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53-422: Agrobacterium is a genus of Gram-negative bacteria established by H. J. Conn that uses horizontal gene transfer to cause tumors in plants. Agrobacterium tumefaciens is the most commonly studied species in this genus. Agrobacterium is well known for its ability to transfer DNA between itself and plants, and for this reason it has become an important tool for genetic engineering . Leading up to

106-557: A species : see Botanical name and Specific name (zoology) . The rules for the scientific names of organisms are laid down in the nomenclature codes , which allow each species a single unique name that, for animals (including protists ), plants (also including algae and fungi ) and prokaryotes ( bacteria and archaea ), is Latin and binomial in form; this contrasts with common or vernacular names , which are non-standardized, can be non-unique, and typically also vary by country and language of usage. Except for viruses ,

159-481: A Ri-plasmid whilst laboratory studies have shown that non- Agrobacterium strains can also harbour a Ti-plasmid. Some environmental strains of Agrobacterium possess neither a Ti nor Ri-plasmid. These strains are avirulent. The plasmid T-DNA is integrated semi-randomly into the genome of the host cell, and the tumor morphology genes on the T-DNA are expressed, causing the formation of a gall. The T-DNA carries genes for

212-651: A later homonym of a validly published name is a nomen illegitimum or nom. illeg. ; for a full list refer to the International Code of Nomenclature for algae, fungi, and plants and the work cited above by Hawksworth, 2010. In place of the "valid taxon" in zoology, the nearest equivalent in botany is " correct name " or "current name" which can, again, differ or change with alternative taxonomic treatments or new information that results in previously accepted genera being combined or split. Prokaryote and virus codes of nomenclature also exist which serve as

265-628: A long time and redescribed as new by a range of subsequent workers, or if a range of genera previously considered separate taxa have subsequently been consolidated into one. For example, the World Register of Marine Species presently lists 8 genus-level synonyms for the sperm whale genus Physeter Linnaeus, 1758, and 13 for the bivalve genus Pecten O.F. Müller, 1776. Within the same kingdom, one generic name can apply to one genus only. However, many names have been assigned (usually unintentionally) to two or more different genera. For example,

318-433: A non-compromised immune system, and can, in some cases, act as commensals until the balance of the immune system is disrupted. Opportunistic infections can also be attributed to pathogens which cause mild illness in healthy individuals but lead to more serious illness when given the opportunity to take advantage of an immunocompromised host. A wide variety of pathogens are involved in opportunistic infection and can cause

371-412: A plant. This method transforms only cells in immediate contact with the bacteria, and results in transient expression of plasmid DNA. Agroinfiltration is commonly used to transform tobacco ( Nicotiana ). A common transformation protocol for Arabidopsis is the floral dip method: An inflorescence is dipped in a suspension of Agrobacterium , and the bacterium transforms the germline cells that make

424-622: A primary pathogen in otherwise healthy individuals. One of the earliest associations of human disease caused by Agrobacterium radiobacter was reported by Dr. J. R. Cain in Scotland (1988). A later study suggested that Agrobacterium attaches to and genetically transforms several types of human cells by integrating its T-DNA into the human cell genome. The study was conducted using cultured human tissue and did not draw any conclusions regarding related biological activity in nature. The ability of Agrobacterium to transfer genes to plants and fungi

477-409: A reference for designating currently accepted genus names as opposed to others which may be either reduced to synonymy, or, in the case of prokaryotes, relegated to a status of "names without standing in prokaryotic nomenclature". An available (zoological) or validly published (botanical) name that has been historically applied to a genus but is not regarded as the accepted (current/valid) name for

530-415: A similarly wide range in pathologies. A partial list of opportunistic pathogens and their associated presentations includes: Immunodeficiency or immunosuppression are characterized by the absence of or disruption in components of the immune system, leading to lower-than-normal levels of immune function and immunity against pathogens. They can be caused by a variety of factors, including: The lack of or

583-427: A taxon; however, the names published in suppressed works are made unavailable via the relevant Opinion dealing with the work in question. In botany, similar concepts exist but with different labels. The botanical equivalent of zoology's "available name" is a validly published name . An invalidly published name is a nomen invalidum or nom. inval. ; a rejected name is a nomen rejiciendum or nom. rej. ;

