A bioassay is an analytical method to determine concentration or potency of a substance by its effect on living cells or tissues. Bioassays were used to estimate the potency of agents by observing their effects on living animals or tissues. A bioassay experiment can either be direct or indirect. If the measured response is binary, the assay is qualititative, if not, it is quantitative. Bioassay is used to give a quality assessment of a mixture. Bioassay is used to monitor water quality and sewage discharge and its impact on surrounding, it is used to assess the environmental impact and safety of new technologies and facilities. Bioassay is a biochemical test to estimate the relative potency of a sample compound to a standard compound. Typical bioassay involves a stimulus applied to a subject and a response of the subject is triggered and measured; the intensity of stimulus is varied by doses and depending on this intensity of stimulus, a change/response will be followed by a subject.. The first uses of bioassay dates back to as early as the late 19th century, when the foundation of bioassays was laid down by a German physician, Paul Ehrlich.
He introduced the concept of standardization by the reactions of living matter. His bioassay on diphtheria antitoxin was the first bioassay to receive recognition, his use of bioassay was able to discover that administration of increasing dose of diphteria in animals stimulated production of antiserum. Many of the early bioassays consisted of using animals to test carcinogenicity of chemicals. One well known example is a "canary in the coal mine" experiment. To test for methane, miners would take methane-sensitive canaries to coal mines to ensure safe air. In 1915, Yamaigiwa Katsusaburo and Koichi Ichikawa tested the carcinogenicity of coal tar using inner surface of rabbit's ears. Through 1940s and 1960s, animal bioassay was used to test for toxicity and safety of drugs, food additives and pesticides. In late 1960s and 1970s, reliance on bioassay increased as the public concern for occupational and environmental hazards increased. While before this health risks of certain chemicals such as pesticide was tested in animal bioassay, it was still rare and testing was not seen often.
- The stimulus/standard sufficiently produces measurable and specific response. The response must be clear recognized, directly measured. - The relationship between the dose and the response is first ascertained. The dose corresponding to a given response is obtained from the relation for each preparation separately. - The assay involves ` none' response. The response is produced by threshold effect. - quantitative analytical method that measures absorbance of color change from antigen-antibody reaction. ELISA is used to measure variety of substances in human body from cortisol levels for stress to glucose level for diabetes. Home pregnancy test involves ELISA to detect the increase of human chorionic gonadotropin during pregnancy. HIV test uses indirect ELISA to detect HIV antibody caused by infection. Assay Immunoassay
OCLC Online Computer Library Center, Incorporated d/b/a OCLC is an American nonprofit cooperative organization "dedicated to the public purposes of furthering access to the world's information and reducing information costs". It was founded in 1967 as the Ohio College Library Center. OCLC and its member libraries cooperatively produce and maintain WorldCat, the largest online public access catalog in the world. OCLC is funded by the fees that libraries have to pay for its services. OCLC maintains the Dewey Decimal Classification system. OCLC began in 1967, as the Ohio College Library Center, through a collaboration of university presidents, vice presidents, library directors who wanted to create a cooperative computerized network for libraries in the state of Ohio; the group first met on July 5, 1967 on the campus of the Ohio State University to sign the articles of incorporation for the nonprofit organization, hired Frederick G. Kilgour, a former Yale University medical school librarian, to design the shared cataloging system.
Kilgour wished to merge the latest information storage and retrieval system of the time, the computer, with the oldest, the library. The plan was to merge the catalogs of Ohio libraries electronically through a computer network and database to streamline operations, control costs, increase efficiency in library management, bringing libraries together to cooperatively keep track of the world's information in order to best serve researchers and scholars; the first library to do online cataloging through OCLC was the Alden Library at Ohio University on August 26, 1971. This was the first online cataloging by any library worldwide. Membership in OCLC is based on use of services and contribution of data. Between 1967 and 1977, OCLC membership was limited to institutions in Ohio, but in 1978, a new governance structure was established that allowed institutions from other states to join. In 2002, the governance structure was again modified to accommodate participation from outside the United States.
