Strain (biology)#Microbiology and virology
{{short description|Genetic variant, subtype or culture within a biological species}}
{{about|strains in biology|strain in chemistry|Strain (chemistry)}}
In biology, a strain is a genetic variant, a subtype or a culture within a biological species. Strains are often seen as inherently artificial concepts, characterized by a specific intent for genetic isolation.{{Cite journal|last1=DIJKSHOORN|first1=L.|last2=URSING|first2=B.M.|last3=URSING|first3=J.B.|date=2000|title=Strain, clone and species: comments on three basic concepts of bacteriology|journal=Journal of Medical Microbiology|volume=49|issue=5|pages=397–401|doi=10.1099/0022-1317-49-5-397|pmid=10798550|doi-access=free}} This is most easily observed in microbiology where strains are derived from a single cell colony and are typically quarantined by the physical constraints of a Petri dish. Strains are also commonly referred to within virology, botany, and with rodents used in experimental studies.{{cn|date=June 2022}}
Microbiology and virology
It has been said that "there is no universally accepted definition for the terms 'strain', 'variant', and 'isolate' in the virology community, and most virologists simply copy the usage of terms from others".{{cite journal|last1=Kuhn|first1=Jens H.|last2=Bao|first2=Yiming|last3=Bavari|first3=Sina|last4=Becker|first4=Stephan|last5=Bradfute|first5=Steven|last6=Brister|first6=J. Rodney|last7=Bukreyev|first7=Alexander A.|last8=Chandran|first8=Kartik|last9=Davey|first9=Robert A.|last10=Dolnik|first10=Olga|last11=Dye|first11=John M.|last12=Enterlein|first12=Sven|last13=Hensley|first13=Lisa E.|last14=Honko|first14=Anna N.|last15=Jahrling|first15=Peter B.|last16=Johnson|first16=Karl M.|author17-link=Gary Kobinger|last17=Kobinger|first17=Gary|last18=Leroy|first18=Eric M.|last19=Lever|first19=Mark S.|last20=Mühlberger|first20=Elke|last21=Netesov|first21=Sergey V.|last22=Olinger|first22=Gene G.|last23=Palacios|first23=Gustavo|last24=Patterson|first24=Jean L.|last25=Paweska|first25=Janusz T.|last26=Pitt|first26=Louise|last27=Radoshitzky|first27=Sheli R.|last28=Saphire|first28=Erica Ollmann|last29=Smither|first29=Sophie J.|last30=Swanepoel|first30=Robert|last31=Towner|first31=Jonathan S.|last32=van der Groen|first32=Guido|last33=Volchkov|first33=Viktor E.|last34=Wahl-Jensen|first34=Victoria|last35=Warren|first35=Travis K.|last36=Weidmann|first36=Manfred|last37=Nichol|first37=Stuart T.|title=Virus nomenclature below the species level: a standardized nomenclature for natural variants of viruses assigned to the family Filoviridae|journal=Archives of Virology|volume=158|issue=1|year=2012|pages=301–311|issn=0304-8608|doi=10.1007/s00705-012-1454-0|pmid=23001720|pmc=3535543|doi-access=free}}
A strain is a genetic variant or subtype of a microorganism such as a bacterial strain or a specific strain of a virus, or fungus. For example, a "flu strain" is a certain biological form of the influenza or "flu" virus. These flu strains are characterized by their differing isoforms of surface proteins. New viral strains can be created due to mutation or swapping of genetic components when two or more viruses infect the same cell in nature.{{Cite journal|last=Yong|first=Ed|title=Scientists create hybrid flu that can go airborne|journal=Nature|language=en|doi= 10.1038/nature.2013.12925|year=2013|s2cid=181077199}} These phenomena are known respectively as antigenic drift and antigenic shift. Microbial strains can also be differentiated by their genetic makeup using metagenomic methods to maximize resolution within species.{{Cite journal|last=Marx|first=Vivien|date=2016-04-28|title=Microbiology: the road to strain-level identification|journal=Nature Methods|language=En|volume=13|issue=5| pages=401–404|doi=10.1038/nmeth.3837|pmid=27123815|doi-access=free}} This has become a valuable tool to analyze the microbiome. {{Citation needed|date=November 2023}}