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636-455: A total of c. 520,000 published names (including synonyms) as at end 2019, increasing at some 2,500 published generic names per year. "Official" registers of taxon names at all ranks, including genera, exist for a few groups only such as viruses and prokaryotes, while for others there are compendia with no "official" standing such as Index Fungorum for fungi, Index Nominum Algarum and AlgaeBase for algae, Index Nominum Genericorum and

689-411: A variety of sources, such as a weakened immune system (as can occur in acquired immunodeficiency syndrome or when being treated with immunosuppressive drugs , as in cancer treatment ), an altered microbiome (such as a disruption in gut microbiota ), or breached integumentary barriers (as in penetrating trauma ). Many of these pathogens do not necessarily cause disease in a healthy host that has

742-544: A virally-associated cancer, has higher incidence rates in HIV-positive patients than in the general population. As immune function declines and HIV-infection progresses to AIDS, individuals are at an increased risk of opportunistic infections that their immune systems are no longer capable of responding properly to. Because of this, opportunistic infections are a leading cause of HIV/AIDS-related deaths. Since opportunistic infections can cause severe disease, much emphasis

795-428: Is approximated using the person's CD4 T-cell count and other indications. The table below provides information regarding the treatment management of common opportunistic infections. Alternative agents can be used instead of the preferred agents. These alternative agents may be used due to allergies, availability, or clinical presentation. The alternative agents are listed in the table below. Treatment depends on

848-612: Is discouraged by both the International Code of Zoological Nomenclature and the International Code of Nomenclature for algae, fungi, and plants , there are some five thousand such names in use in more than one kingdom. For instance, A list of generic homonyms (with their authorities), including both available (validly published) and selected unavailable names, has been compiled by the Interim Register of Marine and Nonmarine Genera (IRMNG). The type genus forms

901-403: Is modified to include DNA elements to select for transformed fungal strains, after co-incubation of Agrobacterium strains carrying these plasmids with fungal species. The Agrobacterium genome consists of three parts: a circular chromosome , a linear chromosome/ chromid , and (in some species) a Ti plasmid . The sequencing of the genomes of several species of Agrobacterium has permitted

954-414: Is needed for plant transformation. The genes to be introduced into the plant are cloned into a plant binary vector that contains the T-DNA region of the disarmed plasmid , together with a selectable marker (such as antibiotic resistance ) to enable selection for plants that have been successfully transformed. Plants are grown on media containing antibiotic following transformation, and those that do not have

1007-543: Is placed on measures to prevent infection. Such a strategy usually includes restoration of the immune system as soon as possible, avoiding exposures to infectious agents, and using antimicrobial medications ("prophylactic medications") directed against specific infections. The following may be avoided as a preventative measure to reduce the risk of infection: Individuals at higher risk are often prescribed prophylactic medication to prevent an infection from occurring. A person's risk level for developing an opportunistic infection

1060-460: Is somewhat arbitrary. Although all species within a genus are supposed to be "similar", there are no objective criteria for grouping species into genera. There is much debate among zoologists about whether enormous, species-rich genera should be maintained, as it is extremely difficult to come up with identification keys or even character sets that distinguish all species. Hence, many taxonomists argue in favor of breaking down large genera. For instance,

1113-474: Is the type species , and the generic name is permanently associated with the type specimen of its type species. Should the specimen turn out to be assignable to another genus, the generic name linked to it becomes a junior synonym and the remaining taxa in the former genus need to be reassessed. In zoological usage, taxonomic names, including those of genera, are classified as "available" or "unavailable". Available names are those published in accordance with

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1166-493: Is used in biotechnology , in particular, genetic engineering for plant improvement . Genomes of plants and fungi can be engineered by use of Agrobacterium for the delivery of sequences hosted in T-DNA binary vectors . A modified Ti or Ri plasmid can be used. The plasmid is 'disarmed' by deletion of the tumor inducing genes; the only essential parts of the T-DNA are its two small (25 base pair) border repeats, at least one of which

