text stringlengths 11 320k | source stringlengths 26 161 |
|---|---|
Generic Network Virtualization Encapsulation ( Geneve ) is a network encapsulation protocol created by the IETF in order to unify the efforts made by other initiatives like VXLAN and NVGRE , [ 1 ] with the intent to eliminate the wild growth of encapsulation protocols. [ 1 ] [ 2 ]
Open vSwitch is an example of a software-based virtual network switch that supports Geneve overlay networks. It is also supported by AWS Gateway Load Balancers.
This computer networking article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Generic_Network_Virtualization_Encapsulation |
A generic drug is a pharmaceutical drug that contains the same chemical substance as a drug that was originally protected by chemical patents . Generic drugs are allowed for sale after the patents on the original drugs expire. Because the active chemical substance is the same, the medical profile of generics is equivalent in performance compared to their performance at the time when they were patented drugs. [ 1 ] [ 2 ] A generic drug has the same active pharmaceutical ingredient (API) as the original, but it may differ in some characteristics such as the manufacturing process, formulation , excipients , color, taste, and packaging. [ 2 ]
Although they may not be associated with a particular company, generic drugs are usually subject to government regulations in the countries in which they are dispensed. They are labeled with the name of the manufacturer and a generic non-proprietary name such as the United States Adopted Name (USAN) or International Nonproprietary Name (INN) of the drug. A generic drug must contain the same active ingredients as the original brand-name formulation. The U.S. Food and Drug Administration (FDA) requires generics to be identical to or within an acceptable bioequivalent range of their brand-name counterparts, with respect to pharmacokinetic and pharmacodynamic properties. [ 3 ]
Biopharmaceuticals , such as monoclonal antibodies , differ biologically from small-molecule drugs . Biosimilars have active pharmaceutical ingredients that are almost identical to the original product and are typically regulated under an extended set of rules, but they are not the same as generic drugs as the active ingredients are not the same as those of their reference products. [ 4 ] In most cases, generic products become available after the patent protections afforded to the drug's original developer expire. Once generic drugs enter the market, competition often leads to substantially lower prices for both the original brand-name product and its generic equivalents. In most countries, patents give 20 years of protection. However, many countries and regions, such as the European Union and the United States , [ 5 ] may grant up to five years of additional protection ("patent term restoration") if manufacturers meet specific goals, such as conducting clinical trials for pediatric patients. [ 6 ]
Manufacturers, wholesalers, insurers, and drugstores can all increase prices at various stages of production and distribution. [ 7 ] In 2014, according to an analysis by the Generic Pharmaceutical Association, generic drugs accounted for 88 percent of the 4.3 billion prescriptions filled in the United States. [ 8 ] : 2 "Branded generics" on the other hand are defined by the FDA and National Health Service as "products that are (a) either novel dosage forms of off-patent products produced by a manufacturer that is not the originator of the molecule, or (b) a molecule copy of an off-patent product with a trade name." [ 9 ] Since the company making branded generics can spend little on research and development , it is able to spend on marketing alone, thus earning higher profits and driving costs down. [ 10 ] For example, the largest revenues of Ranbaxy , now owned by Sun Pharma , came from branded generics. [ 11 ] [ 12 ]
Generic drug names are constructed using standardized affixes that distinguish drugs between and within classes and suggest their action. [ citation needed ]
When a pharmaceutical company first markets a drug, it is usually under a patent that, until it expires, the company can use to exclude competitors by suing them for patent infringement . [ 13 ] Pharmaceutical companies that develop new drugs generally only invest in drug candidates with strong patent protection as a strategy to recoup their costs of drug development (including the costs of the drug candidates that fail) and to make a profit. [ 14 ] The average cost to a brand-name company of discovering, testing, and obtaining regulatory approval for a new drug, with a new chemical entity , was estimated to be as much as US$800 million in 2003 [ 15 ] and US$2.6 billion in 2014. [ 16 ] Drug companies that bring new products have several product line extension strategies they use to extend their exclusivity, some of which are seen as gaming the system and labeled " evergreening " by critics, but at some point there is no patent protection available. [ 13 ] For as long as a drug patent lasts, a brand-name company enjoys a period of market exclusivity, or monopoly , in which the company is able to set the price of the drug at a level that maximizes profit. This profit often greatly exceeds the development and production costs of the drug, allowing the company to offset the cost of research and development of other drugs that are not profitable or do not pass clinical trials. [ 7 ] The impact of loss of patent exclusivity on pharmaceutical products varies significantly across different product classes (e.g., biologics vs. small molecules), largely due to regulatory, legal and manufacturing hurdles associated with such products. Indeed, the greater degree of 'brand-brand' competitive dynamics seen in the biologics and complex generics space allows manufacturers of originators to better protect market share following loss of patent exclusivity. [ 17 ]
Large pharmaceutical companies often spend millions protecting their patents from generic competition. [ 7 ] Apart from litigation, they may reformulate a drug or license a subsidiary (or another company) to sell generics under the original patent. Generics sold under license from the patent holder are known as authorized generics . [ 18 ] Generic drugs are usually sold for significantly lower prices than their branded equivalents and at lower profit margins . [ 19 ] One reason for this is that competition increases among producers when a drug is no longer protected by patents. [ 19 ] Generic companies incur fewer costs in creating generic drugs—only the cost of manufacturing, without the costs of drug discovery and drug development —and are therefore able to maintain profitability at a lower price. [ 19 ] [ 20 ] [ 21 ] The prices are often low enough for users in less-prosperous countries to afford them. [ citation needed ] Generic drug companies may also receive the benefit of the previous marketing efforts of the brand-name company, including advertising, presentations by drug representatives, and distribution of free samples. Many drugs introduced by generic manufacturers have already been on the market for a decade or more and may already be well known to patients and providers, although often under their branded name. [ citation needed ]
India is a leading country in the world's generic drugs market, exporting US$20.0 billion worth of drugs in the 2019–20 (April–March) year. [ 22 ] India exports generic drugs to the United States and the European Union. [ 23 ] Also according to the market research community the Global Generic Drugs Market was evaluated US$465.96 million in 2021 and is expected to rise with a CAGR of 5.5% from 2022- 2028 during the forecast period. [ 24 ] In the United Kingdom, generic drug pricing is controlled by the government's reimbursement rate. The price paid by pharmacists and doctors is determined mainly by the number of license holders, the sales value of the original brand, and the ease of manufacture. A typical price decay graph will show a "scalloped" curve, [ 25 ] which usually starts at the brand-name price on the day of generic launch and then falls as competition intensifies. After some years, the graph typically flattens out at approximately 20% of the original brand price. In about 20% of cases, the price "bounces": Some license holders withdraw from the market when the selling price dips below their cost of goods, and the price then rises for a while until the license holders re-enter the market with new stock. [ 26 ] [ 27 ] The NHS spent about £4.3 billion on generic medicines in 2016–17. [ 28 ] In 2012, 84 percent of prescriptions in the US were filled with generic drugs, [ 29 ] and in 2014, the use of generic drugs in the United States led to US$254 billion in health care savings. [ 8 ] : 2
In the mid-2010s the generics industry began transitioning to the end of an era of giant patent cliffs in the pharmaceutical industry; patented drugs with sales of around US$28 billion were set to come off patent in 2018, but in 2019 only about US$10 billion in revenue was set to open for competition, and less the next year. Companies in the industry have responded with consolidation or turning to try to generate new drugs. [ 30 ] Most developed nations require generic drug manufacturers to prove that their formulations are bioequivalent to their brand-name counterparts. [ 31 ] [ 32 ] [ 33 ] [ 34 ] [ 35 ] [ 36 ] Bioequivalence does not mean generic drugs must be exactly the same as the brand-name product ("pharmaceutical equivalent"). Chemical differences may exist; a different salt or ester may be used, for instance. Different inactive ingredients means that the generic may look different from the originator brand; [ 37 ] however, the therapeutic effect of the drug must be the same ("pharmaceutical alternative"). [ citation needed ] Most small molecule drugs are accepted as bioequivalent if their pharmacokinetic parameters of area under the curve (AUC) and maximum concentration (C max ) are within a 90% confidence interval of 80–125%; most approved generics in the US are well within this limit. [ 38 ] For more complex products—such as inhalers , patch delivery systems , liposomal preparations , or biosimilar drugs—demonstrating pharmacodynamic or clinical equivalence is more challenging. [ 39 ]
Enacted in 1984, the Drug Price Competition and Patent Term Restoration Act , informally known as the Hatch–Waxman Act, standardized procedures for recognition of generic drugs. In 2007, the FDA launched the Generic Initiative for Value and Efficiency (GIVE): [ 40 ] an effort to modernize and streamline the generic drug approval process, and to increase the number and variety of generic products available. [ citation needed ]
Before a company can market a generic drug, it needs to file an Abbreviated New Drug Application (ANDA) with the Food and Drug Administration, seeking to demonstrate therapeutic equivalence to a previously approved "reference-listed drug" and proving that it can manufacture the drug safely and consistently. [ 41 ] For an ANDA to be approved, the FDA requires that the 90% confidence interval of the geometric mean test/reference ratios for the total drug exposure (represented by the area under the curve or AUC) and the maximum plasma concentration (Cmax) should fall within limits of 80–125%. [ 42 ] (This range is part of a statistical calculation, and does not mean that generic drugs are allowed to differ from their brand-name counterparts by up to 25 percent.) The FDA evaluated 2,070 studies conducted between 1996 and 2007 that compared the absorption of brand-name and generic drugs into a person's body. The average difference in absorption between the generic and the brand-name drug was 3.5 percent, comparable to the difference between two batches of a brand-name drug. [ 43 ] [ 44 ] Non-innovator versions of biologic drugs, or biosimilars, require clinical trials for immunogenicity in addition to tests establishing bioequivalency. These products cannot be entirely identical because of batch-to-batch variability and their biological nature, and they are subject to extra rules. [ 45 ]
When an application is approved, the FDA adds the generic drug to its Approved Drug Products with Therapeutic Equivalence Evaluations list and annotates the list to show the equivalence between the reference-listed drug and the generic. The FDA also recognizes drugs that use the same ingredients with different bioavailability and divides them into therapeutic equivalence groups. [ 41 ] For example, as of 2006, diltiazem hydrochloride had four equivalence groups, all using the same active ingredient, but considered equivalent only within each group. [ 46 ]
In order to start selling a drug promptly after the patent on innovator drug expires, a generic company has to file its ANDA well before the patent expires. This puts the generic company at risk of being sued for patent infringement, since the act of filing the ANDA is considered "constructive infringement" of the patent. [ 41 ] In order to incentivize generic companies to take that risk the Hatch-Waxman act granted a 180-day administrative exclusivity period to generic drug manufacturers who are the first to file an ANDA. [ 47 ]
When faced with patent litigation from the drug innovator or patent holder, generic companies will often counter-sue, challenging the validity of the patent. [ 48 ] [ 49 ] [ 50 ] [ 51 ] [ 52 ] Like any litigation between private parties, the innovator and generic companies may choose to settle the litigation. Some of these settlement agreements have been struck down by courts when they took the form of reverse payment patent settlement agreements, in which the generic company basically accepts a payment to drop the litigation, delaying the introduction of the generic product and frustrating the purpose of the Hatch–Waxman Act. [ 53 ] [ 54 ]
Innovator companies sometimes try to maintain some of the revenue from their drug after patents expire by allowing another company to sell an authorized generic ; a 2011 FTC report found that consumers benefitted from lower costs when an authorized generic was introduced during the 180 day exclusivity period, as it created competition. [ 55 ] [ 56 ] Innovator companies may also present arguments to the FDA that the ANDA should not be accepted by filing an FDA citizen petition . The right of individuals or organizations to petition the federal government is guaranteed by the First Amendment to the United States Constitution. [ 57 ] For this reason, the FDA has promulgated regulations that provide, among other things, that at any time, any "interested person" can request that the FDA "issue, amend, or revoke a regulation or order," and set forth a procedure for doing so. [ 58 ] [ 59 ]
Some generic drugs are viewed with suspicion by doctors. For example, warfarin (Coumadin) has a narrow therapeutic window and requires frequent blood tests to make sure patients do not have a subtherapeutic or a toxic level. A study performed in Ontario showed that replacing Coumadin with generic warfarin was safe, [ 60 ] but many physicians are not comfortable with their patients taking branded generic equivalents. [ 61 ] In some countries (for example, Australia) where a drug is prescribed under more than one brand name, doctors may choose not to allow pharmacists to substitute a brand different from the one prescribed unless the consumer requests it. [ 62 ]
A series of scandals around the approval of generic drugs in the late 1980s shook public confidence in generic drugs; there were several instances in which companies obtained bioequivalence data fraudulently, by using the branded drug in their tests instead of their own product, and a congressional investigation found corruption at the FDA, where employees were accepting bribes to approve some generic companies' applications and delaying or denying others. [ 29 ] [ 63 ] [ 64 ] [ 65 ]
In 2007, North Carolina Public Radio 's The People's Pharmacy began reporting on consumers' complaints that generic versions of bupropion (Wellbutrin) were yielding unexpected effects. [ 66 ] Subsequently, Impax Laboratories 's 300 mg extended-release tablets, marketed by Teva Pharmaceutical Industries , were withdrawn from the US market after the FDA determined in 2012 that they were not bioequivalent. [ 67 ] [ 68 ]
Problems with the quality of generic drugs – especially those produced outside the United States – are widespread as of 2019. [ 69 ] The FDA does infrequent – less than annual – inspections of production sites outside the United States. The FDA normally gives advance notice of inspections, which can lead to cover-ups of problems before inspectors arrive; inspections performed with little or no advance notice have produced evidence of serious problems at a majority of generic drug manufacturing sites in India and China. [ 69 ]
Two women, each claiming to have suffered severe medical complications from a generic version of metoclopramide , lost their Supreme Court appeal on June 23, 2011. In a 5–4 ruling in PLIVA, Inc. v. Mensing , [ 70 ] [ 71 ] the court held that generic companies cannot be held liable for information, or the lack of information, on the originator's label. [ 72 ] [ 73 ] [ 74 ]
The Indian government began encouraging more drug manufacturing by Indian companies in the early 1960s, and with the Patents Act in 1970. [ 75 ] The Patents Act removed composition patents for foods and drugs, and though it kept process patents , these were shortened to a period of five to seven years. The resulting lack of patent protection created a niche in both the Indian and global markets that Indian companies filled by reverse-engineering new processes for manufacturing low-cost drugs. [ 76 ] The code of ethics issued by the Medical Council of India in 2002 calls for physicians to prescribe drugs by their generic names only. [ 77 ] India is a leading country in the world's generic drugs market, with Sun Pharmaceuticals being the largest pharmaceutical company in India. Indian generics companies exported US$17.3 billion worth of drugs in the 2017–18 (April–March) year. In 1945–2017, bioequivalence studies were only required for generics of drugs that are less than four years old. Since 2017, all generic drugs of certain classes, irrespective of age, require bioequivalence to be approved. [ 78 ]
Generic drug production is a large part of the pharmaceutical industry in China. Western observers have said that China lacks administrative protection for patents. [ 79 ] However, entry to the World Trade Organization has brought a stronger patent system. [ 80 ] China remains the largest exporter of active pharmaceutical ingredients , accounting for 40% of the world market per a 2017 estimate. [ 81 ]
Bioequivalence studies are required for new generic drugs starting from 2016, with older drugs planned as well. In addition, in vitro dissolution behavior is required to match. [ 82 ] Since 2018, 44 classes of drugs are exempt from testing (requiring only a dissolution check), and 13 classes only require simplified testing. [ 83 ]
As of 2021, several major companies traditionally dominate the generic drugs market, including Viatris (merger of Mylan and Upjohn ), Teva , Novartis' Sandoz , and Sun Pharma . [ 84 ] Prices in traditional generic drugs have declined and newer companies such as India-based Sun Pharma , Aurobindo Pharma , and Dr. Reddy's Laboratories , as well as Canada-based Apotex , have taken market share, which has led to a focus on biosimilars . | https://en.wikipedia.org/wiki/Generic_drug |
Genesee Scientific Corporation is a global life sciences supplier.
Genesee Scientific was founded by Ken Fry in 1995 as a provider of supplies to laboratories located along Genesee Avenue in University City, San Diego.
Today, Genesee Scientific serves life science laboratories around the United States and the world.
Timeline
Genesee Scientific is the world leader in innovation for and supply to the Drosophila (fruit fly) research community. [ citation needed ] Drosophila are widely used as a model organism in the field of genetics.
Genesee Scientific has been awarded three patents by the United States Patent and Trademark Office for its revolutionary Drosophila vial racking system (patent numbers D673,296 S; 8,136,679 B2; and 8,430,251 B2). This Drosophila vial racking system significantly decreases time spent racking vials and is more environmentally friendly compared to traditional vial packaging configurations.
Genesee Scientific has also developed the first atlas of Drosophila phenotypic markers available on mobile devices. [ citation needed ] .
Following is a list of links to articles published in scientific journals that cite Genesee Scientific: | https://en.wikipedia.org/wiki/Genesee_Scientific |
Mary Ann Liebert, Inc. is a publishing company founded by its president , Mary Ann Liebert, in 1980 and a subsidiary of Sage Publishing . [ 2 ] [ 3 ] The company publishes peer-reviewed academic journals , books , and trade magazines in the areas of biotechnology , biomedical sciences , medical research , and life sciences ; clinical medicine , surgery , and nursing ; technology and engineering ; environmental science ; public health and policy ; law , regulation , and education .
The company's headquarters is in New Rochelle, New York . [ 3 ] [ 1 ]
The company has been described as the first to establish a specialty in genetic engineering . [ 4 ]
Eschewing traditional market research , the publisher seeks out niche topics overlooked by larger publishers. [ 1 ] Its portfolio of more than ninety peer-reviewed journals includes: [ 1 ] [ 5 ] [ 6 ] [ 7 ]
Publications focused on topics outside of the medical field include Westchester Wag , which covers the social scene in Westchester County, New York , and Rinkmagazine , a skating periodical. [ 1 ]
The company's first publication was the Journal of Interferon Research , launched in 1981. [ 1 ] Genetic Engineering News was launched the same year, attaining a circulation of 50,000 by 2000. [ 1 ] The combined circulation of all titles from the publisher in 2000 was 250,000. [ 1 ]
The company's top five publications by revenue as of 2000 were Genetic Engineering News (50,000), Westchester Wag (50,000), Journal of Women's Health and Gender-Based Medicine (5,000), Human Gene Therapy (2,300), and AIDS Research and Human Retrovirus (2,150). [ 1 ]
In February 2018, the company launched The CRISPR Journal , a bimonthly journal devoted to research advances and commentary in the field of CRISPR and genome editing . [ 8 ]
In December 2024, Mary Ann Liebert, Inc. was acquired by Sage Publishing . Journals would continue to be published under the Mary Ann Liebert name. [ 9 ] [ 10 ] | https://en.wikipedia.org/wiki/Genetic_Engineering_&_Biotechnology_News |
Jon Entine (born April 30, 1952) is an American science journalist . After working as a network news writer and producer for NBC News and ABC News , Entine moved into print journalism. Entine has written seven books and is a contributing columnist to newspapers and magazines. He is the founder and executive director of the science advocacy group the Genetic Literacy Project, and a former visiting scholar at the American Enterprise Institute . [ 1 ] He is also the founder of the consulting company ESG Mediametrics. [ 2 ] [ 3 ]
Entine was born in Philadelphia , Pennsylvania into an Ashkenazi Jewish family from eastern Europe [ 4 ] and was raised in Reform Judaism . [ 5 ] He graduated from Trinity College in Hartford , Connecticut , in 1974 [ 6 ] with a B.A. in philosophy. [ citation needed ]
In high school, Entine worked as a weekend copyboy for the CBS owned-and-operated TV station then known as WCAU. In 1975, Entine was hired to write for the ABC News program AM America , which was renamed Good Morning America the following year. Entine worked for ABC News as a writer, assignment desk editor, and producer in New York City and Chicago from 1975 to 1983 for programs including the ABC Evening News , 20/20 and Nightline . He took a leave of absence from ABC News in 1981–1982 to study at the University of Michigan under a National Endowment for the Humanities fellowship in journalism. [ citation needed ]
Entine joined NBC News in New York in 1984 as a special segment producer for NBC Nightly News with Tom Brokaw , where he worked until 1990. In 1989, Entine and Brokaw collaborated to write and produce Black Athletes: Fact and Fiction , which was named Best International Sports Film of 1989. [ 7 ] From 1989 to 1990, Entine served as executive in charge of documentaries at NBC News. He rejoined ABC News in 1991 as an investigative producer for Primetime . In 1993 Entine produced a story with reporter Sam Donaldson on eye surgery clinics that led to a lawsuit against ABC News, Entine, and Donaldson. [ 8 ] [ 9 ] The suit was dismissed by a federal appeals court, which concluded: "The only scheme here was a scheme to expose publicly any bad practices that the investigative team discovered, which is nothing fraudulent." [ 10 ] In 1994, Entine produced a prime time special on the Miss America Pageant , "Miss America: Beyond the Crown" for NBC Entertainment. [ citation needed ]
In September 1994, Entine wrote an investigative article titled "Shattered Image: Is The Body Shop Too Good to Be True?" The article caused an international controversy and led to articles in The New York Times [ citation needed ] and a report on ABC World News Tonight . [ citation needed ] The Body Shop [ broken anchor ] , the British-based international cosmetics company, which until that point had been considered a model " socially responsible " company, tried to block the story from being published. [ 11 ] Following the controversy, The Body Shop's stock suffered a temporary 50% drop in market value. [ citation needed ] The case has become the subject of business and management ethics studies. [ 12 ] [ 13 ]
Entine is the executive director of the Genetic Literacy Project (GLP), an organization he founded. [ 14 ] [ 15 ] The GLP is a non-profit organization that promotes public awareness and discussion of genetics , biotechnology , evolution and science literacy . [ 15 ] [ 16 ] [ 17 ] [ 18 ] The site presents articles on topics related to food and agricultural genetics, as well as human genetics. [ 19 ] It also aggregates articles from various published sources. GLP has posted articles taking positions against labeling GMO foods . [ 20 ] [ 21 ] In a Financial Times article, the Genetic Literacy Project site was described as a provider of information on genomics that is not readily accessible to the general public. [ 22 ]
US Right to Know, an advocacy group funded in large part by the Organic Consumers Association , [ 23 ] [ 24 ] raised concerns after the GLP ran a series of articles in 2014 supportive of crop biotechnology after the scientists had been encouraged to do so by American agrochemical and agricultural biotechnology corporation Monsanto . [ 25 ] The GLP said the authors were not paid for their articles. Entine remarked that he had total control of the editing process and that there was nothing to disclose. [ 25 ]
In 2020 and 2021 the GLP received US$741,183 and US$494,075 in donations, respectively. [ 26 ]
Entine has written three books on genetics and two on chemicals. Let Them Eat Precaution: How Politics is Undermining the Genetic Revolution examines the controversy over genetic modification in agriculture. [ citation needed ]
Entine's first book, Taboo: Why Black Athletes Dominate Sports and Why We're Afraid to Talk About It was inspired by the documentary on black athletes written with Brokaw in 1989. [ 27 ] It received reviews ranging from mostly positive to highly negative in The New York Times . [ 27 ] [ 28 ] [ 29 ] Physical anthropologist Jonathan Marks characterized the book as "make-believe genetics applied to naively conceptualized groups of people." [ 29 ]
In 2007, Entine published Abraham's Children: Race, Identity and the DNA of the Chosen People which examined the shared ancestry of Jews, Christians and Muslims, and addressed the question "Who is a Jew?" as seen through the prism of DNA. In a review of this book, geneticist Harry Ostrer wrote that Entine's "understanding of the genetics is limited and uncritical, but his broad, well-documented sweep of Jewish history will inform even the most knowledgeable of readers." [ 30 ]
He was previously senior research fellow at the Center for Health & Risk Communication at George Mason University where he began in 2011 [ 31 ] and at GMU's STATS ( Statistical Assessment Service ). [ 32 ]
Entine joined the conservative American Enterprise Institute for Public Policy Research as an adjunct scholar in 2002 and was subsequently a visiting scholar. [ citation needed ] His research focuses on science and society and corporate sustainability. AEI Press has published three books written and edited by Entine: Crop Chemophobia : Will Precaution Kill the Green Revolution? , which analyzes the impact of chemicals in agriculture; Pension Fund Politics: The Dangers of Socially Responsible Investing , which focuses on the growing influence of social investing in pension funds; and Let Them Eat Precaution: How Politics Is Undermining the Genetic Revolution in Agriculture , which examined the debate over genetic modification (GMOs), food, and farming.
As of 2016, Entine was a senior fellow at the Institute Food and Agricultural Literacy at University of California Davis . [ 1 ]
In 2012 when asked about affiliations between the agrochemical and agricultural biotechnology corporation Monsanto and his consulting company ESG Mediametrics, Entine said, "Nine years ago, I did a $2000 research project for v-Fluence, a social media company formed by former Monsanto executives. That's the entirety of my Monsanto relationship." [ 3 ]
The [Genetic Literacy Project] said that such a disclosure isn't necessary because [Monsanto] didn't pay the authors and wasn't involved in writing or editing the articles.
I got independent articles written by independent professors," Entine said [. . .]. "I ended up working with the professors to edit their pieces and I had total control over the final product. There is nothing to disclose. | https://en.wikipedia.org/wiki/Genetic_Literacy_Project |
Genetic Savings & Clone, Inc. was a company headquartered in Sausalito, California that offered commercial pet gene banking and cloning services, between 2004 and 2006. The company was launched by billionaire John Sperling , the founder of University of Phoenix . Its Chief Executive Officer was Lou Hawthorne. [ 1 ]
The company was founded as a result of the efforts to clone Lou Hawthorne's favorite family dog, Missy. The Missyplicity project generated enough interest that Lou Hawthorne decided to build a company devoted to dog and cat cloning.
The company opened for business in February 2000, funded production of the first cloned cat, CC , in 2001, and launched its pet cloning service in February 2004, operating a "petbank", to which pet owners could send tissue samples for later use in cloning. The company delivered the world's first commercially cloned cat, Little Nicky , in December 2004. Little Nicky was sold to a Texas woman for a reported US$ 50,000. He was a genetic twin of "Nicky," a 17-year-old Maine Coon cat that had been kept as a pet. Musician Liam Lynch 's cat was cloned after its death, presumably making him the first celebrity to own a cloned pet.
As well as their success in cloning cats, the company also made significant advances in dog cloning research, although the technology was not mature enough to sustain the business. The company closed in 2006. Letters to this effect were sent out to clients at the end of September 2006, informing them of this decision and offering to transfer any genetic material to another facility. [ 2 ]
The company spurred widespread debate regarding the ethics and morality of pet cloning especially in light of the fact that animals are euthanized by their owners every day. Though the topic lost currency with the closure of the company, divergent arguments about these issues can still be found on some web sites. [ 3 ] | https://en.wikipedia.org/wiki/Genetic_Savings_&_Clone |
Genetic admixture occurs when previously isolated populations interbreed resulting in a population that is descended from multiple sources. It can occur between species, such as with hybrids , or within species, such as when geographically distant individuals migrate to new regions. It results in gene pool that is a mix of the source populations. [ 1 ] [ 2 ] [ 3 ]
Climatic cycles facilitate genetic admixture in cold periods and genetic diversification in warm periods. [ 4 ] Natural flooding can cause genetic admixture within populations of migrating fish species. [ 5 ] Genetic admixture may have an important role for the success of populations that colonise a new area and interbreed with individuals of native populations. [ 6 ]
Admixture mapping is a method of gene mapping that uses a population of mixed ancestry (an admixed population) to find the genetic loci that contribute to differences in diseases or other phenotypes found between the different ancestral populations. The method is best applied to populations with recent admixture from two populations that were previously genetically isolated. The method attempts to correlate the degree of ancestry near a genetic locus with the phenotype or disease of interest. Genetic markers that differ in frequency between the ancestral populations are needed across the genome. [ 7 ]
Admixture mapping is based on the assumption that differences in disease rates or phenotypes are due in part to differences in the frequencies of disease-causing or phenotype-causing genetic variants between populations. In an admixed population, these causal variants occur more frequently on chromosomal segments inherited from one or another ancestral population. The first admixture scans were published in 2005 and since then genetic contributors to a variety of disease and trait differences have been mapped. [ 8 ] By 2010, high-density mapping panels had been constructed for African Americans, Latino/Hispanics, and Uyghurs . | https://en.wikipedia.org/wiki/Genetic_admixture |
Genetic analysis is the overall process of studying and researching in fields of science that involve genetics and molecular biology . There are a number of applications that are developed from this research, and these are also considered parts of the process. The base system of analysis revolves around general genetics. Basic studies include identification of genes and inherited disorders . This research has been conducted for centuries on both a large-scale physical observation basis and on a more microscopic scale.
Genetic analysis can be used generally to describe methods both used in and resulting from the sciences of genetics and molecular biology, or to applications resulting from this research.
Genetic analysis may be done to identify genetic/inherited disorders and also to make a differential diagnosis in certain somatic diseases such as cancer . Genetic analyses of cancer include detection of mutations , fusion genes , and DNA copy number changes.
Much of the research that set the foundation of genetic analysis began in prehistoric times. Early humans found that they could practice selective breeding to improve crops and animals. They also identified inherited traits in humans that were eliminated over the years. The many genetic analyses gradually evolved over time.
Modern genetic analysis began in the mid-1800s with research conducted by Gregor Mendel . Mendel, who is known as the "father of modern genetics", was inspired to study variation in plants. Between 1856 and 1863, Mendel cultivated and tested some 29,000 pea plants (i.e., Pisum sativum). This study showed that one in four pea plants had purebred recessive alleles, two out of four were hybrid and one out of four were purebred dominant. His experiments led him to make two generalizations, the Law of Segregation and the Law of Independent Assortment , which later became known as Mendel's Laws of Inheritance. Lacking the basic understanding of heredity, Mendel observed various organisms and first utilized genetic analysis to find that traits were inherited from parents and those traits could vary between children. Later, it was found that units within each cell are responsible for these traits. These units are called genes. Each gene is defined by a series of amino acids that create proteins responsible for genetic traits.
Genetic analyses include molecular technologies such as PCR , RT-PCR , DNA sequencing , and DNA microarrays , and cytogenetic methods such as karyotyping and fluorescence in situ hybridisation .
DNA sequencing is essential to the applications of genetic analysis. This process is used to determine the order of nucleotide bases . Each molecule of DNA is made from adenine , guanine , cytosine and thymine , which determine what function the genes will possess. This was first discovered during the 1970s. DNA sequencing encompasses biochemical methods for determining the order of the nucleotide bases, adenine, guanine, cytosine, and thymine, in a DNA oligonucleotide. By generating a DNA sequence for a particular organism, you are determining the patterns that make up genetic traits and in some cases behaviors.
Sequencing methods have evolved from relatively laborious gel-based procedures to modern automated protocols based on dye labelling and detection in capillary electrophoresis that permit rapid large-scale sequencing of genomes and transcriptomes. [ 1 ] Knowledge of DNA sequences of genes and other parts of the genome of organisms has become indispensable for basic research studying biological processes, as well as in applied fields such as diagnostic or forensic research. The advent of DNA sequencing has significantly accelerated biological research and discovery.
Cytogenetics is a branch of genetics that is concerned with the study of the structure and function of the cell, especially the chromosomes. Polymerase chain reaction studies the amplification of DNA. Because of the close analysis of chromosomes in cytogenetics, abnormalities are more readily seen and diagnosed.
A karyotype is the number and appearance of chromosomes in the nucleus of a eukaryotic cell. The term is also used for the complete set of chromosomes in a species, or an individual organism.
Karyotypes describe the number of chromosomes, and what they look like under a light microscope. Attention is paid to their length, the position of the centromeres , banding pattern, any differences between the sex chromosomes, and any other physical characteristics. Karyotyping uses a system of studying chromosomes to identify genetic abnormalities and evolutionary changes in the past.
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome. When a gene is expressed in a cell, it generates messenger RNA (mRNA). Overexpressed genes generate more mRNA than underexpressed genes. This can be detected on the microarray.
Since an array can contain tens of thousands of probes, a microarray experiment can accomplish many genetic tests in parallel. Therefore, arrays have dramatically accelerated many types of investigations.
The polymerase chain reaction (PCR) is a biochemical technology in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
PCR is now a common and often indispensable technique used in medical and biological research labs for a variety of applications. These include DNA cloning for sequencing, DNA-based phylogeny , or functional analysis of genes; the diagnosis of hereditary diseases ; the identification of genetic fingerprints (used in forensic sciences and paternity testing); and the detection and diagnosis of infectious diseases.
Numerous practical advancements have been made in the field of genetics and molecular biology through the processes of genetic analysis. One of the most prevalent advancements during the late 20th and early 21st centuries is a greater understanding of cancer's link to genetics. By identifying which genes in the cancer cells are working abnormally, doctors can better diagnose and treat cancers.
Research has been able to identify the concepts of genetic mutations, fusion genes and changes in DNA copy numbers, and advances are made in the field every day. Much of these applications have led to new types of sciences that use the foundations of genetic analysis. Reverse genetics uses the methods to determine what is missing in a genetic code or what can be added to change that code. Genetic linkage studies analyze the spatial arrangements of genes and chromosomes. There have also been studies to determine the legal and social and moral effects of the increase of genetic analysis. Genetic analysis may be done to identify genetic/inherited disorders and also to make a differential diagnosis in certain somatic diseases such as cancer. Genetic analyses of cancer include detection of mutations , fusion genes , and DNA copy number changes. | https://en.wikipedia.org/wiki/Genetic_analysis |
In evolutionary biology , genetic anthropomorphism refers to "thinking like a gene ". The central question is "if I were a gene, what would I do in order to reproduce myself". The question is an obvious fallacy since genes are incapable of thought . However, natural selection does act in such a way that those that are most successful at reproducing themselves (by following the optimum strategy ) prosper. Thinking like a gene enables the results to be visualised. This is related to a philosophical tool known as the intentional stance .
The most notable genetic anthropomorphist was the British biologist, W. D. Hamilton . Hamilton's friend, Richard Dawkins , popularised the idea.
Anthropomorphism has been criticised on a number of grounds, including that it is reductionist .
This evolution -related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genetic_anthropomorphism |
Genetic architecture is the underlying genetic basis of a phenotypic trait and its variational properties. [ 1 ] Phenotypic variation for quantitative traits is, at the most basic level, the result of the segregation of alleles at quantitative trait loci (QTL) . [ 2 ] Environmental factors and other external influences can also play a role in phenotypic variation. Genetic architecture is a broad term that can be described for any given individual based on information regarding gene and allele number, the distribution of allelic and mutational effects, and patterns of pleiotropy , dominance , and epistasis . [ 1 ]
There are several different experimental views of genetic architecture. Some researchers recognize that the interplay of various genetic mechanisms is incredibly complex, but believe that these mechanisms can be averaged and treated, more or less, like statistical noise. [ 3 ] Other researchers claim that each and every gene interaction is significant and that it is necessary to measure and model these individual systemic influences on evolutionary genetics. [ 1 ]
Genetic architecture can be studied and applied at many different levels. At the most basic, individual level, genetic architecture describes the genetic basis for differences between individuals, species, and populations. This can include, among other details, how many genes are involved in a specific phenotype and how gene interactions, such as epistasis, influence that phenotype. [ 1 ] Line-cross analyses and QTL analyses can be used to study these differences. [ 2 ] This is perhaps the most common way that genetic architecture is studied, and though it is useful for supplying pieces of information, it does not generally provide a complete picture of the genetic architecture as a whole.
Genetic architecture can also be used to discuss the evolution of populations. [ 1 ] Classical quantitative genetics models, such as that developed by R.A. Fisher , are based on analyses of phenotype in terms of the contributions from different genes and their interactions. [ 3 ] Genetic architecture is sometimes studied using a genotype–phenotype map , which graphically depicts the relationship between the genotype and the phenotype. [ 4 ]
Genetic architecture is incredibly important for understanding evolutionary theory because it describes phenotypic variation in its underlying genetic terms, and thus it gives us clues about the evolutionary potential of these variations. Therefore, genetic architecture can help us to answer biological questions about speciation, the evolution of sex and recombination, the survival of small populations, inbreeding, understanding diseases, animal and plant breeding, and more. [ 1 ]
Evolvability is literally defined as the ability to evolve. In terms of genetics, evolvability is the ability of a genetic system to produce and maintain potentially adaptive genetic variants. There are several aspects of genetic architecture that contribute strongly to the evolvability of a system, including autonomy, mutability, coordination, epistasis, pleiotropy, polygeny, and robustness. [ 1 ] [ 2 ]
A study published in 2006 used phylogeny to compare the genetic architecture of differing human skin color. In this study, researchers were able to suggest a speculative framework for the evolutionary history underlying current-day phenotypic variation in human skin pigmentation based on the similarities and differences they found in the genotype. [ 7 ] Evolutionary history is an important consideration in understanding the genetic basis of any trait, and this study was among the first to utilize these concepts in a paired fashion to determine information about the underlying genetics of a phenotypic trait.
In 2013, a group of researchers used genome-wide association studies (GWAS) and genome-wide interaction studies (GWIS) to determine the risk of congenital heart defects in patients with Down Syndrome . [ 8 ] Down Syndrome is a genetic disorder caused by trisomy of human chromosome 21. The current hypothesis regarding congenital heart defect phenotypes in Down Syndrome individuals is that three copies of functional genomic elements on chromosome 21 and genetic variation of chromosome 21 and non-chromosome 21 loci predispose patients to abnormal heart development. This study identified several congenital heart defect risk loci in Down Syndrome individuals, as well as three copy number variation (CNV) regions that may contribute to congenital heart defects in Down Syndrome individuals.
Another study, which was published in 2014, sought to identify the genetic architecture of psychiatric disorders. The researchers in this study suggested that there are a large number of contributing loci that are related to various psychiatric disorders. [ 9 ] Additionally, they, like many others, suggested that the genetic risk of psychiatric disorders involves the combined effects of many common variants with small effects - in other words, the small effects of a wide number of variants at specific loci add together to produce a large, combined effect on the overall phenotype of the individual. They also acknowledged the presence of large but rare mutations that have a large effect on phenotype. This study showcases the intricacy of genetic architecture by providing an example of many different SNPs and mutations working together, each with a varying effect, to generate a given phenotype.
Other studies regarding genetic architecture are many and varied, but most use similar types of analyses to provide specific information regarding loci involved in producing a phenotype. A study of the human immune system in 2015 [ 10 ] uses the same general concepts to identify several loci involved in the development of the immune system, but, like the other studies outlined here, failed to consider other aspects of genetic architecture, such as environmental influences. Unfortunately, many other aspects of genetic architecture remain difficult to quantify.
Although there are a few studies that seek to explore the other aspects of genetic architecture, there is little ability with current technologies to link all of the pieces together to build a truly comprehensive model of genetic architecture. For example, in 2003, a study of genetic architecture and the environment was able to show an association of social environment with variation in body size in Drosophila melanogaster . [ 11 ] However, this study was not able to tie a direct link to specific genes involved in this variation. | https://en.wikipedia.org/wiki/Genetic_architecture |
Genetic codes is a simple ASN.1 database hosted by the National Center for Biotechnology Information and listing all the known Genetic codes . [ 1 ]
This Biological database -related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genetic_codes_(database) |
In biology, genetic demixing [ 1 ] refers to a phenomenon in which an initial mixture of individuals with
two or more distinct genotypes rearranges in the course of time,
giving birth to a spatial organization where some or all genotypes are concentrated in distinct patches.
This genetics article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genetic_demixing |
Genetic distance is a measure of the genetic divergence between species or between populations within a species, whether the distance measures time from common ancestor or degree of differentiation. [ 2 ] Populations with many similar alleles have small genetic distances. This indicates that they are closely related and have a recent common ancestor.
Genetic distance is useful for reconstructing the history of populations, such as the multiple human expansions out of Africa . [ 3 ] It is also used for understanding the origin of biodiversity . For example, the genetic distances between different breeds of domesticated animals are often investigated in order to determine which breeds should be protected to maintain genetic diversity. [ 4 ]
Life on earth began from very simple unicellular organisms evolving into most complex multicellular organisms through the course of over three billion years. [ 5 ] Creating a comprehensive tree of life that represents all the organisms that have ever lived on earth is important for understanding the evolution of life in the face of all challenges faced by living organisms to deal with similar challenges in future. Evolutionary biologists have attempted to create evolutionary or phylogenetic trees encompassing as many organisms as possible based on the available resources. Fossil dating and molecular clock are the two means of generating evolutionary history of living organisms. Fossil record is random, incomplete and does not provide a continuous chain of events like a movie with missing frames cannot tell the whole plot of the movie. [ 5 ]
Molecular clocks on the other hand are specific sequences of DNA , RNA or proteins (amino acids) that are used to determine at molecular level the similarities and differences among species, to find out the timeline of divergence, [ 6 ] and to trace back the common ancestor of species based on the mutation rates and sequence changes being accumulated in those specific sequences. [ 6 ] The primary driver of evolution is the mutation or changes in genes and accounting for those changes over time determines the approximate genetic distance between species. These specific molecular clocks are fairly conserved across a range of species and have a constant rate of mutation like a clock and are calibrated based on evolutionary events (fossil records). For example, gene for alpha-globin (constituent of hemoglobin) mutates at a rate of 0.56 per base pair per billion years. [ 6 ] The molecular clock can fill those gaps created by missing fossil records.
In the genome of an organism , each gene is located at a specific place called the locus for that gene. Allelic variations at these loci cause phenotypic variation within species (e.g. hair colour, eye colour). However, most alleles do not have an observable impact on the phenotype. Within a population new alleles generated by mutation either die out or spread throughout the population. When a population is split into different isolated populations (by either geographical or ecological factors), mutations that occur after the split will be present only in the isolated population. Random fluctuation of allele frequencies also produces genetic differentiation between populations. This process is known as genetic drift . By examining the differences between allele frequencies between the populations and computing genetic distance, we can estimate how long ago the two populations were separated. [ 7 ]
Let’s suppose a sequence of DNA or a hypothetical gene that has mutation rate of one base per 10 million years. Using this sequence of DNA, the divergence of two different species or genetic distance between two different species can be determined by counting the number of base pair differences among them. For example, in Figure 2 a difference of 4 bases in the hypothetical sequence among those two species would indicate that they diverged 40 million years ago, and their common ancestor would have lived at least 20 million years ago before their divergence. Based on molecular clock, the equation below can be used to calculate the time since divergence. [ 8 ]
Number of mutation ÷ Mutation per year (rate of mutation) = time since divergence
Recent advancement in sequencing technology and the availability of comprehensive genomic databases and bioinformatics tools that are capable of storing and processing colossal amount of data generated by the advanced sequencing technology has tremendously improved evolutionary studies and the understanding of evolutionary relationships among species. [ 9 ] [ 10 ]
Different biomolecular markers such DNA, RNA and amino acid sequences (protein) can be used for determining the genetic distance. [ 11 ] [ 12 ]
The selection criteria [ 13 ] of appropriate biomarker for genetic distance entails the following three steps:
The choice of variability depends on the intended outcome. For example, very high level of variability is recommended for demographic studies and parentage analyses , medium to high variability for comparing distinct populations, and moderate to very low variability is recommended for phylogenetic studies. [ 13 ] The genomic localization and ploidy of the marker is also an important factor. For example, the gene copy number is inversely proportional to the robustness with haploid genome ( mitochondrial DNA ) more prone to genetic drift than diploid genome ( nuclear DNA ).
The choice and examples of molecular markers for evolutionary biology studies. [ 13 ]
loci = ( Multilocus )
genotype
Evolutionary forces such as mutation, genetic drift, natural selection , and gene flow drive the process of evolution and genetic diversity. All these forces play significant role in genetic distance within and among species. [ 19 ]
Different statistical measures exist that aim to quantify genetic deviation between populations or species. By utilizing assumptions gained from experimental analysis of evolutionary forces, a model that more accurately suits a given experiment can be selected to study a genetic group. Additionally, comparing how well different metrics model certain population features such as isolation can identify metrics that are more suited for understanding newly studied groups [ 20 ] The most commonly used genetic distance metrics are Nei's genetic distance, [ 7 ] Cavalli-Sforza and Edwards measure, [ 21 ] and Reynolds, Weir and Cockerham's genetic distance. [ 22 ]
One of the most basic and straight forward distance measures is Jukes-Cantor distance . This measure is constructed based on the assumption that no insertions or deletions occurred, all substitutions are independent, and that each nucleotide change is equally likely. With these presumptions, we can obtain the following equation: [ 23 ]
where d A B {\displaystyle d_{AB}} is the Jukes-Cantor distance between two sequences A, and B, and f A B {\displaystyle f_{AB}} being the dissimilarity between the two sequences.
In 1972, Masatoshi Nei published what came to be known as Nei's standard genetic distance. This distance has the nice property that if the rate of genetic change (amino acid substitution) is constant per year or generation then Nei's standard genetic distance ( D ) increases in proportion to divergence time. This measure assumes that genetic differences are caused by mutation and genetic drift . [ 7 ]
This distance can also be expressed in terms of the arithmetic mean of gene identity. Let j X {\displaystyle j_{X}} be the probability for the two members of population X {\displaystyle X} having the same allele at a particular locus and j Y {\displaystyle j_{Y}} be the corresponding probability in population Y {\displaystyle Y} . Also, let j X Y {\displaystyle j_{XY}} be the probability for a member of X {\displaystyle X} and a member of Y {\displaystyle Y} having the same allele. Now let J X {\displaystyle J_{X}} , J Y {\displaystyle J_{Y}} and J X Y {\displaystyle J_{XY}} represent the arithmetic mean of j X {\displaystyle j_{X}} , j Y {\displaystyle j_{Y}} and j X Y {\displaystyle j_{XY}} over all loci, respectively. In other words,
where L {\displaystyle L} is the total number of loci examined. [ 24 ]
Nei's standard distance can then be written as [ 7 ]
In 1967 Luigi Luca Cavalli-Sforza and A. W. F. Edwards published this measure. It assumes that genetic differences arise due to genetic drift only. One major advantage of this measure is that the populations are represented in a hypersphere, the scale of which is one unit per gene substitution. The chord distance in the hyperdimensional sphere is given by [ 2 ] [ 21 ]
Some authors drop the factor 2 π {\displaystyle {\frac {2}{\pi }}} to simplify the formula at the cost of losing the property that the scale is one unit per gene substitution.
In 1983, this measure was published by John Reynolds, Bruce Weir and C. Clark Cockerham .
This measure assumes that genetic differentiation occurs only by genetic drift without mutations. It estimates the coancestry coefficient Θ {\displaystyle \Theta } which provides a measure of the genetic divergence by: [ 22 ]
The Kimura two parameter model (K2P) was developed in 1980 by Japanese biologist Motoo Kimura. It is compatible with the neutral theory of evolution, which was also developed by the same author. As depicted in Figure 4, this measure of genetic distance accounts for the type of mutation occurring, namely whether it is a transition (i.e. purine to purine or pyrimidine to pyrimidine) or a transversion (i.e. purine to pyrimidine or vice versa). With this information, the following formula can be derived:
where P is n 1 n {\displaystyle {\frac {n_{1}}{n}}} and Q is n 2 n {\displaystyle {\frac {n_{2}}{n}}} , with n 1 {\displaystyle n_{1}} being the number of transition type conversions, n 2 {\displaystyle n_{2}} being the number of transversion type conversions, and n {\displaystyle n} being the number of nucleotides sites compared. [ 25 ]
It is worth noting when transition and transversion type substitutions have an equal chance of occurring, and P {\displaystyle P} is assumed to equal Q 2 {\displaystyle {\frac {Q}{2}}} , then the above formula can be reduced down to the Jukes Cantor model. In practice however, P {\displaystyle P} is typically larger than Q {\displaystyle Q} . [ 25 ]
It has been shown that while K2P works well in classifying distantly-related species, it is not always the best choice for comparing closely-related species. In these cases, it may be better to use p-distance instead. [ 26 ]
The Kimura three parameter (K3P) model was first published in 1981. This measure assumes three rates of substitution when nucleotides mutate, which can be seen in Figure 5. There is one rate for transition type mutations, one rate for transversion type mutations to corresponding bases (e.g. G to C; transversion type 1 in the figure), and one rate for transversion type mutations to non-corresponding bases (e.g. G to T; transversion type 2 in the figure).