= Artificial constructs =
Scientists have modified strains of viruses in order to study their behavior, as in the case of the H5N1 influenza virus. While funding for such research has aroused controversy at times due to safety concerns, leading to a temporary pause, it has subsequently proceeded.{{Cite journal|last=Butler|first=Declan|title=Scientists call for 60-day suspension of mutant flu research|journal=Nature|language=en|doi=10.1038/nature.2012.9873|year=2012|s2cid=84203734}}{{cite web |title=Mutant flu |url=https://www.nature.com/collections/wntqfnjrxb |website=Nature News Special |access-date=21 April 2019}}
In biotechnology, microbial strains have been constructed to establish metabolic pathways suitable for treating a variety of applications.{{Cite journal|last=Lee|first=Sang Yup|date=2012-11-16|title=Metabolic altered and Synthetic Biology in Strain Development|journal=ACS Synthetic Biology|volume=1|issue=11|pages=491–492|doi=10.1021/sb300109d|pmid=23656224|doi-access=free}} Historically, a major effort of metabolic research has been devoted to the field of biofuel production.{{Cite journal|last1=Liu|first1=Tiangang|last2=Khosla|first2=Chaitan|date=2010-11-03|title=Genetic modification of Escherichia coli for Biofuel Production|journal=Annual Review of Genetics|volume=44| issue=1|pages=53–69|doi=10.1146/annurev-genet-102209-163440|pmid=20822440|issn=0066-4197}} Escherichia coli is most common species for prokaryotic strain engineering. Scientists have succeeded in establishing viable minimal genomes from which new strains can be developed.{{Cite journal|last1=Sung|first1=Bong Hyun|last2=Choe|first2=Donghui|last3=Kim|first3=Sun Chang|last4=Cho|first4=Byung-Kwan|date=2016-11-30|title=Construction of a minimal genome as a chassis for synthetic biology|journal=Essays in Biochemistry|language=en|volume=60|issue=4|pages=337–346|doi=10.1042/ebc20160024|issn=0071-1365|pmid=27903821|doi-access=free}} These minimal strains provide a near guarantee that experiments on genes outside the minimal framework will not be effected by non-essential pathways. Optimized strains of E. coli are typically used for this application. E. coli are also often used as a chassis for the expression of simple proteins. These strains, such as BL21, are genetically modified to minimize protease activity, hence enabling potential for high efficiency industrial scale protein production.{{cite journal |last1=Jeong |first1=H |last2=Kim |first2=HJ |last3=Lee |first3=SJ |title=Complete Genome Sequence of Escherichia coli Strain BL21. |journal=Genome Announcements |date=19 March 2015 |volume=3 |issue=2 |doi= 10.1128/genomeA.00134-15 |pmid=25792055 |pmc=4395058}}
Strains of yeasts are the most common subjects of eukaryotic genetic modification, especially with respect to industrial fermentation.{{Cite journal|last1=Steensels|first1=Jan|last2=Snoek|first2=Tim|last3=Meersman| first3=Esther|last4=Nicolino|first4=Martina Picca|last5=Voordeckers|first5=Karin|last6=Verstrepen|first6=Kevin J.|date=2014-09-01|title=Improving industrial yeast strains: exploiting natural and artificial diversity|journal=FEMS Microbiology Reviews| language=en|volume=38|issue=5|pages=947–995|doi=10.1111/1574-6976.12073|pmid=24724938|issn=0168-6445|pmc=4293462}}
Plants
The term has no official ranking status in botany; the term refers to the collective descendants produced from a common ancestor that share a uniform morphological or physiological character.{{Citation | last = Usher | first = George | year = 1996 | title = The Wordsworth Dictionary of Botany | pages = 361 | isbn = 978-1-85326-374-3 | publisher = Wordsworth Reference | location = Ware, Hertfordshire}} A strain is a designated group of offspring that are either descended from a modified plant (produced by conventional breeding or by biotechnological means), or which result from genetic mutation. {{Citation needed|date=November 2023}}