1219-621: The International Code of Zoological Nomenclature ; the earliest such name for any taxon (for example, a genus) should then be selected as the " valid " (i.e., current or accepted) name for the taxon in question. Consequently, there will be more available names than valid names at any point in time; which names are currently in use depending on the judgement of taxonomists in either combining taxa described under multiple names, or splitting taxa which may bring available names previously treated as synonyms back into use. "Unavailable" names in zoology comprise names that either were not published according to

1272-824: The International Plant Names Index for plants in general, and ferns through angiosperms, respectively, and Nomenclator Zoologicus and the Index to Organism Names for zoological names. Totals for both "all names" and estimates for "accepted names" as held in the Interim Register of Marine and Nonmarine Genera (IRMNG) are broken down further in the publication by Rees et al., 2020 cited above. The accepted names estimates are as follows, broken down by kingdom: The cited ranges of uncertainty arise because IRMNG lists "uncertain" names (not researched therein) in addition to known "accepted" names;

1325-404: The platypus belongs to the genus Ornithorhynchus although George Shaw named it Platypus in 1799 (these two names are thus synonyms ) . However, the name Platypus had already been given to a group of ambrosia beetles by Johann Friedrich Wilhelm Herbst in 1793. A name that means two different things is a homonym . Since beetles and platypuses are both members of the kingdom Animalia,

1378-463: The 1990s, the genus Agrobacterium was used as a wastebasket taxon . With the advent of 16S sequencing , many Agrobacterium species (especially the marine species) were reassigned to genera such as Ahrensia , Pseudorhodobacter , Ruegeria , and Stappia . The remaining Agrobacterium species were assigned to three biovars: biovar 1 ( Agrobacterium tumefaciens ), biovar 2 ( Agrobacterium rhizogenes ), and biovar 3 ( Agrobacterium vitis ). In

1431-473: The French botanist Joseph Pitton de Tournefort (1656–1708) is considered "the founder of the modern concept of genera". The scientific name (or the scientific epithet) of a genus is also called the generic name ; in modern style guides and science, it is always capitalised. It plays a fundamental role in binomial nomenclature , the system of naming organisms , where it is combined with the scientific name of

1484-463: The T-DNA integrated into their genome will die. An alternative method is agroinfiltration . Transformation with Agrobacterium can be achieved in multiple ways. Protoplasts or alternatively leaf-discs can be incubated with the Agrobacterium and whole plants regenerated using plant tissue culture . In agroinfiltration the Agrobacterium may be injected directly into the leaf tissue of

1537-442: The base for higher taxonomic ranks, such as the family name Canidae ("Canids") based on Canis . However, this does not typically ascend more than one or two levels: the order to which dogs and wolves belong is Carnivora ("Carnivores"). The numbers of either accepted, or all published genus names is not known precisely; Rees et al., 2020 estimate that approximately 310,000 accepted names (valid taxa) may exist, out of

1590-419: The biosynthetic enzymes for the production of unusual amino acids , typically octopine or nopaline . It also carries genes for the biosynthesis of the plant hormones , auxin and cytokinins , and for the biosynthesis of opines , providing a carbon and nitrogen source for the bacteria that most other micro-organisms can't use, giving Agrobacterium a selective advantage . By altering the hormone balance in

1643-639: The disruption of normal vaginal microbiota allows the proliferation of opportunistic microorganisms and will cause the opportunistic infection bacterial vaginosis . HIV is a virus that targets T cells of the immune system and, as a result, HIV infection can lead to progressively worsening immunodeficiency, a condition ideal for the development of opportunistic infection. Because of this, respiratory and central nervous system opportunistic infections, including tuberculosis and meningitis, respectively, are associated with later-stage HIV infection, as are numerous other infectious pathologies. Kaposi's sarcoma,

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1696-427: The early 2000s, Agrobacterium was synonymized with the genus Rhizobium . This move proved to be controversial. The debate was finally resolved when the genus Agrobacterium was reinstated after it was demonstrated that it was phylogenetically distinct from Rhizobium and that Agrobacterium species were unified by a unique synapomorphy : the presence of the protelomerase gene, telA , which causes all members of