With these rates of substitution, the following formula can be derived:
where P {\displaystyle P} is the probability of a transition type mutation, Q {\displaystyle Q} is the probability of a transversion type mutation to a corresponding base, and R {\displaystyle R} is the probability of a transversion type mutation to a non-corresponding base. When Q {\displaystyle Q} and R {\displaystyle R} are assumed to be equal, this reduces down to the Kimura 2 parameter distance. [ 27 ]
Many other measures of genetic distance have been proposed with varying success.
Nei's D A distance was created by Masatoshi Nei, a Japanese-American biologist in 1983. This distance assumes that genetic differences arise due to mutation and genetic drift , but this distance measure is known to give more reliable population trees than other distances particularly for microsatellite DNA data. This method is not ideal in cases where natural selection plays a significant role in a populations genetics. [ 28 ] [ 29 ]
D A {\displaystyle D_{A}} : Nei's DA distance, the genetic distance between populations X and Y
ℓ {\displaystyle \ell } : A locus or gene studied with ∑ ℓ {\displaystyle \sum _{\ell }} being the sum of loci or genes
X u {\displaystyle X_{u}} and Y u {\displaystyle Y_{u}} : The frequencies of allele u in populations X and Y, respectively
L: The total number of loci examined
Euclidean distance is a formula brought about from Euclid's Elements, a 13 book set detailing the foundation of all euclidean mathematics. The foundational principles outlined in these works is used not only in euclidean spaces but expanded upon by Issac Newton and Gottfried Leibniz in isolated pursuits to create calculus. [ 31 ] The euclidean distance formula is used to convey, as simply as possible, the genetic dissimilarity between populations, with a larger distance indicating greater dissimilarity. [ 32 ] As seen in figure 6, this method can be visualized in a graphical manner, this is due to the work of René Descartes who created the fundamental principle of analytic geometry, or the cartesian coordinate system. In an interesting example of historical repetitions, René Descartes was not the only one who discovered the fundamental principle of analytical geometry, this principle was as discovered in an isolated pursuit by Pierre de Fermat who left his work unpublished. [ 33 ] [ 34 ]
D E U {\displaystyle D_{EU}} : Euclidean genetic distance between populations X and Y
X u {\displaystyle X_{u}} and Y u {\displaystyle Y_{u}} : Allele frequencies at locus u in populations X and Y, respectively
It was specifically developed for microsatellite markers and is based on the stepwise-mutation model (SMM). The Goldstein distance formula is modeled in such a way that expected value will increase linearly with time, this property is maintained even when the assumptions of single-step mutations and symmetrical mutation rate are violated. Goldstein distance is derived from the average square distance model, of which Goldstein was also a contributor. [ 35 ]
This calculation represents the minimum amount of codon differences for each locus . [ 36 ] The measurement is based on the assumption that genetic differences arise due to mutation and genetic drift . [ 37 ]
D m = J X + J Y 2 − J X Y {\displaystyle D_{m}={\frac {J_{X}+J_{Y}}{2}}-J_{XY}}
D m {\textstyle D_{m}} : Minimum amount of codon difference per locus
J X {\displaystyle J_{X}} and J Y {\displaystyle J_{Y}} : Average probability of two members of the X population having the same allele
J X Y {\displaystyle J_{XY}} : Average probability of members of the X and Y populations having the same allele
Similar to Euclidean distance, Czekanowski distance involves calculated the distance between points of allele frequency that are graphed on an axis created by . However, Czekanowski assumes a direct path is not available and sums the sides of the triangle formed by the data points instead of finding the hypotenuse. This formula is nicknamed the Manhattan distance because its methodology is similar to the nature of the New York City burrow. Manhattan is mainly built on a grid system requiring resentence to only make 90 degree turns during travel, which parallels the thinking of the formula.
D C z = 1 2 | X u − Y u | {\displaystyle D_{Cz}={\frac {1}{2}}|X_{u}-Y_{u}|}
| X u − Y u | = | P X x − P Y x | + | P X y − P Y y | {\displaystyle |X_{u}-Y_{u}|=|P_{Xx}-P_{Yx}|+|P_{Xy}-P_{Yy}|}
X u {\displaystyle X_{u}} and Y u {\displaystyle Y_{u}} : Allele frequencies at locus u in populations X and Y, respectively
P X x {\displaystyle P_{Xx}} and P Y x {\displaystyle P_{Yx}} : X-axis value of the frequency of an allele for X and Y populations
P X y {\displaystyle P_{Xy}} and P Y y {\displaystyle P_{Yy}} : Y-axis value of the frequency of an allele for X and Y populations
Similar to Czekanowski distance, Roger's distance involves calculating the distance between points of allele frequency. However, this method takes the direct distance between the points.
D R = 1 L ∑ u ( X u − Y u ) 2 2 {\displaystyle D_{R}={\frac {1}{L}}{\sqrt {\frac {\sum \limits _{u}(X_{u}-Y_{u})^{2}}{2}}}} [ 38 ]
X u {\displaystyle X_{u}} and Y u {\displaystyle Y_{u}} : Allele frequencies at locus u in populations X and Y, respectively
L {\displaystyle L} : Total number of microsatallite loci examined
While these formulas are easy and quick calculations to make, the information that is provided gives limited information. The results of these formulas do not account for the potential effects of the number of codon changes between populations, or separation time between populations. [ 39 ]
A commonly used measure of genetic distance is the fixation index (F ST ) which varies between 0 and 1. A value of 0 indicates that two populations are genetically identical (minimal or no genetic diversity between the two populations) whereas a value of 1 indicates that two populations are genetically different (maximum genetic diversity between the two populations). No mutation is assumed. Large populations between which there is much migration, for example, tend to be little differentiated whereas small populations between which there is little migration tend to be greatly differentiated. F ST is a convenient measure of this differentiation, and as a result F ST and related statistics are among the most widely used descriptive statistics in population and evolutionary genetics. But F ST is more than a descriptive statistic and measure of genetic differentiation. F ST is directly related to the Variance in allele frequency among populations and conversely to the degree of resemblance among individuals within populations. If F ST is small, it means that allele frequencies within each population are very similar; if it is large, it means that allele frequencies are very different. | https://en.wikipedia.org/wiki/Genetic_distance |
Genetic divergence is the process in which two or more populations of an ancestral species accumulate independent genetic changes ( mutations ) through time, often leading to reproductive isolation and continued mutation even after the populations have become reproductively isolated for some period of time, as there is not any genetic exchange anymore. [ 1 ] In some cases, subpopulations cover living in ecologically distinct peripheral environments can exhibit genetic divergence from the remainder of a population, especially where the range of a population is very large (see parapatric speciation ). The genetic differences among divergent populations can involve silent mutations (that have no effect on the phenotype ) or give rise to significant morphological and/or physiological changes. Genetic divergence will always accompany reproductive isolation, either due to novel adaptations via selection and/or due to genetic drift, and is the principal mechanism underlying speciation .
On a molecular genetics level, genetic divergence is due to changes in a small number of genes in a species, resulting in speciation . [ 2 ] However, researchers argue that it is unlikely that divergence is a result of a significant, single, dominant mutation in a genetic locus because if that were so, the individual with that mutation would have zero fitness . [ 3 ] Consequently, they could not reproduce and pass the mutation on to further generations. Hence, it is more likely that divergence, and subsequently reproductive isolation , are the outcomes of multiple small mutations over evolutionary time accumulating in a population isolated from gene flow . [ 2 ]
One possible cause of genetic divergence is the founder effect , which is when a few individuals become isolated from their original population. Those individuals might overrepresent a certain genetic pattern, which means that certain biological characteristics are overrepresented. These individuals can form a new population with different gene pools from the original population. For example, 10% of the original population has blue eyes and 90% has brown eyes. By chance, 10 individuals are separated from the original population. If this small group has 80% blue eyes and 20% brown eyes, then their offspring would be more likely to have the allele for the blue eyes. As a result, the percentage of the population with blue eyes would be higher than the population with brown eyes, which is different from the original population.
Another possible cause of genetic divergence is the bottleneck effect . The bottleneck effect is when an event, such as a natural disaster, causes a large portion of the population to die. By chance, certain genetic patterns will be overrepresented in the remaining population, which is similar to what happens with the founder effect . [ 4 ]
Genetic divergence can occur without geographic separation, through Disruptive selection . This occurs when individuals in a population with both high and low phenotypic extremes are fitter than the intermediate phenotype. [ 5 ] These individuals occupy two different niches, within each niche there is Gaussian trait distribution . [ 6 ] If the genetic variation between niches is high then there will be strong reproductive isolation. [ 6 ] If genetic variation is below a certain threshold than introgression will occur but if variation is above a certain threshold the population can split resulting in speciation. [ 6 ]
Disruptive selection is seen in the bimodal population of Darwin's finches , Geospiza fortis . [ 7 ] The two modes specialize in eating different types of seeds small and soft versus large and hard, this results in beaks of different sizes with different force capacities. [ 7 ] Individuals with intermediate beak sizes are selected against. [ 7 ] The song structure and response to song also differs between the two modes. [ 7 ] There is minimal gene flow between the two modes of G. fortis. [ 7 ] | https://en.wikipedia.org/wiki/Genetic_divergence |
Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species. It ranges widely, from the number of species to differences within species , and can be correlated to the span of survival for a species. [ 1 ] It is distinguished from genetic variability , which describes the tendency of genetic characteristics to vary.
Genetic diversity serves as a way for populations to adapt to changing environments. With more variation, it is more likely that some individuals in a population will possess variations of alleles that are suited for the environment. Those individuals are more likely to survive to produce offspring bearing that allele. The population will continue for more generations because of the success of these individuals. [ 2 ]
The academic field of population genetics includes several hypotheses and theories regarding genetic diversity. The neutral theory of evolution proposes that diversity is the result of the accumulation of neutral substitutions. Diversifying selection is the hypothesis that two subpopulations of a species live in different environments that select for different alleles at a particular locus. This may occur, for instance, if a species has a large range relative to the mobility of individuals within it. Frequency-dependent selection is the hypothesis that as alleles become more common, they become more vulnerable. This occurs in host–pathogen interactions , where a high frequency of a defensive allele among the host means that it is more likely that a pathogen will spread if it is able to overcome that allele .
A study conducted by the National Science Foundation in 2007 found that genetic diversity (within-species diversity) and biodiversity are dependent upon each other — i.e. that diversity within a species is necessary to maintain diversity among species, and vice versa. According to the lead researcher in the study, Dr. Richard Lankau, "If any one type is removed from the system, the cycle can break down, and the community becomes dominated by a single species." [ 3 ] Genotypic and phenotypic diversity have been found in all species at the protein , DNA , and organismal levels; in nature, this diversity is nonrandom, heavily structured, and correlated with environmental variation and stress . [ 4 ]
The interdependence between genetic and species diversity is delicate. Changes in species diversity lead to changes in the environment, leading to adaptation of the remaining species. Changes in genetic diversity, such as in loss of species, leads to a loss of biological diversity . [ 2 ] Loss of genetic diversity in domestic animal populations has also been studied and attributed to the extension of markets and economic globalization . [ 5 ] [ 6 ]
Neutral genetic diversity consists of genes that do not increase fitness and are not responsible for adaptability. [ 7 ] Natural selection does not act on these neutral genes. [ 7 ] Adaptive genetic diversity consists of genes that increase fitness and are responsible for adaptability to changes in the environment. [ 7 ] Adaptive genes are responsible for ecological, morphological, and behavioral traits. [ 8 ] Natural selection acts on adaptive genes which allows the organisms to evolve. [ 7 ] The rate of evolution on adaptive genes is greater than on neutral genes due to the influence of selection. [ 8 ] However, it has been difficult to identify alleles for adaptive genes and thus adaptive genetic diversity is most often measured indirectly. [ 7 ] For example, heritability can be measured as h 2 = V A / V P {\displaystyle h^{2}=V_{A}/V_{P}} or adaptive population differentiation can be measured as Q S T = V G / ( V G + 2 V A ) {\displaystyle Q_{ST}=V_{G}/(V_{G}+2V_{A})} . [ 7 ] It may be possible to identify adaptive genes through genome-wide association studies by analyzing genomic data at the population level. [ 9 ]
Identifying adaptive genetic diversity is important for conservation because the adaptive potential of a species may dictate whether it survives or becomes extinct , especially as the climate changes . [ 7 ] [ 10 ] This is magnified by a lack of understanding whether low neutral genetic diversity is correlated with high genetic drift and high mutation load . [ 10 ] In a review of current research, Teixeira and Huber (2021), discovered some species, such as those in the genus Arabidopsis , appear to have high adaptive potential despite suffering from low genetic diversity overall due to severe bottlenecks . [ 10 ] Therefore species with low neutral genetic diversity may possess high adaptive genetic diversity, but since it is difficult to identify adaptive genes, a measurement of overall genetic diversity is important for planning conservation efforts and a species that has experienced a rapid decline in genetic diversity may be highly susceptible to extinction. [ 10 ] [ 9 ]
Variation in the populations gene pool allows natural selection to act upon traits that allow the population to adapt to changing environments. Selection for or against a trait can occur with changing environment – resulting in an increase in genetic diversity (if a new mutation is selected for and maintained) or a decrease in genetic diversity (if a disadvantageous allele is selected against). [ 11 ] Hence, genetic diversity plays an important role in the survival and adaptability of a species. [ 12 ] The capability of the population to adapt to the changing environment will depend on the presence of the necessary genetic diversity. [ 13 ] [ 14 ] The more genetic diversity a population has, the more likelihood the population will be able to adapt and survive. Conversely, the vulnerability of a population to changes, such as climate change or novel diseases will increase with reduction in genetic diversity. [ 15 ] For example, the inability of koalas to adapt to fight Chlamydia and the koala retrovirus (KoRV) has been linked to the koala's low genetic diversity. [ 16 ] This low genetic diversity also has geneticists concerned for the koalas' ability to adapt to climate change and human-induced environmental changes in the future. [ 16 ]
Large populations are more likely to maintain genetic material and thus generally have higher genetic diversity. [ 11 ] Small populations are more likely to experience the loss of diversity over time by random chance, which is an example of genetic drift . When an allele (variant of a gene) drifts to fixation, the other allele at the same locus is lost, resulting in a loss in genetic diversity. [ 17 ] In small population sizes, inbreeding , or mating between individuals with similar genetic makeup, is more likely to occur, thus perpetuating more common alleles to the point of fixation, thus decreasing genetic diversity. [ 18 ] Concerns about genetic diversity are therefore especially important with large mammals due to their small population size and high levels of human-caused population effects. [16]
A genetic bottleneck can occur when a population goes through a period of low number of individuals, resulting in a rapid decrease in genetic diversity. Even with an increase in population size, the genetic diversity often continues to be low if the entire species began with a small population, since beneficial mutations (see below) are rare, and the gene pool is limited by the small starting population. [ 19 ] This is an important consideration in the area of conservation genetics , when working toward a rescued population or species that is genetically healthy.
Random mutations consistently generate genetic variation . [ 11 ] A mutation will increase genetic diversity in the short term, as a new gene is introduced to the gene pool. However, the persistence of this gene is dependent of drift and selection (see above). Most new mutations either have a neutral or negative effect on fitness, while some have a positive effect. [ 11 ] A beneficial mutation is more likely to persist and thus have a long-term positive effect on genetic diversity. Mutation rates differ across the genome, and larger populations have greater mutation rates. [ 11 ] In smaller populations a mutation is less likely to persist because it is more likely to be eliminated by drift. [ 11 ]
Gene flow , often by migration, is the movement of genetic material (for example by pollen in the wind, or the migration of a bird). Gene flow can introduce novel alleles to a population. These alleles can be integrated into the population, thus increasing genetic diversity. [ 20 ]
For example, an insecticide -resistant mutation arose in Anopheles gambiae African mosquitoes. Migration of some A. gambiae mosquitoes to a population of Anopheles coluzziin mosquitoes resulted in a transfer of the beneficial resistance gene from one species to the other. The genetic diversity was increased in A. gambiae by mutation and in A. coluzziin by gene flow. [ 21 ]
When humans initially started farming, they used selective breeding to pass on desirable traits of the crops while omitting the undesirable ones. Selective breeding leads to monocultures : entire farms of nearly genetically identical plants. Little to no genetic diversity makes crops extremely susceptible to widespread disease; bacteria morph and change constantly and when a disease-causing bacterium changes to attack a specific genetic variation, it can easily wipe out vast quantities of the species. If the genetic variation that the bacterium is best at attacking happens to be that which humans have selectively bred to use for harvest, the entire crop will be wiped out. [ 22 ]
The nineteenth-century Great Famine in Ireland was caused in part by a lack of biodiversity. Since new potato plants do not come as a result of reproduction, but rather from pieces of the parent plant, no genetic diversity is developed, and the entire crop is essentially a clone of one potato, it is especially susceptible to an epidemic. In the 1840s, much of Ireland's population depended on potatoes for food. They planted namely the "lumper" variety of potato, which was susceptible to a rot-causing oomycete called Phytophthora infestans . [ 23 ] The fungus destroyed the vast majority of the potato crop, and left one million people to starve to death.
Genetic diversity in agriculture does not only relate to disease, but also herbivores . Similarly, to the above example, monoculture agriculture selects for traits that are uniform throughout the plot. If this genotype is susceptible to certain herbivores, this could result in the loss of a large portion of the crop. [ 24 ] [ 25 ] One way farmers get around this is through inter-cropping . By planting rows of unrelated, or genetically distinct crops as barriers between herbivores and their preferred host plant, the farmer effectively reduces the ability of the herbivore to spread throughout the entire plot. [ 26 ] [ 27 ] [ 28 ]
The genetic diversity of livestock species permits animal husbandry in a range of environments and with a range of different objectives. It provides the raw material for selective breeding programmes and allows livestock populations to adapt as environmental conditions change. [ 29 ]
Livestock biodiversity can be lost as a result of breed extinctions and other forms of genetic erosion . As of June 2014, among the 8,774 breeds recorded in the Domestic Animal Diversity Information System ( DAD-IS ), operated by the Food and Agriculture Organization of the United Nations ( FAO ), 17 percent were classified as being at risk of extinction and 7 percent already extinct. [ 29 ] There is now a Global Plan of Action for Animal Genetic Resources that was developed under the auspices of the Commission on Genetic Resources for Food and Agriculture in 2007, that provides a framework and guidelines for the management of animal genetic resources.
Awareness of the importance of maintaining animal genetic resources has increased over time. FAO has published two reports on the state of the world's animal genetic resources for food and agriculture , which cover detailed analyses of our global livestock diversity and ability to manage and conserve them.
High genetic diversity in viruses must be considered when designing vaccinations. High genetic diversity results in difficulty in designing targeted vaccines, and allows for viruses to quickly evolve to resist vaccination lethality. For example, malaria vaccinations are impacted by high levels of genetic diversity in the protein antigens. [ 30 ] In addition, HIV-1 genetic diversity limits the use of currently available viral load and resistance tests. [ 31 ]
Coronavirus populations have considerable evolutionary diversity due to mutation and homologous recombination . [ 32 ] For example, the sequencing of 86 SARS-CoV-2 coronavirus samples obtained from infected patients revealed 93 mutations indicating the presence of considerable genetic diversity. [ 33 ] Replication of the coronavirus RNA genome is catalyzed by an RNA-dependent RNA polymerase . During replication this polymerase may undergo template switching, a form of homologous recombination. [ 34 ] This process which also generates genetic diversity appears to be an adaptation for coping with RNA genome damage. [ 35 ]
The natural world has several ways of preserving or increasing genetic diversity. Among oceanic plankton , viruses aid in the genetic shifting process. Ocean viruses, which infect the plankton, carry genes of other organisms in addition to their own. When a virus containing the genes of one cell infects another, the genetic makeup of the latter changes. This constant shift of genetic makeup helps to maintain a healthy population of plankton despite complex and unpredictable environmental changes. [ 36 ]
Cheetahs are a threatened species . Low genetic diversity and resulting poor sperm quality has made breeding and survivorship difficult for cheetahs. Moreover, only about 5% of cheetahs survive to adulthood. [ 37 ] However, it has been recently discovered that female cheetahs can mate with more than one male per litter of cubs. They undergo induced ovulation, which means that a new egg is produced every time a female mates. By mating with multiple males, the mother increases the genetic diversity within a single litter of cubs. [ 38 ]
Attempts to increase the viability of a species by increasing genetic diversity is called genetic rescue. For example, eight panthers from Texas were introduced to the Florida panther population, which was declining and suffering from inbreeding depression. Genetic variation was thus increased and resulted in a significant increase in population growth of the Florida Panther. [ 39 ] Creating or maintaining high genetic diversity is an important consideration in species rescue efforts, in order to ensure the longevity of a population.
Genetic diversity of a population can be assessed by some simple measures.
Furthermore, stochastic simulation software is commonly used to predict the future of a population given measures such as allele frequency and population size. [ 41 ]
Genetic diversity can also be measured. The various recorded ways of measuring genetic diversity include: [ 42 ] | https://en.wikipedia.org/wiki/Genetic_diversity |
Genetic ecology is the study of the stability and expression of varying genetic material within abiotic mediums. [ 1 ] Typically, genetic data is not thought of outside of any organism save for criminal forensics. However, genetic material has the ability to be taken up by various organisms that exist within an abiotic medium through natural transformations that may occur. [ 2 ] Thus, this field of study focuses on interaction, exchange, and expression of genetic material that may not be shared by species had they not been in the same environment.
E.B. Ford was the first geneticist to begin work in this field of study. E.B. Ford worked mostly during the 1950s and is most noted for his work with Maniola jurtina and published a book entitled Ecological Genetics in 1975. [ 3 ] [ 4 ] This type of evolutionary biological study was only possible after gel electrophoresis had been designed in 1937. [ 5 ] Prior to this, a high throughput method for DNA analysis did not exist. This field of study began to become more popular following the 1980s with the development of polymerase chain reaction (PCR 1985) and poly- acrylamide gel electrophoresis (p. 1967). [ 6 ] [ 7 ] With this technology, segments of DNA could be sequenced, amplified, and proteins produced using bacterial transformations. The genetic material along with the proteins could be analyzed and more correct phylogenetic trees could be created.
Since E.B. Ford's research, multiple other genetic ecologists have continued study within the field of genetic ecology such as PT Hanford [ 8 ] Alina von Thaden, [ 9 ] and many others. [ 10 ] [ 11 ] [ 12 ] [ 13 ] [ 14 ]
Genetic information may transfer throughout an ecosystem in multiple ways. The first of which, on the smallest scale, being bacterial gene transfer (see bacterial transformation ). Bacteria have the ability to exchange DNA. This DNA exchange, or horizontal gene transfer , may provide various species of bacteria with the genetic information they need to survive in an environment. [ 15 ] This can help many bacterial species survive within an environment.
A similar event has the ability to happen between plants and bacteria. For example, Agrobacterium tumefaciens has the ability to introduce genes into plants to cause the development of Gall disease. This occurs through genetic transfer between the A. tumefaciens and between the plant in question. [ 16 ]
In fact, a similar event occurs each time viral infections occur within living organisms. The viruses , whether positive or negative sense viruses, require a living organism to replicate their genes and produce more viruses. Once a virus is inside a living organism, it utilizes polymerases, ribosomes, and other biomolecules to replicate its own genetic material and to produce more virus genetic material similar to the original virus. [ 17 ] Thus, gene transfer may occur through many varying means. Thus, the study of this gene transfer throughout each ecosystem, whether it be through a bacterial ecosystem or through the ecosystem of an organism, genetic ecology is the study of this gene transfer and its causes. | https://en.wikipedia.org/wiki/Genetic_ecology |
Genetic engineering techniques allow the modification of animal and plant genomes . Techniques have been devised to insert, delete, and modify DNA at multiple levels, ranging from a specific base pair in a specific gene to entire genes. There are a number of steps that are followed before a genetically modified organism (GMO) is created. Genetic engineers must first choose what gene they wish to insert, modify, or delete. The gene must then be isolated and incorporated, along with other genetic elements, into a suitable vector . This vector is then used to insert the gene into the host genome, creating a transgenic or edited organism.
The ability to genetically engineer organisms is built on years of research and discovery on gene function and manipulation. Important advances included the discovery of restriction enzymes , DNA ligases , and the development of polymerase chain reaction and sequencing .
Added genes are often accompanied by promoter and terminator regions as well as a selectable marker gene. The added gene may itself be modified to make it express more efficiently. This vector is then inserted into the host organism's genome. For animals, the gene is typically inserted into embryonic stem cells , while in plants it can be inserted into any tissue that can be cultured into a fully developed plant.
Tests are carried out on the modified organism to ensure stable integration, inheritance and expression. First generation offspring are heterozygous , requiring them to be inbred to create the homozygous pattern necessary for stable inheritance. Homozygosity must be confirmed in second generation specimens.
Early techniques randomly inserted the genes into the genome. Advances allow targeting specific locations, which reduces unintended side effects. Early techniques relied on meganucleases and zinc finger nucleases . Since 2009 more accurate and easier systems to implement have been developed. Transcription activator-like effector nucleases (TALENs) and the Cas9-guideRNA system (adapted from CRISPR ) are the two most common.
Many different discoveries and advancements led to the development of genetic engineering . Human-directed genetic manipulation began with the domestication of plants and animals through artificial selection in about 12,000 BC. [ 1 ] : 1 Various techniques were developed to aid in breeding and selection. Hybridization was one way rapid changes in an organism's genetic makeup could be introduced. Crop hybridization most likely first occurred when humans began growing genetically distinct individuals of related species in close proximity. [ 2 ] : 32 Some plants were able to be propagated by vegetative cloning . [ 2 ] : 31
Genetic inheritance was first discovered by Gregor Mendel in 1865, following experiments crossing peas. [ 3 ] In 1928 Frederick Griffith proved the existence of a "transforming principle" involved in inheritance, which was identified as DNA in 1944 by Oswald Avery, Colin MacLeod, and Maclyn McCarty . Frederick Sanger developed a method for sequencing DNA in 1977, greatly increasing the genetic information available to researchers.
After discovering the existence and properties of DNA , tools had to be developed that allowed it to be manipulated. In 1970 Hamilton Smiths lab discovered restriction enzymes , enabling scientists to isolate genes from an organism's genome. [ 4 ] DNA ligases , which join broken DNA together, were discovered earlier in 1967. [ 5 ] By combining the two enzymes it became possible to "cut and paste" DNA sequences to create recombinant DNA . Plasmids , discovered in 1952, [ 6 ] became important tools for transferring information between cells and replicating DNA sequences. Polymerase chain reaction (PCR), developed by Kary Mullis in 1983, allowed small sections of DNA to be amplified (replicated) and aided identification and isolation of genetic material.
As well as manipulating DNA, techniques had to be developed for its insertion into an organism's genome. Griffith's experiment had already shown that some bacteria had the ability to naturally uptake and express foreign DNA . Artificial competence was induced in Escherichia coli in 1970 by treating them with calcium chloride solution (CaCl 2 ). [ 7 ] Transformation using electroporation was developed in the late 1980s, increasing the efficiency and bacterial range. [ 8 ] In 1907 a bacterium that caused plant tumors, Agrobacterium tumefaciens , had been discovered. In the early 1970s it was found that this bacteria inserted its DNA into plants using a Ti plasmid . [ 9 ] By removing the genes in the plasmid that caused the tumor and adding in novel genes, researchers were able to infect plants with A. tumefaciens and let the bacteria insert their chosen DNA into the genomes of the plants. [ 10 ]
The first step is to identify the target gene or genes to insert into the host organism. This is driven by the goal for the resultant organism. In some cases only one or two genes are affected. For more complex objectives entire biosynthetic pathways involving multiple genes may be involved. Once found genes and other genetic information from a wide range of organisms can be inserted into bacteria for storage and modification, creating genetically modified bacteria in the process. Bacteria are cheap, easy to grow, clonal , multiply quickly, relatively easy to transform and can be stored at -80 °C almost indefinitely. Once a gene is isolated it can be stored inside the bacteria providing an unlimited supply for research. [ 11 ]
Genetic screens can be carried out to determine potential genes followed by other tests that identify the best candidates. A simple screen involves randomly mutating DNA with chemicals or radiation and then selecting those that display the desired trait. For organisms where mutation is not practical, scientists instead look for individuals among the population who present the characteristic through naturally-occurring mutations. Processes that look at a phenotype and then try and identify the gene responsible are called forward genetics . The gene then needs to be mapped by comparing the inheritance of the phenotype with known genetic markers . Genes that are close together are likely to be inherited together. [ 12 ]
Another option is reverse genetics . This approach involves targeting a specific gene with a mutation and then observing what phenotype develops. [ 12 ] The mutation can be designed to inactivate the gene or only allow it to become active under certain conditions. Conditional mutations are useful for identifying genes that are normally lethal if non-functional. [ 13 ] As genes with similar functions share similar sequences ( homologous ) it is possible to predict the likely function of a gene by comparing its sequence to that of well-studied genes from model organisms . [ 12 ] The development of microarrays , transcriptomes and genome sequencing has made it much easier to find desirable genes. [ 14 ]
The bacteria Bacillus thuringiensis was first discovered in 1901 as the causative agent in the death of silkworms . Due to these insecticidal properties, the bacteria was used as a biological insecticide , developed commercially in 1938. The cry proteins were discovered to provide the insecticidal activity in 1956, and by the 1980s, scientists had successfully cloned the gene that encodes this protein and expressed it in plants. [ 15 ] The gene that provides resistance to the herbicide glyphosate was found after seven years of searching in bacteria living in the outflow pipe of a Monsanto RoundUp manufacturing facility. [ 16 ] In animals, the majority of genes used are growth hormone genes. [ 17 ]
All genetic engineering processes involve the modification of DNA. Traditionally DNA was isolated from the cells of organisms. Later, genes came to be cloned from a DNA segment after the creation of a DNA library or artificially synthesised . Once isolated, additional genetic elements are added to the gene to allow it to be expressed in the host organism and to aid selection.
First the cell must be gently opened , exposing the DNA without causing too much damage to it. The methods used vary depending on the type of cell. Once it is open, the DNA must be separated from the other cellular components. A ruptured cell contains proteins and other cell debris. By mixing with phenol and/or chloroform , followed by centrifuging , the nucleic acids can be separated from this debris into an upper aqueous phase . This aqueous phase can be removed and further purified if necessary by repeating the phenol-chloroform steps. The nucleic acids can then be precipitated from the aqueous solution using ethanol or isopropanol . Any RNA can be removed by adding a ribonuclease that will degrade it. Many companies now sell kits that simplify the process. [ 18 ]
The gene researchers are looking to modify (known as the gene of interest) must be separated from the extracted DNA. If the sequence is not known then a common method is to break the DNA up with a random digestion method. This is usually accomplished using restriction enzymes (enzymes that cut DNA). A partial restriction digest cuts only some of the restriction sites, resulting in overlapping DNA fragment segments. The DNA fragments are put into individual plasmid vectors and grown inside bacteria. Once in the bacteria the plasmid is copied as the bacteria divides . To determine if a useful gene is present in a particular fragment, the DNA library is screened for the desired phenotype . If the phenotype is detected then it is possible that the bacteria contains the target gene.
If the gene does not have a detectable phenotype or a DNA library does not contain the correct gene, other methods must be used to isolate it. If the position of the gene can be determined using molecular markers then chromosome walking is one way to isolate the correct DNA fragment. If the gene expresses close homology to a known gene in another species, then it could be isolated by searching for genes in the library that closely match the known gene. [ 19 ]
For known DNA sequences, restriction enzymes that cut the DNA on either side of the gene can be used. Gel electrophoresis then sorts the fragments according to length. [ 20 ] Some gels can separate sequences that differ by a single base-pair . The DNA can be visualised by staining it with ethidium bromide and photographing under UV light . A marker with fragments of known lengths can be laid alongside the DNA to estimate the size of each band. The DNA band at the correct size should contain the gene, where it can be excised from the gel. [ 18 ] : 40–41 Another technique to isolate genes of known sequences involves polymerase chain reaction (PCR). [ 21 ] PCR is a powerful tool that can amplify a given sequence, which can then be isolated through gel electrophoresis. Its effectiveness drops with larger genes and it has the potential to introduce errors into the sequence.
It is possible to artificially synthesise genes . [ 22 ] Some synthetic sequences are available commercially, forgoing many of these early steps. [ 23 ]
The gene to be inserted must be combined with other genetic elements in order for it to work properly. The gene can be modified at this stage for better expression or effectiveness. As well as the gene to be inserted most constructs contain a promoter and terminator region as well as a selectable marker gene. The promoter region initiates transcription of the gene and can be used to control the location and level of gene expression, while the terminator region ends transcription. A selectable marker, which in most cases confers antibiotic resistance to the organism it is expressed in, is used to determine which cells are transformed with the new gene. The constructs are made using recombinant DNA techniques, such as restriction digests , ligations and molecular cloning . [ 24 ]
Once the gene is constructed it must be stably integrated into the genome of the target organism or exist as extrachromosomal DNA . There are a number of techniques available for inserting the gene into the host genome and they vary depending on the type of organism targeted. In multicellular eukaryotes , if the transgene is incorporated into the host's germline cells, the resulting host cell can pass the transgene to its progeny . If the transgene is incorporated into somatic cells, the transgene can not be inherited. [ 25 ]
Transformation is the direct alteration of a cell's genetic components by passing the genetic material through the cell membrane . About 1% of bacteria are naturally able to take up foreign DNA , but this ability can be induced in other bacteria. [ 26 ] Stressing the bacteria with a heat shock or electroporation can make the cell membrane permeable to DNA that may then be incorporated into the genome or exist as extrachromosomal DNA. Typically the cells are incubated in a solution containing divalent cations (often calcium chloride ) under cold conditions, before being exposed to a heat pulse (heat shock). Calcium chloride partially disrupts the cell membrane, which allows the recombinant DNA to enter the host cell. It is suggested that exposing the cells to divalent cations in cold condition may change or weaken the cell surface structure, making it more permeable to DNA. The heat-pulse is thought to create a thermal imbalance across the cell membrane, which forces the DNA to enter the cells through either cell pores or the damaged cell wall. Electroporation is another method of promoting competence. In this method the cells are briefly shocked with an electric field of 10-20 kV /cm, which is thought to create holes in the cell membrane through which the plasmid DNA may enter. After the electric shock, the holes are rapidly closed by the cell's membrane-repair mechanisms. Up-taken DNA can either integrate with the bacterials genome or, more commonly, exist as extrachromosomal DNA .
In plants the DNA is often inserted using Agrobacterium -mediated recombination , [ 27 ] taking advantage of the Agrobacterium s T-DNA sequence that allows natural insertion of genetic material into plant cells. [ 28 ] Plant tissue are cut into small pieces and soaked in a fluid containing suspended Agrobacterium . The bacteria will attach to many of the plant cells exposed by the cuts. The bacteria uses conjugation to transfer a DNA segment called T-DNA from its plasmid into the plant. The transferred DNA is piloted to the plant cell nucleus and integrated into the host plants genomic DNA.The plasmid T-DNA is integrated semi-randomly into the genome of the host cell. [ 29 ]
By modifying the plasmid to express the gene of interest, researchers can insert their chosen gene stably into the plants genome. The only essential parts of the T-DNA are its two small (25 base pair) border repeats, at least one of which is needed for plant transformation. [ 30 ] [ 31 ] The genes to be introduced into the plant are cloned into a plant transformation vector that contains the T-DNA region of the plasmid . An alternative method is agroinfiltration . [ 32 ] [ 33 ]
Another method used to transform plant cells is biolistics , where particles of gold or tungsten are coated with DNA and then shot into young plant cells or plant embryos. [ 34 ] Some genetic material enters the cells and transforms them. This method can be used on plants that are not susceptible to Agrobacterium infection and also allows transformation of plant plastids . Plants cells can also be transformed using electroporation, which uses an electric shock to make the cell membrane permeable to plasmid DNA. Due to the damage caused to the cells and DNA the transformation efficiency of biolistics and electroporation is lower than agrobacterial transformation. [ citation needed ]
Transformation has a different meaning in relation to animals, indicating progression to a cancerous state, so the process used to insert foreign DNA into animal cells is usually called transfection. [ 35 ] There are many ways to directly introduce DNA into animal cells in vitro . Often these cells are stem cells that are used for gene therapy . Chemical based methods uses natural or synthetic compounds to form particles that facilitate the transfer of genes into cells. [ 36 ] These synthetic vectors have the ability to bind DNA and accommodate large genetic transfers. [ 37 ] One of the simplest methods involves using calcium phosphate to bind the DNA and then exposing it to cultured cells. The solution, along with the DNA, is encapsulated by the cells. [ 38 ] Liposomes and polymers can be used as vectors to deliver DNA into cultured animal cells. Positively charged liposomes bind with DNA, while polymers can designed that interact with DNA. [ 36 ] They form lipoplexes and polyplexes respectively, which are then up-taken by the cells. Other techniques include using electroporation and biolistics. [ 39 ] In some cases, transfected cells may stably integrate external DNA into their own genome, this process is known as stable transfection . [ 40 ]
To create transgenic animals the DNA must be inserted into viable embryos or eggs. This is usually accomplished using microinjection , where DNA is injected through the cell's nuclear envelope directly into the nucleus . [ 26 ] Superovulated fertilised eggs are collected at the single cell stage and cultured in vitro . When the pronuclei from the sperm head and egg are visible through the protoplasm the genetic material is injected into one of them. The oocyte is then implanted in the oviduct of a pseudopregnant animal. [ 41 ] Another method is Embryonic Stem Cell-Mediated Gene Transfer. The gene is transfected into embryonic stem cells and then they are inserted into mouse blastocysts that are then implanted into foster mothers. The resulting offspring are chimeric , and further mating can produce mice fully transgenic with the gene of interest. [ 42 ]
Transduction is the process by which foreign DNA is introduced into a cell by a virus or viral vector . [ 43 ] Genetically modified viruses can be used as viral vectors to transfer target genes to another organism in gene therapy . [ 44 ] First the virulent genes are removed from the virus and the target genes are inserted instead. The sequences that allow the virus to insert the genes into the host organism must be left intact. Popular virus vectors are developed from retroviruses or adenoviruses . Other viruses used as vectors include, lentiviruses , pox viruses and herpes viruses . The type of virus used will depend on the cells targeted and whether the DNA is to be altered permanently or temporarily.
As often only a single cell is transformed with genetic material, the organism must be regenerated from that single cell. In plants this is accomplished through the use of tissue culture . [ 45 ] [ 46 ] Each plant species has different requirements for successful regeneration. If successful, the technique produces an adult plant that contains the transgene in every cell. [ 47 ] In animals it is necessary to ensure that the inserted DNA is present in the embryonic stem cells . [ 27 ] Offspring can be screened for the gene. All offspring from the first generation are heterozygous for the inserted gene and must be inbred to produce a homozygous specimen. [ citation needed ] Bacteria consist of a single cell and reproduce clonally so regeneration is not necessary. Selectable markers are used to easily differentiate transformed from untransformed cells.
Cells that have been successfully transformed with the DNA contain the marker gene, while those not transformed will not. By growing the cells in the presence of an antibiotic or chemical that selects or marks the cells expressing that gene, it is possible to separate modified from unmodified cells. Another screening method involves a DNA probe that sticks only to the inserted gene. These markers are usually present in the transgenic organism, although a number of strategies have been developed that can remove the selectable marker from the mature transgenic plant. [ 48 ]
Finding that a recombinant organism contains the inserted genes is not usually sufficient to ensure that they will be appropriately expressed in the intended tissues. Further testing using PCR, Southern hybridization , and DNA sequencing is conducted to confirm that an organism contains the new gene. [ 49 ] These tests can also confirm the chromosomal location and copy number of the inserted gene. Once confirmed methods that look for and measure the gene products (RNA and protein) are also used to assess gene expression, transcription, RNA processing patterns and expression and localization of protein product(s). These include northern hybridisation , quantitative RT-PCR , Western blot , immunofluorescence , ELISA and phenotypic analysis. [ 50 ] When appropriate, the organism's offspring are studied to confirm that the transgene and associated phenotype are stably inherited.
Traditional methods of genetic engineering generally insert the new genetic material randomly within the host genome. This can impair or alter other genes within the organism. Methods were developed that inserted the new genetic material into specific sites within an organism genome. Early methods that targeted genes at certain sites within a genome relied on homologous recombination (HR). [ 51 ] By creating DNA constructs that contain a template that matches the targeted genome sequence, it is possible that the HR processes within the cell will insert the construct at the desired location. Using this method on embryonic stem cells led to the development of transgenic mice with targeted knocked out . It has also been possible to knock in genes or alter gene expression patterns. [ 52 ]
If a vital gene is knocked out it can prove lethal to the organism. In order to study the function of these genes, site specific recombinases (SSR) were used. The two most common types are the Cre-LoxP and Flp-FRT systems. Cre recombinase is an enzyme that removes DNA by homologous recombination between binding sequences known as Lox-P sites. The Flip-FRT system operates in a similar way, with the Flip recombinase recognizing FRT sequences. By crossing an organism containing the recombinase sites flanking the gene of interest with an organism that expresses the SSR under control of tissue specific promoters , it is possible to knock out or switch on genes only in certain cells. This has also been used to remove marker genes from transgenic animals. Further modifications of these systems allowed researchers to induce recombination only under certain conditions, allowing genes to be knocked out or expressed at desired times or stages of development . [ 52 ]
Genome editing uses artificially engineered nucleases that create specific double-stranded breaks at desired locations in the genome. The breaks are subject to cellular DNA repair processes that can be exploited for targeted gene knock-out, correction or insertion at high frequencies. If a donor DNA containing the appropriate sequence (homologies) is present, then new genetic material containing the transgene will be integrated at the targeted site with high efficiency by homologous recombination . [ 53 ] There are four families of engineered nucleases: meganucleases , [ 54 ] [ 55 ] ZFNs , [ 56 ] [ 57 ] transcription activator-like effector nucleases (TALEN), [ 58 ] [ 59 ] t he CRISPR/Cas (clustered regularly interspaced short palindromic repeat/CRISPRassociated protein (e.g. CRISPR/Cas9) . [ 60 ] [ 61 ] Among the four types, TALEN and CRISPR/Cas are the two most commonly used. [ 62 ] Recent advances have looked at combining multiple systems to exploit the best features of both (e.g. megaTAL that are a fusion of a TALE DNA binding domain and a meganuclease). [ 63 ] Recent research has also focused on developing strategies to create gene knock-out or corrections without creating double stranded breaks (base editors). [ 62 ]
Meganucleases were first used in 1988 in mammalian cells. [ 64 ] Meganucleases are endodeoxyribonucleases that function as restriction enzymes with long recognition sites, making them more specific to their target site than other restriction enzymes . This increases their specificity and reduces their toxicity as they will not target as many sites within a genome. The most studied meganucleases are the LAGLIDADG family . While meganucleases are still quite susceptible to off-target binding, which makes them less attractive than other gene editing tools, their smaller size still makes them attractive particularly for viral vectorization perspectives. [ 65 ] [ 53 ]
Zinc-finger nucleases (ZFNs), used for the first time in 1996, are typically created through the fusion of Zinc-finger domains and the Fok I nuclease domain. ZFNs have thus the ability to cleave DNA at target sites. [ 53 ] By engineering the zinc finger domain to target a specific site within the genome, it is possible to edit the genomic sequence at the desired location . [ 65 ] [ 66 ] [ 53 ] ZFNs have a greater specificity, but still hold the potential to bind to non-specific sequences.. While a certain amount of off-target cleavage is acceptable for creating transgenic model organisms, they might not be optimal for all human gene therapy treatments. [ 65 ]
Access to the code governing the DNA recognition by transcription activator-like effectors (TALE) in 2009 opened the way to the development of a new class of efficient TAL-based gene editing tools. TALE, proteins secreted by the Xanthomonas plant pathogen, bind with great specificity to genes within the plant host and initiate transcription of the genes helping infection. Engineering TALE by fusing the DNA binding core to the Fok I nuclease catalytic domain allowed creation of a new tool of designer nucleases, the TALE nuclease (TALEN). [ 67 ] They have one of the greatest specificities of all the current engineered nucleases. Due to the presence of repeat sequences, they are difficult to construct through standard molecular biology procedure and rely on more complicated method of such as Golden gate cloning . [ 62 ]
In 2011, another major breakthrough technology was developed based on CRISPR/Cas (clustered regularly interspaced short palindromic repeat / CRISPR associated protein) systems that function as an adaptive immune system in bacteria and archaea . The CRISPR/Cas system allows bacteria and archaea to fight against invading viruses by cleaving viral DNA and inserting pieces of that DNA into their own genome. The organism then transcribes this DNA into RNA and combines this RNA with Cas9 proteins to make double-stranded breaks in the invading viral DNA. The RNA serves as a guide RNA to direct the Cas9 enzyme to the correct spot in the virus DNA. By pairing Cas proteins with a designed guide RNA CRISPR/Cas9 can be used to induce double-stranded breaks at specific points within DNA sequences. The break gets repaired by cellular DNA repair enzymes, creating a small insertion/deletion type mutation in most cases. Targeted DNA repair is possible by providing a donor DNA template that represents the desired change and that is (sometimes) used for double-strand break repair by homologous recombination. It was later demonstrated that CRISPR/Cas9 can edit human cells in a dish. Although the early generation lacks the specificity of TALEN, the major advantage of this technology is the simplicity of the design. It also allows multiple sites to be targeted simultaneously, allowing the editing of multiple genes at once. CRISPR/Cpf1 is a more recently discovered system that requires a different guide RNA to create particular double-stranded breaks (leaves overhangs when cleaving the DNA) when compared to CRISPR/Cas9. [ 62 ]
CRISPR/Cas9 is efficient at gene disruption. The creation of HIV-resistant babies by Chinese researcher He Jiankui is perhaps the most famous example of gene disruption using this method. [ 68 ] It is far less effective at gene correction. Methods of base editing are under development in which a “nuclease-dead” Cas 9 endonuclease or a related enzyme is used for gene targeting while a linked deaminase enzyme makes a targeted base change in the DNA. [ 69 ] The most recent refinement of CRISPR-Cas9 is called Prime Editing. This method links a reverse transcriptase to an RNA-guided engineered nuclease that only makes single-strand cuts but no double-strand breaks. It replaces the portion of DNA next to the cut by the successive action of nuclease and reverse transcriptase, introducing the desired change from an RNA template. [ 70 ] | https://en.wikipedia.org/wiki/Genetic_engineering_techniques |
Genetic erosion (also known as genetic depletion or genomic erosion ) [ 1 ] is a process where the limited gene pool of an endangered species diminishes even more when reproductive individuals die off before reproducing with others in their endangered low population . The term is sometimes used in a narrow sense, such as when describing the loss of particular alleles or genes, as well as being used more broadly, as when referring to the loss of a phenotype or whole species.