As OCLC expanded services in the United States outside Ohio, it relied on establishing strategic partnerships with "networks", organizations that provided training and marketing services. By 2008, there were 15 independent United States regional service providers. OCLC networks played a key role in OCLC governance, with networks electing delegates to serve on the OCLC Members Council. During 2008, OCLC commissioned two studies to look at distribution channels. In early 2009, OCLC negotiated new contracts with the former networks and opened a centralized support center. OCLC provides bibliographic and full-text information to anyone. OCLC and its member libraries cooperatively produce and maintain WorldCat—the OCLC Online Union Catalog, the largest online public access catalog in the world. WorldCat has holding records from private libraries worldwide; the Open WorldCat program, launched in late 2003, exposed a subset of WorldCat records to Web users via popular Internet search and bookselling sites.
In October 2005, the OCLC technical staff began a wiki project, WikiD, allowing readers to add commentary and structured-field information associated with any WorldCat record. WikiD was phased out; the Online Computer Library Center acquired the trademark and copyrights associated with the Dewey Decimal Classification System when it bought Forest Press in 1988. A browser for books with their Dewey Decimal Classifications was available until July 2013; until August 2009, when it was sold to Backstage Library Works, OCLC owned a preservation microfilm and digitization operation called the OCLC Preservation Service Center, with its principal office in Bethlehem, Pennsylvania. The reference management service QuestionPoint provides libraries with tools to communicate with users; this around-the-clock reference service is provided by a cooperative of participating global libraries. Starting in 1971, OCLC produced catalog cards for members alongside its shared online catalog. OCLC commercially sells software, such as CONTENTdm for managing digital collections.
It offers the bibliographic discovery system WorldCat Discovery, which allows for library patrons to use a single search interface to access an institution's catalog, database subscriptions and more. OCLC has been conducting research for the library community for more than 30 years. In accordance with its mission, OCLC makes its research outcomes known through various publications; these publications, including journal articles, reports and presentations, are available through the organization's website. OCLC Publications – Research articles from various journals including Code4Lib Journal, OCLC Research, Reference & User Services Quarterly, College & Research Libraries News, Art Libraries Journal, National Education Association Newsletter; the most recent publications are displayed first, all archived resources, starting in 1970, are available. Membership Reports – A number of significant reports on topics ranging from virtual reference in libraries to perceptions about library funding. Newsletters – Current and archived newsletters for the library and archive community.
Presentations – Presentations from both guest speakers and OCLC research from conferences and other events. The presentations are organized into five categories: Conference presentations, Dewey presentations, Distinguished Seminar Series, Guest presentations, Research staff
Bruce Nathan Ames is an American biochemist. He is a professor of Biochemistry and Molecular Biology Emeritus at the University of California, a senior scientist at Children's Hospital Oakland Research Institute, he is the inventor of the Ames test, a system for and cheaply testing the mutagenicity of compounds. Ames, raised in New York City, is a graduate of the Bronx High School of Science, his undergraduate studies were at Cornell University in Ithaca, New York, his graduate studies were completed at the California Institute of Technology. Ames was elected a Fellow of the American Academy of Arts and Sciences in 1970, he is a recipient of the Bolton S. Corson Medal in 1980, Tyler Prize for Environmental Achievement in 1985, the Japan Prize in 1997, the National Medal of Science in 1998 and the Thomas Hunt Morgan Medal in 2004, among many others, his research focuses on cancer and aging and he has authored over 550 scientific publications. He is among the few hundred most-cited scientists in all fields.