1749-489: The female gametes . The seeds can then be screened for antibiotic resistance (or another marker of interest). Plants that have not integrated the plasmid DNA will die when exposed to the antibiotic. Agrobacterium is listed as being the vector of genetic material that was transferred to these USA GMOs: The transformation of fungi using Agrobacterium is used primarily for research purposes, and follows similar approaches as for plant transformation. The Ti plasmid system

1802-457: The first to demonstrate that the virulence genes could be removed without adversely affecting the ability of Agrobacterium to insert its own DNA into the plant genome (1983). Genus The composition of a genus is determined by taxonomists . The standards for genus classification are not strictly codified, so different authorities often produce different classifications for genera. There are some general practices used, however, including

1855-446: The form "author, year" in zoology, and "standard abbreviated author name" in botany. Thus in the examples above, the genus Canis would be cited in full as " Canis Linnaeus, 1758" (zoological usage), while Hibiscus , also first established by Linnaeus but in 1753, is simply " Hibiscus L." (botanical usage). Each genus should have a designated type , although in practice there is a backlog of older names without one. In zoology, this

1908-737: The generic name (or its abbreviated form) still forms the leading portion of the scientific name, for example, Canis lupus lupus for the Eurasian wolf subspecies, or as a botanical example, Hibiscus arnottianus ssp. immaculatus . Also, as visible in the above examples, the Latinised portions of the scientific names of genera and their included species (and infraspecies, where applicable) are, by convention, written in italics . The scientific names of virus species are descriptive, not binomial in form, and may or may not incorporate an indication of their containing genus; for example,

1961-599: The genome sequences of Agrobacterium species will continue to increase, resulting in substantial insights into the function and evolutionary history of this group of plant-associated microbes. Marc Van Montagu and Jozef Schell at the University of Ghent ( Belgium ) discovered the gene transfer mechanism between Agrobacterium and plants, which resulted in the development of methods to alter Agrobacterium into an efficient delivery system for gene engineering in plants. A team of researchers led by Mary-Dell Chilton were

2014-417: The genus to have a linear chromid . By this time, however, the three Agrobacterium biovars had become defunct; biovar 1 remained with Agrobacterium , biovar 2 was renamed Rhizobium rhizogenes , and biovar 3 was renamed Allorhizobium vitis . Agrobacterium tumefaciens causes crown-gall disease in plants. The disease is characterised by a tumour -like growth or gall on the infected plant, often at

2067-420: The genus, Agrobacterium tumefaciens , Agrobacterium rhizogenes , and Agrobacterium vitis . Strains within Agrobacterium tumefaciens and Agrobacterium rhizogenes are known to be able to harbour either a Ti or Ri- plasmid , whilst strains of Agrobacterium vitis , generally restricted to grapevines, can harbour a Ti-plasmid. Non- Agrobacterium strains have been isolated from environmental samples which harbour

2120-432: The idea that a newly defined genus should fulfill these three criteria to be descriptively useful: Moreover, genera should be composed of phylogenetic units of the same kind as other (analogous) genera. The term "genus" comes from Latin genus , a noun form cognate with gignere ('to bear; to give birth to'). The Swedish taxonomist Carl Linnaeus popularized its use in his 1753 Species Plantarum , but

2173-421: The junction between the root and the shoot. Tumors are incited by the conjugative transfer of a DNA segment ( T-DNA ) from the bacterial tumour-inducing (Ti) plasmid . The closely related species, Agrobacterium rhizogenes , induces root tumors, and carries the distinct Ri (root-inducing) plasmid. Although the taxonomy of Agrobacterium is currently under revision it can be generalised that 3 biovars exist within

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2226-633: The largest component, with 23,236 ± 5,379 accepted genus names, of which 20,845 ± 4,494 are angiosperms (superclass Angiospermae). By comparison, the 2018 annual edition of the Catalogue of Life (estimated >90% complete, for extant species in the main) contains currently 175,363 "accepted" genus names for 1,744,204 living and 59,284 extinct species, also including genus names only (no species) for some groups. The number of species in genera varies considerably among taxonomic groups. For instance, among (non-avian) reptiles , which have about 1180 genera,