Genetic erosion occurs because each individual organism has many unique genes which get lost when it dies without getting a chance to breed. Low genetic diversity in a population of wild animals and plants leads to a further diminishing gene pool – inbreeding and a weakening immune system can then "fast-track" that species towards eventual extinction .
By definition, endangered species suffer varying degrees of genetic erosion. Many species benefit from a human-assisted breeding program to keep their population viable, [ citation needed ] thereby avoiding extinction over long time-frames. Small populations are more susceptible to genetic erosion than larger populations.
Genetic erosion gets compounded and accelerated by habitat loss and habitat fragmentation – many endangered species are threatened by habitat loss and (fragmentation) habitat . Fragmented habitat create barriers in gene flow between populations.
The gene pool of a species or a population is the complete set of unique alleles that would be found by inspecting the genetic material of every living member of that species or population. A large gene pool indicates extensive genetic diversity , which is associated with robust populations that can survive bouts of intense selection . Meanwhile, low genetic diversity (see inbreeding and population bottlenecks ) can cause reduced biological fitness and increase the chance of extinction of that species or population.
Population bottlenecks create shrinking gene pools, which leave fewer and fewer fertile mating partners. The genetic implications can be illustrated by considering the analogy of a high-stakes poker game with a crooked dealer. Consider that the game begins with a 52-card deck (representing high genetic diversity). Reduction of the number of breeding pairs with unique genes resembles the situation where the dealer deals only the same five cards over and over, producing only a few limited "hands".
As specimens begin to inbreed, both physical and reproductive congenital effects and defects appear more often. Abnormal sperm increases, infertility rises, and birthrates decline. "Most perilous are the effects on the immune defense systems, which become weakened and less and less able to fight off an increasing number of bacterial, viral, fungal, parasitic, and other disease-producing threats. Thus, even if an endangered species in a bottleneck can withstand whatever human development may be eating away at its habitat, it still faces the threat of an epidemic that could be fatal to the entire population." [ 2 ]
Genetic erosion in agricultural and livestock is the loss of biological genetic diversity – including the loss of individual genes, and the loss of particular recombinants of genes (or gene complexes) – such as those manifested in locally adapted landraces of domesticated animals or plants that have become adapted to the natural environment in which they originated.
The major driving forces behind genetic erosion in crops are variety replacement, land clearing, overexploitation of species, population pressure , environmental degradation , overgrazing , governmental policy, and changing agricultural systems. The main factor, however, is the replacement of local varieties of domestic plants and animals by other varieties or species that are non-local. A large number of varieties can also often be dramatically reduced when commercial varieties are introduced into traditional farming systems. Many researchers believe that the main problem related to agro-ecosystem management is the general tendency towards genetic and ecological uniformity imposed by the development of modern agriculture.
In the case of Animal Genetic Resources for Food and Agriculture , major causes of genetic erosion are reported to include indiscriminate cross-breeding, increased use of exotic breeds, weak policies and institutions in animal genetic resources management, neglect of certain breeds because of a lack of profitability or competitiveness, the intensification of production systems, the effects of diseases and disease management, loss of pastures or other elements of the production environment, and poor control of inbreeding. [ 3 ]
With advances in modern bioscience, several techniques and safeguards have emerged to check the relentless advance of genetic erosion and the resulting acceleration of endangered species towards eventual extinction. However, many of these techniques and safeguards are too expensive yet to be practical, and so the best way to protect species is to protect their habitat and to let them live in it as naturally as possible. Complicating matters, the conservation of substantial amounts of genetic diversity often requires the maintenance of multiple independent populations across a species distribution. [ 4 ] For example, to conserve at least 90% of the genetic diversity of the northern quoll requires the conservation of at least eight populations across the continent of Australia. [ 4 ]
Wildlife sanctuaries and national parks have been created to preserve entire ecosystems with all the web of species native to the area. Wildlife corridors are created to join fragmented habitats (see Habitat fragmentation ) to enable endangered species to travel, meet, and breed with others of their kind. Scientific conservation and modern wildlife management techniques, with the expertise of scientifically trained staff, help manage these protected ecosystems and the wildlife found in them. Wild animals are also translocated and reintroduced to other locations physically when fragmented wildlife habitats are too far and isolated to be able to link together via a wildlife corridor, or when local extinctions have already occurred.
Modern policies of zoo associations and zoos around the world have begun putting dramatically increased emphasis on keeping and breeding wild-sourced species and subspecies of animals in their registered endangered species breeding programs. These specimens are intended to have a chance to be reintroduced and survive back in the wild. The main objectives of zoos today have changed, and greater resources are being invested in breeding species and subspecies for then ultimate purpose of assisting conservation efforts in the wild. Zoos do this by maintaining extremely detailed scientific breeding records ( i.e. studbooks )) and by loaning their wild animals to other zoos around the country (and often globally) for breeding, to safeguard against inbreeding by attempting to maximize genetic diversity however possible.
Costly (and sometimes controversial) ex-situ conservation techniques aim to increase the genetic biodiversity on our planet, as well as the diversity in local gene pools . by guarding against genetic erosion. Modern concepts like seedbanks , sperm banks , and tissue banks have become much more commonplace and valuable. Sperm , eggs , and embryos can now be frozen and kept in banks, which are sometimes called "Modern Noah's Arks" or " Frozen Zoos ". Cryopreservation techniques are used to freeze these living materials and keep them alive in perpetuity by storing them submerged in liquid nitrogen tanks at very low temperatures. Thus, preserved materials can then be used for artificial insemination , in vitro fertilization , embryo transfer , and cloning methodologies to protect diversity in the gene pool of critically endangered species.
It can be possible to save an endangered species from extinction by preserving only parts of specimens, such as tissues, sperm, eggs, etc. – even after the death of a critically endangered animal, or collected from one found freshly dead, in captivity or from the wild . A new specimen can then be "resurrected" with the help of cloning, so as to give it another chance to breed its genes into the living population of the respective threatened species. Resurrection of dead critically endangered wildlife specimens with the help of cloning is still being perfected, and is still too expensive to be practical, but with time and further advancements in science and methodology it may well become a routine procedure not too far into the future. | https://en.wikipedia.org/wiki/Genetic_erosion |
Genetic exceptionalism is the belief that genetic information is special and so must be treated differently from other types of medical data or other personally identifiable information .
For example, patients are able to obtain information about their blood pressure without involving any medical professionals, but to obtain information about their genetic profile might require an order from a physician and expensive counseling sessions. Disclosure of an individual's genetic information or its meaning, such as telling a woman with red hair that she has a higher risk of skin cancer, has been legally restricted in some places, as providing medical advice . [ 1 ]
That policy approach has been taken by state legislatures to safeguard individuals' genetic information in the United States from individuals, their families, their employers, and the government. The approach builds upon the existing protection required of general health information provided by such laws as the Health Insurance Portability and Accountability Act .
There is ongoing debate over whether or when certain genetic information should be considered exceptional. [ 2 ] In some cases, the predictive power of genetic information (such as a risk for a disease like Huntington's disease , which is highly penetrant) may justify special considerations for genetic exceptionalism, in that individuals with a high risk for developing this condition may face a certain amount of discrimination. However, for most common human health conditions, a specific genetic variant only plays a partial role, interacting with other genetic variants and environmental and lifestyle influences to contribute to disease development. In these cases, genetic information is often considered similarly to other medical and lifestyle data, such as smoking status, age, or biomarkers . | https://en.wikipedia.org/wiki/Genetic_exceptionalism |
Genetic imbalance is to describe situation when the genome of a cell or organism has more copies of some genes than other genes due to chromosomal rearrangements or aneuploidy .
Changes in gene dosage , the number of times a given gene is present in the cell nucleus , can create a genetic imbalance.
This imbalance in gene dosage alters the amount of a particular protein relative to all other proteins, and this alternation in the relative amounts of protein can have a variety of phenotypic effects. These effects are depending on how the proteins function and how critical the maintenance of a precise ratio of proteins is to the survival of the organism.
Diminishing the dosage of most genes produces no obvious change in phenotype . For some genes the phenotypic consequences of a decrease in gene dosage are noticeable but not catastrophic. For example, Drosophila containing only one copy of the wild type Notch gene has visible wing abnormalities but otherwise seems to function normally. For some rare genes, the normal diploid level of gene expression is essential to individual survival; fewer than two copies of such a gene results in lethality . In Drosophila , a single dose of the locus known as Triplolethal is in an otherwise diploid individual.
Although a single dose of any gene may not cause substantial harm to the individual, the genetic imbalance resulting from a single dose of many genes at the same time can be lethal. Humans, for example, cannot survive, even as heterozygotes , with deletions that remove more than about 3% of any part of their haploid genome . | https://en.wikipedia.org/wiki/Genetic_imbalance |
Genetic interaction networks represent the functional interactions between pairs of genes in an organism and are useful for understanding the relation between genotype and phenotype . The majority of genes do not code for particular phenotypes. Instead, phenotypes often result from the interaction between several genes. In humans , "Each individual carries ~4 million genetic variants and polymorphisms , the overwhelming majority of which cannot be pinpointed as the single cause for a given phenotype. Instead, the effects of genetic variants may combine with one another both additively and synergistically, and each variant's contribution to a quantitative trait or disease risk could depend on the genotypes of dozens of other variants. Interactions between genetic variants, along with the environmental conditions , are likely to play a major role in determining the phenotype that arises from a given genotype. [ 1 ] " Genetic interaction networks help to understand genetic interactions by identifying such interactions between pairs of genes. [ 1 ]
Because genetic interactions provide insight into how genotype connects to phenotype in an organism, improved knowledge of genetic interactions in humans could provide crucial insight into complex diseases. Unfortunately, due to the impossibility of isolating subjects with single genetic variants, it is not possible to directly map the genetic interaction networks in humans. Researchers hope that learning about the characteristics of genetic interaction networks in suitable organisms will provide tools for constructing the genetic interaction network of humans. [ 1 ]
A genetic interaction occurs when the interactions between two or more genes results in a phenotype that differs from the phenotype expected if the genes were independent of each other. In the context of genetic interaction networks, a genetic interaction is defined as "the difference between an experimentally measured double- mutant phenotype and an expected double-mutant phenotype, the latter of which is predicted from the combination of the single-mutant effects, assuming the mutations act independently. [ 1 ] " In this context, a commonly studied phenotype is fitness which measures the relative reproduction rate of a mutant. A strong phenotype refers to a low level of fitness while a weak phenotype refers to a level of fitness close to that of the non-mutant strain . [ 1 ]
A negative genetic interaction occurs when the phenotype of the double mutant is stronger than expected. A special case is a synthetic lethal interaction which occurs when the removal of individual genes does not significantly harm an organism but the removal of both genes results in an inviable organism. A positive genetic interaction occurs when the phenotype of the double mutant is weaker than expected. A special case is genetic suppression which occurs when the phenotype of the double mutant is weaker than that of the least-fit single mutant. [ 1 ] [ 2 ]
In order to measure the interaction between two genes, one must have some standard for the expected phenotype if the genes do not interact. Some common models for how the phenotypes of independent genes combine include the min, additive, and multiplicative models. [ 1 ] [ 3 ] In the min model, the expected fitness resulting from the mutation of two independent genes is the same as the fitness of the least-fit single mutant. [ 3 ] In the additive model, the expected phenotype resulting from the mutation of two independent genes is the sum of the phenotypes due to the individual mutations. In the multiplicative model, the expected phenotype resulting from the mutation of two independent genes is the product of the phenotypes due to the individual mutations. Which model is best depends on the situation. [ 1 ] [ 3 ] It turns out in the case that fitness is used as the phenotype, the multiplicative model is best option.
Methods exist to measure genetic interactions even when one of the genes is essential to an organism. [ 2 ]
Genetic interaction networks have been studied extensively in several organisms including Saccharomyces cerevisiae , Schizosaccharomyces pombe , Escherichia coli , Caenorhabditis elegans , and Drosophila melanogaster . [ 1 ] [ 2 ] [ 4 ] These studies have given insight into properties of genetic interaction networks, including the topology of genetic interaction networks, how genetic interaction networks provide information about gene function, and what characteristics of genetic interaction networks are conserved by evolution. Researchers hope that an understanding of the general properties of genetic interaction networks as well as how they relate to other biological information such as protein-protein interaction networks will make it possible to infer the genetic interaction networks in organisms such as humans for which it is not possible to determine genetic interaction networks directly. [ 1 ] [ 3 ]
The hubs of genetic interaction networks tend to be essential proteins. [ 3 ] [ 2 ]
When two genes interact with a similar set of neighbors, this, along with the particular nature of those interactions, provides information about how the functions of the two genes are related. For example, genes that share a common set of synthetic lethal interactions tend to be involved in the same biological pathway . The set of genes with which a gene interacts and the type of those interactions (i.e. synthetic lethal) make up that gene's interaction profile. This information allows the creation of a genetic profile similarity network from a genetic interaction network. In a genetic profile similarity network, edges connect genes with similar interaction profiles. The result is a network consisting of clusters of genes that tend to be involved in the same biological process and where the connections between these clusters provide information about the interdependencies of these biological processes. This can provide a powerful tool for predicting the function of uncharacterized genes. [ 1 ] [ 3 ] [ 2 ] [ 4 ]
Some studies have looked into how genetic networks are conserved across evolutionary distance. [ 1 ] [ 3 ] [ 5 ] While it is not clear the degree to which individual gene-gene interactions are conserved, the general properties of genetic interaction networks appear to be conserved such as the network hubs and the ability of genetic interaction profiles to predict biological function. [ 1 ] [ 3 ]
Genetic interactions have important implications for the connection between genotype and phenotype. [ 3 ] [ 2 ] [ 6 ] For example, they have been proposed as an explanation for missing heritability . Missing heritability refers to the fact that the genetic sources of many heritable phenotypes are yet to be discovered. While a variety of explanations have been proposed, genetic interactions could majorly decrease the amount of missing heritability by increasing the explanatory power of known genetic sources. Such genetic interactions would most likely go beyond the pairwise interactions considered in genetic interaction networks. [ 1 ] [ 2 ] [ 6 ] | https://en.wikipedia.org/wiki/Genetic_interaction_network |
Genetic load is the difference between the fitness of an average genotype in a population and the fitness of some reference genotype, which may be either the best present in a population , or may be the theoretically optimal genotype. The average individual taken from a population with a low genetic load will generally, when grown in the same conditions , have more surviving offspring than the average individual from a population with a high genetic load. [ 1 ] [ 2 ] Genetic load can also be seen as reduced fitness at the population level compared to what the population would have if all individuals had the reference high-fitness genotype. [ 3 ] High genetic load may put a population in danger of extinction .
Consider n genotypes A 1 , … , A n {\displaystyle \mathbf {A} _{1},\dots ,\mathbf {A} _{n}} , which have the fitnesses w 1 , … , w n {\displaystyle w_{1},\dots ,w_{n}} and frequencies p 1 , … , p n {\displaystyle p_{1},\dots ,p_{n}} , respectively. Ignoring frequency-dependent selection , the genetic load L {\displaystyle L} may be calculated as:
where w max {\displaystyle w_{\max }} is either some theoretical optimum, or the maximum fitness observed in the population. In calculating the genetic load, w 1 … w n {\displaystyle w_{1}\dots w_{n}} must be actually found in at least a single copy in the population, and w ¯ {\displaystyle {\bar {w}}} is the average fitness calculated as the mean of all the fitnesses weighted by their corresponding frequencies:
where the i t h {\displaystyle i^{\mathrm {th} }} genotype is A i {\displaystyle \mathbf {A} _{i}} and has the fitness and frequency w i {\displaystyle w_{i}} and p i {\displaystyle p_{i}} respectively.
One problem with calculating genetic load is that it is difficult to evaluate either the theoretically optimal genotype, or the maximally fit genotype actually present in the population. [ 4 ] This is not a problem within mathematical models of genetic load, or for empirical studies that compare the relative value of genetic load in one setting to genetic load in another.
Deleterious mutation load is the main contributing factor to genetic load overall. [ 5 ] The Haldane-Muller theorem of mutation–selection balance says that the load depends only on the deleterious mutation rate and not on the selection coefficient . [ 6 ] Specifically, relative to an ideal genotype of fitness 1, the mean population fitness is exp ( − U ) {\displaystyle \exp(-U)} where U is the total deleterious mutation rate summed over many independent sites. The intuition for the lack of dependence on the selection coefficient is that while a mutation with stronger effects does more harm per generation, its harm is felt for fewer generations.
A slightly deleterious mutation may not stay in mutation–selection balance but may instead become fixed by genetic drift when its selection coefficient is less than one divided by the effective population size . [ 7 ] Over time, drift load can seriously impact the fitness of a population. [ 8 ] [ 9 ] In asexual populations, the stochastic accumulation of mutation load is called Muller's ratchet , and occurs in the absence of beneficial mutations, when after the most-fit genotype has been lost, it cannot be regained by genetic recombination . Deterministic accumulation of mutation load occurs in asexuals when the deleterious mutation rate exceeds one per replication. [ 10 ] Sexually reproducing species are expected to have lower genetic loads. [ 11 ] This is one hypothesis for the evolutionary advantage of sexual reproduction . Purging of deleterious mutations in sexual populations is facilitated by synergistic epistasis among deleterious mutations. [ 12 ]
High load can lead to a small population size , which in turn increases the accumulation of mutation load, culminating in extinction via mutational meltdown . [ 13 ] [ 14 ]
The accumulation of deleterious mutations in humans has been of concern to many geneticists, including Hermann Joseph Muller , [ 15 ] James F. Crow , [ 12 ] Alexey Kondrashov , [ 16 ] W. D. Hamilton , [ 17 ] and Michael Lynch . [ 18 ]
In sufficiently genetically loaded populations, new beneficial mutations create fitter genotypes than those previously present in the population. When load is calculated as the difference between the fittest genotype present and the average, this creates a substitutional load . The difference between the theoretical maximum (which may not actually be present) and the average is known as the "lag load". [ 19 ] Motoo Kimura 's original argument for the neutral theory of molecular evolution was that if most differences between species were adaptive, this would exceed the speed limit to adaptation set by the substitutional load. [ 20 ] However, Kimura's argument confused the lag load with the substitutional load, using the former when it is the latter that in fact sets the maximal rate of evolution by natural selection. [ 21 ]
More recent "travelling wave" models of rapid adaptation derive a term called the "lead" that is equivalent to the substitutional load, and find that it is a critical determinant of the rate of adaptive evolution. [ 22 ] [ 23 ]
Inbreeding increases homozygosity . In the short run, an increase in inbreeding increases the probability with which offspring get two copies of a recessive deleterious alleles, lowering fitnesses via inbreeding depression . [ 24 ] In a species that habitually inbreeds, e.g. through self-fertilization , a proportion of recessive deleterious alleles can be purged . [ 25 ] [ 26 ]
Likewise, in a small population of humans practicing endogamy , deleterious alleles can either overwhelm the population's gene pool, causing it to become extinct, or alternately, make it fitter. [ 27 ]
Combinations of alleles that have evolved to work well together may not work when recombined with a different suite of coevolved alleles, leading to outbreeding depression . Segregation load occurs in the presence of overdominance , i.e. when heterozygotes are more fit than either homozygote. In such a case, the heterozygous genotype gets broken down by Mendelian segregation , resulting in the production of homozygous offspring. Therefore, there is segregation load as not all individuals have the theoretical optimum genotype. Recombination load arises through unfavorable combinations across multiple loci that appear when favorable linkage disequilibria are broken down. [ 28 ] Recombination load can also arise by combining deleterious alleles subject to synergistic epistasis , i.e. whose damage in combination is greater than that predicted from considering them in isolation. [ 29 ] Evidence was reviewed indicating that meiosis reduces recombination load, thus providing a selective advantage of sexual reproduction . [ 30 ]
Migration load is hypothesized to occur when maladapted non-native organisms enter a new environment. [ 31 ]
On one hand, beneficial genes from migrants can increase the fitness of local populations. [ 32 ] On the other hand, migration may reduce the fitness of local populations by introducing maladaptive alleles. This is hypothesized to occur when the migration rate is "much greater" than the selection coefficient. [ 32 ]
Migration load may occur by reducing the fitness of local organisms, or through natural selection imposed on the newcomers, such as by being eliminated by local predators. [ 33 ] [ 34 ] Most studies have only found evidence for this theory in the form of selection against immigrant populations, however, one study found evidence for increased mutational burden in recipient populations, as well. [ 35 ] | https://en.wikipedia.org/wiki/Genetic_load |
In genetics , mapping functions are used to model the relationship between map distances (measured in map units or centimorgans ) and recombination frequencies, particularly as these measurements relate to regions encompassed between genetic markers . One utility of this approach is that it allows one to obtain values for distances in genetic mapping units directly from recombination fractions, as map distances cannot typically be obtained from empirical experiments. [ 1 ]
The simplest mapping function is the Morgan Mapping Function , eponymously devised by Thomas Hunt Morgan . Other well-known mapping functions include the Haldane Mapping Function introduced by J. B. S. Haldane in 1919, [ 2 ] and the Kosambi Mapping Function introduced by Damodar Dharmananda Kosambi in 1944. [ 3 ] [ 4 ] Few mapping functions are used in practice other than Haldane and Kosambi. [ 5 ] The main difference between them is in how crossover interference is incorporated. [ 6 ]
Where d is the distance in map units, the Morgan Mapping Function states that the recombination frequency r can be expressed as r = d {\displaystyle \ r=d} . This assumes that one crossover occurs, at most, in an interval between two loci, and that the probability of the occurrence of this crossover is proportional to the map length of the interval.
Where d is the distance in map units, the recombination frequency r can be expressed as:
r = 1 2 [ 1 − ( 1 − 2 d ) ] = d {\displaystyle \ r={\frac {1}{2}}[1-(1-2d)]=d}
The equation only holds when 1 2 ≥ d ≥ 0 {\displaystyle {\frac {1}{2}}\geq d\geq 0} as, otherwise, recombination frequency would exceed 50%. Therefore, the function cannot approximate recombination frequencies beyond short distances. [ 4 ]
Two properties of the Haldane Mapping Function is that it limits recombination frequency up to, but not beyond 50%, and that it represents a linear relationship between the frequency of recombination and map distance up to recombination frequencies of 10%. [ 7 ] It also assumes that crossovers occur at random positions and that they do so independent of one another. This assumption therefore also assumes no crossover interference takes place; [ 5 ] but using this assumption allows Haldane to model the mapping function using a Poisson distribution . [ 4 ]
r = 1 2 ( 1 − e − 2 d ) {\displaystyle \ r={\frac {1}{2}}(1-e^{-2d})}
d = − 1 2 ln ( 1 − 2 r ) {\displaystyle \ d=-{\frac {1}{2}}\ln(1-2r)}
The Kosambi mapping function was introduced to account for the impact played by crossover interference on recombination frequency. It introduces a parameter C, representing the coefficient of coincidence , and sets it equal to 2r. For loci which are strongly linked , interference is strong; otherwise, interference decreases towards zero. [ 5 ] Interference declines according to the linear function i = 1 - 2r. [ 8 ]
r = 1 2 tanh ( 2 d ) = 1 2 e 4 d − 1 e 4 d + 1 {\displaystyle \ r={\frac {1}{2}}\tanh(2d)={\frac {1}{2}}{\frac {e^{4d}-1}{e^{4d}+1}}}
d = 1 2 tanh − 1 ( 2 r ) = 1 4 ln ( 1 + 2 r 1 − 2 r ) {\displaystyle \ d={\frac {1}{2}}\tanh ^{-1}(2r)={\frac {1}{4}}\ln({\frac {1+2r}{1-2r}})}
Below 10% recombination frequency, there is little mathematical difference between different mapping functions and the relationship between map distance and recombination frequency is linear (that is, 1 map unit = 1% recombination frequency). [ 8 ] When genome-wide SNP sampling and mapping data is present, the difference between the functions is negligible outside of regions of high recombination, such as recombination hotspots or ends of chromosomes. [ 6 ]
While many mapping functions now exist, [ 9 ] [ 10 ] [ 11 ] in practice functions other than Haldane and Kosambi are rarely used. [ 5 ] More specifically, the Haldane function is preferred when distance between markers is relatively small, whereas the Kosambi function is preferred when distances between markers is larger and crossovers need to be accounted for. [ 12 ] | https://en.wikipedia.org/wiki/Genetic_map_function |
A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species . It can be described as a variation (which may arise due to mutation or alteration in the genomic loci) that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change ( single nucleotide polymorphism , SNP), or a long one, like minisatellites .
For many years, gene mapping was limited to identifying organisms by traditional phenotypes markers. This included genes that encoded easily observable characteristics, such as blood types or seed shapes. The insufficient number of these types of characteristics in several organisms limited the possible mapping efforts. This prompted the development of gene markers, which could identify genetic characteristics that are not readily observable in organisms (such as protein variation). [ 1 ]
Some commonly used types of genetic markers are:
Molecular genetic markers can be divided into two classes: a) biochemical markers which detect variation at the gene product level such as changes in proteins and amino acids and b) molecular markers which detect variation at the DNA level such as nucleotide changes: deletion, duplication, inversion and/or insertion. Markers can exhibit two modes of inheritance, i.e. dominant/recessive or co-dominant. If the genetic pattern of homo-zygotes can be distinguished from that of hetero-zygotes, then a marker is said to be co-dominant. Generally co-dominant markers are more informative than the dominant markers. [ 3 ]
Genetic markers can be used to study the relationship between an inherited disease and its genetic cause (for example, a particular mutation of a gene that results in a defective protein ). It is known that pieces of DNA that lie near each other on a chromosome tend to be inherited together. This property enables the use of a marker, which can then be used to determine the precise inheritance pattern of the gene that has not yet been exactly localized.
Genetic markers are employed in genealogical DNA testing for genetic genealogy to determine genetic distance between individuals or populations. Uniparental markers (on mitochondrial or Y chromosomal DNA) are studied for assessing maternal or paternal lineages . Autosomal markers are used for all ancestry.
Genetic markers have to be easily identifiable, associated with a specific locus , and highly polymorphic , because homozygotes do not provide any information. Detection of the marker can be direct by RNA sequencing, or indirect using allozymes .
Some of the methods used to study the genome or phylogenetics are RFLP, AFLP, RAPD, SSR. They can be used to create genetic maps of whatever organism is being studied.
There was a debate over what the transmissible agent of CTVT ( canine transmissible venereal tumor ) was. Many researchers hypothesized that virus like particles were responsible for transforming the cell, while others thought that the cell itself was able to infect other canines as an allograft . With the aid of genetic markers, researchers were able to provide conclusive evidence that the cancerous tumor cell evolved into a transmissible parasite. Furthermore, molecular genetic markers were used to resolve the issue of natural transmission, the breed of origin ( phylogenetics ), and the age of the canine tumor. [ 4 ]
Genetic markers have also been used to measure the genomic response to selection in livestock. Natural and artificial selection leads to a change in the genetic makeup of the cell. The presence of different alleles due to a distorted segregation at the genetic markers is indicative of the difference between selected and non-selected livestock. [ 5 ]
Media related to Genetic markers at Wikimedia Commons | https://en.wikipedia.org/wiki/Genetic_marker |
Genetic matchmaking is the idea of matching couples for romantic relationships based on their biological compatibility. The initial idea was conceptualized by Claus Wedekind through his "sweaty t-shirt" experiment. [ 1 ] Males were asked to wear T-shirts for two consecutive nights, and then females were asked to smell the T-shirts and rate the body odors for attractiveness. Human body odor has been associated with the human leukocyte antigens (HLA) genomic region. They discovered that females were attracted to men who had dissimilar HLA alleles from them. Furthermore, these females reported that the body odors of HLA-dissimilar males reminded them of their current partners or ex-partners providing further evidence of biological compatibility.
Following research done by Dr. Wedekind, [ 1 ] several studies found corroborating evidence for biological compatibility. Garver-Apgar et al. [ 2 ] presented evidence for HLA-dissimilar alleles playing a factor in the healthiness of romantic relationships. They discovered that as the proportion of HLA-similar alleles increased between couples, females reported being less sexually responsive to their partners, less satisfaction from being aroused by their partners, and having additional sexual partners (while with their current partner). Additionally, Ober et al. [ 3 ] conducted an independent study on a population of American Hutterites by comparing the HLA alleles of married couples. They discovered that married couples were less likely to share HLA alleles than expected from random chance; thus their results were consistent with tendencies for same-HLA alleled partners to avoid mating. Further evidence of the importance of genetic compatibility can be found in the finding that couples sharing a higher proportion of HLA alleles tend to have recurring spontaneous abortions, [ 4 ] reduced body mass in babies, [ 4 ] and longer intervals between successive births. [ 5 ]
The application of this research to find romantic partners via genetic testing has been described as "dubious". [ 6 ] Analyses of data from the International HapMap Project has not found a consistent relationship between marital partners and genes related to the immune system. [ 7 ]
There are several biological reasons why women would be attracted to and mate with men with dissimilar HLA alleles: [ 8 ] | https://en.wikipedia.org/wiki/Genetic_matchmaking |
Genetic monitoring is the use of molecular markers to (i) identify individuals, species or populations, or (ii) to quantify changes in population genetic metrics (such as effective population size , genetic diversity and population size) over time. Genetic monitoring can thus be used to detect changes in species abundance and/or diversity, and has become an important tool in both conservation and livestock management. The types of molecular markers used to monitor populations are most commonly mitochondrial , microsatellites or single-nucleotide polymorphisms (SNPs), while earlier studies also used allozyme data. Species gene diversity is also recognized as an important biodiversity metric for implementation of the Convention on Biological Diversity . [ 1 ]
Types of population changes that can be detected by genetic monitoring include population growth and decline, spread of pathogens, adaptation to environmental change, hybridization, introgression and habitat fragmentation events. Most of these changes are monitored using ‘neutral’ genetic markers (markers for which mutational changes do not change their adaptive fitness within a population). However markers showing adaptive responses to environmental change can be ‘non-neutral’ (e.g. mutational changes affect their relative fitness within a population).
Two broad categories of genetic monitoring have been defined: [ 2 ] Category I encompasses the use of genetic markers as identifiers of individuals (Category Ia), populations and species (Category Ib) for traditional population monitoring. Category II represents the use of genetic markers to monitor changes of population genetic parameters, which include estimators of effective population size (Ne), genetic variation, population inter-mixing, structure and migration.
At the individual level, genetic identification can enable estimation of population abundance and population increase rates within the framework of mark-recapture models. The abundance of cryptic or elusive species that are difficult to monitor can be estimated by collecting non-invasive biological samples in the field (e.g. feathers, scat or fur) and using these to identify individuals through microsatellite or single-nucleotide polymorphism (SNP) genotyping. This census of individuals can then be used to estimate population abundance via mark-recapture analysis. For example, this technique has been used to monitor populations of grizzly bear , [ 3 ] brush-tailed rock-wallaby , [ 4 ] Bengal tiger [ 5 ] and snow leopard . [ 6 ] Population growth rates are a product of rates of population recruitment and survival , and can be estimated through open mark-recapture models. For example, DNA from feathers shed by the eastern imperial eagle shows lower cumulative survival over time than seen for other long-lived raptors. [ 7 ]
Use of molecular genetic techniques to identify species can be useful for a number of reasons. Species identification in the wild can be used to detect changes in population ranges or site occupancy, rates of hybridization and the emergence and spread of pathogens and invasive species . Changes in population ranges have been investigated for Iberian lynx [ 8 ] and wolverine , [ 9 ] while monitoring of westslope cutthroat trout shows widespread ongoing hybridization with introduced rainbow trout [ 10 ] (see cutbow ) and Canada lynx - bobcat hybrids have been detected at the southern periphery of the current population range for lynx. [ 11 ] [ 12 ] The emergence and spread of pathogens can be tracked using diagnostic molecular assays – for example, identifying the spread of West Nile virus among mosquitoes in the eastern US to identify likely geographical origins of infection [ 13 ] and identifying gene loci associated with parasite susceptibility in bighorn sheep . [ 14 ] Genetic monitoring of invasive species is of conservation and economic interest, as invasions often affect the ecology and range of native species and may also bring risks of hybridization (e.g. for copepods , [ 15 ] ducks , [ 16 ] barred owl and spotted owl , [ 17 ] and Lessepsian rabbitfish [ 18 ] ).
Species identification is also of considerable utility in monitoring fisheries and wildlife trade , where conventional visual identification of butchered or flensed products is difficult or impossible. [ 19 ] Monitoring of trade and consumption of species of conservation interest can be carried out using molecular amplification and identification of meat or fish obtained from markets. For example, genetic market surveys have been used to identify protected species and populations of whale (e.g., North Pacific minke whale ) and dolphin species appearing in the marketplace. [ 20 ] Other surveys of market trade have focused on pinnipeds , [ 21 ] sea horses [ 22 ] and sharks . [ 23 ] Such surveys are used to provide ongoing monitoring of the quantity and movement of fisheries and wildlife products through markets and for detecting poaching or other illegal, unreported or unregulated (IUU) exploitation [ 19 ] (e.g. IUU fishing ).
Although initial applications focused on species identification and population assessments, market surveys also provide the opportunity for a range of molecular ecology investigations including capture-recapture, assignment tests and population modeling. [ 19 ] These developments are potentially relevant to genetic monitoring Category II.
Monitoring of population changes through genetic means can be done retrospectively, through analysis of 'historical' DNA recovered from museum-archived species and comparison with contemporary DNA of that species. It can also be used as a tool for evaluating ongoing changes in the status and persistence of current populations. Genetic measures of relative population change include changes in diversity (e.g. heterozygosity and allelic richness). Monitoring of relative population changes through these metrics has been performed retrospectively for Beringian bison , [ 24 ] Galapagos tortoise , [ 25 ] houting , [ 26 ] Atlantic salmon , [ 27 ] northern pike , [ 28 ] New Zealand snapper , [ 29 ] steelhead trout , [ 30 ] greater prairie chicken , [ 31 ] Mauritius kestrel [ 32 ] and Hector's dolphin [ 33 ] and is the subject of many ongoing studies, including Danish and Swedish brown trout populations. [ 34 ] [ 35 ] Measuring absolute population changes (e.g. effective population size (Ne)) can be carried out by measuring changes in population allele frequencies (‘Ftemporal’) or levels of linkage disequilibrium over time (‘LDNe’), while changing patterns of gene flow between populations can also be monitored by estimating differences in allele frequencies between populations over time. Subjects of such studies include grizzly bears , [ 3 ] [ 36 ] [ 37 ] cod , [ 38 ] red deer , [ 39 ] Leopard frogs [ 40 ] and Barrel Medic . [ 41 ] [ 42 ]
Genetic monitoring has also been increasingly used in studies that monitor environmental changes through changes in the frequency of adaptively selected markers. For example, the genetically controlled photo-periodic response (hibernating time) of pitcher-plant mosquitos ( Wyeomyia smithii ) has shifted in response to longer growing seasons for pitcher plants brought on by warmer weather. [ 43 ] Experimental wheat populations grown in contrasting environments over a period of 12 generations found that changes in flowering time were closely correlated with regulatory changes in one gene, suggesting a pathway for genetic adaptation to changing climate in plants. [ 44 ] [ 45 ]
Genetic monitoring is also useful in monitoring the ongoing health of small, relocated populations. Good examples of this are found for New Zealand birds , many species of which were greatly impacted by habitat destruction and the appearance of numerous mammalian predators in the last century and have recently become part of relocation programs that transfer a few ‘founder’ individuals to predator-free offshore “ecological” islands . E.g. black robin , [ 46 ] and kākāpō . [ 47 ]
Category II genetic monitoring of population genetic diversity (PGD) of wild species, for purposes of biodiversity conservation and sustainable management, is unevenly distributed among countries in Europe. Country size and per capita Gross Domestic Product (GDP) are statistically associated in different ways with the number of documented monitoring projects, suggesting that available habitat for species and country financial resources influence monitoring effort. There is relatively little genetic monitoring for PGD conducted in southeastern Europe. Much attention has been directed towards monitoring of large carnivores, and relatively little effort towards monitoring species in other groups, such as amphibians. [ 48 ]
In February 2007 an international summit was held at the Institute of the Environment at UCLA , concerning ‘Evolutionary Change in Human Altered Environments: An International Summit to translate Science into Policy’. This led to a special issue of the journal of Molecular Ecology [ 49 ] organized around our understanding of genetic effects in three main categories: (i) habitat disturbance and climate change (ii) exploitation and captive breeding (iii) invasive species and pathogens .
In 2007 a Working Group on Genetic Monitoring was launched with joint support from NCEAS [ 50 ] and NESCent [ 51 ] to further develop the techniques involved and provide general monitoring guidance for policy makers and managers. [ 52 ]
Currently the topic is covered in several well known text books, including McComb et al. (2010) and Allendorf et al. (2013).
Many natural resource agencies see genetic monitoring as a cost-effective and defensible way to monitor fish and wildlife populations. As such scientists in the U.S. Geological Survey , U.S. Forest Service , [ 53 ] National Park Service , and National Marine Fisheries Service have been developing new methods and tools to use genetic monitoring, and applying such tools across broad geographic scales. [ 2 ] [ 36 ] Currently the USFWS hosts a website that informs managers as to the best way to use genetic tools for monitoring (see below). | https://en.wikipedia.org/wiki/Genetic_monitoring |
Genetic pollution is a term for uncontrolled [ 1 ] [ 2 ] gene flow into wild populations. It is defined as "the dispersal of contaminated altered genes from genetically engineered organisms to natural organisms, esp. by cross-pollination", [ 3 ] but has come to be used in some broader ways. It is related to the population genetics concept of gene flow, and genetic rescue , which is genetic material intentionally introduced to increase the fitness of a population. [ 4 ] It is called genetic pollution when it negatively impacts the fitness of a population, such as through outbreeding depression and the introduction of unwanted phenotypes which can lead to extinction.
Conservation biologists and conservationists have used the term to describe gene flow from domestic, feral, and non-native species into wild indigenous species , which they consider undesirable. They promote awareness of the effects of introduced invasive species that may " hybridize with native species, causing genetic pollution ". In the fields of agriculture , agroforestry and animal husbandry , genetic pollution is used to describe gene flows between genetically engineered species and wild relatives. The use of the word "pollution" is meant to convey the idea that mixing genetic information is bad for the environment, but because the mixing of genetic information can lead to a variety of outcomes, "pollution" may not always be the most accurate descriptor.
Some conservation biologists and conservationists have used genetic pollution for a number of years as a term to describe gene flow from a non-native , invasive subspecies , domestic , or genetically-engineered population to a wild indigenous population. [ 1 ] [ 5 ] [ 6 ]
The introduction of genetic material into the gene pool of a population by human intervention can have both positive and negative effects on populations. When genetic material is intentionally introduced to increase the fitness of a population, this is called genetic rescue . When genetic material is unintentionally introduced to a population, this is called genetic pollution and can negatively affect the fitness of a population (primarily through outbreeding depression ), introduce other unwanted phenotypes, or theoretically lead to extinction.
An introduced species is one that is not native to a given population that is either intentionally or accidentally brought into a given ecosystem. Effects of introduction are highly variable, but if an introduced species has a major negative impact on its new environment, it can be considered an invasive species. One such example is the introduction of the Asian Longhorned beetle in North America, which was first detected in 1996 in Brooklyn, New York. It is believed that these beetles were introduced through cargo at trade ports. The beetles are highly damaging to the environment, and are estimated to cause risk to 35% of urban trees, excluding natural forests. [ 7 ] These beetles cause severe damage to the wood of trees by larval funneling. Their presence in the ecosystem destabilizes community structure, having a negative influence on many species in the system.
Introduced species are not always disruptive to an environment, however. Tomás Carlo and Jason Gleditch of Penn State University found that the number of "invasive" honeysuckle plants in the area correlated with the number and diversity of the birds in the Happy Valley Region of Pennsylvania, suggesting introduced honeysuckle plants and birds formed a mutually beneficial relationship. [ 8 ] Presence of introduced honeysuckle was associated with higher diversity of the bird populations in that area, demonstrating that introduced species are not always detrimental to a given environment and it is completely context dependent.
Conservation biologists and conservationists have, for a number of years, used the term to describe gene flow from domestic, feral, and non-native species into wild indigenous species , which they consider undesirable. [ 1 ] [ 5 ] [ 6 ] For example, TRAFFIC is the international wildlife trade monitoring network that works to limit trade in wild plants and animals so that it is not a threat to conservationist goals. They promote awareness of the effects of introduced invasive species that may " hybridize with native species, causing genetic pollution ". [ 9 ] Furthermore, the Joint Nature Conservation Committee , the statutory adviser to the UK government , has stated that invasive species "will alter the genetic pool (a process called genetic pollution ), which is an irreversible change." [ 10 ]
Invasive species can invade both large and small native populations and have a profound effect. Upon invasion, invasive species interbreed with native species to form sterile or more evolutionarily fit hybrids that can outcompete the native populations. Invasive species can cause extinctions of small populations on islands that are particularly vulnerable due to their smaller amounts of genetic diversity. In these populations, local adaptations can be disrupted by the introduction of new genes that may not be as suitable for the small island environments. For example, the Cercocarpus traskiae of the Catalina Island off the coast of California has faced near extinction with only a single population remaining due to the hybridization of its offspring with Cercocarpus betuloides . [ 11 ]
Increased contact between wild and domesticated populations of organisms can lead to reproductive interactions that are detrimental to the wild population's ability to survive. A wild population is one that lives in natural areas and is not regularly looked after by humans. This contrasts with domesticated populations that live in human controlled areas and are regularly, and historically, in contact with humans. Genes from domesticated populations are added to wild populations as a result of reproduction. In many crop populations this can be the result of pollen traveling from farmed crops to neighboring wild plants of the same species. For farmed animals, this reproduction may happen as the result of escaped or released animals.
A popular example of this phenomenon is the gene flow between wolves and domesticated dogs. The New York Times cites, from the words of biologist Luigi Boitani, "Although wolves and dogs have always lived in close contact in Italy and have presumably mated in the past, the newly worrisome element, in Dr. Boitani's opinion, is the increasing disparity in numbers, which suggests that interbreeding will become fairly common. As a result, 'genetic pollution of the wolf gene pool might reach irreversible levels', he warned. 'By hybridization, dogs can easily absorb the wolf genes and destroy the wolf, as it is,' he said. The wolf might survive as a more doglike animal, better adapted to living close to people, he said, but it would not be 'what we today call a wolf.'" [ 1 ]
Aquaculture is the practice of farming aquatic animals or plants for the purpose of consumption. This practice is becoming increasingly common for the production of salmon . This is specifically termed aquaculture of salmonids . One of the dangers of this practice is the possibility of domesticated salmon breaking free from their containment. The occurrence of escaping incidents is becoming increasingly common as aquaculture gains popularity. [ 12 ] [ 13 ] [ 14 ] Farming structures may be ineffective at holding the vast number of fast growing animals they house. [ 15 ] Natural disasters, high tides, and other environmental occurrences can also trigger aquatic animal escapes. [ 16 ] [ 17 ] The reason these escapes are considered dangers is the impact they pose for the wild population they reproduce with after escaping. In many instances the wild population experiences a decreased likelihood of survival after reproducing with domesticated populations of salmon. [ 18 ] [ 19 ]
The Washington Department of Fish and Wildlife cites that "commonly expressed concerns surrounding escaped Atlantic salmon include competition with native salmon, predation, disease transfer, hybridization, and colonization." [ 20 ] A report done by that organization in 1999 did not find that escaped salmon posed a significant risk to wild populations. [ 21 ]
Crops refer to groups of plants grown for consumption. Despite domestication over many years, these plants are not so far removed from their wild relatives that they couldn't reproduce if brought together. Many crops are still grown in the areas they originated and gene flow between crops and wild relatives impacts the evolution of wild populations. [ 22 ] Farmers can avoid reproduction between the different populations by timing their planting of crops so that crops are not flowering when wild relatives would be. Domesticated crops have been changed through artificial selection and genetic engineering. The genetic make-ups of many crops is different from those of their wild relatives, [ 23 ] but the closer they grow to one another the more likely they are to share genes through pollen. Gene flow persists between crops and wild counterparts.
Genetically engineered organisms are genetically modified in a laboratory, and therefore distinct from those that were bred through artificial selection. In the fields of agriculture , agroforestry and animal husbandry , genetic pollution is being used to describe gene flows between GE species and wild relatives. [ 24 ] An early use of the term " genetic pollution" in this later sense appears in a wide-ranging review of the potential ecological effects of genetic engineering in The Ecologist magazine in July 1989 . It was also popularized by environmentalist Jeremy Rifkin in his 1998 book The Biotech Century . [ 25 ] While intentional crossbreeding between two genetically distinct varieties is described as hybridization with the subsequent introgression of genes, Rifkin, who had played a leading role in the ethical debate for over a decade before, used genetic pollution to describe what he considered to be problems that might occur due to the unintentional process of (modernly) genetically modified organisms (GMOs) dispersing their genes into the natural environment by breeding with wild plants or animals. [ 24 ] [ 26 ] [ 27 ]
Concerns about negative consequences from gene flow between genetically engineered organisms and wild populations are valid. Most corn and soybean crops grown in the midwestern USA are genetically modified. There are corn and soybean varieties that are resistant to herbicides like glyphosate [ 28 ] and corn that produces neonicotinoid pesticide within all of its tissues. [ 29 ] These genetic modifications are meant to increase yields of crops but there is little evidence that yields actually increase. [ 29 ] While scientists are concerned genetically engineered organisms can have negative effects on surrounding plant and animal communities, the risk of gene flow between genetically engineered organisms and wild populations is yet another concern. Many farmed crops may be weed resistant and reproduce with wild relatives. [ 30 ] More research is necessary to understand how much gene flow between genetically engineered crops and wild populations occurs, and the impacts of genetic mixing.
Mutations within organisms can be executed through the process of exposing the organism to chemicals or radiation in order to generate mutations. This has been done in plants in order to create mutants that have a desired trait. These mutants can then be bred with other mutants or individuals that are not mutated in order to maintain the mutant trait. However, similar to the risks associated with introducing individuals to a certain environment, the variation created by mutated individuals could have a negative impact on native populations as well.
Since 2005 there has existed a GM Contamination Register , launched for GeneWatch UK and Greenpeace International that records all incidents of intentional or accidental [ 31 ] [ 32 ] release of organisms genetically modified using modern techniques. [ 33 ]
Genetic use restriction technologies (GURTs) were developed for the purpose of property protection, but could be beneficial in preventing the dispersal of transgenes. GeneSafe technologies introduced a method that became known as "Terminator." This method is based on seeds that produce sterile plants. This would prevent movement of transgenes into wild populations as hybridization would not be possible. [ 34 ] However, this technology has never been deployed as it disproportionately negatively affects farmers in developing countries, who save seeds to use each year (whereas in developed countries, farmers generally buy seeds from seed production companies). [ 34 ]
Physical containment has also been utilized to prevent the escape of transgenes. Physical containment includes barriers such as filters in labs, screens in greenhouses, and isolation distances in the field. Isolation distances have not always been successful, such as transgene escape from an isolated field into the wild in herbicide-resistant bentgrass Agrostis stolonifera . [ 35 ]
Another suggested method that applies specifically to protection traits (e.g. pathogen resistance) is mitigation. Mitigation involves linking the positive trait (beneficial to fitness) to a trait that is negative (harmful to fitness) to wild but not domesticated individuals. [ 35 ] In this case, if the protection trait was introduced to a weed, the negative trait would also be introduced in order to decrease overall fitness of the weed and decrease possibility of the individual’s reproduction and thus propagation of the transgene.