As an example, some rice strains are made by inserting new genetic material into a rice plant,{{cite news| url=http://www.latimes.com/news/science/la-me-wu18feb18,0,4864548.story | work=Los Angeles Times | first=Thomas H. | last=Maugh II | title=Geneticist shaped hybrid rice strains - Los Angeles Times | date=18 February 2008}} all the descendants of the genetically modified rice plant are a strain with unique genetic information that is passed on to later generations; the strain designation, which is normally a number or a formal name, covers all the plants that descend from the originally modified plant. The rice plants in the strain can be bred to other rice strains or cultivars, and if desirable plants are produced, these are further bred to stabilize the desirable traits; the stabilized plants that can be propagated and "come true" (remain identical to the parent plant) are given a cultivar name and released into production to be used by farmers. {{Citation needed|date=November 2023}}
Rodents
{{Further|Model organism}}
A laboratory mouse or rat strain is a group of animals that is genetically uniform. Strains are used in laboratory experiments. Mouse strains can be inbred, mutated, or genetically modified, while rat strains are usually inbred. A given inbred rodent population is considered genetically identical after 20 generations of sibling-mating. Many rodent strains have been developed for a variety of disease models, and they are also often used to test drug toxicity.{{Cite journal|last1=Anderson|first1=Mark S.|last2=Bluestone|first2=Jeffrey A.|date=2004-11-29|title=THE NOD MOUSE: A Model of Immune Dysregulation|journal=Annual Review of Immunology|volume=23|issue=1|pages=447–485|doi=10.1146/annurev.immunol.23.021704.115643|pmid=15771578|issn=0732-0582}}{{Cite journal|last1=Cheon|first1=Dong-Joo|last2=Orsulic|first2=Sandra|date=2011-01-24|title=Mouse Models of Cancer|journal=Annual Review of Pathology: Mechanisms of Disease|volume=6|issue=1|pages=95–119|doi=10.1146/annurev.pathol.3.121806.154244|pmid=20936938|issn=1553-4006}}{{Cite journal|last1=Yang|first1=Guang|last2=Zhao|first2=Lifen|last3=Liu|first3=Bing|last4=Shan|first4=Yujia|last5=Li|first5=Yang|last6=Zhou|first6=Huimin|last7=Jia|first7=Li|title=Nutritional support contributes to recuperation in a rat model of aplastic anemia by enhancing mitochondrial function|journal=Nutrition|volume=46|pages=67–77|doi=10.1016/j.nut.2017.09.002|pmid=29290359|year=2018}}
Insects
{{Main|Drosophila melanogaster#Model organism in genetics}}
The common fruit fly (Drosophila melanogaster) was among the first organisms used for genetic analysis, has a simple genome, and is very well understood. It has remained a popular model organism for many other reasons, like the ease of its breeding and maintenance, and the speed and volume of its reproduction. Various specific strains have been developed, including a flightless version with stunted wings (also used in the pet trade as live food for small reptiles and amphibians).{{citation needed|date=December 2022}}
See also
{{Portal|Biology}}
References
{{Reflist}}
External links
- [http://cgsc.biology.yale.edu/index.php Coli Genetic Stock Center]
- [http://ecoliwiki.net/colipedia/index.php/Category:Strains EcoliWiki E. coli strain index] {{Webarchive|url=https://web.archive.org/web/20190519231433/http://ecoliwiki.net/colipedia/index.php/Category:Strains |date=2019-05-19 }}
- [http://www.informatics.jax.org/imsr/index.jsp International Mouse Strain Resource (IMSR)]
- [http://www.informatics.jax.org/external/festing/rat/STRAINS.shtml Rat strain index]