2279-415: The lizard genus Anolis has been suggested to be broken down into 8 or so different genera which would bring its ~400 species to smaller, more manageable subsets. Opportunistic infection An opportunistic infection is an infection caused by pathogens ( bacteria , fungi , parasites or viruses ) that take advantage of an opportunity not normally available. These opportunities can stem from

2332-403: The most (>300) have only 1 species, ~360 have between 2 and 4 species, 260 have 5–10 species, ~200 have 11–50 species, and only 27 genera have more than 50 species. However, some insect genera such as the bee genera Lasioglossum and Andrena have over 1000 species each. The largest flowering plant genus, Astragalus , contains over 3,000 species. Which species are assigned to a genus

2385-428: The name could not be used for both. Johann Friedrich Blumenbach published the replacement name Ornithorhynchus in 1800. However, a genus in one kingdom is allowed to bear a scientific name that is in use as a generic name (or the name of a taxon in another rank) in a kingdom that is governed by a different nomenclature code. Names with the same form but applying to different taxa are called "homonyms". Although this

2438-425: The plant cell, the division of those cells cannot be controlled by the plant, and tumors form. The ratio of auxin to cytokinin produced by the tumor genes determines the morphology of the tumor (root-like, disorganized or shoot-like). Although generally seen as an infection in plants, Agrobacterium can be responsible for opportunistic infections in humans with weakened immune systems , but has not been shown to be

2491-541: The provisions of the ICZN Code, e.g., incorrect original or subsequent spellings, names published only in a thesis, and generic names published after 1930 with no type species indicated. According to "Glossary" section of the zoological Code, suppressed names (per published "Opinions" of the International Commission of Zoological Nomenclature) remain available but cannot be used as the valid name for

2544-497: The specific name particular to the wolf. A botanical example would be Hibiscus arnottianus , a particular species of the genus Hibiscus native to Hawaii. The specific name is written in lower-case and may be followed by subspecies names in zoology or a variety of infraspecific names in botany . When the generic name is already known from context, it may be shortened to its initial letter, for example, C. lupus in place of Canis lupus . Where species are further subdivided,

2597-412: The standard format for a species name comprises the generic name, indicating the genus to which the species belongs, followed by the specific epithet, which (within that genus) is unique to the species. For example, the gray wolf 's scientific name is Canis lupus , with Canis ( Latin for 'dog') being the generic name shared by the wolf's close relatives and lupus (Latin for 'wolf') being

2650-462: The study of the evolutionary history of these organisms and has provided information on the genes and systems involved in pathogenesis, biological control and symbiosis . One important finding is the possibility that chromosomes are evolving from plasmids in many of these bacteria. Another discovery is that the diverse chromosomal structures in this group appear to be capable of supporting both symbiotic and pathogenic lifestyles. The availability of

2703-403: The taxon is termed a synonym ; some authors also include unavailable names in lists of synonyms as well as available names, such as misspellings, names previously published without fulfilling all of the requirements of the relevant nomenclatural code, and rejected or suppressed names. A particular genus name may have zero to many synonyms, the latter case generally if the genus has been known for

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2756-576: The values quoted are the mean of "accepted" names alone (all "uncertain" names treated as unaccepted) and "accepted + uncertain" names (all "uncertain" names treated as accepted), with the associated range of uncertainty indicating these two extremes. Within Animalia, the largest phylum is Arthropoda , with 151,697 ± 33,160 accepted genus names, of which 114,387 ± 27,654 are insects (class Insecta). Within Plantae, Tracheophyta (vascular plants) make up

2809-429: The virus species " Salmonid herpesvirus 1 ", " Salmonid herpesvirus 2 " and " Salmonid herpesvirus 3 " are all within the genus Salmonivirus ; however, the genus to which the species with the formal names " Everglades virus " and " Ross River virus " are assigned is Alphavirus . As with scientific names at other ranks, in all groups other than viruses, names of genera may be cited with their authorities, typically in

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