Ames' current research includes identifying agents that delay the mitochondrial decay of aging, understanding the role of mitochondrial decay in aging in the brain, optimizing micronutrient intakes in the population to prevent disease and obesity. He is interested in mutagens as they relate to cancer prevention and aging. Dr. Ames received more than $650,000 in support from the National Foundation for Cancer Research between 1998 and 2007, he is married to Giovanna Ferro-Luzzi Ames, a professor at the University of California, Berkeley In the 1970s, Bruce Ames developed the Ames test, a cheap and convenient assay for mutagens and therefore potential carcinogens. Previous carcinogenic testing used live animals, the procedures are expensive and time-consuming; this made animal testing impractical for use in screening on a wide scale, reduced the number of compounds that could be tested. The Ames test on the other hand uses the bacteria Salmonella typhimurium to test for mutagens, is cheaper and faster.
The Ames test became used as an initial screen for possible carcinogens and has been used to identify potential carcinogens used in commercial products. Their identification led to some of those formulations, such as chemicals used in hair dye, being withdrawn from commercial use; the ease with which Ames test allows used chemicals to be identified as possible carcinogens made him an early hero of environmentalism. Subsequent work in Ames' lab involved looking at an overview of what was mutagenic or carcinogenic, to what degree. Scientists tended to only look for positive or negative results without considering the magnitude of the effect, which meant that as more and more items were shown to be mutagenic, there was no system for evaluating the relative dangers, he continued to test various natural and man-made compounds, discovered that, despite what he and others had assumed occurring compounds were not turning out to be benign as compared to man-made ones. His continued work led to his falling out of favor with many environmentalists.
As natural chemicals turned out to be mutagenic, he argued that environmental exposure to manufactured chemicals may be of limited relevance to human cancer when such chemicals are mutagenic in an Ames test and carcinogenic in rodent assays. He contended that most human genetic damage arises from essential micronutrients lacking in poor diets and the oxidation of DNA during normal metabolism, that the most important environmental carcinogens may include some whose chief effect is to cause the chronic division of stem cells whereby the normal protective mechanisms of a cell become less effective, he argued against the banning of synthetic pesticides and other chemicals such as Alar which have been shown to be carcinogenic. Ames published results showing that many ordinary food products would be found carcinogenic according to the same criteria. Ames was concerned that overzealous attention to the minor health effects of trace quantities of carcinogens may divert scarce financial resources away from major health risks, cause public confusion about the relative importance of different hazards.
Ames considered himself a leading “contrarian in the hysteria over tiny traces of chemicals that may or may not cause cancer", said that "if you have thousands of hypothetical risks that you are supposed to pay attention to, that drives out the major risks you should be aware of." Eli Lilly Award of the American Chemical Society 1964 Elected to American Academy of Arts and Sciences 1970 Elected to National Academy of Sciences 1972 Fellow of the American Association for the Advancement of Science 1980 Wadsworth Award 1981 Charles S. Mott Prize, GM Cancer Research Foundation 1983 IBM-Princess Takamatsu Cancer Res Fund Lectureship 1984 Elected Foreign Member, The Royal Swedish Academy of Sciences 1989 Elected Fellow, Academy of Toxicological Sciences 1992 Elected Fellow, American Academy of Microbiology 1992 Röntgen Prize of the Accademia Nazionale de Lincei 1993 Messel Medal, British Society of Chemical Industry 1996 Society of Toxicology Public Communications Award 1996 Honda Prize 1996 Japan Prize 1997 Kehoe Award, American College of Occup. and Environ.
Med 1997 Medal of the City of Paris 1998 U. S. National Medal of Science 1998 American Society for Microbiology Lifetime Achievement Award 2001 Linus Pauling Institute Prize for Health Research 2001 Thomas Hunt Morgan Medal, Genetics Society Am 2004 American Society for Nutrition/CRN M. S. Rose Award 2008 Orthomolecular Medicine Hall of Fame 2010 SOT Lifetime Achievement Award 2012 American Society of Nutrition Class of 2018 Fellows 2018 Off
University of California, Berkeley
The University of California, Berkeley is a public research university in Berkeley, California. It was founded in 1868 and serves as the flagship institution of the ten research universities affiliated with the University of California system. Berkeley has since grown to instruct over 40,000 students in 350 undergraduate and graduate degree programs covering numerous disciplines. Berkeley is one of the 14 founding members of the Association of American Universities, with $789 million in R&D expenditures in the fiscal year ending June 30, 2015. Today, Berkeley maintains close relationships with three United States Department of Energy National Laboratories—Lawrence Berkeley National Laboratory, Lawrence Livermore National Laboratory and Los Alamos National Laboratory—and is home to many institutes, including the Mathematical Sciences Research Institute and the Space Sciences Laboratory. Through its partner institution University of California, San Francisco, Berkeley offers a joint medical program at the UCSF Medical Center.