Not all genetically engineered organisms cause genetic pollution. Genetic engineering has a variety of uses and is specifically defined as a direct manipulation of the genome of an organism. Genetic pollution can occur in response to the introduction of a species that is not native to a particular environment, and genetically engineered organisms are examples of individuals that could cause genetic pollution following introduction. Due to these risks, studies have been done in order to assess the risks of genetic pollution associated with organisms that have been genetically engineered:
Not only are there risks in terms of genetic engineering, but there are risks that emerge from species hybridization. In Czechoslovakia, ibex were introduced from Turkey and Sinai to help promote the ibex population there, which caused hybrids that produced offspring too early, which caused the overall population to disappear completely. [ 4 ] The genes of each population of the ibex in Turkey and Sinai were locally adapted to their environments so when placed in a new environmental context did not flourish. Additionally, the environmental toll that may arise from the introduction of a new species may be so disruptive that the ecosystem is no longer able to sustain certain populations.
The use of the word "pollution" in the term genetic pollution has a deliberate negative connotation and is meant to convey the idea that mixing genetic information is bad for the environment. However, because the mixing of genetic information can lead to a variety of outcomes, "pollution" may not be the most accurate descriptor. Gene flow is undesirable according to some environmentalists and conservationists , including groups such as Greenpeace , TRAFFIC , and GeneWatch UK . [ 44 ] [ 31 ] [ 33 ] [ 45 ] [ 5 ] [ 9 ] [ 46 ]
" Invasive species have been a major cause of extinction throughout the world in the past few hundred years. Some of them prey on native wildlife, compete with it for resources, or spread disease, while others may hybridize with native species, causing " genetic pollution ". In these ways, invasive species are as big a threat to the balance of nature as the direct overexploitation by humans of some species. " [ 47 ]
It can also be considered undesirable if it leads to a loss of fitness in the wild populations. [ 48 ] The term can be associated with the gene flow from a mutation bred , synthetic organism or genetically engineered organism to a non GE organism, [ 24 ] by those who consider such gene flow detrimental. [ 44 ] These environmentalist groups stand in complete opposition to the development and production of genetically engineered organisms.
From a governmental perspective, genetic pollution is defined as follows by the Food and Agriculture Organization of the United Nations :
"Uncontrolled spread of genetic information (frequently referring to transgenes) into the genomes of organisms in which such genes are not present in nature." [ 49 ]
Use of the term 'genetic pollution' and similar phrases such as genetic deterioration , genetic swamping , genetic takeover , and genetic aggression , are being debated by scientists as many do not find it scientifically appropriate. Rhymer and Simberloff argue that these types of terms:
...imply either that hybrids are less fit than the parentals, which need not be the case, or that there is an inherent value in "pure" gene pools. [ 47 ]
They recommend that gene flow from invasive species be termed genetic mixing since:
"Mixing" need not be value-laden, and we use it here to denote mixing of gene pools whether or not associated with a decline in fitness. [ 47 ] | https://en.wikipedia.org/wiki/Genetic_pollution |
Genetic predisposition refers to a genetic characteristic which influences the possible phenotypic development of an individual organism within a species or population under the influence of environmental conditions. The term genetic susceptibility is often used synonymously with genetic predisposition and is further defined as the inherited risk for specific conditions, based on genetic variants. While environmental factors can influence disease onset, genetic predisposition plays a role in inherited risk of conditions, such as various cancers. [ 1 ] At the molecular level, genetic predisposition often involves specific gene mutation, regulatory pathways, or epigenetic modifications that alter cellular processes, increasing disease risk. [ 2 ]
There are several approaches commonly used in the field of genetics to predict a genetic predisposition toward a disease.
As individuals, one’s genetic makeup or genotype , which is passed down from their parents, defines how they look and what genetic conditions they could have inherited, or be at risk for. These traits are exclusive, and therefore one's susceptibility to specific diseases is unique as well. The inheritance of specific genes reflect phenotypes based on one allele that comes from the mother and one from the father of each gene. [ 2 ]
Phenotypes that display genetic conditions are often caused by random mutations within the DNA sequence that makes up a gene. Somatic mutations are mutations that occur within the DNA of a non-reproductive cell post-conception, and therefore cannot be inherited, nor will they contribute to one’s genetic predisposition to disease. However, germline mutations occur within the DNA of reproductive cells and can be inherited by offspring, thereby influencing the individual's susceptibility to the specific genetic issue. [ 7 ] Upon diagnosing individuals with particular conditions via genetic testing, their genetic predisposition can be measured with pedigree trees. These trees trace inheritance patterns throughout a family to see if the mutation of interest can also be found in other blood-related individuals.
Genetic diseases can be autosomal recessive, autosomal dominant, X chromosome-linked recessive, X chromosome-linked dominant or Y chromosome-linked. They will be inherited differently based on their composition. Autosomal inheritance patterns will affect specific autosomes , non-sex chromosomes, depending on the genetic disease. Autosomal recessive diseases occur only when both inherited alleles have the mutation, while autosomal dominant diseases will be demonstrated in individuals with only one mutant version of the allele. Therefore, besides solely inheritance, the type of disease that is being considered plays a large role in susceptiblity. Genetic predisposition can also be impacted by one’s gender, as sex chromosomes define inheritance of X-linked and Y-linked alleles. Males are far more likely to inherit X-linked recessive diseases, because they only have one copy of the X chromosome, while females have two and therefore need mutations in both for this phenotype to be demonstrated. X-linked dominant diseases are equally shown in both males and females, while Y-linked diseases will only be demonstrated in males, as females do not have a Y chromosome. [ 8 ]
Cancers are a major consideration when examining genetic predisposition to diseases, as they often arise from inherited genetic mutations that trigger uncontrolled cell growth. As genetic diseases, these mutations can be passed down through families, increasing an individual's risk of developing various types of cancer. Understanding an individual's genetic predisposition to cancer plays a key role in managing risk among family members and optimizing treatment. [ 9 ]
Genetic predisposition to breast cancer is categorized into three main risk groups. The first group consists of high-penetrance genes, such as BRCA1 , BRCA2 , and TP53. Mutations in these genes are inherited and significantly increase an individual's susceptibility to breast cancer. The second group includes intermediate-penetrance genes, such as CHEK2 and ATM . These genes are identified through mutational screening of DNA repair genes and increase an individual's risk of breast cancer, though not as severely as high-penetrance genes. The last category consists of low-penetrance alleles, which are SNPs more commonly found in populations, however still contribute to a slight increase in susceptibility to breast cancer. [ 10 ] Genetic testing for high penetrance genes serves as an important indicator of breast cancer risk. Having the knowledge of predisposition to these genes can allow precautional measures to be taken towards prevention and treatment options early on, rather than not knowing until the disease has already progressed. [ 9 ]
Individuals with a genetic predisposition to colorectal cancer can benefit greatly from early and consistent monitoring. [ 9 ] Hereditary Colorectal Cancer (HCRC) is typically associated with several genetic syndromes, each characterized by specific gene mutations that play a critical role in diagnosis and risk assessment. Lynch Syndrome is the most common, and results from inherited pathogenic variants in DNA mismatch repair genes such as MLH1 , MSH2 , and MSH6 . Inheriting these mutations impairs the body's ability to correct DNA replication errors, significantly increasing the risk of developing colorectal and other cancers. Familial adenomatous polyposis (FAP) is another hereditary condition, caused by pathogenic mutations in the APC gene. If left untreated, it leads to a severe risk of developing colorectal cancer, typically before the age of 50. [ 11 ] Genetic testing and screening is essential for identifying individuals at increased risk, enabling early detection strategies such as regular colonoscopies and informing preventive care for both patients and their family members. Early implementation of these measures has been shown to improve long term outcomes for those with inherited susceptibility. [ 9 ] [ 11 ]
Genetic predisposition can also have an impact on psychological and behavioural phenotypes, as well as physical. An individual’s predisposition towards certain human behaviors can be examined in an attempt to identify behavioural patterns that appear to be historically and evolutionarily invariant within a variety of different cultures.
Studies have shown that heritability and other genetic factors can greatly contribute to the risk of depression and suicidal behaviours. [ 12 ] [ 13 ] Genetic predisposition to depressive disorders is typically caused through interactions between specific genes with each other and their environment. More than 100 candidate genes have been identified that have the ability to increase risk of depression and contribute to its symptoms, which can be assessed via methodological approaches. [ 12 ] Growing research is investigating how suicide can aggregate within families, further providing evidence that the alleles contributing to suicidal thoughts can be inherited. This has been further investigated through twin studies and adoption studies to measure the impacts of genetic information versus environment on one’s behaviour. [ 13 ] | https://en.wikipedia.org/wiki/Genetic_predisposition |
Genetic purging is the increased pressure of natural selection against deleterious alleles prompted by inbreeding . [ 1 ]
Purging occurs because deleterious alleles tend to be recessive, which means that they only express all their harmful effects when they are present in the two copies of the individual (i.e., in homozygosis). During inbreeding, as related individuals mate, they produce offspring that are more likely to be homozygous so that deleterious alleles express all their harmful effects more often, making individuals less fit.
Purging reduces both the overall number of recessive deleterious alleles and the decline of mean fitness caused by inbreeding (the inbreeding depression for fitness).
The term "purge" is sometimes used for selection against deleterious alleles in a general way. It would avoid ambiguity to use " purifying selection " in that general context, and to reserve "purging" to its more strict meaning defined above.
Deleterious alleles segregating in populations of diploid organisms have a remarkable trend to be, at least, partially recessive. This means that, when they occur in homozygosis (double copies), they reduce fitness by more than twice than when they occur in heterozygosis (single copy). In other words, part of their potential deleterious effect is hidden in heterozygosis but expressed in homozygosis, so that selection is more efficient against them when they occur in homozygosis. Since inbreeding increases the probability of being homozygous, it increases the fraction of the potential deleterious effect that is expressed and, therefore, exposed to selection. This causes some increase in the selective pressure against (partially) recessive deleterious alleles, which is known as purging. Of course, it also causes some reduction in fitness, which is known as inbreeding depression .
Purging can reduce the average frequency of deleterious alleles across the genome below the value expected in a non-inbred population during long periods. [ 2 ] which reduces the negative impact of inbreeding on fitness. If inbreeding is due just to random mating in a finite population, due to purging the fitness mean fitness declines less than would be expected just from inbreeding and, after some initial decline, it can even rebound up to almost its value before inbreeding. Another consequence is the reduction of the so-called inbreeding load. This means that, after purging, further inbreeding is expected to be less harmful. The efficiency of purging is reduced by genetic drift and, therefore, in the long term, purging is less efficient in smaller populations. [ 1 ] Purging can be increased if individuals mate with relatives more often than expected by random mating.
Accounting for purging when predicting inbreeding depression is important in evolutionary genetics, because the fitness decline caused by inbreeding can be determinant in the evolution of diploidy , sexual reproduction and other main biological features. It is also important in animal breeding and, of course, in conservation genetics , because inbreeding depression may be a relevant factor determining the extinction risk of endangered populations, and because conservation programs can allow some breeding handling in order to control inbreeding. [ 3 ]
In brief: due to purging, inbreeding depression does not depend on the standard measure of inbreeding (Wright's inbreeding coefficient F ), since this measure only applies to neutral alleles. Instead, fitness decline it depends on the "purged inbreeding coefficient" g , which takes into account how deleterious alleles are being purged.
Purging reduces inbreeding depression in two ways: first, it slows its progress; second, it reduces the overall inbreeding depression expected in the long term. The slower the progress of inbreeding, the more efficient is purging.
In the absence of natural selection, mean fitness would be expected to decline exponentially as inbreeding increases, where inbreeding is measured using Wright's inbreeding coefficient F [ 4 ] (the reason why decline is exponential on F instead of linear is just that fitness is usually considered a multiplicative trait). The rate at which fitness declines as F increases (the inbreeding depression rate δ ) depends on the frequencies and deleterious effects of the alleles present in the population before inbreeding.
The above coefficient F is the standard measure of inbreeding, and gives the probability that, at any given neutral locus, an individual has inherited two copies of a same gene of a common ancestor (i.e. the probability of being homozygous "by descent"). In simple conditions, F can be easily computed in terms of population size or of genealogical information. F is often denoted using lowercase ( f ), but should not be confused with the coancestry coefficient.
However, the above prediction for the fitness decline rarely applies, since it was derived assuming no selection, and fitness is precisely the target trait of natural selection . Thus, Wright's inbreeding coefficient F for neutral loci does not apply to deleterious alleles, unless inbreeding increases so fast that the change in gene frequency is governed just by random sampling (i.e., by genetic drift ).
Therefore, according to the model , the decline of fitness can be predicted using, instead of the standard inbreeding coefficient F , a "purged inbreeding coefficient" ( g ) that gives the probability of being homozygous by descent for (partially) recessive deleterious alleles, taking into account how their frequency is reduced by purging. [ 1 ] Due to purging, fitness declines at the same rate δ than in the absence of selection, but as a function of g instead of F .
This purged inbreeding coefficient g can also be computed, to a good approximation, using simple expressions in terms of the population size, as explained below, or of the genealogy of individuals. However this requires some information on the magnitude of the deleterious effects that are hidden in the heterozygous condition but become expressed in homozygosis. The larger this magnitude, denoted purging coefficient d , the more efficient is purging.
An interesting property of purging is that, during inbreeding, while F increases approaching a final value F = 1 , g can approach a much smaller final value. Hence, it is not just that purging slows the fitness decline, but also that it reduces the overall fitness loss produced by inbreeding in the long term. This is illustrated below for the extreme case of inbreeding depression caused by recessive lethals, which are alleles that cause death before reproduction but only when they occur in homozygosis. Purging is less effective against mildly deleterious alleles than against lethal ones but, in general, the slower is the increase of inbreeding F , the smaller becomes the final value of the purged inbreeding coefficient g and, therefore, the final reduction in fitness. This implies that, if inbreeding progresses slowly enough, no relevant inbreeding depression is expected in the long term. implies, for example, that the average fitness of a population that has been moderately small for a long time, can be very similar to that of a large population with more genetic diversity. In conservation genetics, it would be very useful to ascertain the maximum rate of increase of inbreeding that allows for such efficient purging.
Consider a large non-inbred population with mean fitness W . Then, the size of the population reduces to a new smaller value N (in fact, the effective population size should be used here), leading to a progressive increase of inbreeding.
Then inbreeding depression occurs at a rate δ , due to (partially) recessive deleterious alleles that were present at low frequencies at different loci. This means that, in the absence of selection, the expected value for mean fitness after t generations of inbreeding, would be:
where F t {\displaystyle F_{t}} is the population mean for Wright's inbreeding coefficient after t generations of inbreeding. [ 4 ]
However, since selection operates upon fitness, mean fitness should be predicted taking into account both inbreeding and purging, as
In the above equation, g t {\displaystyle g_{t}} is the average "purged inbreeding coefficient" after t generations of inbreeding. [ 1 ] It depends upon the "purging coefficient" d , which represents the deleterious effects that are hidden in heterozygosis but exposed in homozygosis.
The average "purged inbreeding coefficient" can be approximated using the recurrent expression
There are also predictive equations to be used with genealogical information.
As an example of genetic purging, consider a large population where there are recessive lethal alleles segregating at very low frequency in many loci, so that each gamete carries on the average one of these alleles. Although about 63% of the gametes carry at least one of these lethal alleles, almost no individual carry two copies of the same lethal. Therefore, since lethals are considered completely recessive (i.e., they are harmless in heterozygosis), they cause almost no deaths. Now assume that population size reduces to a small value (say N =10), and remains that small for many generations. As inbreeding increases, the probability of being homozygous for one (or more) of these lethal alleles also increases, causing fitness to decline. However, as those lethals begin to occur in homozygosis, natural selection begins purging them. The figure to the right gives the expected decline of fitness against the number of generations, taking into account just the increase in inbreeding F (red line), or both inbreeding and purging (blue line, computed using the purged inbreeding coefficient g ). This example shows that purging can be very efficient in preventing inbreeding depression. However, for non-lethal deleterious alleles, the efficiency of purging would be smaller, and it can require larger populations to overcome genetic drift.
Inbreeding depression and purging play a major role in the evolution of reproductive systems. As an example, they determine when selfing becomes at an advantage compared to outcrossing. [ 5 ] [ 6 ] Another example is the genomic renewal in yeasts. Saccharomyces cerevisiae and Saccharomyces paradoxus have a life cycle that alternates between long periods of asexual reproduction as a diploid, ending in meiosis that is usually immediately followed selfing , with only rare outcrossing . [ 7 ] Recessive deleterious mutations accumulate during the diploid expansion phase, and are purged during selfing: this purging has been termed "genome renewal". [ 8 ] [ 9 ]
When a previously stable population undergoes inbreeding, if nothing else changes, natural selection should consist mainly of purging. The joint consequences of inbreeding and purging on fitness vary depending on many factors: the previous history of the population, the rate of increase of inbreeding, the harshness of the environment or of the competitive conditions, etc. The effects of purging were first noted by Darwin [ 10 ] in plants, and have been detected in laboratory experiments and in vertebrate populations undergoing inbreeding in zoos or in the wild, as well as in humans. [ 11 ] The detection of purging is often obscured by many factors, but there is consistent evidence that, in agreement with the predictions explained above, slow inbreeding results in more efficient purging, so that a given inbreeding F leads to less threat to population viability if it has been produced more slowly. [ 12 ] [ 13 ]
Nevertheless, in practical situations, the genetic change in fitness also depends on many other factors, besides inbreeding and purging. For example, adaptation to changing environmental conditions often causes relevant genetic changes during inbreeding. Furthermore, if inbreeding is due to a reduction in population size, selection against new deleterious mutations can become less efficient, and this can induce additional fitness decline in the medium-long term.
In addition, part of the inbreeding depression could be not due to deleterious alleles, but to an intrinsic advantage of being heterozygous compared to being homozygous for any available allele, which is known as overdominance. Inbreeding depression caused by overdominance cannot be purged, but seems to be a minor cause of overall inbreeding depression, although its actual importance is still a matter of debate. [ 14 ]
Therefore, predicting the actual evolution of fitness during inbreeding is highly elusive. However, the component of fitness decline expected from inbreeding and purging on deleterious alleles could be predicted using g .
Understanding genetic purging and predicting its consequences is of great importance in evolutionary and conservation genetics. Endangered populations use to undergo inbreeding due to their reduced numbers, and purging can play a relevant role in determining their extinction risk and the success of conservation strategies. [ 15 ] | https://en.wikipedia.org/wiki/Genetic_purging |
Genetic recombination (also known as genetic reshuffling ) is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes , genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) int er chromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes (random orientation of pairs of homologous chromosomes in meiosis I); & (2) int ra chromosomal recombination, occurring through crossing over. [ 1 ]
During meiosis in eukaryotes , genetic recombination involves the pairing of homologous chromosomes . This may be followed by information transfer between the chromosomes. The information transfer may occur without physical exchange (a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed) (see SDSA – Synthesis Dependent Strand Annealing pathway in Figure); or by the breaking and rejoining of DNA strands, which forms new molecules of DNA (see DHJ pathway in Figure).
Recombination may also occur during mitosis in eukaryotes where it ordinarily involves the two sister chromosomes formed after chromosomal replication. In this case, new combinations of alleles are not produced since the sister chromosomes are usually identical. In meiosis and mitosis, recombination occurs between similar molecules of DNA ( homologous sequences ). In meiosis, non-sister homologous chromosomes pair with each other so that recombination characteristically occurs between non-sister homologues. In both meiotic and mitotic cells, recombination between homologous chromosomes is a common mechanism used in DNA repair .
Gene conversion – the process during which homologous sequences are made identical also falls under genetic recombination.
Genetic recombination and recombinational DNA repair also occurs in bacteria and archaea , which use asexual reproduction .
Recombination can be artificially induced in laboratory ( in vitro ) settings, producing recombinant DNA for purposes including vaccine development.
V(D)J recombination in organisms with an adaptive immune system is a type of site-specific genetic recombination that helps immune cells rapidly diversify to recognize and adapt to new pathogens .
During meiosis, synapsis (the pairing of homologous chromosomes) ordinarily precedes genetic recombination.
Genetic recombination is catalyzed by many different enzymes . Recombinases are key enzymes that catalyse the strand transfer step during recombination. RecA , the chief recombinase found in Escherichia coli , is responsible for the repair of DNA double strand breaks (DSBs). In yeast and other eukaryotic organisms there are two recombinases required for repairing DSBs. The RAD51 protein is required for mitotic and meiotic recombination, whereas the DNA repair protein, DMC1 , is specific to meiotic recombination. In the archaea, the ortholog of the bacterial RecA protein is RadA.
Bacteria regularly undergo genetic recombination in three main ways:
Sometimes a strand of DNA is transferred into the target cell but fails to be copied as the target divides. This is called an abortive transfer .
In eukaryotes , recombination during meiosis is facilitated by chromosomal crossover . The crossover process leads to offspring having different combinations of genes from those of their parents, and can occasionally produce new chimeric alleles . [ citation needed ] The shuffling of genes brought about by genetic recombination produces increased genetic variation . It also allows sexually reproducing organisms to avoid Muller's ratchet , in which the genomes of an asexual population tend to accumulate more deleterious mutations over time than beneficial or reversing mutations. [ citation needed ]
Chromosomal crossover involves recombination between the paired chromosomes inherited from each of one's parents, generally occurring during meiosis . [ citation needed ] During prophase I (pachytene stage) the four available chromatids are in tight formation with one another. [ citation needed ] While in this formation, homologous sites on two chromatids can closely pair with one another, and may exchange genetic information. [ 6 ]
Because there is a small probability of recombination at any location along a chromosome, the frequency of recombination between two locations depends on the distance separating them. [ citation needed ] Therefore, for genes sufficiently distant on the same chromosome, the amount of crossover is high enough to destroy the correlation between alleles. [ citation needed ]
Tracking the movement of genes resulting from crossovers has proven quite useful to geneticists. Because two genes that are close together are less likely to become separated than genes that are farther apart, geneticists can deduce roughly how far apart two genes are on a chromosome if they know the frequency of the crossovers. [ citation needed ] Geneticists can also use this method to infer the presence of certain genes. Genes that typically stay together during recombination are said to be linked . One gene in a linked pair can sometimes be used as a marker to deduce the presence of the other gene. This is typically used to detect the presence of a disease-causing gene. [ 7 ]
The recombination frequency between two loci observed is the crossing-over value . It is the frequency of crossing over between two linked gene loci ( markers ), and depends on the distance between the genetic loci observed. For any fixed set of genetic and environmental conditions, recombination in a particular region of a linkage structure ( chromosome ) tends to be constant, and the same is then true for the crossing-over value which is used in the production of genetic maps . [ 5 ] [ 8 ]
In gene conversion, a section of genetic material is copied from one chromosome to another, without the donating chromosome being changed. Gene conversion occurs at high frequency at the actual site of the recombination event during meiosis . It is a process by which a DNA sequence is copied from one DNA helix (which remains unchanged) to another DNA helix, whose sequence is altered. Gene conversion has often been studied in fungal crosses [ 9 ] where the 4 products of individual meioses can be conveniently observed. Gene conversion events can be distinguished as deviations in an individual meiosis from the normal 2:2 segregation pattern (e.g. a 3:1 pattern).
Recombination can occur between DNA sequences that contain no sequence homology . This can cause chromosomal translocations , sometimes leading to cancer.
B cells of the immune system perform genetic recombination, called immunoglobulin class switching . It is a biological mechanism that changes an antibody from one class to another, for example, from an isotype called IgM to an isotype called IgG .
In genetic engineering , recombination can also refer to artificial and deliberate recombination of disparate pieces of DNA, often from different organisms, creating what is called recombinant DNA . A prime example of such a use of genetic recombination is gene targeting , which can be used to add, delete or otherwise change an organism's genes. This technique is important to biomedical researchers as it allows them to study the effects of specific genes. Techniques based on genetic recombination are also applied in protein engineering to develop new proteins of biological interest.
Examples include Restriction enzyme mediated integration , Gibson assembly and Golden Gate Cloning .
DNA damages caused by a variety of exogenous agents (e.g. UV light , X-rays , chemical cross-linking agents) can be repaired by homologous recombinational repair (HRR). [ 10 ] [ 11 ] These findings suggest that DNA damages arising from natural processes , such as exposure to reactive oxygen species that are byproducts of normal metabolism, are also repaired by HRR. In humans, deficiencies in the gene products necessary for HRR during meiosis likely cause infertility [ 12 ] In humans, deficiencies in gene products necessary for HRR, such as BRCA1 and BRCA2 , increase the risk of cancer (see DNA repair-deficiency disorder ).
In bacteria, transformation is a process of gene transfer that ordinarily occurs between individual cells of the same bacterial species. Transformation involves integration of donor DNA into the recipient chromosome by recombination. This process appears to be an adaptation for repairing DNA damages in the recipient chromosome by HRR. [ 13 ] Transformation may provide a benefit to pathogenic bacteria by allowing repair of DNA damage, particularly damages that occur in the inflammatory, oxidizing environment associated with infection of a host.
When two or more viruses, each containing lethal genomic damages, infect the same host cell, the virus genomes can often pair with each other and undergo HRR to produce viable progeny. This process, referred to as multiplicity reactivation, has been studied in lambda and T4 bacteriophages , [ 14 ] as well as in several pathogenic viruses. In the case of pathogenic viruses, multiplicity reactivation may be an adaptive benefit to the virus since it allows the repair of DNA damages caused by exposure to the oxidizing environment produced during host infection. [ 13 ] See also reassortment .
A molecular model for the mechanism of meiotic recombination presented by Anderson and Sekelsky [ 15 ] is outlined in the first figure in this article. Two of the four chromatids present early in meiosis (prophase I) are paired with each other and able to interact. Recombination, in this model, is initiated by a double-strand break (or gap) shown in the DNA molecule (chromatid) at the top of the figure. Other types of DNA damage may also initiate recombination. For instance, an inter-strand cross-link (caused by exposure to a cross-linking agent such as mitomycin C) can be repaired by HRR.
Two types of recombinant product are produced. Indicated on the right side is a "crossover" (CO) type, where the flanking regions of the chromosomes are exchanged, and on the left side, a "non-crossover" (NCO) type where the flanking regions are not exchanged. The CO type of recombination involves the intermediate formation of two "Holliday junctions" indicated in the lower right of the figure by two X-shaped structures in each of which there is an exchange of single strands between the two participating chromatids. This pathway is labeled in the figure as the DHJ (double-Holliday junction) pathway.
The NCO recombinants (illustrated on the left in the figure) are produced by a process referred to as "synthesis dependent strand annealing" (SDSA). Recombination events of the NCO/SDSA type appear to be more common than the CO/DHJ type. [ 16 ] The NCO/SDSA pathway contributes little to genetic variation, since the arms of the chromosomes flanking the recombination event remain in the parental configuration. Thus, explanations for the adaptive function of meiosis that focus exclusively on crossing-over are inadequate to explain the majority of recombination events.
Achiasmy is the phenomenon where autosomal recombination is completely absent in one sex of a species. Achiasmatic chromosomal segregation is well documented in male Drosophila melanogaster . The "Haldane-Huxley rule" states that achiasmy usually occurs in the heterogametic sex . [ 17 ]
Heterochiasmy occurs when recombination rates differ between the sexes of a species. [ 17 ] In humans, each oocyte has on average 41.6 ± 11.3 recombinations, 1.63-fold higher than sperms. This sexual dimorphic pattern in recombination rate has been observed in many species. In mammals, females most often have higher rates of recombination. [ 18 ]
Numerous RNA viruses are capable of genetic recombination when at least two viral genomes are present in the same host cell. [ 19 ] [ 20 ] Recombination is largely responsible for RNA virus diversity and immune evasion. [ 21 ] RNA recombination appears to be a major driving force in determining genome architecture and the course of viral evolution among picornaviridae ( (+)ssRNA ) (e.g. poliovirus ). [ 22 ] In the retroviridae ((+)ssRNA)(e.g. HIV ), damage in the RNA genome appears to be avoided during reverse transcription by strand switching, a form of recombination. [ 23 ] [ 24 ]
Recombination also occurs in the reoviridae (dsRNA)(e.g. reovirus), orthomyxoviridae ((-)ssRNA)(e.g. influenza virus ) [ 24 ] and coronaviridae ((+)ssRNA) (e.g. SARS ). [ 25 ] [ 26 ]
Recombination in RNA viruses appears to be an adaptation for coping with genome damage. [ 19 ] Switching between template strands during genome replication, referred to as copy-choice recombination, was originally proposed to explain the positive correlation of recombination events over short distances in organisms with a DNA genome (see first Figure, SDSA pathway). [ 27 ]
Recombination can occur infrequently between animal viruses of the same species but of divergent lineages. The resulting recombinant viruses may sometimes cause an outbreak of infection in humans. [ 25 ]
Especially in coronaviruses, recombination may also occur even among distantly related evolutionary groups (subgenera), due to their characteristic transcription mechanism, that involves subgenomic mRNAs that are formed by template switching. [ 28 ] [ 26 ]
When replicating its (+)ssRNA genome , the poliovirus RNA-dependent RNA polymerase (RdRp) is able to carry out recombination. Recombination appears to occur by a copy choice mechanism in which the RdRp switches (+)ssRNA templates during negative strand synthesis. [ 29 ] Recombination by RdRp strand switching also occurs in the (+)ssRNA plant carmoviruses and tombusviruses . [ 30 ]
Recombination appears to be a major driving force in determining genetic variability within coronaviruses, as well as the ability of coronavirus species to jump from one host to another and, infrequently, for the emergence of novel species, although the mechanism of recombination in is unclear. [ 25 ]
In early 2020, many genomic sequences of Australian SARS‐CoV‐2 isolates have deletions or mutations (29742G>A or 29742G>U; "G19A" or "G19U") in the s2m, suggesting that RNA recombination may have occurred in this RNA element. 29742G("G19"), 29744G("G21"), and 29751G("G28") were predicted as recombination hotspots. [ 31 ] During the first months of the COVID-19 pandemic, such a recombination event was suggested to have been a critical step in the evolution of SARS-CoV-2's ability to infect humans. [ 32 ] Linkage disequilibrium analysis confirmed that RNA recombination with the 11083G > T mutation also contributed to the increase of mutations among the viral progeny. The findings indicate that the 11083G > T mutation of SARS-CoV-2 spread during Diamond Princess shipboard quarantine and arose through de novo RNA recombination under positive selection pressure. In three patients on the Diamond Princess cruise, two mutations, 29736G > T and 29751G > T (G13 and G28) were located in Coronavirus 3′ stem-loop II-like motif (s2m) of SARS-CoV-2. Although s2m is considered an RNA motif highly conserved in 3' untranslated region among many coronavirus species, this result also suggests that s2m of SARS-CoV-2 is RNA recombination /mutation hotspot. [ 33 ]
SARS-CoV-2's entire receptor binding motif appeared, based on preliminary observations, to have been introduced through recombination from coronaviruses of pangolins . [ 34 ] However, more comprehensive analyses later refuted this suggestion and showed that SARS-CoV-2 likely evolved solely within bats and with little or no recombination. [ 35 ] [ 36 ]
Nowak and Ohtsuki [ 37 ] noted that the origin of life ( abiogenesis ) is also the origin of biological evolution . They pointed out that all known life on earth is based on biopolymers and proposed that any theory for the origin of life must involve biological polymers that act as information carriers and catalysts. Lehman [ 38 ] argued that recombination was an evolutionary development as ancient as the origins of life. Smail et al. [ 39 ] proposed that in the primordial Earth, recombination played a key role in the expansion of the initially short informational polymers (presumed to be RNA ) that were the precursors to life.
This article incorporates public domain material from Science Primer . NCBI . Archived from the original on 2009-12-08. | https://en.wikipedia.org/wiki/Genetic_recombination |
Genetic redundancy is a term typically used to describe situations where a given biochemical function is redundantly encoded by two or more genes . In these cases, mutations (or defects) in one of these genes will have a smaller effect on the fitness of the organism than expected from the genes’ function. Characteristic examples of genetic redundancy include (Enns, Kanaoka et al. 2005) and (Pearce, Senis et al. 2004). Many more examples are thoroughly discussed in (Kafri, Levy & Pilpel. 2006).
The main source of genetic redundancy is the process of gene duplication which generates multiplicity in gene copy number. A second and less frequent source of genetic redundancy are convergent evolutionary processes leading to genes that are close in function but unrelated in sequence (Galperin, Walker & Koonin 1998). Genetic redundancy is typically associated with signaling networks, in which many proteins act together to accomplish teleological functions. In contrast to expectations, genetic redundancy is not associated with gene duplications [Wagner, 2007], neither do redundant genes mutate faster than essential genes [Hurst 1999]. Therefore, genetic redundancy has classically aroused much debate in the context of evolutionary biology (Nowak et al., 1997; Kafri, Springer & Pilpel . 2009).
From an evolutionary standpoint, genes with overlapping functions imply minimal, if any, selective pressures acting on these genes. One therefore expects that the genes participating in such buffering of mutations will be subject to severe mutational drift diverging their functions and/or expression patterns with considerably high rates. Indeed it has been shown that the functional divergence of paralogous pairs in both yeast and human is an extremely rapid process. Taking these notions into account, the very existence of genetic buffering, and the functional redundancies required for it, presents a paradox in light of the evolutionary concepts. On one hand, for genetic buffering to take place there is a necessity for redundancies of gene function, on the other hand such redundancies are clearly unstable in face of natural selection and are therefore unlikely to be found in evolved genomes.
Duplicated genes that diverge in function may undergo subfunctionalization or can become degenerate . When two protein coding genes are degenerate there will be conditions where the gene products appear functionally redundant and also conditions where the gene products take on unique functions. | https://en.wikipedia.org/wiki/Genetic_redundancy |
Genetic rescue is seen as a mitigation strategy designed to restore genetic diversity and reduce extinction risks in small, isolated and frequently inbred populations. [ 1 ] It is largely implemented through translocation, a type of demographic rescue and technical migration that adds individuals to a population to prevent its potential extinction. This demographic rescue may be similar to genetic rescue, as each increase population size and/or fitness. This overlap in meaning has led some researchers to consider a more detailed definition for each type of rescue that details 'assessment and documentation of pre- and post-translocation genetic ancestry'. [ 1 ] Not every example of genetic rescue is clearly successful and the current definition of genetic rescue does not mandate that the process result in a 'successful' outcome. Despite an ambiguous definition, genetic rescue is viewed positively, with many perceived successes. [ 2 ]
The conceptual foundation of genetic rescue can be traced back to the work of geneticist Sewall Wright , who studied the effect of immigration among populations linked by gene flow. [ 3 ] More recently, genetic rescue has been defined by scientific reviews as: "when population fitness, inferred from some demographic vital rate or phenotypic trait, increases by more than can be attributed to the demographic contribution of immigrants." [ 4 ] [ 5 ] Genetic mixing leading to fitness recovery could be described as "genetic rescue", but perpetuates the unclear differences between genetic rescue and pollution.
When a species' population becomes too small, they are subject to genetic processes such as inbreeding depression from a lack of gene flow, allelic fixation from genetic drift , and loss of diversity. In combination these can lead to a decrease in population fitness, and increase the risk of extinction. [ 3 ] Genetic rescue is a conservation tool which tries to address these genetic factors by moving genes from one population to another to increase the overall genetic diversity and minimize inbreeding. [ 6 ] This conservation technique intended to increase the fitness of a small, imperiled population [ 2 ] [ 3 ] through the introduction of beneficial alleles through migration. [ 2 ] It is often used for populations of species that are at a high risk of extinction. A successful genetic rescue occurs when the addition of new genes effectively introduces genetic diversity that leads to increased population size and growth rate, as well as a greater population fitness. [ 2 ] An unsuccessful genetic rescue may occur if the addition of new genes causes outbreeding depression , which decreases their population fitness. [ 3 ] Too much gene flow may lead to genetic swamping through extensive hybridization. [ 2 ] Genetic rescue can occur through multiple pathways, including heterosis and adaptive evolution . [ 2 ] It is closely related to, but distinctly different from the concepts of genetic pollution , evolutionary rescue , genetic restoration , and assisted gene flow. [ 2 ]
Gene flow (migration) is the introduction of new individuals (and genes) into a target population. [ 7 ] Predicting the impact of a migrant on a population will depend on combination of complex genetic and non-genetic factors. Whether migration increases population fitness will depend if the genes brought in are adapted to local conditions and if they decrease levels of inbreeding in the target population. An Introduced individuals can also positively or negatively affect genetic rescue through behaviors such as mate choice , dominance hierarchies, and infanticide. [ 3 ]
Genetic drift is the fixation of alleles by chance, hence reducing the overall diversity in the population. Genetic rescue can restore diversity by adding new genes to a population, counteracting fixation. [ 8 ]
Natural selection occurs when variations in heritable traits determines reproductive success of an individual, and thereby determines the persistence of that trait in that population. [ 9 ] Genetic rescue may introduce traits that are advantageous to the target population or reduced the frequency of disadvantageous traits, increasing the net fitness of a population to ensure the continued survival as a species.
Genetic rescue can be a controversial tool because it is hard to predict how a population will be affected by a migration event. Genetic rescue has the possibility of actually lowering the fitness of a population by swamping the population or increasing rare deleterious alleles. [ 10 ] This instance may simply be termed genetic pollution instead of being referred to genetic rescue. Rescue may also only be a short-term solution, as shown by the case of the Isle Royale Wolves. In that case, genetic rescue of the wolves resulted in a large initial increase in population fitness followed by a large decline in subsequent years. [ 10 ] Many conservationists argue that genetic rescue could create unforeseen problems for species at risk, and that it overlooks the underlying problems that push so many species to the brink of extinction, including habitat loss due to human development. [ 11 ]
As with the term genetic pollution, 'genetic rescue' has political connotations. Some of the more controversial practices which can be considered genetic rescue include
A case of successful genetic rescue can be observed in the Florida panther population. Habitat loss and other anthropogenic influences led to small, inbred population which increased the decline of this population ( Puma concolor cougar ), . [ 16 ] Inbreeding depression resulted in kinked tails and cowlicks, sperm defects, and heart abnormalities. [ 16 ] The population reached a low of approximately 22 panthers. [ 3 ] Fearing inevitable extinction, eight panthers from Texas were translocated to Florida in the mid 1990s. [ 16 ] This effort was deemed successful after analysis showed a 4% annual population growth rate following the immigration event. [ 3 ] Additionally, researchers found that the resulting hybrid kittens were three times more likely to survive to adulthood than “purebred” kittens. [ 16 ] The Florida panther population increased from around 25 to over 100 individuals in roughly a decade. [ 4 ]
A case of unsuccessful genetic rescue can be observed in the Isle Royale wolf population. In 1997, a single wolf arrived on the island and bred with the wolf population of about 25 individuals. [ 10 ] Initially, the addition of his genetic variation resulted in a positive effects on the population , shown by a large increase in population fitness. [ 10 ] However, the addition of genetic variation by this immigrant was only beneficial in the short term. The population swiftly declined, with only two wolves sighted in 2016. [ 10 ] it is possible that the new immigrant brought a new detrimental allele that increased in frequency as he interbred with the original population or that a single individual was insufficient to overcome the negative impact of genetic load. [ 10 ]
The greater prairie chicken is a ground-nesting bird with ecological and evolutionary hurdles that necessitated genetic rescue to avoid extinction. [ 1 ] It was widely distributed across the North American great plains but now requires population management in small remnant areas. In Illinois, the greater prairie chicken declined from millions of individuals in the mid 19th century to 46 by 1998. This prompted genetic rescue efforts and movement of individuals from neighboring states to increase Illinois greater prairie chicken numbers. This has been considered an early and successful case of genetic rescue. Although the initial genetic rescue actions seem to have led to an increase in fitness, prairie habitat is now limiting recovery. Exclusively genetic efforts to rescue the species are considered insufficient and more focus on habitat protection may be required to save the species. [ 1 ]
Mountain lions in the Santa Monica Mountains face a lack of genetic diversity due to their isolation caused by U.S. 101 , and several documented cases of inbreeding [ 17 ] [ 18 ] and physical deformations [ 19 ] have occurred in the area. In 2008, P-12 crossed U.S. 101 and in doing so brought fresh genetic material to the area. His successful breeding was considered a genetic rescue, although the effects were mitigated when he began mating with his offspring as well. [ 18 ]
The Wallis Annenberg Wildlife Crossing , meant to de-isolate the Santa Monica Mountains by connecting it over U.S. 101 to the Simi Hills , [ 20 ] is currently being built to increase genetic diversity and alleviate inbreeding in mountain lions in the Santa Monica Mountains. [ 21 ] The crossing is located near where P-12 crossed U.S. 101, and when completed, it will be the largest of its kind in the world. [ 20 ] [ 22 ] | https://en.wikipedia.org/wiki/Genetic_rescue |
Genetic resources are genetic material of actual or potential value, where genetic material means any material of plant, animal, microbial or other origin containing functional units of heredity . [ 1 ] Genetic resources is one of the three levels of biodiversity defined by the Convention on Biological Diversity in Rio, 1992. | https://en.wikipedia.org/wiki/Genetic_resources |
Genetic resources means genetic material of actual or potential value where genetic material means any material of plant, animal, microbial or other origin containing functional units of heredity... [ 1 ] Genetic resources thus refer to the part of genetic diversity that has or could have practical use, such as in plant breeding. The term was introduced by Otto Frankel and Erna Bennett for a technical conference on the exploration, utilization and conservation of plant genetic resources, organized by the Food and Agriculture Organisation (FAO) and the International Biological Program (IBP), held in Rome, Italy, 18–26 September 1967. [ 2 ]
Genetic resources is one of the three levels of biodiversity defined by Article 2 of the Convention on Biological Diversity (CBD) in Rio, 1992 [ 3 ]
Under the CBD, discussions and negotiations regarding genetic resources are organized by the FAO Commission of Genetic Resources for Food and Agriculture . This commission distinguishes the following domains of genetic resources:
Genetic resources are threatened by genetic erosion and conservation activities are undertaken to prevent loss of diversity.
Before the introduction of the term, the Russian scientist Nikolai Vavilov initiated comprehensive studies on plant genetic resources and conservation work in the 1920’s. The American botanist Jack Harlan stressed the tight link between plant genetic resources and man in a seminal publication "Crops and Man". [ 5 ]
There are two complementary ways to conserve genetics resources:
Policies are key to ensure the fair and equitable sharing of benefits derived from the use of genetic resources, for present and future generations. The main international policy framework that regulates genetic resources exchange and use is the Nagoya Protocol which entered into force in 2014. It defines and protects the owners of genetic resources and it sets the rules for Access and Benefit Sharing (ABS) [ 9 ]
The following scientific journals are dedicated to the topic of genetic resources conservation and sustainable use: | https://en.wikipedia.org/wiki/Genetic_resources_conservation_and_sustainable_use |
Genetic saturation is the result of multiple substitutions at the same site in a sequence, or identical substitutions in different sequences, such that the apparent sequence divergence rate is lower than the actual divergence that has occurred. [ 1 ] When comparing two or more genetic sequences consisting of single nucleotides, differences in sequence observed are only differences in the final state of the nucleotide sequence. Single nucleotides that undergoing genetic saturation change multiple times, sometimes back to their original nucleotide or to a nucleotide common to the compared genetic sequence. Without genetic information from intermediate taxa, it is difficult to know how much, or if any saturation has occurred on an observed sequence. [ 2 ] Genetic saturation occurs most rapidly on fast-evolving sequences, such as the hypervariable region of mitochondrial DNA, or in short tandem repeats such as on the Y-chromosome . [ 3 ] [ 4 ]
In phylogenetics, saturation effects result in long branch attraction , where the most distant lineages have misleadingly short branch lengths. It also decreases phylogenetic information contained in the sequences. [ 5 ]
Multiple substitutions take place when single nucleotides undergo multiple changes before reaching their final nucleotide identity. A sequence is said to be saturated because mutation has acted multiple times upon nucleotides and observed change in sequence is, in fact, less than the historical change in sequence. [ 1 ]
It is possible to estimate the amount of saturation that a sequence might have undergone by estimating the substitution rate of a genetic sequence and how much time has passed since divergence. Divergence rates are estimated from a variety of sources including ancestral DNA, fossil records and biographical events. [ 6 ] This use of molecular clocks to determine divergence is controversial because of its potential for inaccuracy and assumptions made in the model (such as consistent mutation rate for all branches) and is used mostly as an estimation tool. [ 6 ] Genetic saturation can also be estimated by comparing the number of observed differences in nucleotide sequences between multiple pairs of species. The number of observed substitutions between sequences of different species can be compared to the number of inferred substitutions based on branch length to find the approximate point where the number of inferred substitutions surpasses the number of observed substitutions. [ 6 ] [ 7 ] This method can give researchers an idea of the level of saturation of a particular gene but is thought to underestimate the amount of saturation, especially for very large branch lengths. [ 2 ]
In the field of molecular phylogenetics , the distances and relationships between species are investigated by looking at the DNA, RNA or amino acid sequences of an organism. When phylogenetic trees are constructed without considering possible saturation, the possibility of multiple substitutions can cause the distance between taxa to appear much smaller than the true distance. Multiple sequence alignment , a common technique to construct phylogenies, relies on the comparison of homologous sequences. It can easily be confounded by genetic saturation because the homologous loci under investigation show no indication whether or not more than one substitution on each nucleotide separates the taxa being described. [ 1 ] Substitution decreases the amount of phylogenetic information that can be contained in sequences, especially when deep branches are involved. This is particularly evident in studies examining arthropod groups. [ 8 ] Furthermore, saturation effects can lead to a gross underestimation of divergence time. This is mainly attributed to the randomization of the phylogenetic signal with the number of observed sequence mutations and substitutions. The effects of saturation can mask the true amount of divergence time leading to inaccurate phylogenetic trees. [ 1 ] [ 2 ]
Parsimony plays a fundamental role in genetic saturation analysis. This principle gives preference to the simplest explanation that can explain the data. In regards to genetic saturation, parsimony means that the hypothesized relationship is one that has the smallest number of character changes. Using parsimony to analyze genetic saturation can lead to conflict when creating a phylogenetic tree. [ 7 ] When only sequence data is used, it is possible to come up with numerous phylogenetic trees with the same amount of parsimony.
