology 3: 722-732. This genetics article is a stub . You can help by expanding it . * v * t * e Retrieved from "https://en.wikipedia.org/w/index.php?title= Mobilome additional terms may apply. By using this site, you agree to the Terms of Use and Privacy Policy .® is a registered trademark of the Wikimedia Foundation, Inc
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Caudovirales
Myoviridae Podoviridae Siphoviridae The CAUDOVIRALES are an order of viruses also known as the tailed bacteriophages (cauda is Latin for "tail"). Under the Baltimore classification scheme, the Caudovirales
Caudovirales
are group I viruses as they have double stranded DNA
DNA
(dsDNA) genomes, which can be anywhere from 18,000 base pairs to 500,000 base pairs in length. The virus particles have a distinct shape; each virion has an icosohedral head that contains the viral genome, and is attached to a flexible tail by a connector protein. The order encompasses a wide range of viruses, many of which containing genes of similar nucleotide sequence and function. Some tailed bacteriophage genomes can vary quite significantly in nucleotide sequence, however, even among the same genus. Due to their characteristic structure and possession of potentially homologous genes, it is believed these bacteriophages possess a common origin. There are at least 350 recognised species in this order
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Zygotic Induction
ZYGOTIC INDUCTION occurs when a bacterial cell carrying the silenced DNA of a bacterial virus in its chromosome transfers the viral DNA along with its own DNA to another bacterial cell lacking the virus, causing the recipient of the DNA to break open. In the donor cell, a repressor protein encoded by the prophage (viral DNA) keeps the viral genes turned off so that virus is not produced. When DNA is transferred to the recipient cell by conjugation , the viral genes in the transferred DNA are immediately turned on because the recipient cell lacks the repressor. As a result, lots of virus is made in the recipient cell, and lysis eventually occurs to release the new virus. Zygotic induction was discovered by Élie Wollman and François Jacob in 1954. Historically, zygotic induction provided insight into the nature of bacterial conjugation. It also contributed to the development of the early repression model of gene regulation that explained how the lac operon and λ bacteriophage genes are negatively regulated. NATURE OF BACTERIAL CONJUGATIONIn 1947, Joshua Lederberg and Edward Tatum discovered that nutritional mutants of the bacterium E. coli , when incubated in mixed cultures, exchanged genetic markers to generate new recombinants, although the mating efficiency was inefficient. Later experiments with E
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PubMed Central
PUBMED CENTRAL (PMC) is a free digital repository that archives publicly accessible full-text scholarly articles that have been published within the biomedical and life sciences journal literature. As one of the major research databases within the suite of resources that have been developed by the National Center for Biotechnology Information (NCBI), PubMed Central is much more than just a document repository. Submissions into PMC undergo an indexing and formatting procedure which results in enhanced metadata, medical ontology , and unique identifiers which all enrich the XML structured data for each article on deposit. Content within PMC can easily be interlinked to many other NCBI databases and accessed via Entrez search and retrieval systems, further enhancing the public's ability to freely discover, read and build upon this portfolio of biomedical knowledge. PubMed Central should not be confused with PubMed . These are two very different services at their core. While PubMed is a searchable database of biomedical citations and abstracts, the full-text article referenced in the PubMed record will physically reside elsewhere. (Sometimes in print, sometimes online, sometimes free, sometimes behind a toll-wall accessible only to paying subscribers). PubMed Central is a free digital archive of articles, accessible to anyone from anywhere via a basic web browser
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Pubmed Identifier
PUBMED is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine (NLM) at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval . From 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries . PubMed, first released in January 1996, ushered in the era of private, free, home- and office-based MEDLINE searching. The PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore
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