As of October 2018, Berkeley alumni, faculty members and researchers include 107 Nobel laureates, 25 Turing Award winners, 14 Fields Medalists. They have won 9 Wolf Prizes, 45 MacArthur Fellowships, 20 Academy Awards, 14 Pulitzer Prizes and 207 Olympic medals. In 1930, Ernest Lawrence invented the cyclotron at Berkeley, based on which UC Berkeley researchers along with Berkeley Lab have discovered or co-discovered 16 chemical elements of the periodic table – more than any other university in the world. During the 1940s, Berkeley physicist J. R. Oppenheimer, the "Father of the Atomic Bomb," led the Manhattan project to create the first atomic bomb. In the 1960s, Berkeley was noted for the Free Speech Movement as well as the Anti-Vietnam War Movement led by its students. In the 21st century, Berkeley has become one of the leading universities in producing entrepreneurs and its alumni have founded a large number of companies worldwide. Berkeley is ranked among the top 20 universities in the world by the Academic Ranking of World Universities, the Times Higher Education World University Rankings, the U.
S. News & World Report Global University Rankings, it is considered one of the "Public Ivies", meaning that it is a public university thought to offer a quality of education comparable to that of the Ivy League. In 1866, the private College of California purchased the land comprising the current Berkeley campus in order to re-sell it in subdivided lots to raise funds; the effort failed to raise the necessary funds, so the private college merged with the state-run Agricultural and Mechanical Arts College to form the University of California, the first full-curriculum public university in the state. Upon its founding, The Dwinelle Bill stated that the "University shall have for its design, to provide instruction and thorough and complete education in all departments of science and art, industrial and professional pursuits, general education, special courses of instruction in preparation for the professions". Ten faculty members and 40 students made up the new University of California when it opened in Oakland in 1869.
Frederick H. Billings was a trustee of the College of California and suggested that the new site for the college north of Oakland be named in honor of the Anglo-Irish philosopher George Berkeley. In 1870, Henry Durant, the founder of the College of California, became the first president. With the completion of North and South Halls in 1873, the university relocated to its Berkeley location with 167 male and 22 female students where it held its first classes. Beginning in 1891, Phoebe Apperson Hearst made several large gifts to Berkeley, funding a number of programs and new buildings and sponsoring, in 1898, an international competition in Antwerp, where French architect Émile Bénard submitted the winning design for a campus master plan. In 1905, the University Farm was established near Sacramento becoming the University of California, Davis. In 1919, Los Angeles State Normal School became the southern branch of the University, which became University of California, Los Angeles. By 1920s, the number of campus buildings had grown and included twenty structures designed by architect John Galen Howard.
Robert Gordon Sproul served as president from 1930 to 1958. In the 1930s, Ernest Lawrence helped establish the Radiation Laboratory and invented the cyclotron, which won him the Nobel physics prize in 1939. Based on the cyclotron, UC Berkeley scientists and researchers, along with Berkeley Lab, went on to discover 16 chemical elements of the periodic table – more than any other university in the world. In particular, during World War II and following Glenn Seaborg's then-secret discovery of plutonium, Ernest Orlando Lawrence's Radiation Laboratory began to contract with the U. S. Army to develop the atomic bomb. UC Berkeley physics professor J. Robert Oppenheimer was named scientific head of the Manhattan Project in 1942. Along with the Lawrence Berkeley National Laboratory, Berkeley was a partner in managing two other labs, Los Alamos National Laboratory and Lawrence Livermore National Laboratory. By 1942, the American Council on Education ranked Berkeley second only to Harvard in the number of distinguished departments.