Genetic saturation contributes to long-branch attraction in its ability to greatly mix up genetic code without easily observable associated phenotypic changes. Long branch attraction occurs when two relatively outgrouped taxa are seemingly closely linked. [ 1 ] The more substitution mutations, the more likely it is for previously dissimilar sequences to share nucleotides and as a result, show homology in phylogenetic tree calculations. Long-branch attraction due to saturation has been proposed to be the cause of links in ancient phylogenies and puts into question even some of the earliest relationships between eukaryotes , archaea , and eubacteria . [ 2 ]
Gene site saturation mutagenesis (GSSM) is mutagenesis technique of one or more codons in a gene to create a library of variants covering all other codons at that position. [ 9 ] It is used in biochemistry and protein engineering to explore the functions and characteristics of specific amino acid sequences. [ 9 ] This systemic identification of amino acid substitutions allows researchers to look at every possible variant of each position. This will provide crucial structural information about the protein of interest and will identify amino acid sequences that are more vital to the function of the protein. [ 9 ] [ 10 ]
Researchers often lean towards using a one-step PCR-based to explore the specific effects of different variations in an amino acid of interest within a protein with GSSM. [ 11 ] With a one-step PCR-based approached, researchers create a primer that has a corresponding sequence to the protein of interest at its two ends. Only one codon of a three codon amino acid sequence is substituted. [ 10 ]
The type of codon set, will determine the number of sequences that can be derived from GSSM. To determine which codon set to use, researchers will need to check the library quality on the DNA level, which means that massive sequence data is needed. If all 3 positions can be substituted for each of the four different nucleotides, researchers can code for all 20 amino acids. [ 10 ] Although it’s possible to code for all 20 amino acids, this is not the most efficient method. The most efficient method is to use an NNK codon degeneracy, also known as a limited codon set. [ 12 ] This method, will result in only 32 codons rather than 64. [ 10 ]
In comparison to other techniques, GSSM is able to offer unique advantages such as:
GSSM was able to open up a whole frontier in genetic research, as it revolutionized fundamental beliefs about DNA. Before GSSM, researchers mutated DNA through radiation or with various chemicals. Both of these methods are imprecise. [ 13 ] | https://en.wikipedia.org/wiki/Genetic_saturation |
A genetic screen or mutagenesis screen is an experimental technique used to identify and select individuals who possess a phenotype of interest in a mutagenized population. [ 1 ] Hence a genetic screen is a type of phenotypic screen . Genetic screens can provide important information on gene function as well as the molecular events that underlie a biological process or pathway. While genome projects have identified an extensive inventory of genes in many different organisms, genetic screens can provide valuable insight as to how those genes function. [ 2 ] [ 3 ] [ 4 ] [ 5 ] [ 6 ]
Forward genetics (or a forward genetic screen) starts with a phenotype and then attempts to identify the causative mutation and thus gene(s) responsible for the phenotype. For instance, the famous screen by Christiane Nüsslein-Volhard and Eric Wieschaus mutagenized fruit flies and then set out to find the genes causing the observed mutant phenotypes. [ 7 ]
Successful forward genetic screens often require a defined genetic background and a simple experimental procedure. That is, when multiple individuals are mutagenized they should be genetically identical so that their wild-type phenotype is identical too and mutant phenotypes are easier to identify. A simple screening method allows for a larger number of individuals to be screened, thereby increasing the probability of generating and identifying mutants of interest. [ 3 ]
Since natural allelic mutations are rare prior to screening geneticists often mutagenize a population of individuals by exposing them to a known mutagen , such as a chemical or radiation, thereby generating a much higher frequency of chromosomal mutations . [ 1 ] In some organisms mutagens are used to perform saturation screens , that is, a screen used to uncover all genes involved in a particular phenotype. Christiane Nüsslein-Volhard and Eric Wieschaus were the first individuals to perform this type of screening procedure in animals. [ 8 ]
Reverse genetics (or a reverse genetic screen), starts with a known gene and assays the effect of its disruption by analyzing the resultant phenotypes. For example, in a knock-out screen, one or more genes are completely deleted and the deletion mutants are tested for phenotypes. Such screens have been done for all genes in many bacteria and even complex organisms, such as C. elegans . [ 1 ] A reverse genetic screen typically begins with a gene sequence followed by targeted inactivation. [ 9 ] Moreover, it induces mutations in model organisms to learn their role in disease. [ 10 ] Reverse genetics is also used to provide extremely accurate statistics on mutations that occur in specific genes. From these screens you are able to determine how fortuitous the mutations are, and how often the mutations occur. [ 11 ]
Many screening variations have been devised to elucidate a gene that leads to a mutant phenotype of interest.
An enhancer screen begins with a mutant individual that has an affected process of interest with a known gene mutation. The screen can then be used to identify additional genes or gene mutations that play a role in that biological or physiological process. A genetic enhancer screen identifies mutations that enhance a phenotype of interest in an already mutant individual. The phenotype of the double mutant (individual with both the enhancer and original background mutation) is more prominent than either of the single mutant phenotypes. The enhancement must surpass the expected phenotypes of the two mutations on their own, and therefore each mutation may be considered an enhancer of the other. Isolating enhancer mutants can lead to the identification of interacting genes or genes which act redundantly with respect to one another. [ 12 ]
A suppressor screen is used to identify suppressor mutations that alleviate or revert the phenotype of the original mutation, in a process defined as synthetic viability . [ 13 ] Suppressor mutations can be described as second mutations at a site on the chromosome distinct from the mutation under study, which suppress the phenotype of the original mutation. [ 14 ] If the mutation is in the same gene as the original mutation it is known as intragenic suppression , whereas a mutation located in a different gene is known as extragenic suppression or intergenic suppression . [ 1 ] Suppressor mutations are extremely useful to define the functions of biochemical pathways within a cell and the relationships between different biochemical pathways.
A temperature-sensitive screen involves performing temperature shifts to enhance a mutant phenotype. A population grown at low temperatures would have a normal phenotype; however, the mutation in the particular gene would make it unstable at a higher temperature. A screen for temperature sensitivity in fruit flies, for example, might involve raising the temperature in the cage until some flies faint, then opening a portal to let the others escape. Individuals selected in a screen are liable to carry an unusual version of a gene involved in the phenotype of interest. An advantage of alleles found in this type of screen is that the mutant phenotype is conditional and can be activated by simply raising the temperature. A null mutation in such a gene may be lethal to the embryo and such mutants would be missed in a basic screen. A famous temperature-sensitive screen was carried out independently by Lee Hartwell and Paul Nurse to identify mutants defective in the cell cycle in S. cerevisiae and S. pombe , respectively.
RNA interference (RNAi) screen is essentially a forward genetics screen using a reverse genetics technique. Similar to classical genetic screens in the past, large-scale RNAi surveys success depends on a careful development of phenotypic assays and their interpretation. [ 9 ] In Drosophila , RNAi has been applied in cultured cells or in vivo to investigate gene functions and to effect the function of single genes on a genome-wide scale. RNAi is used to silence gene expression in Drosophila by injecting dsRNA into early embryos, and interfering with Frizzled and Frizzled2 genes creating defects in embryonic patterning that mimic loss of wingless function. [ 15 ]
CRISPR/Cas is primarily used for reverse genetic screens. CRISPR has the ability to create libraries of thousands of precise genetic mutations and can identify new tumors as well as validate older tumors in cancer research. Genome-scale CRISPR-Cas9 knockout (GeCKO) library targeting 18,080 genes with 64,751 unique guide sequences identify genes essential for cell viability in cancer. Bacterial CRISPR–Cas9 system for engineering both loss of function (LOF) and gain of function (GOF) mutations in untransformed human intestinal organoids in order to demonstrate a model of Colorectal cancer (CRC) . It can also be used to study functional consequences of mutations in vivo by enabling direct genome editing in somatic cells. [ 10 ]
By the classical genetics approach, a researcher would then locate (map) the gene on its chromosome by crossbreeding with individuals that carry other unusual traits and collecting statistics on how frequently the two traits are inherited together. Classical geneticists would have used phenotypic traits to map the new mutant alleles . With the advent of genomic sequences for model systems such as Drosophila melanogaster , Arabidopsis thaliana and C. elegans many single nucleotide polymorphisms (SNPs) have now been identified that can be used as traits for mapping. In fact, the Heidelberg screen , allowing mass testing of mutants and developed in 1980 by Nüsslein-Volhard and Wieschaus , cleared the way for future scientists in this field. [ 4 ] SNPs are the preferred traits for mapping since they are very frequent, on the order of one difference per 1000 base pairs, between different varieties of organism. Mutagens such as random DNA insertions by transformation or active transposons can also be used to generate new mutants. These techniques have the advantage of tagging the new alleles with a known molecular (DNA) marker that can facilitate the rapid identification of the gene. [ 8 ]
Positional cloning is a method of gene identification in which a gene for a specific phenotype is identified only by its approximate chromosomal location (but not the function); this is known as the candidate region . Initially, the candidate region can be defined using techniques such as linkage analysis , and positional cloning is then used to narrow the candidate region until the gene and its mutations are found. Positional cloning typically involves the isolation of partially overlapping DNA segments from genomic libraries to progress along the chromosome toward a specific gene. During the course of positional cloning, one needs to determine whether the DNA segment currently under consideration is part of the gene.
Tests used for this purpose include cross-species hybridization, identification of unmethylated CpG islands , exon trapping , direct cDNA selection, computer analysis of DNA sequence, mutation screening in affected individuals, and tests of gene expression. For genomes in which the regions of genetic polymorphisms are known, positional cloning involves identifying polymorphisms that flank the mutation. This process requires that DNA fragments from the closest known genetic marker are progressively cloned and sequenced, getting closer to the mutant allele with each new clone. This process produces a contig map of the locus and is known as chromosome walking . With the completion of genome sequencing projects such as the Human Genome Project , modern positional cloning can use ready-made contigs from the genome sequence databases directly.
For each new DNA clone a polymorphism is identified and tested in the mapping population for its recombination frequency compared to the mutant phenotype. When the DNA clone is at or close to the mutant allele, the recombination frequency should be close to zero. If the chromosome walk proceeds through the mutant allele, the new polymorphisms will start to show increase in recombination frequency compared to the mutant phenotype. Depending on the size of the mapping population, the mutant allele can be narrowed down to a small region (<30 Kb). Sequence comparison between wild type and mutant DNA in that region is then required to locate the DNA mutation that causes the phenotypic difference.
Modern positional cloning can more directly extract information from genomic sequencing projects and existing data by analyzing the genes in the candidate region. Potential disease genes from the candidate region can then be prioritized, potentially reducing the amount of work involved. Genes with expression patterns consistent with the disease phenotype, showing a (putative) function related to the phenotype, or homologous to another gene linked to the phenotype are all priority candidates. Generalization of positional cloning techniques in this manner is also known as positional gene discovery.
Positional cloning is an effective method to isolate disease genes in an unbiased manner and has been used to identify disease genes for Duchenne muscular dystrophy , Huntington's disease , and cystic fibrosis . However, complications in the analysis arise if the disease exhibits locus heterogeneity. | https://en.wikipedia.org/wiki/Genetic_screen |
Genetic significant dose ( GSD ), or genetically significant dose , was initially defined by United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) in 1958. [ 1 ]
It represents an estimate of the genetic significance of gonad radiation doses. Annual GSD is calculated by weighting the individual gonad doses received during ionizing imaging by the number of individual examined, and accounting for the number of offspring for each individual.
This article related to medical imaging is a stub . You can help Wikipedia by expanding it .
This radioactivity –related article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genetic_significant_dose |
Genetic structure refers to any pattern in the genetic makeup of individuals within a population. [ 1 ]
Genetic structure allows for information about an individual to be inferred from other members of the same population. In trivial terms, all populations have genetic structure, because all populations can be characterized by their genotype or allele frequencies: if only 1% of a large sample of moths drawn from a single population have spotted wings, then it is safe to assume that any unknown individual is unlikely to have spotted wings.
A more complicated example arises in dense thickets of plants, where plants tend to be pollinated by near neighbours, and seeds tend to fall and germinate near the maternal plant. In such a scenario, plants tend to be more closely related to nearby plants than they are to distant plants; and yet they are more likely to breed with nearby plants than they are with distant plants. Thus an inbreeding cycle is created that perpetuates the pattern of plants being closely related to near neighbors. This is a form of genetic structure because one can infer much about the genetic makeup of any individual plant simply by studying plants in their immediate neighborhoods.
This genetics article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genetic_structure |
Genetic testing , also known as DNA testing , is used to identify changes in DNA sequence or chromosome structure. Genetic testing can also include measuring the results of genetic changes, such as RNA analysis as an output of gene expression , or through biochemical analysis to measure specific protein output. [ 1 ] In a medical setting, genetic testing can be used to diagnose or rule out suspected genetic disorders , predict risks for specific conditions, or gain information that can be used to customize medical treatments based on an individual's genetic makeup. [ 1 ] Genetic testing can also be used to determine biological relatives, such as a child's biological parentage (genetic mother and father) through DNA paternity testing , [ 2 ] or be used to broadly predict an individual's ancestry . [ 3 ] Genetic testing of plants and animals can be used for similar reasons as in humans (e.g. to assess relatedness/ancestry or predict/diagnose genetic disorders), [ 4 ] to gain information used for selective breeding , [ 5 ] or for efforts to boost genetic diversity in endangered populations. [ 6 ]
The variety of genetic tests has expanded throughout the years. Early forms of genetic testing which began in the 1950s involved counting the number of chromosomes per cell. Deviations from the expected number of chromosomes (46 in humans) could lead to a diagnosis of certain genetic conditions such as trisomy 21 ( Down syndrome ) or monosomy X ( Turner syndrome ). [ 7 ] In the 1970s, a method to stain specific regions of chromosomes, called chromosome banding , was developed that allowed more detailed analysis of chromosome structure and diagnosis of genetic disorders that involved large structural rearrangements. [ 8 ] In addition to analyzing whole chromosomes ( cytogenetics ), genetic testing has expanded to include the fields of molecular genetics and genomics which can identify changes at the level of individual genes, parts of genes, or even single nucleotide "letters" of DNA sequence. [ 7 ] According to the National Institutes of Health , there are tests available for more than 2,000 genetic conditions, [ 9 ] and one study estimated that as of 2018 there were more than 68,000 genetic tests on the market. [ 10 ]
Genetic testing is "the analysis of chromosomes ( DNA ), proteins, and certain metabolites in order to detect heritable disease-related genotypes , mutations , phenotypes , or karyotypes for clinical purposes." [ 11 ] It can provide information about a person 's genes and chromosomes throughout life.
Genetic testing is often done as part of a genetic consultation and as of mid-2008 there were more than 1,200 clinically applicable genetic tests available. [ 23 ] Once a person decides to proceed with genetic testing, a medical geneticist, genetic counselor, primary care doctor, or specialist can order the test after obtaining informed consent . [ citation needed ]
Genetic tests are performed on a sample of blood , hair , skin , amniotic fluid (the fluid that surrounds a fetus during pregnancy), or other tissue. For example, a medical procedure called a buccal smear uses a small brush or cotton swab to collect a sample of cells from the inside surface of the cheek. Alternatively, a small amount of saline mouthwash may be swished in the mouth to collect the cells. The sample is sent to a laboratory where technicians look for specific changes in chromosomes, DNA, or proteins, depending on the suspected disorders, often using DNA sequencing . The laboratory reports the test results in writing to a person's doctor or genetic counselor. [ citation needed ]
Routine newborn screening tests are done on a small blood sample obtained by pricking the baby's heel with a lancet .
The physical risks associated with most genetic tests are very small, particularly for those tests that require only a blood sample or buccal smear (a procedure that samples cells from the inside surface of the cheek). The procedures used for prenatal testing carry a small but non-negligible risk of losing the pregnancy (miscarriage) because they require a sample of amniotic fluid or tissue from around the fetus. [ 24 ]
Many of the risks associated with genetic testing involve the emotional, social, or financial consequences of the test results. People may feel angry, depressed, anxious, or guilty about their results. The potential negative impact of genetic testing has led to an increasing recognition of a "right not to know". [ 25 ] In some cases, genetic testing creates tension within a family because the results can reveal information about other family members in addition to the person who is tested. [ 26 ] The possibility of genetic discrimination in employment or insurance is also a concern. Some individuals avoid genetic testing out of fear it will affect their ability to purchase insurance or find a job. [ 27 ] Health insurers do not currently require applicants for coverage to undergo genetic testing, and when insurers encounter genetic information, it is subject to the same confidentiality protections as any other sensitive health information. [ 28 ] In the United States, the use of genetic information is governed by the Genetic Information Nondiscrimination Act (GINA) (see discussion below in the section on government regulation).
Genetic testing can provide only limited information about an inherited condition. The test often can't determine if a person will show symptoms of a disorder, how severe the symptoms will be, or whether the disorder will progress over time. Another major limitation is the lack of treatment strategies for many genetic disorders once they are diagnosed. [ 24 ]
Another limitation to genetic testing for a hereditary linked cancer, is the variants of unknown clinical significance. Because the human genome has over 22,000 genes, there are 3.5 million variants in the average person's genome. These variants of unknown clinical significance means there is a change in the DNA sequence, however the increase for cancer is unclear because it is unknown if the change affects the gene's function. [ 29 ]
A genetics professional can explain in detail the benefits, risks, and limitations of a particular test. It is important that any person who is considering genetic testing understand and weigh these factors before making a decision. [ 24 ]
Other risks include incidental findings —a discovery of some possible problem found while looking for something else. [ 30 ] In 2013 the American College of Medical Genetics and Genomics (ACMG) recommended that certain genes always be included any time a genomic sequencing was done, and that labs should report the results. [ 31 ]
DNA studies have been criticised for a range of methodological problems and providing misleading, interpretations on racial classifications. [ 32 ] [ 33 ] [ 34 ] [ 35 ] [ 36 ]
Direct-to-consumer (DTC) genetic testing (also called at-home genetic testing) is a type of genetic test that is accessible directly to the consumer without having to go through a health care professional. Usually, to obtain a genetic test, health care professionals such as physicians, nurse practitioners, or genetic counselors acquire their patient's permission and then order the desired test, which may or may not be covered by health insurance. DTC genetic tests, however, allow consumers to bypass this process and purchase DNA tests themselves. DTC genetic testing can entail primarily genealogical/ancestry-related information, health and trait-related information, or both. [ 37 ] Genetic testing has been taken on by private companies, such as 23andMe , Ancestry.com , and Family Tree DNA . These companies will send the consumer a kit at their home address, with which they will provide a saliva sample for their lab to analyze. The company will then send back the consumer's results in a few weeks, which is a breakdown of their ancestral heritage and possible health risks that accompany it. [ 38 ]
There are a variety of DTC genetic tests, ranging from tests for breast cancer alleles to mutations linked to cystic fibrosis . Possible benefits of DTC genetic testing are the accessibility of tests to consumers, promotion of proactive healthcare, and the privacy of genetic information . Possible additional risks of DTC genetic testing are the lack of governmental regulation, the potential misinterpretation of genetic information, issues related to testing minors, privacy of data , and downstream expenses for the public health care system. [ 39 ] In the United States, most DTC genetic test kits are not reviewed by the Food and Drug Administration (FDA) , with the exception of a few tests offered by the company 23andMe . [ 40 ] As of 2019, the tests that have received marketing authorization by the FDA include 23andMe's genetic health risk reports for select variants of BRCA1/BRCA2 , [ 41 ] pharmacogenetic reports that test for selected variants associated with metabolism of certain pharmaceutical compounds, a carrier screening test for Bloom syndrome , and genetic health risk reports for a handful of other medical conditions, such as celiac disease and late-onset Alzheimer's . [ 40 ]
DTC genetic testing has been controversial due to outspoken opposition within the medical community. Critics of DTC genetic testing argue against the risks involved in several steps of the testing process, such as the unregulated advertising and marketing claims , the potential reselling of genetic data to third parties, and the overall lack of governmental oversight. [ 42 ] [ 43 ] [ 44 ] [ 45 ]
DTC genetic testing involves many of the same risks associated with any genetic test. One of the more obvious and dangerous of these is the possibility of misreading of test results. Without professional guidance, consumers can potentially misinterpret genetic information, causing them to be deluded about their personal health.
Some advertising for DTC genetic testing has been criticized as conveying an exaggerated and inaccurate message about the connection between genetic information and disease risk, utilizing emotions as a selling factor. An advertisement for a BRCA -predictive genetic test for breast cancer stated: "There is no stronger antidote for fear than information." [ 46 ] Apart from rare diseases that are directly caused by specific, single-gene mutation, diseases "have complicated, multiple genetic links that interact strongly with personal environment, lifestyle, and behavior." [ 47 ]
Ancestry.com , a company providing DTC DNA tests for genealogy purposes, has reportedly allowed the warrantless search of their database by police investigating a murder. [ 48 ] The warrantless search led to a search warrant to force the gathering of a DNA sample from a New Orleans filmmaker; however he turned out not to be a match for the suspected killer. [ 49 ]
As part of its healthcare system, Estonia is offering all of its residents genome-wide genotyping. This will be translated into personalized reports for use in everyday medical practice via the national e-health portal. [ 50 ]
The aim is to minimise health problems by warning participants most at risk of conditions such as cardiovascular disease and diabetes. It is also hoped that participants who are given early warnings will adopt healthier lifestyles or take preventative drugs . [ 51 ]
In 2005, National Geographic launched the "Genographic Project", which was a fifteen-year project that was discontinued in 2020. Over one million people participated in the DNA sampling from more than 140 countries, which made the project the largest of its kind ever conducted. [ 52 ] The project asked for DNA samples from indigenous people as well as the general public, which spurred political controversy among some indigenous groups, leading to the coining of the term "biocolonialism". [ 53 ]
With regard to genetic testing and information in general, legislation in the United States called the Genetic Information Nondiscrimination Act prohibits group health plans and health insurers from denying coverage to a healthy person or charging that person higher premiums based solely on a genetic predisposition to developing a disease in the future. The legislation also bars employers from using genetic information when making hiring , firing , job placement, or promotion decisions. [ 54 ] Although GINA protects against genetic discrimination, Section 210 of the law states that once the disease has manifested, employers can use the medical information and not be in violation of the law, even if the condition has a genetic basis. [ 55 ] The legislation, the first of its kind in the United States, [ 56 ] was passed by the United States Senate on April 24, 2008, on a vote of 95–0, and was signed into law by President George W. Bush on May 21, 2008. [ 57 ] [ 58 ] It went into effect on November 21, 2009.
In June 2013 the US Supreme Court issued two rulings on human genetics. The Court struck down patents on human genes, opening up competition in the field of genetic testing. [ 59 ] The Supreme Court also ruled that police were allowed to collect DNA from people arrested for serious offenses. [ 60 ]
Effective as of 25 May 2018, companies that process genetic data must abide by the General Data Protection Regulation (GDPR). [ 61 ] [ 62 ] The GDPR is a set of rules/regulations that helps an individual take control of their data that is collected, used, and stored digitally or in a structured filing system on paper, and restricts a company's use of personal data. [ 62 ] The regulation also applies to companies that offer products/services outside the EU. [ 62 ]
Genetic testing in Germany is governed by the Genetic Diagnostics Act (GenDG), [ 63 ] which mandates that health-related genetic tests can only be carried out under medical supervision to ensure the proper interpretation of results and informed decision-making. The law emphasizes genetic counseling and informed consent, protecting individuals from potential misuse or misunderstanding of their genetic data.
The legal status of genetic testing in France is regulated under strict privacy and data protection laws, including the Bioethics Law. [ 64 ] Direct-to-consumer (DTC) genetic tests, especially those for health-related purposes, are prohibited unless conducted with medical oversight to ensure informed consent and appropriate counseling. [ 65 ] This is due to concerns about the potential misuse of genetic data and privacy violations. While health-related genetic testing is allowed within a medical context, tests for non-medical purposes, such as ancestry or personal traits, also face legal restrictions, particularly regarding consumer access.
Russian law [ 66 ] provides that the processing of special categories of personal data relating to race, nationality, political views, religious or philosophical beliefs, health status, intimate life is allowed if it is necessary in connection with the implementation of international agreements of the Russian Federation on readmission and is carried out in accordance with the legislation of the Russian Federation on citizenship of the Russian Federation. Information characterizing the physiological and biological characteristics of a person, on the basis of which it is possible to establish his identity (biometric personal data), can be processed without the consent of the subject of personal data in connection with the implementation of international agreements of the Russian Federation on readmission, administration of justice and execution of judicial acts, compulsory state fingerprinting registration, as well as in cases stipulated by the legislation of the Russian Federation on defense, security, anti-terrorism, transport security, anti-corruption, operational investigative activities, public service, as well as in cases stipulated by the criminal-executive legislation of Russia, the legislation of Russia on the procedure for leaving the Russian Federation and entering the Russian Federation, citizenship of the Russian Federation and notaries.
Within the framework of this program, it is also planned to include the peoples of neighboring countries, which are the main source of migration, into the genogeographic study on the basis of existing collections. [ 67 ]
By the end of 2021, the UAE Genome Project will be in full swing, as part of the National Innovation Strategy, establishing strategic partnerships with top medical research centers, and making sustainable investments in healthcare services. The project aims to prevent genetic diseases through the use of genetic sciences and innovative modern techniques related to profiling and genetic sequencing, in order to identify the genetic footprint and prevent the most prevalent diseases in the country, such as obesity, diabetes, hypertension, cancer, and asthma. It aims to achieve personalized treatment for each patient based on genetic factors. Additionally, a study by Khalifa University has identified, for the first time, four genetic markers associated with type 2 diabetes among UAE citizens. [ 68 ]
The Israeli Knesset passed the Genetic Information Law in 2000, becoming one of the first countries to establish a regulatory framework for the conducting of genetic testing and genetic counseling and for the handling and use identified genetic information. Under the law, genetic tests must be done in labs accredited by the Ministry of Health ; however, genetic tests may be conducted outside Israel. The law also forbids discrimination for employment or insurance purposes based on genetic test results. Finally, the law takes a strict approach to genetic testing on minors, which is permitted only for the purpose of finding a genetic match with someone ill for the sake of medical treatment, or to see whether the minor carries a gene related to an illness that can be prevented or postponed. [ 69 ] [ 70 ]
Under the Genetic Information Law as of 2019, commercial DNA tests are not permitted to be sold directly to the public, but can be obtained with a court order, due to data privacy, reliability, and misinterpretation concerns. [ 71 ]
Three to five percent of the funding available for the Human Genome Project was set aside to study the many social, ethical, and legal implications that will result from the better understanding of human heredity the rapid expansion of genetic risk assessment by genetic testing which would be facilitated by this project. [ 72 ]
The American Academy of Pediatrics (AAP) and the American College of Medical Genetics (ACMG) have provided new guidelines for the ethical issue of pediatric genetic testing and screening of children in the United States. [ 73 ] [ 74 ] Their guidelines state that performing pediatric genetic testing should be in the best interest of the child. AAP and ACMG recommend holding off on genetic testing for late-onset conditions until adulthood, unless diagnosing genetic disorders during childhood can reduce morbidity or mortality (e.g., to start early intervention). Testing asymptomatic children who are at risk of childhood onset conditions can also be warranted.
Both AAP and ACMG discourage the use of direct-to-consumer and home kit genetic tests because of concerns regarding the accuracy, interpretation and oversight of test content.
Guidelines also state that parents or guardians should be encouraged to inform their child of the results from the genetic test if the minor is of appropriate age. For ethical and legal reasons, health care providers should be cautious in providing minors with predictive genetic testing without the involvement of parents or guardians. Within the guidelines set by AAP and ACMG, health care providers have an obligation to inform parents or guardians on the implication of test results.
AAP and ACMG state that any type of predictive genetic testing should be offered with genetic counseling by clinical genetics , genetic counselors or health care providers. [ 74 ]
In Israel, DNA testing is used to determine if people are eligible for immigration. The policy where "many Jews from the former Soviet Union (FSU) are asked to provide DNA confirmation of their Jewish heritage in the form of paternity tests in order to immigrate as Jews and become citizens under Israel's Law of Return " has generated controversy. [ 75 ] [ 76 ] [ 77 ] [ 78 ]
From the date that a sample is taken, results may take weeks to months, depending upon the complexity and extent of the tests being performed. Results for prenatal testing are usually available more quickly because time is an important consideration in making decisions about a pregnancy. Prior to the testing, the doctor or genetic counselor who is requesting a particular test can provide specific information about the cost and time frame associated with that test. [ 79 ]
This article incorporates public domain material from What are the risks and limitations of genetic testing? . United States Department of Health and Human Services . This article incorporates public domain material from What is the cost of genetic testing, and how long does it take to get the results? . United States Department of Health and Human Services . | https://en.wikipedia.org/wiki/Genetic_testing |
In molecular biology and genetics , transformation is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane (s). For transformation to take place, the recipient bacterium must be in a state of competence , which might occur in nature as a time-limited response to environmental conditions such as starvation and cell density, and may also be induced in a laboratory. [ 1 ]
Transformation is one of three processes that lead to horizontal gene transfer , in which exogenous genetic material passes from one bacterium to another, the other two being conjugation (transfer of genetic material between two bacterial cells in direct contact) and transduction (injection of foreign DNA by a bacteriophage virus into the host bacterium). [ 1 ] In transformation, the genetic material passes through the intervening medium, and uptake is completely dependent on the recipient bacterium. [ 1 ]
As of 2014 about 80 species of bacteria were known to be capable of transformation, about evenly divided between Gram-positive and Gram-negative bacteria ; the number might be an overestimate since several of the reports are supported by single papers. [ 1 ]
"Transformation" may also be used to describe the insertion of new genetic material into nonbacterial cells, including animal and plant cells; however, because " transformation " has a special meaning in relation to animal cells, indicating progression to a cancerous state, the process is usually called " transfection ". [ 2 ]
Transformation in bacteria was first demonstrated in 1928 by the British bacteriologist Frederick Griffith . [ 3 ] Griffith was interested in determining whether injections of heat-killed bacteria could be used to vaccinate mice against pneumonia. However, he discovered that a non-virulent strain of Streptococcus pneumoniae could be made virulent after being exposed to heat-killed virulent strains. Griffith hypothesized that some " transforming principle " from the heat-killed strain was responsible for making the harmless strain virulent. In 1944 this "transforming principle" was identified as being genetic by Oswald Avery , Colin MacLeod , and Maclyn McCarty . They isolated DNA from a virulent strain of S. pneumoniae and using just this DNA were able to make a harmless strain virulent. They called this uptake and incorporation of DNA by bacteria "transformation" (See Avery-MacLeod-McCarty experiment ) [ 4 ] The results of Avery et al.'s experiments were at first skeptically received by the scientific community and it was not until the development of genetic markers and the discovery of other methods of genetic transfer ( conjugation in 1947 and transduction in 1953) by Joshua Lederberg that Avery's experiments were accepted. [ 5 ]
It was originally thought that Escherichia coli , a commonly used laboratory organism, was refractory to transformation. However, in 1970, Morton Mandel and Akiko Higa showed that E. coli may be induced to take up DNA from bacteriophage λ without the use of helper phage after treatment with calcium chloride solution. [ 6 ] Two years later in 1972, Stanley Norman Cohen , Annie Chang and Leslie Hsu showed that CaCl 2 treatment is also effective for transformation of plasmid DNA. [ 7 ] The method of transformation by Mandel and Higa was later improved upon by Douglas Hanahan . [ 8 ] The discovery of artificially induced competence in E. coli created an efficient and convenient procedure for transforming bacteria which allows for simpler molecular cloning methods in biotechnology and research , and it is now a routinely used laboratory procedure.
Transformation using electroporation was developed in the late 1980s, increasing the efficiency of in-vitro transformation and increasing the number of bacterial strains that could be transformed. [ 9 ] Transformation of animal and plant cells was also investigated with the first transgenic mouse being created by injecting a gene for a rat growth hormone into a mouse embryo in 1982. [ 10 ] In 1897 a bacterium that caused plant tumors, Agrobacterium tumefaciens , was discovered and in the early 1970s the tumor-inducing agent was found to be a DNA plasmid called the Ti plasmid . [ 11 ] By removing the genes in the plasmid that caused the tumor and adding in novel genes, researchers were able to infect plants with A. tumefaciens and let the bacteria insert their chosen DNA into the genomes of the plants. [ 12 ] Not all plant cells are susceptible to infection by A. tumefaciens , so other methods were developed, including electroporation and micro-injection . [ 13 ] Particle bombardment was made possible with the invention of the Biolistic Particle Delivery System (gene gun) by John Sanford in the 1980s. [ 14 ] [ 15 ] [ 16 ]
Transformation is one of three forms of horizontal gene transfer that occur in nature among bacteria, in which DNA encoding for a trait passes from one bacterium to another and is integrated into the recipient genome by homologous recombination ; the other two are transduction , carried out by means of a bacteriophage , and conjugation , in which a gene is passed through direct contact between bacteria. [ 1 ] In transformation, the genetic material passes through the intervening medium, and uptake is completely dependent on the recipient bacterium. [ 1 ]
Competence refers to a temporary state of being able to take up exogenous DNA from the environment; it may be induced in a laboratory. [ 1 ]
It appears to be an ancient process inherited from a common prokaryotic ancestor that is a beneficial adaptation for promoting recombinational repair of DNA damage, especially damage acquired under stressful conditions. Natural genetic transformation appears to be an adaptation for repair of DNA damage that also generates genetic diversity . [ 1 ] [ 17 ]
Transformation has been studied in medically important Gram-negative bacteria species such as Helicobacter pylori , Legionella pneumophila , Neisseria meningitidis , Neisseria gonorrhoeae , Haemophilus influenzae and Vibrio cholerae . [ 18 ] It has also been studied in Gram-negative species found in soil such as Pseudomonas stutzeri , Acinetobacter baylyi , and Gram-negative plant pathogens such as Ralstonia solanacearum and Xylella fastidiosa . [ 18 ] Transformation among Gram-positive bacteria has been studied in medically important species such as Streptococcus pneumoniae , Streptococcus mutans , Staphylococcus aureus and Streptococcus sanguinis and in Gram-positive soil bacterium Bacillus subtilis . [ 17 ] It has also been reported in at least 30 species of Pseudomonadota distributed in several different classes. [ 19 ] The best studied Pseudomonadota with respect to transformation are the medically important human pathogens Neisseria gonorrhoeae , Haemophilus influenzae , and Helicobacter pylori . [ 17 ]
"Transformation" may also be used to describe the insertion of new genetic material into nonbacterial cells, including animal and plant cells; however, because " transformation " has a special meaning in relation to animal cells, indicating progression to a cancerous state, the process is usually called " transfection ". [ 2 ]
Naturally competent bacteria carry sets of genes that provide the protein machinery to bring DNA across the cell membrane(s). The transport of the exogenous DNA into the cells may require proteins that are involved in the assembly of type IV pili and type II secretion system , as well as DNA translocase complex at the cytoplasmic membrane. [ 20 ]
Due to the differences in structure of the cell envelope between Gram-positive and Gram-negative bacteria, there are some differences in the mechanisms of DNA uptake in these cells, however most of them share common features that involve related proteins. The DNA first binds to the surface of the competent cells on a DNA receptor, and passes through the cytoplasmic membrane via DNA translocase. [ 21 ] Only single-stranded DNA may pass through, the other strand being degraded by nucleases in the process. The translocated single-stranded DNA may then be integrated into the bacterial chromosomes by a RecA -dependent process. In Gram-negative cells, due to the presence of an extra membrane, the DNA requires the presence of a channel formed by secretins on the outer membrane. Pilin may be required for competence, but its role is uncertain. [ 22 ] The uptake of DNA is generally non-sequence specific, although in some species the presence of specific DNA uptake sequences may facilitate efficient DNA uptake. [ 23 ]
Natural transformation is a bacterial adaptation for DNA transfer that depends on the expression of numerous bacterial genes whose products appear to be responsible for this process. [ 20 ] [ 19 ] In general, transformation is a complex, energy-requiring developmental process. In order for a bacterium to bind, take up and recombine exogenous DNA into its chromosome, it must become competent, that is, enter a special physiological state. Competence development in Bacillus subtilis requires expression of about 40 genes. [ 24 ] The DNA integrated into the host chromosome is usually (but with rare exceptions) derived from another bacterium of the same species, and is thus homologous to the resident chromosome.
In B. subtilis the length of the transferred DNA is greater than 1271 kb (more than 1 million bases). [ 25 ] The length transferred is likely double stranded DNA and is often more than a third of the total chromosome length of 4215 kb. [ 26 ] It appears that about 7-9% of the recipient cells take up an entire chromosome. [ 27 ]
The capacity for natural transformation appears to occur in a number of prokaryotes, and thus far 67 prokaryotic species (in seven different phyla) are known to undergo this process. [ 19 ]
Competence for transformation is typically induced by high cell density and/or nutritional limitation, conditions associated with the stationary phase of bacterial growth. Transformation in Haemophilus influenzae occurs most efficiently at the end of exponential growth as bacterial growth approaches stationary phase. [ 28 ] Transformation in Streptococcus mutans , as well as in many other streptococci, occurs at high cell density and is associated with biofilm formation. [ 29 ] Competence in B. subtilis is induced toward the end of logarithmic growth, especially under conditions of amino acid limitation. [ 30 ] Similarly, in Micrococcus luteus (a representative of the less well studied Actinomycetota phylum), competence develops during the mid-late exponential growth phase and is also triggered by amino acids starvation. [ 31 ] [ 32 ]
By releasing intact host and plasmid DNA, certain bacteriophages are thought to contribute to transformation. [ 33 ]
Competence is specifically induced by DNA damaging conditions. For instance, transformation is induced in Streptococcus pneumoniae by the DNA damaging agents mitomycin C (a DNA cross-linking agent) and fluoroquinolone (a topoisomerase inhibitor that causes double-strand breaks). [ 34 ] In B. subtilis , transformation is increased by UV light, a DNA damaging agent. [ 35 ] In Helicobacter pylori , ciprofloxacin, which interacts with DNA gyrase and introduces double-strand breaks, induces expression of competence genes, thus enhancing the frequency of transformation [ 36 ] Using Legionella pneumophila , Charpentier et al. [ 37 ] tested 64 toxic molecules to determine which of these induce competence. Of these, only six, all DNA damaging agents, caused strong induction. These DNA damaging agents were mitomycin C (which causes DNA inter-strand crosslinks), norfloxacin, ofloxacin and nalidixic acid (inhibitors of DNA gyrase that cause double-strand breaks [ 38 ] ), bicyclomycin (causes single- and double-strand breaks [ 39 ] ), and hydroxyurea (induces DNA base oxidation [ 40 ] ). UV light also induced competence in L. pneumophila . Charpentier et al. [ 37 ] suggested that competence for transformation probably evolved as a DNA damage response. Natural transformation in the extraordinarily radiation resistant bacterium Deinococcus radiodurans is associated with the repair of DNA damage under stressful conditions. [ 41 ]
Logarithmically growing bacteria differ from stationary phase bacteria with respect to the number of genome copies present in the cell, and this has implications for the capability to carry out an important DNA repair process. During logarithmic growth, two or more copies of any particular region of the chromosome may be present in a bacterial cell, as cell division is not precisely matched with chromosome replication. The process of homologous recombinational repair (HRR) is a key DNA repair process that is especially effective for repairing double-strand damages, such as double-strand breaks. This process depends on a second homologous chromosome in addition to the damaged chromosome. During logarithmic growth, a DNA damage in one chromosome may be repaired by HRR using sequence information from the other homologous chromosome. Once cells approach stationary phase, however, they typically have just one copy of the chromosome, and HRR requires input of homologous template from outside the cell by transformation. [ 42 ]
To test whether the adaptive function of transformation is repair of DNA damages, a series of experiments were carried out using B. subtilis irradiated by UV light as the damaging agent (reviewed by Michod et al. [ 43 ] and Bernstein et al. [ 42 ] ) The results of these experiments indicated that transforming DNA acts to repair potentially lethal DNA damages introduced by UV light in the recipient DNA. The particular process responsible for repair was likely HRR. Transformation in bacteria can be viewed as a primitive sexual process, since it involves interaction of homologous DNA from two individuals to form recombinant DNA that is passed on to succeeding generations. Bacterial transformation in prokaryotes may have been the ancestral process that gave rise to meiotic sexual reproduction in eukaryotes (see Evolution of sexual reproduction ; Meiosis .)
Artificial competence can be induced in laboratory procedures that involve making the cell passively permeable to DNA by exposing it to conditions that do not normally occur in nature. [ 44 ] Typically the cells are incubated in a solution containing divalent cations (often calcium chloride ) under cold conditions, before being exposed to a heat pulse (heat shock). Calcium chloride partially disrupts the cell membrane, which allows the recombinant DNA to enter the host cell. Cells that are able to take up the DNA are called competent cells.
It has been found that growth of Gram-negative bacteria in 20 mM Mg reduces the number of protein-to- lipopolysaccharide bonds by increasing the ratio of ionic to covalent bonds, which increases membrane fluidity, facilitating transformation. [ 45 ] The role of lipopolysaccharides here are verified from the observation that shorter O-side chains are more effectively transformed – perhaps because of improved DNA accessibility.
The surface of bacteria such as E. coli is negatively charged due to phospholipids and lipopolysaccharides on its cell surface, and the DNA is also negatively charged. One function of the divalent cation therefore would be to shield the charges by coordinating the phosphate groups and other negative charges, thereby allowing a DNA molecule to adhere to the cell surface.
DNA entry into E. coli cells is through channels known as zones of adhesion or Bayer's junction, with a typical cell carrying as many as 400 such zones. Their role was established when cobalamine (which also uses these channels) was found to competitively inhibit DNA uptake. Another type of channel implicated in DNA uptake consists of poly (HB):poly P:Ca. In this poly (HB) is envisioned to wrap around DNA (itself a polyphosphate), and is carried in a shield formed by Ca ions. [ 45 ]
It is suggested that exposing the cells to divalent cations in cold condition may also change or weaken the cell surface structure, making it more permeable to DNA. The heat-pulse is thought to create a thermal imbalance across the cell membrane, which forces the DNA to enter the cells through either cell pores or the damaged cell wall.
Electroporation is another method of promoting competence. In this method the cells are briefly shocked with an electric field of 10-20 kV /cm, which is thought to create holes in the cell membrane through which the plasmid DNA may enter. After the electric shock, the holes are rapidly closed by the cell's membrane-repair mechanisms.
Most species of yeast , including Saccharomyces cerevisiae , may be transformed by exogenous DNA in the environment. Several methods have been developed to facilitate this transformation at high frequency in the lab. [ 46 ]
Efficiency – Different yeast genera and species take up foreign DNA with different efficiencies. [ 54 ] Also, most transformation protocols have been developed for baker's yeast, S. cerevisiae , and thus may not be optimal for other species. Even within one species, different strains have different transformation efficiencies, sometimes different by three orders of magnitude. For instance, when S. cerevisiae strains were transformed with 10 ug of plasmid YEp13, the strain DKD-5D-H yielded between 550 and 3115 colonies while strain OS1 yielded fewer than five colonies. [ 55 ]
A number of methods are available to transfer DNA into plant cells. Some vector -mediated methods are:
Some vector-less methods include:
There are some methods to produce transgenic fungi most of them being analogous to those used for plants. However, fungi have to be treated differently due to some of their microscopic and biochemical traits:
As stated earlier, an array of methods used for plant transformation do also work in fungi:
Introduction of DNA into animal cells is usually called transfection , and is discussed in the corresponding article.
The discovery of artificially induced competence in bacteria allow bacteria such as Escherichia coli to be used as a convenient host for the manipulation of DNA as well as expressing proteins. Typically plasmids are used for transformation in E. coli . In order to be stably maintained in the cell, a plasmid DNA molecule must contain an origin of replication , which allows it to be replicated in the cell independently of the replication of the cell's own chromosome.
The efficiency with which a competent culture can take up exogenous DNA and express its genes is known as transformation efficiency and is measured in colony forming unit (cfu) per μg DNA used. A transformation efficiency of 1×10 8 cfu/μg for a small plasmid like pUC19 is roughly equivalent to 1 in 2000 molecules of the plasmid used being transformed.
In calcium chloride transformation , the cells are prepared by chilling cells in the presence of Ca 2+ (in CaCl 2 solution), making the cell become permeable to plasmid DNA . The cells are incubated on ice with the DNA, and then briefly heat-shocked (e.g., at 42 °C for 30–120 seconds). This method works very well for circular plasmid DNA. Non-commercial preparations should normally give 10 6 to 10 7 transformants per microgram of plasmid; a poor preparation will be about 10 4 /μg or less, but a good preparation of competent cells can give up to ~10 8 colonies per microgram of plasmid. [ 61 ] Protocols, however, exist for making supercompetent cells that may yield a transformation efficiency of over 10 9 . [ 62 ] The chemical method, however, usually does not work well for linear DNA, such as fragments of chromosomal DNA, probably because the cell's native exonuclease enzymes rapidly degrade linear DNA. In contrast, cells that are naturally competent are usually transformed more efficiently with linear DNA than with plasmid DNA.
The transformation efficiency using the CaCl 2 method decreases with plasmid size, and electroporation therefore may be a more effective method for the uptake of large plasmid DNA. [ 63 ] Cells used in electroporation should be prepared first by washing in cold double-distilled water to remove charged particles that may create sparks during the electroporation process.
Because transformation usually produces a mixture of relatively few transformed cells and an abundance of non-transformed cells, a method is necessary to select for the cells that have acquired the plasmid. [ 64 ] The plasmid therefore requires a selectable marker such that those cells without the plasmid may be killed or have their growth arrested. Antibiotic resistance is the most commonly used marker for prokaryotes. The transforming plasmid contains a gene that confers resistance to an antibiotic that the bacteria are otherwise sensitive to. The mixture of treated cells is cultured on media that contain the antibiotic so that only transformed cells are able to grow. Another method of selection is the use of certain auxotrophic markers that can compensate for an inability to metabolise certain amino acids, nucleotides, or sugars. This method requires the use of suitably mutated strains that are deficient in the synthesis or utility of a particular biomolecule, and the transformed cells are cultured in a medium that allows only cells containing the plasmid to grow.
In a cloning experiment, a gene may be inserted into a plasmid used for transformation. However, in such experiment, not all the plasmids may contain a successfully inserted gene. Additional techniques may therefore be employed further to screen for transformed cells that contain plasmid with the insert. Reporter genes can be used as markers , such as the lacZ gene which codes for β-galactosidase used in blue-white screening . This method of screening relies on the principle of α- complementation , where a fragment of the lacZ gene ( lacZα ) in the plasmid can complement another mutant lacZ gene ( lacZΔM15 ) in the cell. Both genes by themselves produce non-functional peptides, however, when expressed together, as when a plasmid containing lacZ-α is transformed into a lacZΔM15 cells, they form a functional β-galactosidase. The presence of an active β-galactosidase may be detected when cells are grown in plates containing X-gal , forming characteristic blue colonies. However, the multiple cloning site , where a gene of interest may be ligated into the plasmid vector , is located within the lacZα gene. Successful ligation therefore disrupts the lacZα gene, and no functional β-galactosidase can form, resulting in white colonies. Cells containing successfully ligated insert can then be easily identified by its white coloration from the unsuccessful blue ones.
Other commonly used reporter genes are green fluorescent protein (GFP), which produces cells that glow green under blue light, and the enzyme luciferase , which catalyzes a reaction with luciferin to emit light. The recombinant DNA may also be detected using other methods such as nucleic acid hybridization with radioactive RNA probe, while cells that expressed the desired protein from the plasmid may also be detected using immunological methods. | https://en.wikipedia.org/wiki/Genetic_transformation |
Genetic use restriction technology ( GURT ), also known as terminator technology or suicide seeds , is designed to restrict access to "genetic materials and their associated phenotypic traits ." [ 2 ] The technology works by activating (or deactivating) specific genes using a controlled stimulus in order to cause second generation seeds to be either infertile or to not have one or more of the desired traits of the first generation plant. [ 3 ] [ 4 ] GURTs can be used by agricultural firms to enhance protection of their innovations in genetically modified organisms by making it impossible for farmers to reproduce the desired traits on their own. [ 4 ] Another possible use is to prevent the escape of genes from genetically modified organisms into the surrounding environment. [ 5 ]
Patent applications related to a biological switch mechanism emerged in the early 1990's by companies such as DuPont and Zeneca (today Syngenta ). [ 6 ] Though the original GURT technology named "Technology Protection System" or "TPS" was developed under a cooperative research and development agreement between the Agricultural Research Service of the United States Department of Agriculture and Delta & Pine Land Company in the 1990s. The purpose of the development was to protect the intellectual property of biotechnology firms that the United States Department of Agriculture viewed as being a specifically American technological competence. [ 7 ] The United States Patent and Trademark Office (USPTO) granted the application and issued a patent on March 3rd, 1998, the exclusive rights of the license given to the Delta & Pine Land Company through a research agreement. [ 6 ] Monsanto bought Delta & Pine Land Co. acquiring its patents in 2007, although the original patent has since expired. [ 6 ] The technology, while still being developed, is not yet commercially available due to the political and scientific controversies that accompanied its development. [ 8 ]
GURT was first reported on by the Subsidiary Body on Scientific, Technical and Technological Advice (SBSTTA) to the UN Convention on Biological Diversity [ 3 ] and discussed during the 8th Conference of the Parties to the United Nations Convention on Biological Diversity in Curitiba , Brazil, March 20–31, 2006.
The GURT process is typically composed of four genetic components: a target gene, a promoter, a trait switch, and a genetic switch, sometimes with slightly different names given in different papers. [ 5 ] A typical GURT involves the engineering of a plant that has a target gene in its DNA that expresses when activated by a promoter gene . However, it is separated from the target gene by a blocker sequence that prevents the promoter from accessing the target. When the plant receives a given external input, a genetic switch in the plant takes the input, amplifies it, and converts it into a biological signal. When a trait switch receives the amplified signal, it creates an enzyme that cuts the blocker sequence out. With the blocker sequence eliminated, the promoter gene allows the target gene to express itself in the plant. [ 5 ] [ 9 ]
In other versions of the process, an operator must bind to the trait switch in order for it to make the enzymes that cut out the blocker sequence. However, there are repressors that bind to the trait switch and prevent it from doing so. In this case, when the external input is applied, the repressors bond to the input instead of to the trait switch, allowing the enzymes to be created that cut the blocker sequence, thereby allowing the trait to be expressed. [ 7 ]
Other GURTs embody alternative approaches, such as letting the genetic switch directly affect the blocker sequence and bypass the need for a trait switch. [ 7 ]
There are two broad categories of GURTs: Variety-specific genetic use restriction technologies (V-GURTs) and Trait specific genetic use restriction technologies (T-GURTs). [ 10 ] [ 11 ] The two variants have been described as follows [ 5 ] :
V-GURTs are designed to restrict the use of all genetic materials contained in an entire plant variety. Prior to being sold to growers, the seeds of V-GURTs are activated by the seed company. The seeds can germinate, and the plants grow and reproduce normally, but their offspring will be sterile... . Thus, farmers could not save seed from year-to-year to replant. In contrast, T-GURTs only restrict the use of particular traits conferred by a transgene, but seeds are fertile. Growers could replant seed from the previous harvest, but they would not contain the transgenic trait.
Variety-specific genetic use restriction technologies destroy seed development and plant fertility by means of a "genetic process triggered by a chemical inducer that will allow the plant to grow and to form seeds, but will cause the embryo of each of those seeds to produce a cell toxin that will prevent its germination if replanted, thus causing second generation seeds to be sterile... ." [ 7 ] The toxin degrades the DNA or RNA of the plant. Thus, the seed from the crop is not viable and cannot be used as seeds to produce subsequent crops, but only for sale as food or fodder. [ 8 ] [ 12 ]
Trait specific genetic use restriction technologies modify a crop in such a way that the genetic enhancement engineered into the crop does not function until the plant is treated with a specific chemical. [ 8 ] [ 13 ] The chemical acts as the external input, activating the target gene. One difference in T-GURTs is the possibility that the gene could be toggled on and off with different chemical inputs, resulting in the same toggling on or off an associated trait. With T-GURTs, seeds could possibly be saved for planting with a condition that the new plants do not get any enhanced traits unless the external input is added.
GURTs have a number of potential uses, though they have not yet been used in commercial agricultural products available on the market or in pharmaceutical applications. [ 14 ] These uses include protection of intellectual property for biotechnological innovations, and bio-confinement (preventing escape of genetically engineered genes into nature).
The original aim of the developers of GURTs was the protection of intellectual property in agricultural biotechnology. That is, the developers sought to prevent farmers from reusing patented seeds in cases where patents for biological innovations did not exist or could not be easily enforced. [ 8 ] This problem is not generally posed for farmers using hybrid seeds (which, in any case, are not fertile or do not breed true) and, thus, could not be used to grow subsequent crops. However, the V-GURTS make it impossible for farmers to use seeds they have produced to grow crops in subsequent seasons because the entire genome of the targeted cells is destroyed. The T-GURTs could be used by seed companies to allow for the commercialization of seeds that are fertile, but that develop into plants with desired traits only when sprayed with an activator chemical sold by the company. [ 13 ] Corporate seed companies are strongly in favor of GURTs since they can be used as a policing method for Intellectual Property which has brought large opposition from developing nations. These nations fear even more power will be given to these corporations which would no longer have to bring a suit proving infringement but instead the farmer could be presumed guilty and cutoff from their supply immediately. [ 15 ]
An ongoing fear raised by GURTs and other biotechnologies is that the genes of genetically modified plants might escape into nature via sexual reproduction with compatible wild plants or with other cultivated plants. This is known as ' transgene escape' and is among the highest priority risks posed by genetic engineering of plants. [ 4 ] This risk of escape is one of the reasons that the GURT process has not yet been used in commercial applications (indeed, the main producing companies have vowed to not commercialize these products, though they still have related research programs such as Monsanto which spends 40% of its research budget on developing GM seeds). [ 15 ] Ironically, GURTs – themselves a process for the genetic modification of plants – may also be used to secure the 'bio-confinement' of the transgenes of genetically modified plants. GURTs, because they control plant fertility in various ways, could be used to prevent the escape of transgenes into wild relatives and help reduce risks of deleterious impacts on biodiversity . For bio-confinement, both "V- and T GURTs could be targeted to reproductive tissues, most typically pollen and seed (or embryo)." [ 5 ] Crops modified to produce non-food products (eg. in pharmacology, therapeutic proteins, monoclonal antibodies and vaccines) could be armed with GURTs to prevent accidental transmission of these traits into crops meant for foods. [ 8 ] Even then problems could arise, since GURTs require a signal some of these seeds will inevitably not receive the signal passing on the termination step through hybridization to the native gene pool. Since the outright confinement of GM genetic material is likely impossible the terminator trait could attach randomly and possibly decrease the ability of natural species to produce. [ 15 ]
Another possible advantage is that non-viable seeds produced on V-GURT plants may reduce the propagation of volunteer plants . Volunteer plants can become an economic problem for larger-scale mechanized farming systems that incorporate crop rotation . [ 8 ] Furthermore, under warm, wet harvest conditions non V-GURT grain can sprout, lowering the quality of grain produced. It is likely that this problem would not occur with the use of V-GURT grain varieties. [ 8 ]
Another proposed use is in synthetic biology, where a restricted activator chemical must be added to the fermentation medium to produce a desired output chemical. [ 16 ]
There is also the possibility of using GURT seed technology against invasive plant species where the genetically modified plant would fertilize invasive species creating ''terminator seeds''. These seeds would be sterile, possibly stopping the invasive from being as successful especially after fires, droughts, or other disturbances when ecosystems are more prone. This could help lower pressure during restoration projects, and protect native ecosystems. [ 17 ]
As of 2025, GURT seeds have not been commercialized anywhere in the world due to opposition from farmers, consumers, indigenous peoples , NGOs , and some governments. [ 7 ] Using the technology, companies that manufacture genetic use restriction technologies could potentially acquire an advantageous position vis-a-vis farmers because the seeds sold could not be resown. V-GURTs would not have an immediate impact on the many farmers who use hybrid seeds, as they do not produce their own planting seeds, buying instead specialized hybrid seeds from seed production companies. However, in developing countries globally, 80 to 90 percent of the seeds farmers use have been saved from their past harvests. [ 12 ] [ 18 ] Another concern is that farmers purchasing the seeds would be greatly impacted, given they would have to buy new seeds every year. It has been argued that this would result in higher prices in food. [ 19 ]
Some analysts have expressed concerns that GURT seeds might adversely impact biodiversity and threaten native species of plants. [ 20 ] [ 21 ] However, proponents of the technology dispute these claims, arguing that because non-GMO hybrid plants are used in the same way and GURT seeds could help farmers deal with cross pollination, the benefits outweigh the potential negatives. [ 22 ]
In 2000, the United Nations Convention on Biological Diversity recommended a de facto moratorium on field-testing and commercial sale of terminator seeds; the moratorium was re-affirmed and the language strengthened in March 2006, at the COP8 meeting of the UNCBD. [ 23 ] Specifically, the moratorium recommended that, due to a lack of research on the technology's potential risks, no field testing of GURTs nor products using them should be allowed until there was a sufficiently justified reason to do so. Multiple countries have passed legislation prohibiting the technology including India's Protection of Plant Varieties and Farmers' Rights Act, 2001 [ 24 ] and Brazil's Biosecurity Law No.11.105. [ 25 ] | https://en.wikipedia.org/wiki/Genetic_use_restriction_technology |
Genetic viability is the ability of the genes present to allow a cell, organism or population to survive and reproduce. [ 1 ] [ 2 ] The term is generally used to mean the chance or ability of a population to avoid the problems of inbreeding . [ 1 ] Less commonly genetic viability can also be used in respect to a single cell or on an individual level. [ 1 ]
Inbreeding depletes heterozygosity of the genome, meaning there is a greater chance of identical alleles at a locus. [ 1 ] When these alleles are non-beneficial, homozygosity could cause problems for genetic viability. [ 1 ] These problems could include effects on the individual fitness (higher mortality, slower growth, more frequent developmental defects, reduced mating ability, lower fecundity, greater susceptibility to disease, lowered ability to withstand stress, reduced intra- and inter-specific competitive ability) or effects on the entire population fitness (depressed population growth rate, reduced regrowth ability, reduced ability to adapt to environmental change). [ 3 ] See Inbreeding depression . When a population of plants or animals loses their genetic viability, their chance of going extinct increases. [ 4 ]
To be genetically viable, a population of plants or animals requires a certain amount of genetic diversity and a certain population size . [ 5 ] For long-term genetic viability, the population size should consist of enough breeding pairs to maintain genetic diversity. [ 6 ] The precise effective population size can be calculated using a minimum viable population analysis. [ 7 ] Higher genetic diversity and a larger population size will decrease the negative effects of genetic drift and inbreeding in a population. [ 3 ] When adequate measures have been met, the genetic viability of a population will increase. [ 8 ]
The main cause of a decrease in genetic viability is loss of habitat . [ 4 ] [ 9 ] [ 10 ] This loss can occur because of, for example urbanization or deforestation causing habitat fragmentation . [ 4 ] Natural events like earthquakes, floods or fires can also cause loss of habitat. [ 4 ] Eventually, loss of habitat could lead to a population bottleneck . [ 3 ] In a small population, the risk of inbreeding will increase drastically which could lead to a decrease in genetic viability. [ 3 ] [ 4 ] [ 11 ] If they are specific in their diets, this can also lead to habitat isolation and reproductive constraints, leading to greater population bottleneck, and decrease in genetic viability. [ 8 ] Traditional artificial propagation can also lead to decreases in genetic viability in some species. [ 12 ] [ 13 ]
A small highly inbred population of gray wolves ( Canis lupus ) residing in Isle Royale National Park , Michigan, USA has been undergoing population decline and is nearing extinction. [ 14 ] These gray wolves have been experiencing severe inbreeding depression primarily determined by the homozygous expression of strongly deleterious recessive mutations leading to decreased genetic viability. [ 14 ] [ 15 ] Reduced genetic viability due to severe inbreeding was expressed as reduced reproduction and survival as well as specific defects such as malformed vertebrae, probable cataracts, syndactyly, an unusual “rope tail,” and anomalous fur phenotypes. A separate inbred Scandinavian population of gray wolves ( Canis lupus ), also suffering from loss of genetic viability, is experiencing inbreeding depression likely due to the homozygous expression of deleterious recessive mutations. [ 14 ]
Habitat protection is associated with more allelic richness and heterozygosity than in unprotected habitats. [ 16 ] Reduced habitat fragmentation and increased landscape permeability can promote allelic richness by facilitating gene flow between populations that are isolated or smaller. [ 16 ]
The minimum viable population needed to maintain genetic viability is where the loss of genetic variation because of small population size ( genetic drift ) is equal to genetic variation gained through mutation . [ 17 ] When the numbers of one sex is too low, there may be a need for crossbreeding to maintain viability. [ 18 ]
When genetic viability seems to be decreasing within a population, a population viability analysis (PVA) can be done to assess the risk of extinction of this species. [ 19 ] [ 20 ] [ 21 ] The result of a PVA could determine whether further action is needed regarding the preservation of a species. [ 19 ]
Genetic viability is applied by wildlife management staff in zoos, aquariums or other such ex situ habitats. [ 22 ] They use the knowledge of the animals' genetics, usually through their pedigrees, to calculate the PVA and manage the population viability. [ 22 ] | https://en.wikipedia.org/wiki/Genetic_viability |
Genetically encoded voltage indicator (or GEVI ) is a protein that can sense membrane potential in a cell and relate the change in voltage to a form of output, often fluorescent level . [ 1 ] It is a promising optogenetic recording tool that enables exporting electrophysiological signals from cultured cells, live animals, and ultimately human brain. Examples of notable GEVIs include ArcLight, [ 2 ] ASAP1, [ 3 ] ASAP3, [ 4 ] Archons, [ 5 ] SomArchon, [ 6 ] and Ace2N-mNeon. [ 7 ]
Even though the idea of optical measurement of neuronal activity was proposed in the late 1960s, [ 8 ] the first successful GEVI that was convenient enough to put into actual use was not developed until technologies of genetic engineering had become mature in the late 1990s. The first GEVI, coined FlaSh, [ 9 ] was constructed by fusing a modified green fluorescent protein with a voltage-sensitive K + channel ( Shaker ). Unlike fluorescent proteins, the discovery of new GEVIs are seldom inspired by nature, for it is hard to find an organism which naturally has the ability to change its fluorescence based on voltage. Therefore, new GEVIs are mostly the products of genetic and protein engineering.
Two methods can be utilized to find novel GEVIs: rational design and directed evolution . The former method contributes to the most of new GEVI variants, but recent research using directed evolution have shown promising results in GEVI optimization. [ 5 ] [ 10 ]
Conceptually, a GEVI should sense the voltage difference across the cell membrane and report it by a change in fluorescence. Many different structures can be used for the voltage sensing function, [ 11 ] but one essential feature is that it must be imbedded in the cell membrane. Usually, the voltage-sensing domain (VSD) of a GEVI spans across the membrane, and is connected to the fluorescent protein (FP). However, it is not necessary that sensing and reporting must happen in different structures - see, for example, the Archons.
By structure, GEVIs can be classified into four categories based on the current findings: (1) GEVIs contain a fluorescent protein FRET pair, e.g. VSFP1, (2) Single opsin GEVIs, e.g. Arch, (3) Opsin-FP FRET pair GEVIs, e.g. MacQ-mCitrine, (4) single FP with special types of voltage sensing domains, e.g. ASAP1. A majority of GEVIs are based on the Ciona intestinalis voltage sensitive phosphatase (Ci-VSP or Ci-VSD (domain)), which was discovered in 2005 from the genomic survey of the organism. [ 12 ] Some GEVIs may have similar components, but in different positions. For example, ASAP1 and ArcLight both use a VSD and one FP, but the FP of ASAP1 is on the outside of the cell whereas that of ArcLight is on the inside, and the two FPs of VSFP-Butterfly are separated by the VSD, while the two FPs of Mermaid are relatively close to each other.
A GEVI can be evaluated by its many characteristics. These traits can be classified into two categories: performance and compatibility. The performance properties include brightness, photostability , sensitivity, kinetics (speed), linearity of response, etc., while the compatibility properties cover toxicity ( phototoxicity ), plasma membrane localization, adaptability of deep-tissue imaging, etc. [ 43 ] For now, no existing GEVI meets all the desired properties, so searching for a perfect GEVI is still a quite competitive research area.
Different types of GEVIs are being developed in many biological or physiological research areas. It is thought to be superior to conventional voltage detecting methods like electrode-based electrophysiological recordings, calcium imaging , or voltage sensitive dyes . It has subcellular spatial resolution [ 44 ] and temporal resolution as low as 0.2 milliseconds, about an order of magnitude faster than calcium imaging. This allows for spike detection fidelity comparable to electrode-based electrophysiology but without the invasiveness. [ 32 ] Researchers have used it to probe neural communications of an intact brain (of Drosophila [ 45 ] or mouse [ 46 ] ), electrical spiking of bacteria ( E. coli [ 21 ] ), and human stem-cell derived cardiomyocyte . [ 47 ] [ 48 ]
Conversely, any form of voltage indication has inherent limitations. [ 49 ] Imaging must be fast, or short voltage excursions will be missed. This means fewer photons per image. Next, the brightness is inherently less, as about a thousand-fold fewer voltage indicators can fit in the membrane, when compared a cytosolic sensor such as used in calcium imaging. Finally, since the sensor is bound to the membrane (as opposed to the cytosol), it can be ambiguous which cell is responding. | https://en.wikipedia.org/wiki/Genetically_encoded_voltage_indicator |
Genetically modified agriculture includes: | https://en.wikipedia.org/wiki/Genetically_modified_agriculture |
Genetically modified animals are animals that have been genetically modified for a variety of purposes including producing drugs, enhancing yields, increasing resistance to disease, etc. The vast majority of genetically modified animals are at the research stage while the number close to entering the market remains small. [ 1 ]
The process of genetically engineering mammals is a slow, tedious, and expensive process. [ 2 ] As with other genetically modified organisms (GMOs), first genetic engineers must isolate the gene they wish to insert into the host organism. This can be taken from a cell containing the gene [ 3 ] or artificially synthesised . [ 4 ] If the chosen gene or the donor organism's genome has been well studied it may already be accessible from a genetic library . The gene is then combined with other genetic elements, including a promoter and terminator region and usually a selectable marker . [ 5 ]
A number of techniques are available for inserting the isolated gene into the host genome . With animals DNA is generally inserted into using microinjection , where it can be injected through the cell's nuclear envelope directly into the nucleus , or through the use of viral vectors . [ 6 ] The first transgenic animals were produced by injecting viral DNA into embryos and then implanting the embryos in females. [ 7 ] It is necessary to ensure that the inserted DNA is present in the embryonic stem cells . [ 8 ] The embryo would develop and it would be hoped that some of the genetic material would be incorporated into the reproductive cells. Then researchers would have to wait until the animal reached breeding age and then offspring would be screened for presence of the gene in every cell, using PCR , Southern hybridization , and DNA sequencing . [ 9 ]
New technologies are making genetic modifications easier and more precise. [ 2 ] Gene targeting techniques, which creates double-stranded breaks and takes advantage on the cells natural homologous recombination repair systems, have been developed to target insertion to exact locations . Genome editing uses artificially engineered nucleases that create breaks at specific points. There are four families of engineered nucleases: meganucleases , [ 10 ] [ 11 ] zinc finger nucleases , [ 12 ] [ 13 ] transcription activator-like effector nucleases (TALENs), [ 14 ] [ 15 ] and the Cas9-guideRNA system (adapted from CRISPR ). [ 16 ] [ 17 ] TALEN and CRISPR are the two most commonly used and each has its own advantages. [ 18 ] TALENs have greater target specificity, while CRISPR is easier to design and more efficient. [ 18 ] The development of the CRISPR-Cas9 gene editing system has effectively halved the amount of time needed to develop genetically modified animals. [ 19 ]
Humans have domesticated animals since around 12,000 BCE, using selective breeding or artificial selection (as contrasted with natural selection ). The process of selective breeding , in which organisms with desired traits (and thus with the desired genes ) are used to breed the next generation and organisms lacking the trait are not bred, is a precursor to the modern concept of genetic modification [ 20 ] : 1 Various advancements in genetics allowed humans to directly alter the DNA and therefore genes of organisms. In 1972, Paul Berg created the first recombinant DNA molecule when he combined DNA from a monkey virus with that of the lambda virus . [ 21 ] [ 22 ]
In 1974, Rudolf Jaenisch created a transgenic mouse by introducing foreign DNA into its embryo , making it the world's first transgenic animal. [ 23 ] [ 24 ] However it took another eight years before transgenic mice were developed that passed the transgene to their offspring. [ 25 ] [ 26 ] Genetically modified mice were created in 1984 that carried cloned oncogenes , predisposing them to developing cancer. [ 27 ] Mice with genes knocked out ( knockout mouse ) were created in 1989. The first transgenic livestock were produced in 1985 [ 28 ] and the first animal to synthesise transgenic proteins in their milk were mice, [ 29 ] engineered to produce human tissue plasminogen activator in 1987. [ 30 ]
The first genetically modified animal to be commercialised was the GloFish , a Zebra fish with a fluorescent gene added that allows it to glow in the dark under ultraviolet light . [ 31 ] It was released to the US market in 2003. [ 32 ] The first genetically modified animal to be approved for food use was AquAdvantage salmon in 2015. [ 33 ] The salmon were transformed with a growth hormone -regulating gene from a Pacific Chinook salmon and a promoter from an ocean pout enabling it to grow year-round instead of only during spring and summer. [ 34 ]
GM mammals are created for research purposes, production of industrial or therapeutic products, agricultural uses or improving their health. There is also a market for creating genetically modified pets. [ 35 ]
Mammals are the best models for human disease, making genetic engineered ones vital to the discovery and development of cures and treatments for many serious diseases. Knocking out genes responsible for human genetic disorders allows researchers to study the mechanism of the disease and to test possible cures. Genetically modified mice have been the most common mammals used in biomedical research , as they are cheap and easy to manipulate. Examples include humanized mice created by xenotransplantation of human gene products, so as to be utilized as murine human-animal hybrids for gaining relevant insights in the in vivo context for understanding of human-specific physiology and pathologies. [ 36 ] Pigs are also a good target, because they have a similar body size, anatomical features, physiology , pathophysiological response, and diet. [ 37 ] Nonhuman primates are the most similar model organisms to humans, but there is less public acceptance toward using them as research animals. [ 38 ] In 2009, scientists announced that they had successfully transferred a gene into a primate species ( marmosets ) and produced a stable line of breeding transgenic primates for the first time. [ 39 ] [ 40 ] Their first research target for these marmosets was Parkinson's disease , but they were also considering amyotrophic lateral sclerosis and Huntington's disease . [ 41 ]
Human proteins expressed in mammals are more likely to be similar to their natural counterparts than those expressed in plants or microorganisms. Stable expression has been accomplished in sheep, pigs, rats, and other animals. In 2009, the first human biological drug produced from such an animal, a goat , was approved. The drug, ATryn , is an anticoagulant which reduces the probability of blood clots during surgery or childbirth was extracted from the goat's milk. [ 42 ] Human alpha-1-antitrypsin is another protein that is used in treating humans with this deficiency. [ 43 ] Another area is in creating pigs with greater capacity for human organ transplants ( xenotransplantation ). Pigs have been genetically modified so that their organs can no longer carry retroviruses [ 44 ] or have modifications to reduce the chance of rejection. [ 45 ] [ 46 ] Pig lungs from genetically modified pigs are being considered for transplantation into humans. [ 47 ] [ 48 ] There is even potential to create chimeric pigs that can carry human organs. [ 37 ] [ 49 ]
Livestock are modified with the intention of improving economically important traits such as growth-rate, quality of meat, milk composition, disease resistance and survival. Animals have been engineered to grow faster, be healthier [ 50 ] and resist diseases. [ 51 ] Modifications have also improved the wool production of sheep and udder health of cows. [ 1 ]
Goats have been genetically engineered to produce milk with strong spiderweb-like silk proteins. [ 52 ] The goat gene sequence has been modified, using fresh umbilical cords taken from kids, in order to code for the human enzyme lysozyme . Researchers wanted to alter the milk produced by the goats, to contain lysozyme in order to fight off bacteria causing diarrhea in humans. [ 53 ]
Enviropig was a genetically enhanced line of Yorkshire pigs in Canada created with the capability of digesting plant phosphorus more efficiently than conventional Yorkshire pigs. [ 54 ] [ 55 ] The A transgene construct consisting of a promoter expressed in the murine parotid gland and the Escherichia coli phytase gene was introduced into the pig embryo by pronuclear microinjection . [ 56 ] This caused the pigs to produce the enzyme phytase , which breaks down the indigestible phosphorus, in their saliva. [ 54 ] [ 57 ] As a result, they excrete 30 to 70% less phosphorus in manure depending upon the age and diet. [ 54 ] [ 57 ] The lower concentrations of phosphorus in surface runoff reduces algal growth, because phosphorus is the limiting nutrient for algae. [ 54 ] Because algae consume large amounts of oxygen, excessive growth can result in dead zones for fish. Funding for the Enviropig program ended in April 2012, [ 58 ] and as no new partners were found the pigs were killed. [ 59 ] However, the genetic material will be stored at the Canadian Agricultural Genetics Repository Program. In 2006, a pig was engineered to produce omega-3 fatty acids through the expression of a roundworm gene. [ 60 ]
In 1990, the world's first transgenic bovine , Herman the Bull, was developed. Herman was genetically engineered by micro-injected embryonic cells with the human gene coding for lactoferrin . The Dutch Parliament changed the law in 1992 to allow Herman to reproduce. Eight calves were born in 1994 and all calves inherited the lactoferrin gene. [ 61 ] With subsequent sirings, Herman fathered a total of 83 calves. [ 62 ] Dutch law required Herman to be slaughtered at the conclusion of the experiment . However the Dutch Agriculture Minister at the time, Jozias van Aartsen , granted him a reprieve provided he did not have more offspring after public and scientists rallied to his defence. [ 62 ] Together with cloned cows named Holly and Belle, he lived out his retirement at Naturalis , the National Museum of Natural History in Leiden. [ 62 ] On 2 April 2004, Herman was euthanised by veterinarians from the University of Utrecht because he suffered from osteoarthritis . [ 63 ] [ 62 ] At the time of his death Herman was one of the oldest bulls in the Netherlands. [ 63 ] Herman's hide has been preserved and mounted by taxidermists and is permanently on display in Naturalis. They say that he represents the start of a new era in the way man deals with nature, an icon of scientific progress, and the subsequent public discussion of these issues. [ 63 ]
In October 2017, Chinese scientists announced they used CRISPR gene editing technology to create of a line of pigs with better body temperature regulation, resulting in about 24% less body fat than typical livestock. [ 64 ]
Researchers have developed GM dairy cattle to grow without horns (sometimes referred to as " polled ") which can cause injuries to farmers and other animals. DNA was taken from the genome of Red Angus cattle, which is known to suppress horn growth, and inserted into cells taken from an elite Holstein bull called "Randy". Each of the progeny will be a clone of Randy, but without his horns, and their offspring should also be hornless. [ 65 ] In 2011, Chinese scientists generated dairy cows genetically engineered with genes from human beings to produce milk that would be the same as human breast milk. [ 66 ] This could potentially benefit mothers who cannot produce breast milk but want their children to have breast milk rather than formula. [ 67 ] [ 68 ] The researchers claim these transgenic cows to be identical to regular cows. [ 69 ] Two months later, scientists from Argentina presented Rosita, a transgenic cow incorporating two human genes, to produce milk with similar properties as human breast milk. [ 68 ] In 2012, researchers from New Zealand also developed a genetically engineered cow that produced allergy-free milk. [ 70 ]
In 2016 Jayne Raper and a team announced the first trypanotolerant transgenic cow in the world. This team, spanning the International Livestock Research Institute , Scotland's Rural College , the Roslin Institute 's Centre for Tropical Livestock Genetics and Health, and the City University of New York , announced that a Kenyan Boran bull had been born and had already successfully had two children. Tumaini - named for the Swahili word for "hope" - carries a trypanolytic factor from a baboon via CRISPR/Cas9 . [ 71 ] [ 72 ]
Scientists have genetically engineered several organisms, including some mammals, to include green fluorescent protein (GFP), for research purposes. [ 73 ] GFP and other similar reporting genes allow easy visualisation and localisation of the products of the genetic modification. [ 74 ] Fluorescent pigs have been bred to study human organ transplants, regenerating ocular photoreceptor cells , and other topics. [ 75 ] In 2011 green-fluorescent cats were created to find therapies for HIV/AIDS and other diseases [ 76 ] as feline immunodeficiency virus (FIV) is related to HIV. [ 77 ] Researchers from the University of Wyoming have developed a way to incorporate spiders' silk-spinning genes into goats, allowing the researchers to harvest the silk protein from the goats' milk for a variety of applications. [ 78 ]
Genetic modification of the myxoma virus has been proposed to conserve European wild rabbits in the Iberian peninsula and to help regulate them in Australia. To protect the Iberian species from viral diseases, the myxoma virus was genetically modified to immunize the rabbits, while in Australia the same myxoma virus was genetically modified to lower fertility in the Australian rabbit population. [ 79 ] There have also been suggestions that genetic engineering could be used to bring animals back from extinction . It involves changing the genome of a close living relative to resemble the extinct one and is currently being attempted with the passenger pigeon . [ 80 ] Genes associated with the woolly mammoth have been added to the genome of an African Elephant , although the lead researcher says he has no intention of using live elephants. [ 81 ]
Gene therapy [ 82 ] uses genetically modified viruses to deliver genes which can cure disease in humans. Although gene therapy is still relatively new, it has had some successes. It has been used to treat genetic disorders such as severe combined immunodeficiency [ 83 ] and Leber's congenital amaurosis . [ 84 ] Treatments are also being developed for a range of other currently incurable diseases, such as cystic fibrosis , [ 85 ] sickle cell anemia , [ 86 ] Parkinson's disease , [ 87 ] [ 88 ] cancer , [ 89 ] [ 90 ] [ 91 ] diabetes , [ 92 ] heart disease , [ 93 ] and muscular dystrophy . [ 94 ] These treatments only affect somatic cells , which means that any changes would not be inheritable. Germline gene therapy results in any change being inheritable, which has raised concerns within the scientific community. [ 95 ] [ 96 ] In 2015, CRISPR was used to edit the DNA of non-viable human embryos . [ 97 ] [ 98 ] In November 2018, He Jiankui announced that he had edited the genomes of two human embryos, to attempt to disable the CCR5 gene, which codes for a receptor that HIV uses to enter cells. He said that twin girls- Lulu and Nana , had been born a few weeks earlier, and that they carried functional copies of CCR5 along with disabled CCR5 ( mosaicism ), and were still vulnerable to HIV. The work was widely condemned as unethical, dangerous, and premature. [ 99 ]
Genetically modified fish are used for scientific research, as pets, and as a food source. Aquaculture is a growing industry, currently providing over half of the consumed fish worldwide. [ 100 ] Through genetic engineering, it is possible to increase growth rates, reduce food intake, remove allergenic properties, increase cold tolerance, and provide disease resistance.
Fish can also be used to detect aquatic pollution or function as bioreactors. [ 101 ] Several groups have been developing zebrafish to detect pollution by attaching fluorescent proteins to genes activated by the presence of pollutants. The fish will then glow and can be used as environmental sensors. [ 102 ] [ 103 ]
The GloFish is a brand of genetically modified fluorescent zebrafish with bright red, green, and orange fluorescent color. It was originally developed by one of the groups to detect pollution, but is now part of the ornamental fish trade, becoming the first genetically modified animal to become publicly available as a pet when it was introduced for sale in 2003. [ 104 ]
GM fish are widely used in basic research in genetics and development. Two species of fish- zebrafish and medaka , are most commonly modified, because they have optically clear chorions (membranes in the egg), rapidly develop, and the 1-cell embryo is easy to see and microinject with transgenic DNA. [ 105 ] Zebrafish are model organisms for developmental processes, regeneration , genetics, behaviour, disease mechanisms, and toxicity testing. [ 106 ] Their transparency allows researchers to observe developmental stages, intestinal functions, and tumour growth. [ 107 ] [ 108 ] The generation of transgenic protocols (whole organism, cell or tissue specific, tagged with reporter genes) has increased the level of information gained by studying these fish. [ 109 ]
GM fish have been developed with promoters driving an over-production of "all fish" growth hormone for use in the aquaculture industry, to increase the speed of development and potentially reduce fishing pressure on wild stocks. This has resulted in dramatic growth enhancement in several species, including salmon , [ 110 ] trout , [ 111 ] and tilapia . [ 112 ]
AquaBounty Technologies have produced a salmon that can mature in half the time as wild salmon. [ 113 ] The fish is an Atlantic salmon with a Chinook salmon ( Oncorhynchus tshawytscha ) gene inserted. This allows the fish to produce growth hormones all year round compared to the wild-type fish that produces the hormone for only part of the year. [ 114 ] The fish also has a second gene inserted from the eel-like ocean pout that acts like an "on" switch for the hormone. [ 114 ] Pout also have antifreeze proteins in their blood, which allow the GM salmon to survive near-freezing waters and continue their development. [ 115 ] A wild-type salmon takes 24 to 30 months to reach market size (4–6 kg), whereas the producers of the GM salmon say that it requires only 18 months for the GM fish to reach that size. [ 115 ] [ 116 ] [ 117 ] In November 2015, the FDA of the USA approved the AquAdvantage salmon for commercial production, sale, and consumption, [ 118 ] the first non-plant GMO food to be commercialized. [ 119 ]
AquaBounty says that to prevent the genetically modified fish from inadvertently breeding with wild salmon, all of the fish will be female and reproductively sterile, [ 117 ] although a small percentage of the females may remain fertile. [ 114 ] Some opponents of the GM salmon have dubbed it the "Frankenfish". [ 114 ] [ 120 ]
In biological research, transgenic fruit flies ( Drosophila melanogaster ) are model organisms used to study the effects of genetic changes on development. [ 121 ] Fruit flies are often preferred over other animals due to their short life cycle and low maintenance requirements. It also has a relatively simple genome compared to many vertebrates , with typically only one copy of each gene, making phenotypic analysis easy. [ 122 ] Drosophila have been used to study genetics and inheritance, embryonic development, learning, behavior, and aging. [ 123 ] Transposons (particularly P elements) are well developed in Drosophila and provided an early method to add transgenes to their genome, although this has been taken over by more modern gene-editing techniques. [ 124 ]
Due to their significance to human health, scientists are looking at ways to control mosquitoes through genetic engineering. Malaria-resistant mosquitoes have been developed in the laboratory. [ 125 ] by inserting a gene that reduces the development of the malaria parasite [ 126 ] and then use homing endonucleases to rapidly spread that gene throughout the male population (known as a gene drive ). [ 127 ] This has been taken further by swapping it for a lethal gene. [ 128 ] [ 129 ] In trials the populations of Aedes aegypti mosquitoes, the single most important carrier of dengue fever and Zika virus, were reduced by between 80% and by 90%. [ 130 ] [ 131 ] [ 129 ] Another approach is to use the sterile insect technique , whereby males genetically engineered to be sterile out compete viable males, to reduce population numbers. [ 132 ]
Other insect pests that make attractive targets are moths . Diamondback moths cause US$4 to $5 billion of damage a year worldwide. [ 133 ] The approach is similar to the mosquitoes, where males transformed with a gene that prevents females from reaching maturity will be released. [ 134 ] They underwent field trials in 2017. [ 133 ] Genetically modified moths have previously been released in field trials. [ 135 ] A strain of pink bollworm that were sterilised with radiation were genetically engineered to express a red fluorescent protein making it easier for researchers to monitor them. [ 136 ]
Silkworm, the larvae stage of Bombyx mori , is an economically important insect in sericulture . Scientists are developing strategies to enhance silk quality and quantity. There is also potential to use the silk producing machinery to make other valuable proteins. [ 137 ] Proteins expressed by silkworms include; human serum albumin , human collagen α-chain , mouse monoclonal antibody and N-glycanase . [ 138 ] Silkworms have been created that produce spider silk , a stronger but extremely difficult to harvest silk, [ 139 ] and even novel silks. [ 140 ]
Attempts to produce genetically modified birds began before 1980. [ 141 ] Chickens have been genetically modified for a variety of purposes. This includes studying embryo development , [ 142 ] preventing the transmission of bird flu [ 143 ] and providing evolutionary insights using reverse engineering to recreate dinosaur-like phenotypes. [ 144 ] A GM chicken that produces the drug Kanuma , an enzyme that treats a rare condition, in its egg passed regulatory approval in 2015. [ 145 ]
One potential use of GM birds could be to reduce the spread of avian disease. Researchers at Roslin Institute have produced a strain of GM chickens ( Gallus gallus domesticus ) that does not transmit avian flu to other birds; however, these birds are still susceptible to contracting it. The genetic modification is an RNA molecule that prevents the virus reproduction by mimicking the region of the flu virus genome that controls replication. It is referred to as a "decoy" because it diverts the flu virus enzyme, the polymerase , from functions that are required for virus replication. [ 146 ]
A team of geneticists led by University of Montana paleontologist Jack Horner is seeking to modify a chicken to express several features present in ancestral maniraptorans but absent in modern birds, such as teeth and a long tail, [ 147 ] creating what has been dubbed a 'chickenosaurus'. [ 148 ] Parallel projects have produced chicken embryos expressing dinosaur-like skull, [ 149 ] leg, [ 144 ] and foot [ 150 ] anatomy.
Gene editing is one possible tool in the laying hen breeding industry to provide an alternative to Chick culling . With this technology, breeding hens are given a genetic marker that is only passed down to male offspring. These males can then be identified during incubation and removed from the egg supply, so that only females hatch. For example, the Israeli startup eggXYt uses CRISPR to give male eggs a biomarker that makes then glow under certain conditions. [ 151 ] Importantly, the resulting laying hen and the eggs it producers are not themselves genetically edited. The European Union's Director General for Health and Food Safety has confirmed that made in this way eggs can be marketed, [ 152 ] although none are commercially available as of June 2023. [ 153 ]
The first experiments that successfully developed transgenic amphibians into embryos began in the 1980s with Xenopus laevis . [ 154 ] Later, germline transgenic axolotls in Ambystoma mexicanum were produced in 2006 using a technique called I-SceI-mediated transgenesis which utilizes the I-SceI endonuclease enzyme that can break DNA at specific sites and allow for foreign DNA to be inserted into the genome. [ 155 ] Both Xenopus laevis and Ambystoma mexicanum are model organisms used to study regeneration . In addition, transgenic lines have been produced in other salamanders including the Japanese newt Pyrrhogaster and Pleurodeles watl . [ 156 ] Genetically modified frogs, in particular Xenopus laevis and Xenopus tropicalis , are used in development biology . GM frogs can also be used as pollution sensors, especially for endocrine disrupting chemicals . [ 157 ] There are proposals to use genetic engineering to control cane toads in Australia . [ 158 ] [ 159 ] Many lines of transgenic X. laevis are used to study immunology to address how bacteria and viruses cause infectious disease at the University of Rochester Medical Center's X. laevis Research Resource for Immunobiology (XLRRI). [ 160 ] Amphibians can also be used to study and validate regenerative signaling pathways such as the Wnt pathway . [ 161 ] [ 160 ] The wound-healing abilities of amphibians have many practical applications and can potentially provide a foundation for scar-free repair in human plastic surgery, such as treating the skin of burn patients. [ 162 ]
Amphibians like X. laevis are suitable for experimental embryology because they have large embryos that can be easily manipulated and observed during development. [ 163 ] In experiments with axolotls, mutants with white pigmented skin are often used because their semi-transparent skin provides an efficient visualization and tracking method for fluorescently tagged proteins like GFP . [ 155 ] Amphibians are not always ideal when it comes to the resources required to produce genetically modified animals; along with the one to two-year generation time, Xenopus laevis can be considered less than ideal for transgenic experiments because of its pseudotetraploid genome. [ 163 ] Due to the same genes appearing in the genome multiple times, the chance of mutagenesis experiments working is lower. [ 164 ] Current methods of freezing and thawing axolotl sperm render them nonfunctional, meaning transgenic lines must be maintained in a facility and this can get quite costly. [ 155 ] [ 165 ] Producing transgenic axolotls has many challenges due to their large genome size. [ 165 ] Current methods of generating transgenic axolotls are limited to random integration of the transgene cassette into the genome, which can lead to uneven expression or silencing. [ 156 ] Gene duplicates also complicate efforts to generate efficient gene knockouts . [ 165 ]
Despite the costs, axolotls have unique regenerative abilities and ultimately provide useful information in understanding tissue regeneration because they can regenerate their limbs, spinal cord, skin, heart, lungs, and other organs. [ 165 ] [ 166 ] Naturally occurring mutant axolotls like the white strain that are often used in research have a transcriptional mutation at the Edn3 gene locus. [ 167 ] Unlike other model organisms, the first fluorescently labeled cells in axolotls were differentiated muscle cells instead of embryos. In these initial experiments in the early 2000s, scientists were able to visualize muscle cell regeneration in the axolotl tail using a microinjecting technique, but cells could not be traced for the entire course of regeneration due to too harsh conditions that caused early cell death in labeled cells. [ 156 ] [ 168 ] Though the process of producing transgenic axolotls was a challenge, scientists were able to label cells for longer durations using a plasmid transfection technique, which involves injecting DNA into cells using an electrical pulse in a process called electroporation . Transfecting axolotl cells is thought to be more difficult because of the composition of the extracellular matrix (ECM). This technique allows spinal cord cells to be labeled and is very important in studying limb regeneration in many other cells; it has been used to study the role of the immune system in regeneration. Using gene knockout approaches, scientists can target specific regions of DNA using techniques like CRISPR/Cas9 to understand the function of certain genes based on the absence of the gene of interest. For example, gene knockouts of the Sox2 gene confirm this region's role in neural stem cell amplification in the axolotl. The technology to do more complex conditional gene knockouts, or conditional knockouts that give the scientist spatiotemporal control of the gene is not yet suitable for axolotls. [ 165 ] However, research in this field continues to develop and is made easier by recent sequencing of the genome and resources created for scientists, including data portals that contain axolotl genome and transcriptome reference assemblies to identify orthologs . [ 169 ] [ 170 ]
The nematode Caenorhabditis elegans is one of the major model organisms for researching molecular biology . [ 171 ] RNA interference (RNAi) was discovered in C. elegans [ 172 ] and could be induced by simply feeding them bacteria modified to express double stranded RNA . [ 173 ] It is also relatively easy to produce stable transgenic nematodes and this along with RNAi are the major tools used in studying their genes. [ 174 ] The most common use of transgenic nematodes has been studying gene expression and localisation by attaching reporter genes. Transgenes can also be combined with RNAi to rescue phenotypes, altered to study gene function, imaged in real time as the cells develop or used to control expression for different tissues or developmental stages. [ 174 ] Transgenic nematodes have been used to study viruses, [ 175 ] toxicology, [ 176 ] and diseases [ 177 ] [ 178 ] and to detect environmental pollutants. [ 179 ]
Systems have been developed to create transgenic organisms in a wide variety of other animals. The gene responsible for albinism in sea cucumbers has been found, and used to engineer white sea cucumbers , a rare delicacy. The technology also opens the way to investigate the genes responsible for some of the cucumbers more unusual traits, including hibernating in summer, eviscerating their intestines, and dissolving their bodies upon death. [ 180 ] Flatworms have the ability to regenerate themselves from a single cell. [ 181 ] [ 182 ] Until 2017 there was no effective way to transform them, which hampered research. By using microinjection and radiation, scientists have now created the first genetically modified flatworms. [ 183 ] The bristle worm , a marine annelid , has been modified. It is of interest due to its reproductive cycle being synchronized with lunar phases, regeneration capacity and slow evolution rate. [ 184 ] Cnidaria such as Hydra and the sea anemone Nematostella vectensis are attractive model organisms to study the evolution of immunity and certain developmental processes. [ 185 ] Other organisms that have been genetically modified include snails , [ 186 ] geckos , turtles , [ 187 ] crayfish , oysters , shrimp , clams , abalone , [ 188 ] and sponges . [ 189 ]
Food products derived from genetically modified (GM) animals have not yet entered the European market. Nonetheless, the on-going discussion about GM crops [1], and the developing debate about the safety and ethics of foods and pharmaceutical products produced by both GM animals and plants, have provoked varying views across different sectors of society [ 190 ]
Genetic modification and genome editing hold potential for the future, but decisions regarding the use of these technologies must be based not only on what is possible, but also on what is ethically reasonable. Principles such as animal integrity, naturalness, risk identification and animal welfare are examples of ethically important factors that must be taken into consideration, and they also influence public perception and regulatory decisions by authorities. [ 191 ]
The utility of extrapolating animal data to humans has been questioned. This has led ethical committees to adopt the principles of the four Rs (Reduction, Refinement, Replacement, and Responsibility) as a guide for decision-making regarding animal experimentation . However, complete abandonment of laboratory animals has not yet been possible, and further research is needed to develop a roadmap for robust alternatives before their use can be fully discontinued. [ 192 ] | https://en.wikipedia.org/wiki/Genetically_modified_animal |
Genetically modified bacteria were the first organisms to be modified in the laboratory, due to their simple genetics. [ 1 ] These organisms are now used for several purposes, and are particularly important in producing large amounts of pure human proteins for use in medicine. [ 2 ]
The first example of this occurred in 1978 when Herbert Boyer , working at a University of California laboratory, took a version of the human insulin gene and inserted into the bacterium Escherichia coli to produce synthetic "human" insulin . Four years later, it was approved by the U.S. Food and Drug Administration .
Bacteria were the first organisms to be genetically modified in the laboratory, due to the relative ease of modifying their chromosomes. [ 3 ] This ease made them important tools for the creation of other GMOs. Genes and other genetic information from a wide range of organisms can be added to a plasmid and inserted into bacteria for storage and modification. Bacteria are cheap, easy to grow, clonal , multiply quickly, are relatively easy to transform, and can be stored at -80 °C almost indefinitely. Once a gene is isolated it can be stored inside the bacteria, providing an unlimited supply for research. [ 4 ] The large number of custom plasmids make manipulating DNA excised from bacteria relatively easy. [ 5 ]
Their ease of use has made them great tools for scientists looking to study gene function and evolution . Most DNA manipulation takes place within bacterial plasmids before being transferred to another host. Bacteria are the simplest model organism and most of our early understanding of molecular biology comes from studying Escherichia coli . [ 6 ] Scientists can easily manipulate and combine genes within the bacteria to create novel or disrupted proteins and observe the effect this has on various molecular systems. Researchers have combined the genes from bacteria and archaea , leading to insights on how these two diverged in the past. [ 7 ] In the field of synthetic biology , they have been used to test various synthetic approaches, from synthesizing genomes to creating novel nucleotides . [ 8 ] [ 9 ] [ 10 ]
Bacteria have been used in the production of food for a very long time, and specific strains have been developed and selected for that work on an industrial scale. They can be used to produce enzymes , amino acids , flavourings , and other compounds used in food production. With the advent of genetic engineering, new genetic changes can easily be introduced into these bacteria. Most food-producing bacteria are lactic acid bacteria , and this is where the majority of research into genetically engineering food-producing bacteria has gone. The bacteria can be modified to operate more efficiently, reduce toxic byproduct production, increase output, create improved compounds, and remove unnecessary pathways . [ 11 ] Food products from genetically modified bacteria include alpha-amylase , which converts starch to simple sugars, chymosin , which clots milk protein for cheese making, and pectinesterase , which improves fruit juice clarity. [ 12 ]
Chymosin is an enzyme produced in the stomach of young ruminant mammals to digest milk. The digestion of milk proteins via enzymes is essential to cheesemaking. The species Escherichia coli and Bacillus subtilis can be genetically engineered to synthesise and excrete chymosin, [ 13 ] providing a more efficient means of production. The use of bacteria to synthesise chymosin also provides a vegetarian method of cheesemaking, as previously, young ruminants (typically calves) had to be slaughtered to extract the enzyme from the stomach lining.