During the McCarthy era in 1949, the Board of Regents adopted an anti-communist loyalty oath. A number of faculty members led by Edward C. Tolman were dismissed. In 1952, the University of California became; each campus was give
Bacteria are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. 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, are present in most of its habitats. Bacteria inhabit soil, acidic hot springs, radioactive waste, the deep portions of Earth's crust. Bacteria live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, only about half of the bacterial phyla have species that can be grown in the laboratory; the study of bacteria is known as a branch of microbiology. There are 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants and animals. 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 dead bodies. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Data reported by researchers in October 2012 and published in March 2013 suggested that bacteria thrive in the Mariana Trench, 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—they're adaptable to conditions, survive wherever they are."The famous notion that bacterial cells in the human body outnumber human cells by a factor of 10:1 has been debunked. There are 39 trillion bacterial cells in the human microbiota as personified by a "reference" 70 kg male 170 cm tall, whereas there are 30 trillion human cells in the body.
This means that although they do have the upper hand in actual numbers, it is only by 30%, not 900%. The largest number exist in the gut flora, a large number on the skin; the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial in the gut flora. However several species of bacteria are pathogenic and cause infectious diseases, including cholera, anthrax and bubonic plague; the most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year in sub-Saharan Africa. In developed countries, antibiotics are used to treat bacterial infections and are used in farming, making antibiotic resistance a growing problem. In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium and other metals in the mining sector, as well as in biotechnology, the manufacture of antibiotics and other chemicals.
Once regarded as plants 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 harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two different groups of organisms that evolved from an ancient common ancestor; these evolutionary domains are called Archaea. The word bacteria is the plural of the New Latin bacterium, the latinisation of the Greek βακτήριον, the diminutive of βακτηρία, meaning "staff, cane", because the first ones to be discovered were rod-shaped; the ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, about 4 billion years ago. For about 3 billion years, most organisms were microscopic, bacteria and archaea were the dominant forms of life. Although bacterial fossils exist, such as stromatolites, their lack of distinctive morphology prevents them from being used to examine the history of bacterial evolution, or to date the time of origin of a particular bacterial species.
However, gene sequences can be used to reconstruct the bacterial phylogeny, these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. The most recent common ancestor of bacteria and archaea was a hyperthermophile that lived about 2.5 billion–3.2 billion years ago. Bacteria were involved in the second great evolutionary divergence, that of the archaea and eukaryotes. Here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves related to the Archaea; this involved the engulfment by proto-eukaryotic cells of alphaproteobacterial symbionts to form either mitochondria or hydrogenosomes, which are still found in all known Eukarya. Some eukaryotes that contained mitochondria engulfed cyanobacteria-like organisms, leading to the formation of chloroplasts in algae and plants; this is known as primary endosymbiosis. Bacteria display a wide diversity of sizes, called morphologies.
Bacterial cells are about one-tenth the size of eukaryotic cells
Nucleotide excision repair
Nucleotide excision repair is a DNA repair mechanism. DNA damage occurs because of chemicals and other mutagens. Three excision repair pathways exist to repair single stranded DNA damage: Nucleotide excision repair, base excision repair, DNA mismatch repair. While the BER pathway can recognize specific non-bulky lesions in DNA, it can correct only damaged bases that are removed by specific glycosylases; the MMR pathway only targets mismatched Watson-Crick base pairs. Nucleotide excision repair is a important excision mechanism that removes DNA damage induced by ultraviolet light. UV DNA damage results in bulky DNA adducts - these adducts are thymine dimers and 6,4-photoproducts. Recognition of the damage leads to removal of a short single-stranded DNA segment that contains the lesion; the undamaged single-stranded DNA remains and DNA polymerase uses it as a template to synthesize a short complementary sequence. Final ligation to complete NER and form a double stranded DNA is carried out by DNA ligase.