Genetically modified bacteria are used to produce large amounts of proteins for industrial use. Generally the bacteria are grown to a large volume before the gene encoding the protein is activated. The bacteria are then harvested and the desired protein purified from them. [ 14 ] The high cost of extraction and purification has meant that only high value products have been produced at an industrial scale. [ 15 ]
The majority of the industrial products from bacteria are human proteins for use in medicine. [ 16 ] Many of these proteins are impossible or difficult to obtain via natural methods and they are less likely to be contaminated with pathogens, making them safer. [ 14 ] Prior to recombinant protein products, several treatments were derived from cadavers or other donated body fluids and could transmit diseases. [ 17 ] Indeed, transfusion of blood products had previously led to unintentional infection of haemophiliacs with HIV or hepatitis C ; similarly, treatment with human growth hormone derived from cadaver pituitary glands may have led to outbreaks of Creutzfeldt–Jakob disease . [ 17 ] [ 18 ]
The first medicinal use of GM bacteria was to produce the protein insulin to treat diabetes . [ 19 ] Other medicines produced include clotting factors to treat haemophilia , [ 20 ] human growth hormone to treat various forms of dwarfism , [ 21 ] [ 22 ] interferon to treat some cancers, erythropoietin for anemic patients, and tissue plasminogen activator which dissolves blood clots. [ 14 ] Outside of medicine they have been used to produce biofuels . [ 23 ] There is interest in developing an extracellular expression system within the bacteria to reduce costs and make the production of more products economical. [ 15 ]
With greater understanding of the role that the microbiome plays in human health, there is the potential to treat diseases by genetically altering the bacteria to, themselves, be therapeutic agents. Ideas include altering gut bacteria so they destroy harmful bacteria, or using bacteria to replace or increase deficient enzymes or proteins. One research focus is to modify Lactobacillus , bacteria that naturally provide some protection against HIV , with genes that will further enhance this protection. [ 24 ] The bacteria which generally cause tooth decay have been engineered to no longer produce tooth-corroding lactic acid . [ 25 ] These transgenic bacteria, if allowed to colonize a person's mouth, could perhaps reduce the formation of cavities. [ 26 ] Transgenic microbes have also been used in recent research to kill or hinder tumors, and to fight Crohn's disease . [ 27 ]
If the bacteria do not form colonies inside the patient, the person must repeatedly ingest the modified bacteria in order to get the required doses. Enabling the bacteria to form a colony could provide a more long-term solution, but could also raise safety concerns as interactions between bacteria and the human body are less well understood than with traditional drugs.
One example of such an intermediate, which only forms short-term colonies in the gastrointestinal tract , may be Lactobacillus Acidophilus MPH734 . This is used as a specific in the treatment of Lactose Intolerance . This genetically modified version of Lactobacillus acidophilus bacteria produces a missing enzyme called lactase which is used for the digestion of lactose found in dairy products or, more commonly, in food prepared with dairy products. The short term colony is induced over a one-week, 21-pill treatment regimen, after which, the temporary colony can produce lactase for three months or more before it is removed from the body by a natural processes. The induction regimen can be repeated as often as necessary to maintain protection from the symptoms of lactose intolerance, or discontinued with no consequences, except the return of the original symptoms.
There are concerns that horizontal gene transfer to other bacteria could have unknown effects. As of 2018 there are clinical trials underway testing the efficacy and safety of these treatments. [ 24 ]
For over a century bacteria have been used in agriculture. Crops have been inoculated with Rhizobia (and more recently Azospirillum ) to increase their production or to allow them to be grown outside their original habitat . Application of Bacillus thuringiensis (Bt) and other bacteria can help protect crops from insect infestation and plant diseases. With advances in genetic engineering, these bacteria have been manipulated for increased efficiency and expanded host range. Markers have also been added to aid in tracing the spread of the bacteria. The bacteria that naturally colonise certain crops have also been modified, in some cases to express the Bt genes responsible for pest resistance. Pseudomonas strains of bacteria cause frost damage by nucleating water into ice crystals around themselves. This led to the development of ice-minus bacteria , that have the ice-forming genes removed. When applied to crops they can compete with the ice-plus bacteria and confer some frost resistance. [ 28 ]
Other uses for genetically modified bacteria include bioremediation , where the bacteria are used to convert pollutants into a less toxic form. Genetic engineering can increase the levels of the enzymes used to degrade a toxin or to make the bacteria more stable under environmental conditions. [ 29 ] GM bacteria have also been developed to leach copper from ore, [ 30 ] clean up mercury pollution [ 31 ] and detect arsenic in drinking water. [ 32 ] Bioart has also been created using genetically modified bacteria. In the 1980s artist Joe Davis and geneticist Dana Boyd converted the Germanic symbol for femininity (ᛉ) into binary code and then into a DNA sequence, which was then expressed in Escherichia coli . [ 33 ] This was taken a step further in 2012, when a whole book was encoded onto DNA. [ 34 ] Paintings have also been produced using bacteria transformed with fluorescent proteins. [ 33 ] [ 35 ] [ 36 ] | https://en.wikipedia.org/wiki/Genetically_modified_bacteria |
Genetically modified crops ( GM crops ) are plants used in agriculture , the DNA of which has been modified using genetic engineering methods. Plant genomes can be engineered by physical methods or by use of Agrobacterium for the delivery of sequences hosted in T-DNA binary vectors . In most cases, the aim is to introduce a new trait to the plant which does not occur naturally in the species. Examples in food crops include resistance to certain pests, diseases, environmental conditions, reduction of spoilage, resistance to chemical treatments (e.g. resistance to a herbicide ), or improving the nutrient profile of the crop. Examples in non-food crops include production of pharmaceutical agents , biofuels , and other industrially useful goods, as well as for bioremediation . [ 1 ]
Farmers have widely adopted GM technology. Acreage increased from 1.7 million hectares in 1996 to 185.1 million hectares in 2016, some 12% of global cropland. As of 2016, major crop ( soybean , maize , canola and cotton ) traits consist of herbicide tolerance (95.9 million hectares) insect resistance (25.2 million hectares), or both (58.5 million hectares). In 2015, 53.6 million ha of Genetically modified maize were under cultivation (almost 1/3 of the maize crop). GM maize outperformed its predecessors: yield was 5.6 to 24.5% higher with less mycotoxins (−28.8%), fumonisin (−30.6%) and thricotecens (−36.5%). Non-target organisms were unaffected, except for lower populations some parasitoid wasps due to decreased populations of their pest host European corn borer ; European corn borer is a target of Lepidoptera active Bt maize. Biogeochemical parameters such as lignin content did not vary, while biomass decomposition was higher. [ 2 ]
A 2014 meta-analysis concluded that GM technology adoption had reduced chemical pesticide use by 37%, increased crop yields by 22%, and increased farmer profits by 68%. [ 3 ] This reduction in pesticide use has been ecologically beneficial, but benefits may be reduced by overuse. [ 4 ] Yield gains and pesticide reductions are larger for insect-resistant crops than for herbicide-tolerant crops. [ 5 ] Yield and profit gains are higher in developing countries than in developed countries . [ 3 ] Pesticide poisonings were reduced by 2.4 to 9 million cases per year in India alone. [ 6 ] A 2011 review of the relationship between Bt cotton adoption and farmer suicides in India found that "Available data show no evidence of a 'resurgence' of farmer suicides" and that "Bt cotton technology has been very effective overall in India." [ 7 ] During the time period of Bt cotton introduction in India, farmer suicides instead declined by 25%. [ 6 ]
There is a scientific consensus [ 8 ] [ 9 ] [ 10 ] [ 11 ] that currently available food derived from GM crops poses no greater risk to human health than conventional food, [ 12 ] [ 13 ] [ 14 ] [ 15 ] [ 16 ] but that each GM food needs to be tested on a case-by-case basis before introduction. [ 17 ] [ 18 ] [ 19 ] Nonetheless, members of the public are much less likely than scientists to perceive GM foods as safe. [ 20 ] [ 21 ] [ 22 ] [ 23 ] The legal and regulatory status of GM foods varies by country, with some nations banning or restricting them, and others permitting them with widely differing degrees of regulation. [ 24 ] [ 25 ] [ 26 ] [ 27 ]
Humans have directly influenced the genetic makeup of plants to increase their value as a crop through domestication . The first evidence of plant domestication comes from emmer and einkorn wheat found in pre-Pottery Neolithic A villages in Southwest Asia dated about 10,500 to 10,100 BC. [ 28 ] The Fertile Crescent of Western Asia, Egypt , and India were sites of the earliest planned sowing and harvesting of plants that had previously been gathered in the wild. Independent development of agriculture occurred in northern and southern China, Africa's Sahel , New Guinea and several regions of the Americas. [ 29 ] The eight Neolithic founder crops ( emmer wheat , einkorn wheat , barley , peas , lentils , bitter vetch , chick peas and flax ) had all appeared by about 7,000 BC. [ 30 ] Traditional crop breeders have long introduced foreign germplasm into crops by creating novel crosses. A hybrid cereal grain was created in 1875, by crossing wheat and rye . [ 31 ] Since then traits including dwarfing genes and rust resistance have been introduced in that manner. [ 32 ] Plant tissue culture and deliberate mutations have enabled humans to alter the makeup of plant genomes. [ 33 ] [ 34 ]
Modern advances in genetics have allowed humans to more directly alter plants genetics. In 1970 Hamilton Smith's lab discovered restriction enzymes that allowed DNA to be cut at specific places, enabling scientists to isolate genes from an organism's genome. [ 35 ] DNA ligases that join broken DNA together had been discovered earlier in 1967, [ 36 ] and by combining the two technologies, it was possible to "cut and paste" DNA sequences and create recombinant DNA . Plasmids , discovered in 1952, [ 37 ] became important tools for transferring information between cells and replicating DNA sequences. In 1907 a bacterium that caused plant tumors, Agrobacterium tumefaciens , was discovered and in the early 1970s the tumor inducing agent was found to be a DNA plasmid called the Ti plasmid . [ 38 ] By removing the genes in the plasmid that caused the tumor and adding in novel genes researchers were able to infect plants with A. tumefaciens and let the bacteria insert their chosen DNA sequence into the genomes of the plants. [ 39 ] As not all plant cells were susceptible to infection by A. tumefaciens other methods were developed, including electroporation , micro-injection [ 40 ] and particle bombardment with a gene gun (invented in 1987). [ 41 ] [ 42 ] In the 1980s techniques were developed to introduce isolated chloroplasts back into a plant cell that had its cell wall removed. With the introduction of the gene gun in 1987 it became possible to integrate foreign genes into a chloroplast . [ 43 ] Genetic transformation has become very efficient in some model organisms. In 2008 genetically modified seeds were produced in Arabidopsis thaliana by dipping the flowers in an Agrobacterium solution. [ 44 ] In 2013 CRISPR was first used to target modification of plant genomes. [ 45 ]
The first genetically engineered crop plant was tobacco, reported in 1983. [ 46 ] It was developed creating a chimeric gene that joined an antibiotic resistant gene to the T1 plasmid from Agrobacterium . The tobacco was infected with Agrobacterium transformed with this plasmid resulting in the chimeric gene being inserted into the plant. Through tissue culture techniques a single tobacco cell was selected that contained the gene and a new plant grown from it. [ 47 ] The first field trials of genetically engineered plants occurred in France and the US in 1986, tobacco plants were engineered to be resistant to herbicides . [ 48 ] In 1987 Plant Genetic Systems , founded by Marc Van Montagu and Jeff Schell , was the first company to genetically engineer insect-resistant plants by incorporating genes that produced insecticidal proteins from Bacillus thuringiensis (Bt) into tobacco . [ 49 ] The People's Republic of China was the first country to commercialise transgenic plants, introducing a virus-resistant tobacco in 1992. [ 50 ] In 1994 Calgene attained approval to commercially release the Flavr Savr tomato, a tomato engineered to have a longer shelf life. [ 51 ] Also in 1994, the European Union approved tobacco engineered to be resistant to the herbicide bromoxynil , making it the first genetically engineered crop commercialised in Europe. [ 52 ] In 1995 Bt Potato was approved safe by the Environmental Protection Agency , after having been approved by the FDA, making it the first pesticide producing crop to be approved in the US. [ 53 ] In 1996 a total of 35 approvals had been granted to commercially grow 8 transgenic crops and one flower crop (carnation), with 8 different traits in 6 countries plus the EU. [ 48 ] By 2010, 29 countries had planted commercialised genetically modified crops and a further 31 countries had granted regulatory approval for transgenic crops to be imported. [ 54 ]
GM banana cultivar QCAV-4 was approved by Australia and New Zealand in 2024. The banana resists the fungus that is fatal to the Cavendish banana , the dominant cultivar. [ 55 ]
Genetically engineered crops have genes added or removed using genetic engineering techniques, [ 56 ] originally including gene guns , electroporation , microinjection and agrobacterium . More recently, CRISPR and TALEN offered much more precise and convenient editing techniques.
Gene guns (also known as biolistics) "shoot" (direct high energy particles or radiations against [ 57 ] ) target genes into plant cells. It is the most common method. DNA is bound to tiny particles of gold or tungsten which are subsequently shot into plant tissue or single plant cells under high pressure. The accelerated particles penetrate both the cell wall and membranes . The DNA separates from the metal and is integrated into plant DNA inside the nucleus . This method has been applied successfully for many cultivated crops, especially monocots like wheat or maize, for which transformation using Agrobacterium tumefaciens has been less successful. [ 58 ] The major disadvantage of this procedure is that serious damage can be done to the cellular tissue.
Agrobacterium tumefaciens - mediated transformation is another common technique. Agrobacteria are natural plant parasites . [ 59 ] Their natural ability to transfer genes provides another engineering method. To create a suitable environment for themselves, these Agrobacteria insert their genes into plant hosts, resulting in a proliferation of modified plant cells near the soil level ( crown gall ). The genetic information for tumor growth is encoded on a mobile, circular DNA fragment ( plasmid ). When Agrobacterium infects a plant, it transfers this T-DNA to a random site in the plant genome. When used in genetic engineering the bacterial T-DNA is removed from the bacterial plasmid and replaced with the desired foreign gene. The bacterium is a vector , enabling transportation of foreign genes into plants. This method works especially well for dicotyledonous plants like potatoes, tomatoes, and tobacco. Agrobacteria infection is less successful in crops like wheat and maize.
Electroporation is used when the plant tissue does not contain cell walls. In this technique, "DNA enters the plant cells through miniature pores which are temporarily caused by electric pulses."
Microinjection is used to directly inject foreign DNA into cells. [ 60 ]
Plant scientists, backed by results of modern comprehensive profiling of crop composition, point out that crops modified using GM techniques are less likely to have unintended changes than are conventionally bred crops. [ 61 ] [ 62 ]
In research tobacco and Arabidopsis thaliana are the most frequently modified plants, due to well-developed transformation methods, easy propagation and well studied genomes. [ 63 ] [ 64 ] They serve as model organisms for other plant species.
Introducing new genes into plants requires a promoter specific to the area where the gene is to be expressed. For instance, to express a gene only in rice grains and not in leaves, an endosperm -specific promoter is used. The codons of the gene must be optimized for the organism due to codon usage bias .
Transgenic plants have genes inserted into them that are derived from another species. The inserted genes can come from species within the same kingdom (plant to plant), or between kingdoms (for example, bacteria to plant). In many cases the inserted DNA has to be modified slightly in order to be correctly and efficiently expressed in the host organism. Transgenic plants are used to express proteins , like the cry toxins from B. thuringiensis , herbicide -resistant genes, antibodies , [ 65 ] and antigens for vaccinations . [ 66 ] A study led by the European Food Safety Authority (EFSA) also found viral genes in transgenic plants. [ 67 ]
Transgenic carrots have been used to produce the drug Taliglucerase alfa which is used to treat Gaucher's disease . [ 68 ] In the laboratory, transgenic plants have been modified to increase photosynthesis (currently about 2% at most plants versus the theoretic potential of 9–10%). [ 69 ] This is possible by changing the rubisco enzyme (i.e. changing C 3 plants into C 4 plants [ 70 ] ), by placing the rubisco in a carboxysome , by adding CO 2 pumps in the cell wall, [ 71 ] or by changing the leaf form or size. [ 72 ] [ 73 ] [ 74 ] Plants have been engineered to exhibit bioluminescence that may become a sustainable alternative to electric lighting. [ 75 ]
Cisgenic plants are made using genes found within the same species or a sexually-compatible closely related one, where conventional plant breeding can occur. [ 76 ] Some breeders and scientists argue that cisgenic modification is useful for plants that are difficult to crossbreed by conventional means (such as potatoes ), and that plants in the cisgenic category should not require the same regulatory scrutiny as transgenics. [ 77 ]
Genetically modified plants can also be developed using gene knockdown or gene knockout to alter the genetic makeup of a plant without incorporating genes from other plants. In 2014, Chinese researcher Gao Caixia filed patents on the creation of a strain of wheat that is resistant to powdery mildew . The strain lacks genes that encode proteins that repress defenses against the mildew. The researchers deleted all three copies of the genes from wheat's hexaploid genome. Gao used the TALENs and CRISPR gene editing tools without adding or changing any other genes. No field trials were immediately planned. [ 78 ] [ 79 ] The CRISPR technique has also been used by Penn State researcher Yinong Yang to modify white button mushrooms ( Agaricus bisporus ) to be non-browning, [ 80 ] and by DuPont Pioneer to make a new variety of corn. [ 81 ]
With multiple trait integration, several new traits may be integrated into a new crop. [ 82 ]
GM food's economic value to farmers is one of its major benefits, including in developing nations. [ 83 ] [ 84 ] [ 85 ] A 2010 study found that Bt corn provided economic benefits of $6.9 billion over the previous 14 years in five Midwestern states. The majority ($4.3 billion) accrued to farmers producing non-Bt corn. This was attributed to European corn borer populations reduced by exposure to Bt corn, leaving fewer to attack conventional corn nearby. [ 86 ] [ 87 ] Agriculture economists calculated that "world surplus [increased by] $240.3 million for 1996. Of this total, the largest share (59%) went to U.S. farmers. Seed company Monsanto received the next largest share (21%), followed by US consumers (9%), the rest of the world (6%), and the germplasm supplier, Delta & Pine Land Company of Mississippi (5%)." [ 88 ]
According to the International Service for the Acquisition of Agri-biotech Applications (ISAAA), in 2014 approximately 18 million farmers grew biotech crops in 28 countries; about 94% of the farmers were resource-poor in developing countries. 53% of the global biotech crop area of 181.5 million hectares was grown in 20 developing countries. [ 89 ] PG Economics comprehensive 2012 study concluded that GM crops increased farm incomes worldwide by $14 billion in 2010, with over half this total going to farmers in developing countries. [ 90 ]
Forgoing these benefits is costly. [ 91 ] [ 92 ] Wesseler et al. , 2017 estimate the cost of delay for several crops including GM banana in Uganda , GM cowpea in west Africa , and GM maize/corn in Kenya . [ 91 ] They estimate Nigeria alone loses $33–46m annually. [ 91 ] The potential and alleged harms of GM crops must then be compared to these costs of delay. [ 91 ] [ 92 ]
Critics challenged the claimed benefits to farmers over the prevalence of biased observers and by the absence of randomized controlled trials . [ citation needed ] The main Bt crop grown by small farmers in developing countries is cotton. A 2006 review of Bt cotton findings by agricultural economists concluded, "the overall balance sheet, though promising, is mixed. Economic returns are highly variable over years, farm type, and geographical location". [ 93 ]
In 2013 the European Academies Science Advisory Council (EASAC) asked the EU to allow the development of agricultural GM technologies to enable more sustainable agriculture, by employing fewer land, water, and nutrient resources. EASAC also criticizes the EU's "time-consuming and expensive regulatory framework" and said that the EU had fallen behind in the adoption of GM technologies. [ 94 ]
Participants in agriculture business markets include seed companies, agrochemical companies, distributors, farmers, grain elevators and universities that develop new crops/traits and whose agricultural extensions advise farmers on best practices. [ citation needed ] According to a 2012 review based on data from the late 1990s and early 2000s, much of the GM crop grown each year is used for livestock feed and increased demand for meat leads to increased demand for GM feed crops. [ 95 ] Feed grain usage as a percentage of total crop production is 70% for corn and more than 90% of oil seed meals such as soybeans. About 65 million metric tons of GM corn grains and about 70 million metric tons of soybean meals derived from GM soybean become feed. [ 95 ]
In 2014 the global value of biotech seed was US$15.7 billion; US$11.3 billion (72%) was in industrial countries and US$4.4 billion (28%) was in the developing countries. [ 89 ] In 2009, Monsanto had $7.3 billion in sales of seeds and from licensing its technology; DuPont, through its Pioneer subsidiary, was the next biggest company in that market. [ 96 ] As of 2009, the overall Roundup line of products including the GM seeds represented about 50% of Monsanto's business. [ 97 ]
Some patents on GM traits have expired, allowing the legal development of generic strains that include these traits. For example, generic glyphosate-tolerant GM soybean is now available. Another impact is that traits developed by one vendor can be added to another vendor's proprietary strains, potentially increasing product choice and competition. [ 98 ] The patent on the first type of Roundup Ready crop that Monsanto produced (soybeans) expired in 2014 [ 99 ] and the first harvest of off-patent soybeans occurs in the spring of 2015. [ 100 ] Monsanto has broadly licensed the patent to other seed companies that include the glyphosate resistance trait in their seed products. [ 101 ] About 150 companies have licensed the technology, [ 102 ] including Syngenta [ 103 ] and DuPont Pioneer . [ 104 ]
In 2014, the largest review yet concluded that GM crops' effects on farming were positive. The meta-analysis considered all published English-language examinations of the agronomic and economic impacts between 1995 and March 2014 for three major GM crops: soybean, maize, and cotton. The study found that herbicide-tolerant crops have lower production costs, while for insect-resistant crops the reduced pesticide use was offset by higher seed prices, leaving overall production costs about the same. [ 3 ] [ 105 ]
Yields increased 9% for herbicide tolerance and 25% for insect resistant varieties. Farmers who adopted GM crops made 69% higher profits than those who did not. The review found that GM crops help farmers in developing countries, increasing yields by 14 percentage points. [ 105 ]
The researchers considered some studies that were not peer-reviewed and a few that did not report sample sizes. They attempted to correct for publication bias , by considering sources beyond academic journals . The large data set allowed the study to control for potentially confounding variables such as fertilizer use. Separately, they concluded that the funding source did not influence study results. [ 105 ]
Under special conditions meant to reveal only genetic yield factors, many GM crops are known to actually have lower yields. This is variously due to one or both of: Yield drag, wherein the trait itself lowers yield, either by competing for synthesis feedstock or by being inserted slightly inaccurately, into the middle of a yield-relevant gene; and/or yield lag , wherein it takes some time to breed the newest yield genetics into the GM lines. This does not reflect realistic field conditions however, especially leaving out pest pressure which is often the point of the GM trait. [ 106 ] See for example Roundup Ready § Productivity claims .
Gene editing may also increase yields non-specific to the use of any biocides/pesticides. In March 2022, field test results showed CRISPR -based gene knockout of KRN2 in maize and OsKRN2 in rice increased grain yields by ~10% and ~8% without any detected negative effects. [ 107 ] [ 108 ]
GM crops grown today, or under development, have been modified with various traits . These traits include improved shelf life , disease resistance , stress resistance, herbicide resistance , pest resistance , production of useful goods such as biofuel or drugs, and ability to absorb toxins and for use in bioremediation of pollution.
Recently, research and development has been targeted to enhancement of crops that are locally important in developing countries , such as insect-resistant cowpea for Africa [ 109 ] and insect-resistant brinjal (eggplant). [ 110 ]
The first genetically modified crop approved for sale in the U.S. was the FlavrSavr tomato, which had a longer shelf life. [ 51 ] First sold in 1994, FlavrSavr tomato production ceased in 1997. [ 111 ] It is no longer on the market.
In November 2014, the USDA approved a GM potato that prevents bruising. [ 112 ] [ 113 ]
In February 2015 Arctic Apples were approved by the USDA, [ 114 ] becoming the first genetically modified apple approved for US sale. [ 115 ] Gene silencing was used to reduce the expression of polyphenol oxidase (PPO) , thus preventing enzymatic browning of the fruit after it has been sliced open. The trait was added to Granny Smith and Golden Delicious varieties. [ 114 ] [ 116 ] The trait includes a bacterial antibiotic resistance gene that provides resistance to the antibiotic kanamycin . The genetic engineering involved cultivation in the presence of kanamycin, which allowed only resistant cultivars to survive. Humans consuming apples do not acquire kanamycin resistance, per arcticapple.com. [ 117 ] The FDA approved the apples in March 2015. [ 118 ]
Plants use non-photochemical quenching to protect them from excessive amounts of sunlight. Plants can switch on the quenching mechanism almost instantaneously, but it takes much longer for it to switch off again. During the time that it is switched on, the amount of energy that is wasted increases. [ 119 ] A genetic modification in three genes allows to correct this (in a trial with tobacco plants). As a result, yields were 14-20% higher, in terms of the weight of the dry leaves harvested. The plants had larger leaves, were taller and had more vigorous roots. [ 119 ] [ 120 ]
Another improvement that can be made on the photosynthesis process (with C3 pathway plants ) is on photorespiration . By inserting the C4 pathway into C3 plants, productivity may increase by as much as 50% for cereal crops , such as rice. [ 121 ] [ 122 ] [ 123 ] [ 124 ] [ 125 ]
The Harnessing Plants Initiative focuses on creating GM plants that have increased root mass, root depth and suberin content.
Some GM soybeans offer improved oil profiles for processing. [ 126 ] Camelina sativa has been modified to produce plants that accumulate high levels of oils similar to fish oils . [ 127 ] [ 128 ]
Golden rice , developed by the International Rice Research Institute (IRRI), provides greater amounts of vitamin A targeted at reducing vitamin A deficiency . [ 129 ] [ 130 ] As of January 2016, golden rice has not yet been grown commercially in any country. [ 131 ]
A genetically modified cassava under development offers lower cyanogen glucosides and enhanced protein and other nutrients (called BioCassava). [ 132 ]
In November 2014, the USDA approved a potato that prevents bruising and produces less acrylamide when fried. [ 112 ] [ 113 ] They do not employ genes from non-potato species. The trait was added to the Russet Burbank , Ranger Russet and Atlantic varieties. [ 112 ]
Plants have been engineered to tolerate non-biological stressors , such as drought , [ 112 ] [ 113 ] [ 133 ] [ 134 ] frost , [ 135 ] and high soil salinity . [ 64 ] In 2011, Monsanto's DroughtGard maize became the first drought-resistant GM crop to receive US marketing approval. [ 136 ]
Drought resistance occurs by modifying the plant's genes responsible for the mechanism known as the crassulacean acid metabolism (CAM), which allows the plants to survive despite low water levels. This holds promise for water-heavy crops such as rice, wheat, soybeans and poplar to accelerate their adaptation to water-limited environments. [ 137 ] [ 138 ] Several salinity tolerance mechanisms have been identified in salt-tolerant crops. For example, rice, canola and tomato crops have been genetically modified to increase their tolerance to salt stress. [ 139 ] [ 140 ]
The most prevalent GM trait is herbicide tolerance, [ 141 ] where glyphosate -tolerance is the most common. [ 142 ] Glyphosate (the active ingredient in Roundup and other herbicide products) kills plants by interfering with the shikimate pathway in plants, which is essential for the synthesis of the aromatic amino acids phenylalanine , tyrosine , and tryptophan . The shikimate pathway is not present in animals, which instead obtain aromatic amino acids from their diet. More specifically, glyphosate inhibits the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS).
This trait was developed because the herbicides used on grain and grass crops at the time were highly toxic and not effective against narrow-leaved weeds. Thus, developing crops that could withstand spraying with glyphosate would both reduce environmental and health risks, and give an agricultural edge to the farmer. [ 143 ]
Some micro-organisms have a version of EPSPS that is resistant to glyphosate inhibition. One of these was isolated from an Agrobacterium strain CP4 (CP4 EPSPS) that was resistant to glyphosate. [ 144 ] [ 145 ] The CP4 EPSPS gene was engineered for plant expression by fusing the 5' end of the gene to a chloroplast transit peptide derived from the petunia EPSPS. This transit peptide was used because it had shown previously an ability to deliver bacterial EPSPS to the chloroplasts of other plants. This CP4 EPSPS gene was cloned and transfected into soybeans .
The plasmid used to move the gene into soybeans was PV-GMGTO4. It contained three bacterial genes, two CP4 EPSPS genes, and a gene encoding beta-glucuronidase (GUS) from Escherichia coli as a marker. The DNA was injected into the soybeans using the particle acceleration method . Soybean cultivar A54O3 was used for the transformation .
Tobacco plants have been engineered to be resistant to the herbicide bromoxynil . [ 146 ]
Crops have been commercialized that are resistant to the herbicide glufosinate , as well. [ 147 ] Crops engineered for resistance to multiple herbicides to allow farmers to use a mixed group of two, three, or four different chemicals are under development to combat growing herbicide resistance. [ 148 ] [ 149 ]
In October 2014 the US EPA registered Dow 's Enlist Duo maize, which is genetically modified to be resistant to both glyphosate and 2,4-D , in six states. [ 150 ] [ 151 ] [ 152 ] Inserting a bacterial aryloxyalkanoate dioxygenase gene, aad1 makes the corn resistant to 2,4-D. [ 150 ] [ 153 ] The USDA had approved maize and soybeans with the mutation in September 2014. [ 154 ]
Monsanto has requested approval for a stacked strain that is tolerant of both glyphosate and dicamba . The request includes plans for avoiding herbicide drift to other crops. [ 155 ] Significant damage to other non-resistant crops occurred from dicamba formulations intended to reduce volatilization drifting when sprayed on resistant soybeans in 2017. [ 156 ] The newer dicamba formulation labels specify to not spray when average wind speeds are above 10–15 miles per hour (16–24 km/h) to avoid particle drift, average wind speeds below 3 miles per hour (4.8 km/h) to avoid temperature inversions , and rain or high temperatures are in the next day forecast. However, these conditions typically only occur during June and July for a few hours at a time. [ 157 ] [ 158 ]
Tobacco, corn, rice and some other crops have been engineered to express genes encoding for insecticidal proteins from Bacillus thuringiensis (Bt). [ 159 ] [ 160 ] The introduction of Bt crops during the period between 1996 and 2005 has been estimated to have reduced the total volume of insecticide active ingredient use in the United States by over 100 thousand tons. This represents a 19.4% reduction in insecticide use. [ 161 ]
In the late 1990s, a genetically modified potato that was resistant to the Colorado potato beetle was withdrawn because major buyers rejected it, fearing consumer opposition. [ 112 ]
Plant viruses are a cause of around half of the plant diseases emerging worldwide, and an estimated 10–15% of losses in crop yields. [ 162 ] Papaya, potatoes, and squash have been engineered to resist viral pathogens such as cucumber mosaic virus which, despite its name, infects a wide variety of plants. [ 163 ] [ 162 ] Virus resistant papaya were developed in response to a papaya ringspot virus (PRV) outbreak in Hawaii in the late 1990s. They incorporate PRV DNA. [ 164 ] [ 165 ] By 2010, 80% of Hawaiian papaya plants were genetically modified. [ 166 ] [ 167 ]
Potatoes were engineered for resistance to potato leaf roll virus and Potato virus Y in 1998. Poor sales led to their market withdrawal after three years. [ 168 ]
Yellow squash that were resistant to at first two, then three viruses were developed, beginning in the 1990s. The viruses are watermelon, cucumber and zucchini/courgette yellow mosaic. Squash was the second GM crop to be approved by US regulators. The trait was later added to zucchini. [ 169 ]
Many strains of corn have been developed in recent years to combat the spread of Maize dwarf mosaic virus , a costly virus that causes stunted growth which is carried in Johnson grass and spread by aphid insect vectors. These strands are commercially available although the resistance is not standard among GM corn variants. [ 170 ]
In 2012, the FDA approved the first plant-produced pharmaceutical , a treatment for Gaucher's Disease . [ 171 ] Tobacco plants have been modified to produce therapeutic antibodies. [ 172 ]
Algae is under development for use in biofuels . [ 173 ] The focus of Microalgae for mass production for biofuels modifying the algae to produce more lipid has become a focus yet will take years to see results due to the cost of this process to extract lipids. [ 174 ] Researchers in Singapore were working on GM jatropha for biofuel production. [ 175 ] Syngenta has USDA approval to market a maize trademarked Enogen that has been genetically modified to convert its starch to sugar for ethanol . [ 176 ] Some trees have been genetically modified to either have less lignin , or to express lignin with chemically labile bonds. Lignin is the critical limiting factor when using wood to make bio-ethanol because lignin limits the accessibility of cellulose microfibrils to depolymerization by enzymes . [ 177 ] Besides with trees, the chemically labile lignin bonds are also very useful for cereal crops such as maize, [ 178 ] [ 179 ]
Companies and labs are working on plants that can be used to make bioplastics . [ 180 ] Potatoes that produce industrially useful starches have been developed as well. [ 181 ] Oilseed can be modified to produce fatty acids for detergents , substitute fuels and petrochemicals .
Besides the modified oilcrop above, Camelina sativa has also been modified to produce Helicoverpa armigera pheromones and is in progress with a Spodoptera frugiperda version. The H. armigera pheromones have been tested and are effective. [ 182 ]
Scientists at the University of York developed a weed ( Arabidopsis thaliana ) that contains genes from bacteria that could clean TNT and RDX -explosive soil contaminants in 2011. [ 183 ] 16 million hectares in the US (1.5% of the total surface) are estimated to be contaminated with TNT and RDX. However A. thaliana was not tough enough for use on military test grounds. [ 184 ] Modifications in 2016 included switchgrass and bentgrass . [ 185 ]
Genetically modified plants have been used for bioremediation of contaminated soils. Mercury , selenium and organic pollutants such as polychlorinated biphenyls (PCBs). [ 184 ] [ 186 ]
Marine environments are especially vulnerable since pollution such as oil spills are not containable. In addition to anthropogenic pollution, millions of tons of petroleum annually enter the marine environment from natural seepages. Despite its toxicity, a considerable fraction of petroleum oil entering marine systems is eliminated by the hydrocarbon-degrading activities of microbial communities. Particularly successful is a recently discovered group of specialists, the so-called hydrocarbonoclastic bacteria (HCCB) that may offer useful genes. [ 187 ]
Crops such as maize reproduce sexually each year. This randomizes which genes get propagated to the next generation, meaning that desirable traits can be lost. To maintain a high-quality crop, some farmers purchase seeds every year. Typically, the seed company maintains two inbred varieties and crosses them into a hybrid strain that is then sold. Related plants like sorghum and gamma grass are able to perform apomixis , a form of asexual reproduction that keeps the plant's DNA intact. This trait is apparently controlled by a single dominant gene, but traditional breeding has been unsuccessful in creating asexually-reproducing maize. Genetic engineering offers another route to this goal. Successful modification would allow farmers to replant harvested seeds that retain desirable traits, rather than relying on purchased seed. [ 188 ]
Genetic modifications to some crops also exist, which make it easier to process the crop, i.e. by growing it in a more compact form. [ 189 ] Crops such as tomatoes have been modified to be seedless. [ 190 ] Tobacco has been modified to produce chlorophyll c in addition to a and b , increasing growth rates. The transgene was discovered in marine algae , which uses it to gain energy from the blue light that is able to penetrate seawater more effectively than longer wavelengths. [ 191 ] [ 192 ]
Margarine
Emulsifiers in packaged foods [ 194 ]
high-fructose corn syrup
corn starch [ 194 ]
Soybean oil [ 194 ]
high-fructose corn syrup
corn starch [ 194 ]
Margarine
Emulsifiers in packaged foods [ 194 ]
high-fructose corn syrup
corn starch [ 194 ]
Soybean oil [ 194 ]
Several modifications of Camelina sativa have been done, see §Edible oils and §Non-pesticide pest management products above.
The number of USDA-approved field releases for testing grew from 4 in 1985 to 1,194 in 2002 and averaged around 800 per year thereafter. The number of sites per release and the number of gene constructs (ways that the gene of interest is packaged together with other elements) – have rapidly increased since 2005. Releases with agronomic properties (such as drought resistance) jumped from 1,043 in 2005 to 5,190 in 2013. As of September 2013, about 7,800 releases had been approved for corn, more than 2,200 for soybeans, more than 1,100 for cotton, and about 900 for potatoes. Releases were approved for herbicide tolerance (6,772 releases), insect resistance (4,809), product quality such as flavor or nutrition (4,896), agronomic properties like drought resistance (5,190), and virus/fungal resistance (2,616). The institutions with the most authorized field releases include Monsanto with 6,782, Pioneer/DuPont with 1,405, Syngenta with 565, and USDA's Agricultural Research Service with 370. As of September 2013 USDA had received proposals for releasing GM rice, squash, plum, rose, tobacco, flax, and chicory. [ 207 ]
Researchers at North Carolina State University are designing genetically modified plants or seeds to ship to Mars , that can live in habitable greenhouses or bio-domes to help build plant life on the planet. NASA's NIAC is sponsoring this work on designer plants/trees or genetically modified vegetation that could better survive on Mars. CRISPR gene editing from extremophiles on Earth is used to help withstand the harsh Martian regolith and atmosphere , including such challenges as ultraviolet radiation , extreme cold, low atmospheric pressure , perchlorates , and drought tolerance . [ 208 ] The plants and seeds could then be tested outdoors to try and start an ecosystem for the full terraforming of Mars . [ 209 ] [ 210 ] [ 211 ] [ 212 ]
Constant exposure to a toxin creates evolutionary pressure for pests resistant to that toxin. [ 213 ] Over-reliance on glyphosate and a reduction in the diversity of weed management practices allowed the spread of glyphosate resistance in 14 weed species in the US, [ 207 ] and in soybeans. [ 5 ]
To reduce resistance to Bacillus thuringiensis (Bt) crops, the 1996 commercialization of transgenic cotton and maize came with a management strategy to prevent insects from becoming resistant. Insect resistance management plans are mandatory for Bt crops. The aim is to encourage a large population of pests so that any (recessive) resistance genes are diluted within the population. Resistance lowers evolutionary fitness in the absence of the stressor, Bt. In refuges, non-resistant strains outcompete resistant ones. [ 214 ]
With sufficiently high levels of transgene expression, nearly all of the heterozygotes (S/s), i.e., the largest segment of the pest population carrying a resistance allele, will be killed before maturation, thus preventing transmission of the resistance gene to their progeny. [ 215 ] Refuges (i. e., fields of nontransgenic plants) adjacent to transgenic fields increases the likelihood that homozygous resistant (s/s) individuals and any surviving heterozygotes will mate with susceptible (S/S) individuals from the refuge, instead of with other individuals carrying the resistance allele. As a result, the resistance gene frequency in the population remains lower.
Complicating factors can affect the success of the high-dose/refuge strategy. For example, if the temperature is not ideal, thermal stress can lower Bt toxin production and leave the plant more susceptible. More importantly, reduced late-season expression has been documented, possibly resulting from DNA methylation of the promoter . [ 216 ] The success of the high-dose/refuge strategy has successfully maintained the value of Bt crops. This success has depended on factors independent of management strategy, including low initial resistance allele frequencies, fitness costs associated with resistance, and the abundance of non-Bt host plants outside the refuges. [ 217 ]
Companies that produce Bt seed are introducing strains with multiple Bt proteins. Monsanto did this with Bt cotton in India, where the product was rapidly adopted. [ 218 ] Monsanto has also; in an attempt to simplify the process of implementing refuges in fields to comply with Insect Resistance Management(IRM) policies and prevent irresponsible planting practices; begun marketing seed bags with a set proportion of refuge (non-transgenic) seeds mixed in with the Bt seeds being sold. Coined "Refuge-In-a-Bag" (RIB), this practice is intended to increase farmer compliance with refuge requirements and reduce additional labor needed at planting from having separate Bt and refuge seed bags on hand. [ 219 ] This strategy is likely to reduce the likelihood of Bt-resistance occurring for corn rootworm , but may increase the risk of resistance for lepidopteran corn pests, such as European corn borer . Increased concerns for resistance with seed mixtures include partially resistant larvae on a Bt plant being able to move to a susceptible plant to survive or cross pollination of refuge pollen on to Bt plants that can lower the amount of Bt expressed in kernels for ear feeding insects. [ 220 ] [ 221 ]
Best management practices (BMPs) to control weeds may help delay resistance. BMPs include applying multiple herbicides with different modes of action, rotating crops, planting weed-free seed, scouting fields routinely, cleaning equipment to reduce the transmission of weeds to other fields, and maintaining field borders. [ 207 ] The most widely planted GM crops are designed to tolerate herbicides. By 2006 some weed populations had evolved to tolerate some of the same herbicides. Palmer amaranth is a weed that competes with cotton. A native of the southwestern US, it traveled east and was first found resistant to glyphosate in 2006, less than 10 years after GM cotton was introduced. [ 222 ] [ 223 ]
Farmers generally use less insecticide when they plant Bt-resistant crops. Insecticide use on corn farms declined from 0.21 pound per planted acre in 1995 to 0.02 pound in 2010. This is consistent with the decline in European corn borer populations as a direct result of Bt corn and cotton. The establishment of minimum refuge requirements helped delay the evolution of Bt resistance. However, resistance appears to be developing to some Bt traits in some areas. [ 207 ] In Colombia, GM cotton has reduced insecticide usage by 25% and herbicide usage by 5%, and GM corn has reduced insecticide and herbicide usage by 66% and 13%, respectively. [ 224 ]
By leaving at least 30% of crop residue on the soil surface from harvest through planting, conservation tillage reduces soil erosion from wind and water, increases water retention, and reduces soil degradation as well as water and chemical runoff. In addition, conservation tillage reduces the carbon footprint of agriculture. [ 225 ] A 2014 review covering 12 states from 1996 to 2006, found that a 1% increase in herbicde-tolerant (HT) soybean adoption leads to a 0.21% increase in conservation tillage and a 0.3% decrease in quality-adjusted herbicide use. [ 225 ]
Combined features of increased yield, decreased land use, reduced use of fertilizer and reduced farming machinery use create a feedback loop that reduces carbon emissions related to farming. These reductions have been estimated at 7.5% of total agricultural emissions in the EU or 33 millions tons of CO 2 [ 226 ] and an estimated 8.76 million tons of CO 2 in Colombia. [ 224 ]
The use of drought tolerant crops can increase yield in water-scarce locations, making farming possible in new areas. The adoption of drought tolerant maize in Ghana was shown to increase yield by more than 150% and boost commercialization intensity, although it did not significantly affect farm income. [ 227 ]
The regulation of genetic engineering concerns the approaches taken by governments to assess and manage the risks associated with the development and release of genetically modified crops. There are differences in the regulation of GM crops between countries, with some of the most marked differences occurring between the US and Europe. Regulation varies in a given country depending on the intended use of each product. For example, a crop not intended for food use is generally not reviewed by authorities responsible for food safety. [ 228 ] [ 229 ]
In 2013, GM crops were planted in 27 countries; 19 were developing countries and 8 were developed countries. 2013 was the second year in which developing countries grew a majority (54%) of the total GM harvest. 18 million farmers grew GM crops; around 90% were small-holding farmers in developing countries. [ 1 ]
The United States Department of Agriculture (USDA) reports every year on the total area of GM crop varieties planted in the United States. [ 231 ] [ 232 ] According to National Agricultural Statistics Service , the states published in these tables represent 81–86 percent of all corn planted area, 88–90 percent of all soybean planted area, and 81–93 percent of all upland cotton planted area (depending on the year).
Global estimates are produced by the International Service for the Acquisition of Agri-biotech Applications (ISAAA) and can be found in their annual reports, "Global Status of Commercialized Transgenic Crops". [ 1 ] [ 233 ]
Farmers have widely adopted GM technology (see figure). Between 1996 and 2013, the total surface area of land cultivated with GM crops increased by a factor of 100, from 17,000 square kilometers (4,200,000 acres) to 1,750,000 km 2 (432 million acres). [ 1 ] 10% of the world's arable land was planted with GM crops in 2010. [ 54 ] As of 2011, 11 different transgenic crops were grown commercially on 395 million acres (160 million hectares) in 29 countries such as the US, Brazil, Argentina, India, Canada, China, Paraguay, Pakistan, South Africa, Uruguay, Bolivia, Australia, Philippines, Myanmar, Burkina Faso, Mexico and Spain. [ 54 ] One of the key reasons for this widespread adoption is the perceived economic benefit the technology brings to farmers. For example, the system of planting glyphosate-resistant seed and then applying glyphosate once plants emerged provided farmers with the opportunity to dramatically increase the yield from a given plot of land, since this allowed them to plant rows closer together. Without it, farmers had to plant rows far enough apart to control post-emergent weeds with mechanical tillage. [ 234 ] Likewise, using Bt seeds means that farmers do not have to purchase insecticides, and then invest time, fuel, and equipment in applying them. However critics have disputed whether yields are higher and whether chemical use is less, with GM crops. See Genetically modified food controversies article for information.
In the US, by 2014, 94% of the planted area of soybeans, 96% of cotton and 93% of corn were genetically modified varieties. [ 235 ] [ 236 ] [ 237 ] Genetically modified soybeans carried herbicide-tolerant traits only, but maize and cotton carried both herbicide tolerance and insect protection traits (the latter largely Bt protein). [ 238 ] These constitute "input-traits" that are aimed to financially benefit the producers, but may have indirect environmental benefits and cost benefits to consumers. The Grocery Manufacturers of America estimated in 2003 that 70–75% of all processed foods in the U.S. contained a GM ingredient. [ 239 ]
Europe grows relatively few genetically engineered crops [ 240 ] with the exception of Spain, where one fifth of maize is genetically engineered, [ 241 ] and smaller amounts in five other countries. [ 242 ] The EU had a 'de facto' ban on the approval of new GM crops, from 1999 until 2004. [ 243 ] [ 244 ] GM crops are now regulated by the EU. [ 245 ] Developing countries grew 54 percent of genetically engineered crops in 2013. [ 1 ]
In recent years GM crops expanded rapidly in developing countries . In 2013 approximately 18 million farmers grew 54% of worldwide GM crops in developing countries. [ 1 ] 2013's largest increase was in Brazil (403,000 km 2 versus 368,000 km 2 in 2012). GM cotton began growing in India in 2002, reaching 110,000 km 2 in 2013. [ 1 ]
According to the 2013 ISAAA brief: "a total of 36 countries (35 + EU-28) have granted regulatory approvals for biotech crops for food and/or feed use and for environmental release or planting since 1994 ... a total of 2,833 regulatory approvals involving 27 GM crops and 336 GM events (NB: an "event" is a specific genetic modification in a specific species) have been issued by authorities, of which 1,321 are for food use (direct use or processing), 918 for feed use (direct use or processing) and 599 for environmental release or planting. Japan has the largest number (198), followed by the U.S.A. (165, not including "stacked" events), Canada (146), Mexico (131), South Korea (103), Australia (93), New Zealand (83), European Union (71 including approvals that have expired or under renewal process), Philippines (68), Taiwan (65), Colombia (59), China (55) and South Africa (52). Maize has the largest number (130 events in 27 countries), followed by cotton (49 events in 22 countries), potato (31 events in 10 countries), canola (30 events in 12 countries) and soybean (27 events in 26 countries). [ 1 ]
Direct genetic engineering has been controversial since its introduction. Most, but not all of the controversies are over GM foods rather than crops per se. GM foods are the subject of protests, vandalism, referendums, legislation, court action [ 246 ] and scientific disputes. The controversies involve consumers, biotechnology companies, governmental regulators, non-governmental organizations and scientists.