NER can be divided into two subpathways: global genomic NER and transcription coupled NER. The two subpathways differ in how they recognize DNA damage but they share the same process for lesion incision and ligation; the importance of NER is evidenced by the severe human diseases that result from in-born genetic mutations of NER proteins. Xeroderma pigmentosum and Cockayne's syndrome are two examples of NER associated diseases. Nucleotide excision repair is more complex in eukaryotes than prokaryotes, but the general principle is similar. There are 9 major proteins involved in NER in mammalian cells. Deficiencies in certain proteins leads to disease. XPA, XPB, XPC, XPD, XPE, XPF, XPG all derive from хeroderma pigmentosum and CSA and CSB represent proteins linked to Cockayne syndrome. Additionally, the proteins ERCC1, RPA, RAD23A, RAD23B, others participate in nucleotide excision repair. A more complete list of proteins involved in NER is found below. Eukaryotic nucleotide excision repair can be divided into two subpathways: global genomic NER and transcription coupled NER.
Three different sets of proteins are involved in recognizing DNA damage for each subpathway. After damage recognition, the three subpathways converge for the steps of dual incision and ligation. Global genomic NER repairs damage in both transcribed and untranscribed DNA strands in active and inactive genes throughout the genome; this process is not dependent on transcription. This pathway employs several "damage sensing" proteins including the DNA-damage binding and XPC-Rad23B complexes that scan the genome and recognize helix distortions: the XPC-Rad23B complex is responsible for distortion recognition, while DDB1 and DDB2 can recognize some types of damage caused by UV light. Additionally, XPA performs a function in damage recognition, as yet poorly defined. Upon identification of a damaged site, subsequent repair proteins are recruited to the damaged DNA to verify presence of DNA damage, excise the damaged DNA surrounding the lesion fill in the repair patch. Mutations in GG-NER machinery are responsible for multiple genetic disorders including: Xeroderma pigmentosum: severe photosensitivity, high cancer rates in areas of the body exposed to the sun At any given time, most of the genome in an organism is not undergoing transcription.
For many types of lesions, NER repairs the transcribed strands of transcriptionally active genes faster than it repairs nontranscribed strands and transcriptionally silent DNA. TC-NER and GG-NER differ only in the initial steps of DNA damage recognition; the principal difference between TC-NER and GG-NER is that TC-NER does not require XPC or DDB proteins for distortion recognition in mammalian cells. Instead TC-NER initiates when RNA polymerase stalls at a lesion in DNA: the blocked RNA polymerase serves as a damage recognition signal, which replaces the need for the distortion recognition properties of the XPC-RAD23B and DDB complexes. CS proteins bind some types of DNA damage instead of XPC-Rad23B. Other repair mechanisms are less accurate and efficient. TC-NER initiates when RNA polymerase stalls at a lesion in DNA, whereupon protein complexes help move the polymerase backwards. Mutations in TC-NER machinery are responsible for multiple genetic disorders including: Trichothiodystrophy: some individuals are photosensitive, mental/physical retardation Cockayne syndrome: photosensitivity, mental retardation, progeria-like features, microcephaly Transcription factor II H is the key enzyme involved in dual excision.
TFIIH and XPG are first recruited to the site of DNA damage. The TFIIH subunits of XPD and XPB act as a 5'-3' and 3'-5' helicase - they help unwind DNA and generate a junction between the double-stranded and single-stranded DNA around the transcription bubble. In addition to stabilizing TFIIH, XPG has endonuclease activity; the dual incision leads to the removal of a ssDNA with a single strand gap of 25~30 nucleotides. The small, damage-containing DNA oligonucleotides are released from the duplex in complex with TFIIH but dissociate in an ATP-dependent manner and become bound to replication protein A. Inhibition of gap filling DNA synthesis and ligation results in an accumulation of RPA-bound sedDNAs in the cell. Replication p
Auxotrophy is the inability of an organism to synthesize a particular organic compound required for its growth. An auxotroph is an organism. Auxotrophy is the opposite of prototrophy, characterized by the ability to synthesize all the compounds needed for growth. Prototrophic cells are self sufficient producers of required amino acids, while auxotrophs require to be on medium with the amino acid that they cannot produce, it is a term used in relation to something, for example saying a cell is methionine auxotrophic means that it would need to be on a medium containing methionine or else it would not be able to replicate. In this example this is. However, a prototroph or a methionine prototrophic cell would be able to function and replicate on a medium with or without methionine. Replica plating is a technique that transfers colonies from one plate to another in the same spot as the last plate so the different media plates can be compared side by side, it is used to compare the growth of the same colonies on different plates of media to determine which environments the bacterial colony can or cannot grow in (this gives insight to possible auxotrophic characteristics.
The method of replica plating implemented by Esther Lederberg included auxotrophs that were temperature-sensitive. It is possible that an organism is auxotrophic to more than just one organic compound that it requires for growth. In genetics, a strain is said to be auxotrophic if it carries a mutation that renders it unable to synthesize an essential compound. For example, a yeast mutant with an inactivated uracil synthesis pathway gene is a uracil auxotroph; such a strain is unable to synthesize uracil and will only be able to grow if uracil can be taken up from the environment. This is the opposite of a uracil prototroph, or in this case a wild-type strain, which can still grow in the absence of uracil. Auxotrophic genetic markers are used in molecular genetics; this allows for biosynthetic or biochemical pathway mapping that can help determine which enzyme or enzymes are mutated and dysfunctional in the auxotrophic strains of bacteria being studied. Researchers have used strains of E. coli auxotrophic for specific amino acids to introduce non-natural amino acid analogues into proteins.
For instance cells auxotrophic for the amino acid phenylalanine can be grown in media supplemented with an analogue such as para-azido phenylalanine. Many living things, including humans, are auxotrophic for large classes of compounds required for growth and must obtain these compounds through diet; the complex pattern of evolution of vitamin auxotrophy across the eukaryotic tree of life is intimately connected with the interdependence between organisms. The Salmonella Mutagenesis test uses multiple strains of Salmonella typhimurium that are auxotrophic to histidine to test whether a given chemical can cause mutations by observing its auxotrophic property in response to an added chemical compound; the mutation a chemical substance or compound causes is measured by applying it to the bacteria on a plate containing histidine moving the bacteria to a new plate without sufficient histidine for continual growth. If the substance does not mutate the genome of the bacteria from auxotrophic to histidine back to prototrophic to histidine the bacteria would not show growth on the new plate.
So by comparing the ratio of the bacteria on the new plate to the old plate and the same ratio for the control group, it is possible to quantify how mutagenic a substance is, or rather, how it is to cause mutations in DNA. A chemical is considered positive for Ames test if it causes mutations increasing the observed reversion rate and negative if presents similar to the control group. There is a normal, but small, number of revertant colonies expected when an auxotrophic bacteria is plated on a media without the metabolite it needs because it could mutate back to prototrophy; the chances of this are low and therefore cause small colonies to be formed. If a mutagenic substance is added, the number of revertants would be visibly higher than without the mutagenic substance; the Ames test is considered positive if a substance increases chance of mutation in the DNA of the bacteria enough to cause a quantifiable difference in the revertants of the mutagen plate and the control group plate. Negative Ames test means the possible mutagen DID not cause increase in revertants and positive Ames test signifies that the possible mutagen DID increase the chance of mutation.
These mutagenic effects on bacteria are researched as a possible indicator of the same effects on larger organisms, like humans. It is suggested that if a mutation can arise in bacterial DNA under presence of a mutagen the same effect would occur for larger organisms causing cancer. A negative Ames test result could suggest that the substance is not a mutagen and would not cause tumor formation in living organisms; however only few of the positive Ames Test resulting chemicals were considered insignificant when tested in larger organisms but t