Opponents have objected to GM crops on multiple grounds including environmental impacts, food safety, whether GM crops are needed to address food needs, whether they are sufficiently accessible to farmers in developing countries, [ 247 ] concerns over subjecting crops to intellectual property law, and on religious grounds. [ 248 ] Secondary issues include labeling, the behavior of government regulators, the effects of pesticide use and pesticide tolerance.
A significant environmental concern about using genetically modified crops is possible cross-breeding with related crops, giving them advantages over naturally occurring varieties. One example is a glyphosate-resistant rice crop that crossbreeds with a weedy relative, giving the weed a competitive advantage. The transgenic hybrid had higher rates of photosynthesis, more shoots and flowers, and more seeds than the non-transgenic hybrids. [ 249 ] This demonstrates the possibility of ecosystem damage by GM crop usage.
The role of biopiracy in the development of GM crops is also potentially problematic, as developed countries have gotten economic gain by using the genetic resources of developing countries. In the twentieth century, the International Rice Research Institute catalogued the genomes of almost 80,000 varieties of rice from Asian farms, which has since been used to create new higher yielding varieties of rice. These new varieties create almost 655 million dollars of economic gain for Australia, USA, Canada, and New Zealand every year. [ 250 ]
There is a scientific consensus [ 8 ] [ 9 ] [ 10 ] [ 11 ] that currently available food derived from GM crops poses no greater risk to human health than conventional food, [ 12 ] [ 13 ] [ 14 ] [ 15 ] [ 16 ] but that each GM food needs to be tested on a case-by-case basis before introduction. [ 17 ] [ 18 ] [ 19 ] Nonetheless, members of the public are much less likely than scientists to perceive GM foods as safe. [ 20 ] [ 21 ] [ 22 ] [ 23 ] The legal and regulatory status of GM foods varies by country, with some nations banning or restricting them, and others permitting them with widely differing degrees of regulation. [ 24 ] [ 25 ] [ 26 ] [ 27 ]
No reports of ill effects from GM food have been documented in the human population. [ 251 ] [ 252 ] [ 253 ] GM crop labeling is required in many countries, although the United States Food and Drug Administration does not, nor does it distinguish between approved GM and non-GM foods. [ 254 ] The United States enacted a law that requires labeling regulations to be issued by July 2018. It allows indirect disclosure such as with a phone number, bar code, or web site. [ 255 ]
Advocacy groups such as Center for Food Safety , Union of Concerned Scientists , and Greenpeace claim that risks related to GM food have not been adequately examined and managed, that GM crops are not sufficiently tested and should be labelled, and that regulatory authorities and scientific bodies are too closely tied to industry. [ citation needed ] Some studies have claimed that genetically modified crops can cause harm; [ 256 ] [ 257 ] a 2016 review that reanalyzed the data from six of these studies found that their statistical methodologies were flawed and did not demonstrate harm, and said that conclusions about GM crop safety should be drawn from "the totality of the evidence ... instead of far-fetched evidence from single studies". [ 258 ]
But see also:
Domingo JL, Giné Bordonaba J (May 2011). "A literature review on the safety assessment of genetically modified plants" (PDF) . Environment International . 37 (4): 734– 42. Bibcode : 2011EnInt..37..734D . doi : 10.1016/j.envint.2011.01.003 . PMID 21296423 . In spite of this, the number of studies specifically focused on safety assessment of GM plants is still limited. However, it is important to remark that for the first time, a certain equilibrium in the number of research groups suggesting, on the basis of their studies, that a number of varieties of GM products (mainly maize and soybeans) are as safe and nutritious as the respective conventional non-GM plant, and those raising still serious concerns, was observed. Moreover, it is worth mentioning that most of the studies demonstrating that GM foods are as nutritional and safe as those obtained by conventional breeding, have been performed by biotechnology companies or associates, which are also responsible of commercializing these GM plants. Anyhow, this represents a notable advance in comparison with the lack of studies published in recent years in scientific journals by those companies.
Krimsky S (2015). "An Illusory Consensus behind GMO Health Assessment". Science, Technology, & Human Values . 40 (6): 883– 914. doi : 10.1177/0162243915598381 . S2CID 40855100 . I began this article with the testimonials from respected scientists that there is literally no scientific controversy over the health effects of GMOs. My investigation into the scientific literature tells another story.
And contrast:
Panchin AY, Tuzhikov AI (March 2017). "Published GMO studies find no evidence of harm when corrected for multiple comparisons". Critical Reviews in Biotechnology . 37 (2): 213– 217. doi : 10.3109/07388551.2015.1130684 . PMID 26767435 . S2CID 11786594 . Here, we show that a number of articles some of which have strongly and negatively influenced the public opinion on GM crops and even provoked political actions, such as GMO embargo, share common flaws in the statistical evaluation of the data. Having accounted for these flaws, we conclude that the data presented in these articles does not provide any substantial evidence of GMO harm. The presented articles suggesting possible harm of GMOs received high public attention. However, despite their claims, they actually weaken the evidence for the harm and lack of substantial equivalency of studied GMOs. We emphasize that with over 1783 published articles on GMOs over the last 10 years it is expected that some of them should have reported undesired differences between GMOs and conventional crops even if no such differences exist in reality.
and | https://en.wikipedia.org/wiki/Genetically_modified_crops |
A genetically modified mouse , genetically engineered mouse model ( GEMM ) [ 1 ] or transgenic mouse is a mouse ( Mus musculus ) that has had its genome altered through the use of genetic engineering techniques. Genetically modified mice are commonly used for research or as animal models of human diseases and are also used for research on genes. Together with patient-derived xenografts (PDXs), GEMMs are the most common in vivo models in cancer research . The two approaches are considered complementary and may be used to recapitulate different aspects of disease. [ 2 ] GEMMs are also of great interest for drug development , as they facilitate target validation and the study of response, resistance, toxicity and pharmacodynamics . [ 3 ]
In 1974 Beatrice Mintz and Rudolf Jaenisch created the first genetically modified animal by inserting a DNA virus into an early-stage mouse embryo and showing that the inserted genes were present in every cell. [ 4 ] However, the mice did not pass the transgene to their offspring, and the impact and applicability of this experiment were, therefore, limited. In 1981 the laboratories of Frank Ruddle [ 5 ] from Yale University , Frank Costantini and Elizabeth Lacy from Oxford , and Ralph L. Brinster and Richard Palmiter in collaboration from the University of Pennsylvania and the University of Washington injected purified DNA into a single-cell mouse embryo utilizing techniques developed by Brinster in the 1960s and 1970s, showing transmission of the genetic material to subsequent generations for the first time. [ 6 ] [ 7 ] [ 8 ] During the 1980s, Palmiter and Brinster developed and led the field of transgenesis, refining methods of germline modification and using these techniques to elucidate the activity and function of genes in a way not possible before their unique approach. [ 9 ]
There are two basic technical approaches to produce genetically modified mice. The first involves pronuclear injection , a technique developed and refined by Ralph L. Brinster in the 1960s and 1970s, into a single cell of the mouse embryo, where it will randomly integrate into the mouse genome. [ 10 ] This method creates a transgenic mouse and is used to insert new genetic information into the mouse genome or to over-express endogenous genes. The second approach, pioneered by Oliver Smithies and Mario Capecchi , involves modifying embryonic stem cells with a DNA construct containing DNA sequences homologous to the target gene. Embryonic stem cells that recombine with the genomic DNA are selected for and they are then injected into the mice blastocysts . [ 11 ] This method is used to manipulate a single gene, in most cases "knocking out" the target gene, although increasingly more subtle and complex genetic manipulation can occur (e.g. humanisation of a specific protein, or only changing single nucleotides ). A humanised mouse can also be created by direct addition of human genes, thereby creating a murine form of human–animal hybrid . For example, genetically modified mice may be born with human leukocyte antigen genes in order to provide a more realistic environment when introducing human white blood cells into them in order to study immune system responses. [ 12 ] One such application is the identification of hepatitis C virus (HCV) peptides that bind to HLA, and that can be recognized by the human immune system, thereby potentially being targets for future vaccines against HCV. [ 13 ]
Genetically modified mice are used extensively in research as models of human disease. [ 14 ] Mice are a useful model for genetic manipulation and research, as their tissues and organs are similar to that of a human and they carry virtually all the same genes that operate in humans. [ 15 ] They also have advantages over other mammals, in regards to research, in that they are available in hundreds of genetically homogeneous strains. [ 15 ] Also, due to their size, they can be kept and housed in large numbers, reducing the cost of research and experiments. [ 15 ] Transgenic mice are found in two main models of either loss or gain of function. The most common type is loss of function mice or the knockout mouse , where the activity of a single (or in some cases multiple) genes are removed or silenced. Gain of function mice, in other hand, overexpress a specific gene. [ 16 ] They have been used to study and model obesity, heart disease, diabetes, arthritis, substance abuse, anxiety, aging, temperature, pain reception, and Parkinson disease. [ 17 ] [ 18 ] Genetically modified mice further be divided into constitutive mouse model, in which the target gene is permanently activated or inactivated in all the cells of the animal, or conditional mouse model, in which the knockout or the overexpressed gene can be regulated in a spatiotemporal manner, which enables targeting of a specific type or subset of cells in the animal from a specific time in the life of the animal. [ 16 ]
Transgenic mice generated to carry cloned oncogenes and knockout mice lacking tumor suppressing genes have provided good models for human cancer . Hundreds of these oncomice have been developed covering a wide range of cancers affecting most organs of the body and they are being refined to become more representative of human cancer. [ 9 ] The disease symptoms and potential drugs or treatments can be tested against these mouse models.
A mouse has been genetically engineered to have increased muscle growth and strength by overexpressing the insulin-like growth factor I (IGF-I) in differentiated muscle fibers . [ 19 ] [ 20 ] Another mouse has had a gene altered that is involved in glucose metabolism and runs faster, lives longer, is more sexually active and eats more without getting fatter than the average mouse (see Metabolic supermice ). [ 21 ] [ 22 ] Another mouse had the TRPM8 receptor blocked or removed in a study involving capsaicin and menthol . [ 18 ] With the TRPM8 receptor removed, the mouse was unable to detect small changes in temperature and the pain associated with it. [ 18 ]
Great care should be taken when deciding how to use genetically modified mice in research. [ 23 ] Even basic issues like choosing the correct "wild-type" control mouse to use for comparison are sometimes overlooked. [ 24 ] | https://en.wikipedia.org/wiki/Genetically_modified_mouse |
Genetically modified plants have been engineered for scientific research, to create new colours in plants, deliver vaccines, and to create enhanced crops. Plant genomes can be engineered by physical methods or by use of Agrobacterium for the delivery of sequences hosted in T-DNA binary vectors . Many plant cells are pluripotent , meaning that a single cell from a mature plant can be harvested and then under the right conditions form a new plant. This ability is most often taken advantage by genetic engineers through selecting cells that can successfully be transformed into an adult plant which can then be grown into multiple new plants containing transgene in every cell through a process known as tissue culture . [ 1 ]
Much of the advances in the field genetic engineering has come from experimentation with tobacco . Major advances in tissue culture and plant cellular mechanisms for a wide range of plants has originated from systems developed in tobacco. [ 2 ] It was the first plant to be genetically engineered and is considered a model organism for not only genetic engineering, but a range of other fields. [ 3 ] As such the transgenic tools and procedures are well established making it one of the easiest plants to transform. [ 4 ] Another major model organism relevant to genetic engineering is Arabidopsis thaliana . Its small genome and short life cycle makes it easy to manipulate and it contains many homologs to important crop species. [ 5 ] It was the first plant sequenced , has abundant bioinformatic resources and can be transformed by simply dipping a flower in a transformed Agrobacterium solution. [ 6 ]
In research, plants are engineered to help discover the functions of certain genes. The simplest way to do this is to remove the gene and see what phenotype develops compared to the wild type form. Any differences are possibly the result of the missing gene. Unlike mutagenisis , genetic engineering allows targeted removal without disrupting other genes in the organism. [ 1 ] Some genes are only expressed in certain tissue, so reporter genes, like GUS , can be attached to the gene of interest allowing visualisation of the location. [ 7 ] Other ways to test a gene is to alter it slightly and then return it to the plant and see if it still has the same effect on phenotype. Other strategies include attaching the gene to a strong promoter and see what happens when it is over expressed, forcing a gene to be expressed in a different location or at different developmental stages . [ 1 ]
Some genetically modified plants are purely ornamental . They are modified for flower color, fragrance, flower shape and plant architecture. [ 8 ] The first genetically modified ornamentals commercialised altered colour. [ 9 ] Carnations were released in 1997, with the most popular genetically modified organism, a blue rose (actually lavender or mauve) created in 2004. [ 10 ] The roses are sold in Japan, the United States, and Canada. [ 11 ] [ 12 ] Other genetically modified ornamentals include Chrysanthemum and Petunia . [ 8 ] As well as increasing aesthetic value there are plans to develop ornamentals that use less water or are resistant to the cold, which would allow them to be grown outside their natural environments. [ 13 ]
It has been proposed to genetically modify some plant species threatened by extinction to be resistant invasive plants and diseases, such as the emerald ash borer in North American and the fungal disease, Ceratocystis platani , in European plane trees . [ 14 ] The papaya ringspot virus (PRSV) devastated papaya trees in Hawaii in the twentieth century until transgenic papaya plants were given pathogen-derived resistance. [ 15 ] However, genetic modification for conservation in plants remains mainly speculative. A unique concern is that a transgenic species may no longer bear enough resemblance to the original species to truly claim that the original species is being conserved. Instead, the transgenic species may be genetically different enough to be considered a new species, thus diminishing the conservation worth of genetic modification. [ 14 ]
Genetically modified crops are genetically modified plants that are used in agriculture . The first crops provided are used for animal or human food and provide resistance to certain pests, diseases, environmental conditions, spoilage or chemical treatments (e.g. resistance to a herbicide ). [ 16 ] The second generation of crops aimed to improve the quality, often by altering the nutrient profile . Third generation genetically modified crops can be used for non-food purposes, including the production of pharmaceutical agents , biofuels , and other industrially useful goods, as well as for bioremediation . [ 17 ]
There are three main aims to agricultural advancement; increased production, improved conditions for agricultural workers and sustainability . GM crops contribute by improving harvests through reducing insect pressure, increasing nutrient value and tolerating different abiotic stresses . Despite this potential, as of 2018, the commercialised crops are limited mostly to cash crops like cotton, soybean, maize and canola and the vast majority of the introduced traits provide either herbicide tolerance or insect resistance. [ 17 ] Soybeans accounted for half of all genetically modified crops planted in 2014. [ 18 ] Adoption by farmers has been rapid, between 1996 and 2013, the total surface area of land cultivated with GM crops increased by a factor of 100, from 17,000 square kilometers (4,200,000 acres) to 1,750,000 km 2 (432 million acres). [ 19 ] Geographically though the spread has been very uneven, with strong growth in the Americas and parts of Asia and little in Europe and Africa. [ 17 ] Its socioeconomic spread has been more even, with approximately 54% of worldwide GM crops grown in developing countries in 2013. [ 19 ]
The majority of GM crops have been modified to be resistant to selected herbicides, usually a glyphosate or glufosinate based one. Genetically modified crops engineered to resist herbicides are now more available than conventionally bred resistant varieties; [ 20 ] in the USA 93% of soybeans and most of the GM maize grown is glyphosate tolerant. [ 21 ] Most currently available genes used to engineer insect resistance come from the Bacillus thuringiensis bacterium. Most are in the form of delta endotoxin genes known as cry proteins, while a few use the genes that encode for vegetative insecticidal proteins . [ 22 ] The only gene commercially used to provide insect protection that does not originate from B. thuringiensis is the Cowpea trypsin inhibitor (CpTI). CpTI was first approved for use cotton in 1999 and is currently undergoing trials in rice. [ 23 ] [ 24 ] Less than one percent of GM crops contained other traits, which include providing virus resistance, delaying senescence, modifying flower colour and altering the plants composition. [ 18 ] Golden rice is the most well known GM crop that is aimed at increasing nutrient value. It has been engineered with three genes that biosynthesise beta-carotene , a precursor of vitamin A , in the edible parts of rice. [ 25 ] It is intended to produce a fortified food to be grown and consumed in areas with a shortage of dietary vitamin A . [ 26 ] a deficiency which each year is estimated to kill 670,000 children under the age of 5 [ 27 ] and cause an additional 500,000 cases of irreversible childhood blindness. [ 28 ] The original golden rice produced 1.6μg/g of the carotenoids , with further development increasing this 23 times. [ 29 ] In 2018 it gained its first approvals for use as food. [ 30 ]
Plants and plant cells have been genetically engineered for production of biopharmaceuticals in bioreactors , a process known as Pharming . Work has been done with duckweed Lemna minor , [ 31 ] the algae Chlamydomonas reinhardtii [ 32 ] and the moss Physcomitrella patens . [ 33 ] [ 34 ] Biopharmaceuticals produced include cytokines , hormones , antibodies , enzymes and vaccines, most of which are accumulated in the plant seeds. Many drugs also contain natural plant ingredients and the pathways that lead to their production have been genetically altered or transferred to other plant species to produce greater volume and better products. [ 35 ] Other options for bioreactors are biopolymers [ 36 ] and biofuels . [ 37 ] Unlike bacteria, plants can modify the proteins post- translationally , allowing them to make more complex molecules. They also pose less risk of being contaminated. [ 38 ] Therapeutics have been cultured in transgenic carrot and tobacco cells, [ 39 ] including a drug treatment for Gaucher's disease . [ 40 ]
Vaccine production and storage has great potential in transgenic plants. Vaccines are expensive to produce, transport and administer, so having a system that could produce them locally would allow greater access to poorer and developing areas. [ 35 ] As well as purifying vaccines expressed in plants, it is also possible to produce edible vaccines in plants. Edible vaccines stimulate the immune system when ingested to protect against certain diseases. Being stored in plants reduces the long-term cost as they can be disseminated without the need for cold storage, do not need to be purified, and have long term stability. Also being housed within plant cells provides some protection from the gut acids upon digestion; the cost of developing, regulating and containing transgenic plants is high, leading to most current plant-based vaccine development being applied to veterinary medicine , where the controls are not as strict. [ 41 ] | https://en.wikipedia.org/wiki/Genetically_modified_plant |
Most vaccines consist of viruses that have been attenuated , disabled, weakened or killed in some way so that their virulent properties are no longer effective. A simple genetically modified vaccine , based on a thymidine kinase deficient mutant of pseudorabies virus was reportedly available as early as 2001 as a commercial vaccine to control Aujeszky's disease in Europe, North America and Japan. [ 1 ]
This article about vaccines or vaccination is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genetically_modified_vaccine |
A genetically modified virus is a virus that has been altered or generated using biotechnology methods, and remains capable of infection . Genetic modification involves the directed insertion , deletion , artificial synthesis or change of nucleotide bases in viral genomes. Genetically modified viruses are mostly generated by the insertion of foreign genes intro viral genomes for the purposes of biomedical , agricultural, bio-control , or technological objectives. The terms genetically modified virus and genetically engineered virus are used synonymously.
Genetically modified viruses are generated through genetic modification, which involves the directed insertion, deletion, artificial synthesis , or change of nucleotide sequences in viral genomes using biotechnological methods. While most dsDNA viruses have single monopartite genomes, many RNA viruses have multipartite genomes, it is not necessary for all parts of a viral genome to be genetically modified for the virus to be considered a genetically modified virus. Infectious viruses capable of infection that are generated through artificial gene synthesis of all, or part of their genomes (for example based on inferred historical sequences) may also be considered as genetically modified viruses. Viruses that are changed solely through the action of spontaneous mutations , recombination or reassortment events (even in experimental settings), are not generally considered to be genetically modified viruses.
Viruses are generally modified so they can be used as vectors for inserting new genetic information into a host organism or altering its preexisting genetic material. This can be achieved in at least three processes :
None of these three processes are mutually exclusive. Where only process 2. occurs and it results in the expression of a genetically modified gene this will often be referred to as a transient expression approach.
The capacity to infect host cells or tissues is a necessary requirement for all applied uses of genetically modified viruses. However, a capacity for viral transmission (the transfer of infections between host individuals), is either not required or is considered undesirable for most applications. Only in a small minority of proposed uses is viral transmission considered necessary or desirable, an example is transmissible vaccines. [ 2 ] [ 3 ] This is because transmissibility considerably complicates efforts to monitor, control, or contain the spread of viruses. [ 4 ]
In 1972, the earliest report of the insertion of a foreign sequence into a viral genome was published, when Paul Berg used the EcoRI restriction enzyme and DNA ligases to create the first ever recombinant DNA molecules. [ 5 ] This was achieved by joining DNA from the monkey SV40 virus with that of the lambda virus. However, it was not established that either of the two viruses were capable of infection or replication.
In 1974, the first report of a genetically modified virus that could also replicate and infect was submitted for publication by Noreen Murray and Kenneth Murray . [ 6 ] Just two months later in August 1974, Marjorie Thomas, John Cameron and Ronald W. Davis submitted a report for publication of a similar achievement. [ 7 ]
Collectively, these experiments represented the very start of the development of what would eventually become known as biotechnology or recombinant DNA methods.
Gene therapy [ 8 ] uses genetically modified viruses to deliver genes that can cure diseases in human cells.These viruses can deliver DNA or RNA genetic material to the targeted cells. Gene therapy is also used by inactivating mutated genes that are causing the disease using viruses. [ 9 ]
Viruses that have been used for gene therapy are, adenovirus , lentivirus , retrovirus and the herpes simplex virus . [ 10 ] The most common virus used for gene delivery come from adenoviruses as they can carry up to 7.5 kb of foreign DNA and infect a relatively broad range of host cells, although they have been known to elicit immune responses in the host and only provide short term expression. Other common vectors are adeno-associated viruses , which have lower toxicity and longer term expression, but can only carry about 4kb of DNA. [ 11 ] Herpes simplex viruses is a promising vector, have a carrying capacity of over 30kb and provide long term expression, although it is less efficient at gene delivery than other vectors. [ 12 ] The best vectors for long term integration of the gene into the host genome are retroviruses, but their propensity for random integration is problematic. Lentiviruses are a part of the same family as retroviruses with the advantage of infecting both dividing and non-dividing cells, whereas retroviruses only target dividing cells. Other viruses that have been used as vectors include alphaviruses , flaviviruses , measles viruses , rhabdoviruses , Newcastle disease virus , poxviruses , and picornaviruses . [ 11 ]
Although primarily still at trial stages, [ 13 ] it has had some successes. It has been used to treat inherited genetic disorders such as severe combined immunodeficiency [ 14 ] rising from adenosine deaminase deficiency (ADA-SCID), [ 15 ] although the development of leukemia in some ADA-SCID patients [ 11 ] along with the death of Jesse Gelsinger in another trial set back the development of this approach for many years. [ 16 ] In 2009 another breakthrough was achieved when an eight year old boy with Leber’s congenital amaurosis regained normal eyesight [ 16 ] and in 2016 GlaxoSmithKline gained approval to commercialise a gene therapy treatment for ADA-SCID. [ 15 ] As of 2018, there are a substantial number of clinical trials underway, including treatments for hemophilia , glioblastoma , chronic granulomatous disease , cystic fibrosis and various cancers . [ 11 ] Although some successes, gene therapy is still considered a risky technique and studies are still undergoing to ensure safety and effectiveness. [ 9 ]
Another potential use of genetically modified viruses is to alter them so they can directly treat diseases. This can be through expression of protective proteins or by directly targeting infected cells. In 2004, researchers reported that a genetically modified virus that exploits the selfish behaviour of cancer cells might offer an alternative way of killing tumours. [ 17 ] [ 18 ] Since then, several researchers have developed genetically modified oncolytic viruses that show promise as treatments for various types of cancer . [ 19 ] [ 20 ] [ 21 ] [ 22 ] [ 23 ]
Most vaccines consist of viruses that have been attenuated , disabled, weakened or killed in some way so that their virulent properties are no longer effective. Genetic engineering could theoretically be used to create viruses with the virulent genes removed. In 2001, it was reported that genetically modified viruses can possibly be used to develop vaccines [ 24 ] against diseases such as, AIDS, herpes, dengue fever and viral hepatitis by using a proven safe vaccine virus, such as adenovirus , and modify its genome to have genes that code for immunogenic proteins that can spike the immune systems response to then be able to fight the virus. Genetic engineered viruses should not have reduced infectivity , invoke a natural immune response and there is no chance that they will regain their virulence function, which can occur with some other vaccines. As such they are generally considered safer and more efficient than conventional vaccines, although concerns remain over non-target infection, potential side effects and horizontal gene transfer to other viruses. [ 25 ] Another approach is to use vectors to create novel vaccines for diseases that have no vaccines available or the vaccines that are do not work effectively, such as AIDS , malaria , and tuberculosis . Vector-based vaccines have already been approved and many more are being developed. [ 26 ]
In 2012, US researchers reported that they injected a genetically modified virus into the heart of pigs. This virus inserted into the heart muscles a gene called Tbx18 which enabled heartbeats. The researchers forecast that one day this technique could be used to restore the heartbeat in humans who would otherwise need electronic pacemakers . [ 27 ] [ 28 ]
In Spain and Portugal, by 2005 rabbits had declined by as much as 95% over 50 years due diseases such as myxomatosis , rabbit haemorrhagic disease and other causes. This in turn caused declines in predators like the Iberian lynx , a critically endangered species. [ 29 ] [ 30 ] In 2000 Spanish researchers investigated a genetically modified virus which might have protected rabbits in the wild against myxomatosis and rabbit haemorrhagic disease. [ 31 ] However, there was concern that such a virus might make its way into wild populations in areas such as Australia and create a population boom. [ 29 ] [ 4 ] Rabbits in Australia are considered to be such a pest that land owners are legally obliged to control them. [ 32 ]
Genetically modified viruses that make the target animals infertile through immunocontraception have been created [ 33 ] as well as others that target the developmental stage of the animal. [ 34 ] There are concerns over virus containment [ 33 ] and cross species infection. [ 35 ]
Since 2009 genetically modified viruses expressing spinach defensin proteins have been field trialed in Florida (USA). [ 36 ] The virus infection of orange trees aims to combat citrus greening disease , that had reduced orange production in Florida 70% since 2005. [ 37 ] A permit application has been pending since February 13, 2017 (USDA 17-044-101r) to extend the experimental use permit to an area of 513,500 acres , this would make it the largest permit of this kind ever issued by the USDA Biotechnology Regulatory Services.
In 2016 DARPA , an agency of the U.S. Department of Defense , announced a tender for contracts to develop genetically modified plant viruses for an approach involving their dispersion into the environment using insects. [ 38 ] [ 39 ] The work plan stated:
“Plant viruses hold significant promise as carriers of gene editing circuitry and are a natural partner for an insect-transmitted delivery platform.” [ 38 ]
The motivation provided for the program is to ensure food stability by protecting agricultural food supply and commodity crops:
"By leveraging the natural ability of insect vectors to deliver viruses with high host plant specificity, and combining this capability with advances in gene editing, rapid enhancement of mature plants in the field can be achieved over large areas and without the need for industrial infrastructure.” [ 38 ]
Despite its name, the “Insect Allies” program is to a large extent a viral program, developing viruses that would essentially perform gene editing of crops in already-planted fields. [ 40 ] [ 41 ] [ 42 ] [ 43 ] The genetically modified viruses described in the work plan and other public documents are of a class of genetically modified viruses subsequently termed HEGAAs (horizontal environmental gene alteration agents). The Insect Allies program is scheduled to run from 2017 to 2021 with contracts being executed by three consortia. There are no plans to release the genetically modified viruses into the environment, with testing of the full insect dispersed system occurring in greenhouses ( Biosafety level 3 facilities have been mentioned). [ 44 ]
Concerns have been expressed about how this program and any data it generates will impact biological weapon control and agricultural coexistence, [ 45 ] [ 46 ] [ 47 ] though there has also been support for its stated objectives. [ 48 ]
In 2009, MIT scientists created a genetically modified virus that has been used to construct a more environmentally friendly lithium-ion battery . [ 49 ] [ 50 ] [ 51 ] The battery was constructed by genetically engineering different viruses such as, the E4 bacteriophage and the M13 bacteriophage, to be used as a cathode. This was done by editing the genes of the virus that code for the protein coat. The protein coat is edited to coat itself in iron phosphate to be able to adhere to highly conductive carbon-nanotubes . The viruses that have been modified to have a multifunctional protein coat can be used as a nano-structured cathode with causes ionic interactions with cations. Allowing the virus to be used as a small battery. Angela Blecher , the scientist who led the MIT research team on the project, says that the battery is powerful enough to be used as a rechargeable battery, power hybrid electric cars, and a number of personal electronics. [ 52 ] While both the E4 and M13 viruses can infect and replicate within their bacterial host, it unclear if they retain this capacity after being part of a battery.
The National Institute of Health declared a research funding moratorium on select Gain-of-Function virus research in January 2015. [ 53 ] [ 54 ] In January 2017, the U.S. Government released final policy guidance for the review and oversight of research anticipated to create, transfer, or use enhanced potential pandemic pathogens (PPP). [ 55 ] Questions about a potential escape of a modified virus from a biosafety lab and the utility of dual-use-technology , dual use research of concern (DURC), prompted the NIH funding policy revision. [ 56 ] [ 57 ] [ 58 ]
A scientist claims she was infected by a genetically modified virus while working for Pfizer. In her federal lawsuit she says she has been intermittently paralyzed by the Pfizer-designed virus. "McClain, of Deep River, suspects she was inadvertently exposed, through work by a former Pfizer colleague in 2002 or 2003, to an engineered form of the lentivirus , a virus similar to the one that can lead to acquired immune deficiency syndrome, or AIDS." [ 59 ] The court found that McClain failed to demonstrate that her illness was caused by exposure to the lentivirus, [ 60 ] but also that Pfizer violated whistleblower protection laws. [ 61 ] | https://en.wikipedia.org/wiki/Genetically_modified_virus |
Genetics nursing is a nursing specialty that focuses on providing genetic healthcare to patients.
The integration of genetics into nursing began in the 1980s and has been a slow but important process in improving the quality of healthcare for patients receiving genetic and genomic based care from nurses. Modeling the United Kingdom, the United States critically established a set of essential competencies as a set of guidelines for registered nurses . Through the process of consensus the essential competencies were created by the steering committee, and provided the minimalist competency and scope of practice for registered nurses delivering genetic healthcare to patients.
The Nursing Code of Ethics and other ethical foundations were established for field of genetics nursing to provide regulations when ethical issues develop. [ 1 ]
Adopted from the early Christians in 30 AD, the term nurse was created from the Latin origin nutrire, which means to nurture or nourish. Establishing nursing as one of the oldest forms of healthcare and continues to be a growing field of medicine. [ 2 ] Genetics , which is the study of inherited traits and their variation is a much more recent field of medicine. The experiments and theories of Gregor Mendel in the mid-19th century helped to introduce the field of genetics into medicine. Genomics is a subset of genetics that compares and analyzes genomes and how the genes interact with one another. Both genetics and genomics help to reveal how closely related we are to each other and to other species. [ 3 ] This scientific study is ongoing and strives to interpret health, illness, disease risk, and treatment response. The progress in genetics and genomics is applicable to the entire spectrum of health care and all health professionals and as such to the entire nursing profession. [ 4 ] Genetics and genomics are important to healthcare because it provides information in the diagnosis, treatment, and prevention of diseases and illnesses. Even though genetics has been a growing field of medicine since the mid-19th century, the process of integrating genomics into the nursing curriculum, National Council Licensure Examinations, continuing education, and certification was not highlighted until the 1980s. [ 5 ] Genetics and genomics are fundamental to the nursing practice because the basis of genetics can recognize individuals at risk for certain illnesses and diseases, identify the risks of certain disease or illnesses when conceiving children, facilitate drug dosage or selection for certain illnesses or specific patients, and genetics promotes benefits in treatment of particular ailments. [ 6 ]
However, it took twenty more years until the Health Recourses and Services Administration (HRSA) stressed the significance of incorporating genetics into nursing education. [ 5 ] After HRSA's proposal, there was minor advancement and the development that was established contained a lot of inconsistency. The progress of integration continued to be slow and limited. By fall of 2005, only 30% of academic nursing programs contained a curriculum thread in genetics and genomics . [ 5 ] One of the leading factors in the limited progress of genetics integration is the relevance to all nursing practice is not fully appreciated by many, and genetics is also seen by many nurses to be a subspecialty . Also state boards of nursing do not require competency in genomics and genetics as part of licensure and genetics and genomics are not considered in the evaluations of accrediting bodies. The extremely large size and variation of the nursing workforce provides an extra challenge in the many existing barriers needed to be overcome for genetics to be implemented. [ 4 ] Some of the first successful training of genetic practices in the nursing workforce can be seen in the United Kingdom . The main aspect of the U.K. ’s strategy was simplicity. They achieved this by constructing seven essential competencies that were applied to the entire nursing profession. In 2003, the U.K. National Health Service created the NHS National Genetics Education and Development Centre. The main functions of these programs were to enhance genetics education and to dispense materials and resources for educators of all genetic professions. The United States mirrored the efforts and ideas established in the U.K. and adopted similar methods and competencies. The U.S. National Human Genome Research Institute and the National Cancer Institute of the National Institutes of Health united to initiate strategies, training programs, committees, and define the competencies. [ 5 ]
The genetic and genomic competencies are important to the practice of all nurses regardless of academic preparation, practice setting, role, or specialty. [ 6 ] The competencies are significant because they establish a foundation and set of guidelines for the nursing workforce on administering the minimal amount of genetic and genomic based healthcare. Since the competencies would only reflect the minimalist amount of genetic and genomic based healthcare, they were specifically drawn up to focus on the scope of practice for registered nurses . This was done because a registered nurse is a general level of practice for nursing and requires that one has graduated from a college or university nursing program and has passed the NCLEX . The NCLEX is a national licensing exam that signifies minimal competency in practicing nursing if passed. [ 5 ] [ 6 ] [ 7 ]
To begin the development of the competencies, the initial strategy of the U.S. National Human Genome Research Institute and the National Cancer Institute of the National Institutes of Health established the steering committee. It was composed of nurse leaders from a variety of professional nursing agencies, academic settings, and organizations. Two of the major nursing leaders, Jean Jenkins, RN, PhD, FAAN and Kathleen Calzone, RN, MSN, APNG, FAAN were chosen as the Co-Chairs of the committee. The committee's fundamental function was to generate a mechanism for establishing competencies by recognizing, examining, and comparing existing published competencies. [ 5 ] [ 6 ] The published competencies that were being examined targeted all health care professionals, specifically those practicing genetics , nurses with bachelor's degrees, and advanced practice nurses . After the published competencies were reviewed carefully, the developing of the essential competencies was produced in four phases called the process of consensus.
During phase I of the process of consensus, a subset of the committee was created to synthesize competencies from the documents under review that would apply to all registered nurses; then the steering committee reviewed, modified, and approved the recommended competencies. [ 5 ] In 2005, nurse representatives of the National Coalition for Health Professional Education in Genetics also reviewed the proposed competencies and made modifications. Throughout phase II, the American Nursing Association published the competencies during a meeting in 2006 and requested judgment, thoughts, and comments from the public, specifically targeting the insight from the nursing community. [ 5 ] [ 6 ] The 10 comments that were received were recorded and evaluated and the majority of them showed support. Phase III consisted of establishing consensus on the final draft of the essential competencies by the steering committee and the consensus panel, which is also made up of a variety of nursing leaders in different organizations and settings. [ 5 ] The steering committee also constructed strategies for integrating genetic and genomic information into education and practice such as the NCLEX exam, accreditation programs, certification processes, and nursing curriculum. In March 2006, phase IV occurred and consisted of endorsing the final document by the Nursing Organizations Alliance member organizations. [ 6 ]
The essential competencies consists of two domains: professional responsibilities and professional practice. Under the professional responsibilities domain, all professional activities by registered nurses are required to fall within the confines of the Nursing: Scope and Standards of Practice produced by the American Nurses Association. [ 6 ]
Also, competent nursing practice now requires the incorporation of genetic and genomic knowledge and skills in order to:
The competencies for the registered nurse , under the professional practice domain, includes: nursing assessment , which is the application and integration of genetic and genomic knowledge, identification, referral activities, and provision of education, care, and support. [ 5 ]
Nursing Assessment for the registered nurse includes:
Identification for the registered nurse includes:
Referral Activities for the registered nurse includes:
Provision of support, care, and education for the registered nurse includes:
Ethics pertain to the ‘’rightness’’ and ‘’wrongness’’ of human actions, motives, and conduct. Complicated ethical issues in areas such as justice, privacy, and autonomy, tend to follow both the field of genetics and the field of nursing . Ethical problems and dilemmas arise daily in healthcare settings for both the patient and health care provider. For example, all patients and individuals have the right to receive equal health care regardless of gender, religious beliefs, status, or race. A Code of Ethics for Nursing was created by the American Nurses Association, which provides rules, regulations, and guidelines to follow when making a decision that is ethical based. These regulations were mainly established to help provide equal healthcare, protect the rights, safety, and privacy of the patient, and to hold nurses accountable for their actions and choices. Genetics can create ethical issues in nursing for a variety of different situations. Many scenarios, questions, and debates have been encountered such as what individuals can receive genetic testing or information? Who owns or controls the information received from the genetic test and how can the owner use that information? However, the code of ethics does not address genetics or genomics specifically, so ethical foundations were also established to help guide genetics into health care. The foundations provide a set of guidelines to understand and manage an ethical issue if one should arise, and to assist in the translation of genetics into the healthcare environment. [ 8 ] [ 9 ] | https://en.wikipedia.org/wiki/Genetics_nursing |
Genetics of aging is generally concerned with life extension associated with genetic alterations, rather than with accelerated aging diseases leading to reduction in lifespan.
The first mutation found to increase longevity in an animal was the age-1 gene in Caenorhabditis elegans . Michael Klass discovered that lifespan of C. elegans could be altered by mutations, but Klass believed that the effect was due to reduced food consumption ( calorie restriction ). [ 1 ] Thomas Johnson later showed that life extension of up to 65% was due to the mutation itself rather than due to calorie restriction, [ 2 ] and he named the gene age-1 in the expectation that other genes that control aging would be found. The age-1 gene encodes the catalytic subunit of class-I phosphatidylinositol 3-kinase (PI3K).
A decade after Johnson's discovery daf-2 , one of the two genes that are essential for dauer larva formation, [ 3 ] was shown by Cynthia Kenyon to double C. elegans lifespan. [ 4 ] Kenyon showed that the daf-2 mutants, which would form dauers above 25 °C (77 °F) would bypass the dauer state below 20 °C (68 °F) with a doubling of lifespan. [ 4 ] Prior to Kenyon's study it was commonly believed that lifespan could only be increased at the cost of a loss of reproductive capacity, but Kenyon's nematodes maintained youthful reproductive capacity as well as extended youth in general. Subsequent genetic modification (PI3K-null mutation) to C. elegans was shown to extend maximum life span tenfold. [ 5 ] [ 6 ]
Long-lived mutants of C. elegans ( age-1 and daf-2 ) were demonstrated to be resistant to oxidative stress and UV light . [ 7 ] These long-lived mutants had a higher DNA repair capability than wild-type C. elegans . [ 7 ] Knockdown of the nucleotide excision repair gene Xpa-1 increased sensitivity to UV and reduced the life span of the long-lived mutants. These findings support the hypothesis that DNA damage has a significant role in the aging process . [ 7 ]
Genetic modifications in other species have not achieved as great a lifespan extension as have been seen for C. elegans . Drosophila melanogaster lifespan has been doubled. [ 8 ] Genetic mutations in mice can increase maximum lifespan to 1.5 times normal, and up to 1.7 times normal when combined with calorie restriction . [ 9 ]
In yeast, NAD +-dependent histone deacetylase Sir2 is required for genomic silencing at three loci: the yeast mating loci , the telomeres and the ribosomal DNA (rDNA). In some species of yeast, replicative aging may be partially caused by homologous recombination between rDNA repeats; excision of rDNA repeats results in the formation of extrachromosomal rDNA circles (ERCs). These ERCs replicate and preferentially segregate to the mother cell during cell division, and are believed to result in cellular senescence by titrating away (competing for) essential nuclear factors . ERCs have not been observed in other species (nor even all strains of the same yeast species) of yeast (which also display replicative senescence), and ERCs are not believed to contribute to aging in higher organisms such as humans (they have not been shown to accumulate in mammals in a similar manner to yeast). Extrachromosomal circular DNA (eccDNA) has been found in worms, flies, and humans. The origin and role of eccDNA in aging, if any, is unknown.
Despite the lack of a connection between circular DNA and aging in higher organisms, extra copies of Sir2 are capable of extending the lifespan of both worms and flies (though, in flies, this finding has not been replicated by other investigators, and the activator of Sir2 resveratrol does not reproducibly increase lifespan in either species. [ 10 ] ) Whether the Sir2 homologues in higher organisms have any role in lifespan is unclear, but the human SIRT1 protein has been demonstrated to deacetylate p53 , Ku70, and the forkhead family of transcription factors . SIRT1 can also regulate acetylates such as CBP/p300 , and has been shown to deacetylate specific histone residues.
RAS1 and RAS2 also affect aging in yeast and have a human homologue. RAS2 overexpression has been shown to extend lifespan in yeast.
Other genes regulate aging in yeast by increasing the resistance to oxidative stress . Superoxide dismutase , a protein that protects against the effects of mitochondrial free radicals , can extend yeast lifespan in stationary phase when overexpressed.
In higher organisms, aging is likely to be regulated in part through the insulin/IGF-1 pathway. Mutations that affect insulin-like signaling in worms, flies, and the growth hormone/IGF1 axis in mice are associated with extended lifespan. In yeast, Sir2 activity is regulated by the nicotinamidase PNC1. PNC1 is transcriptionally upregulated under stressful conditions such as caloric restriction , heat shock , and osmotic shock . By converting nicotinamide to niacin , nicotinamide is removed, inhibiting the activity of Sir2. A nicotinamidase found in humans, known as PBEF , may serve a similar function, and a secreted form of PBEF known as visfatin may help to regulate serum insulin levels. It is not known, however, whether these mechanisms also exist in humans, since there are obvious differences in biology between humans and model organisms.
Sir2 activity has been shown to increase under calorie restriction. Due to the lack of available glucose in the cells, more NAD+ is available and can activate Sir2. Resveratrol , a stilbenoid found in the skin of red grapes , was reported to extend the lifespan of yeast, worms, and flies (the lifespan extension in flies and worms have proved to be irreproducible by independent investigators [ 10 ] ). It has been shown to activate Sir2 and therefore mimics the effects of calorie restriction, if one accepts that caloric restriction is indeed dependent on Sir2.
According to the GenAge database of aging-related genes, there are over 1800 genes altering lifespan in model organisms : 838 in the soil roundworm ( Caenorhabditis elegans ), 883 in the bakers' yeast ( Saccharomyces cerevisiae ), 170 in the fruit fly ( Drosophila melanogaster ) and 126 in the mouse ( Mus musculus ). [ 11 ]
The following is a list of genes connected to longevity through research [ 11 ] on model organisms :
In July 2020 scientists, using public biological data on 1.75 m people with known lifespans overall, identify 10 genomic loci which appear to intrinsically influence healthspan , lifespan, and longevity – of which half have not been reported previously at genome-wide significance and most being associated with cardiovascular disease – and identify haem metabolism as a promising candidate for further research within the field. Their study suggests that high levels of iron in the blood likely reduce, and genes involved in metabolising iron likely increase healthy years of life in humans. [ 13 ] [ 12 ]
Ned Sharpless and collaborators demonstrated the first in vivo link between p16 -expression and lifespan. [ 14 ] They found reduced p16 expression in some tissues of mice with mutations that extend lifespan, as well as in mice that had their lifespan extended by food restriction. Jan van Deursen and Darren Baker in collaboration with Andre Terzic at the Mayo Clinic in Rochester, Minn., provided the first in vivo evidence for a causal link between cellular senescence and aging by preventing the accumulation of senescent cells in BubR1 progeroid mice. [ 15 ] In the absence of senescent cells, the mice's tissues showed a major improvement in the usual burden of age-related disorders. They did not develop cataracts , avoided the usual wasting of muscle with age. They retained the fat layers in the skin that usually thin out with age and, in people, cause wrinkling. A second study led by Jan van Deursen in collaboration with a team of collaborators at the Mayo Clinic and Groningen University, provided the first direct in vivo evidence that cellular senescence causes signs of aging by eliminating senescent cells from progeroid mice by introducing a drug-inducible suicide gene and then treating the mice with the drug to kill senescent cells selectively, as opposed to decreasing whole body p16. [ 16 ] Another Mayo study led by James Kirkland in collaboration with Scripps and other groups demonstrated that senolytics, drugs that target senescent cells, enhance cardiac function and improve vascular reactivity in old mice, alleviate gait disturbance caused by radiation in mice, and delay frailty, neurological dysfunction, and osteoporosis in progeroid mice. Discovery of senolytic drugs was based on a hypothesis-driven approach: the investigators leveraged the observation that senescent cells are resistant to apoptosis to discover that pro-survival pathways are up-regulated in these cells. They demonstrated that these survival pathways are the "Achilles heel" of senescent cells using RNA interference approaches, including Bcl-2-, AKT-, p21-, and tyrosine kinase-related pathways. They then used drugs known to target the identified pathways and showed these drugs kill senescent cells by apoptosis in culture and decrease senescent cell burden in multiple tissues in vivo. Importantly, these drugs had long term effects after a single dose, consistent with removal of senescent cells, rather than a temporary effect requiring continued presence of the drugs. This was the first study to show that clearing senescent cells enhances function in chronologically aged mice. [ 17 ]
The genetically determined capability to repair DNA damage appears to be a key aging factor in comparisons of several species of birds and animals. When the rate of accumulation of DNA damage (double-strand breaks) in the leukocytes of dolphins, goats, reindeer, American flamingos, and griffon vultures was compared to the longevity of individuals of these different species, it was found that the species with longer lifespans have slower accumulation of DNA damage. [ 18 ] The activity of the enzyme PARP1, employed in several DNA repair process, was compared in thirteen different mammalian species and its activity was found to correlate with the maximum lifespan of the species. [ 19 ] In humans, genetically determined DNA repair capability appears to influence lifespan. Lymphoblastoid cell lines established from blood samples of humans who lived past 100 years (centenarians) were found to have a significantly higher activity of the DNA repair protein Poly (ADP-ribose) polymerase ( PARP ) than cell lines from younger individuals (20 to 70 years old). [ 20 ]
A 2008 paper found a U-shaped association between paternal age and the overall mortality rate in children (i.e., mortality rate up to age 18). [ 21 ] Although the relative mortality rates were higher, the absolute numbers were low, because of the relatively low occurrence of genetic abnormality. The study has been criticized for not adjusting for maternal health, which could have a large effect on child mortality. [ 22 ] The researchers also found a correlation between paternal age and offspring death by injury or poisoning, indicating the need to control for social and behavioral confounding factors. [ 23 ] | https://en.wikipedia.org/wiki/Genetics_of_aging |
About 10–15% of human couples are infertile , unable to conceive. In approximately in half of these cases, the underlying cause is related to the male. The underlying causative factors in the male infertility can be attributed to environmental toxins, systemic disorders such as, hypothalamic–pituitary disease , testicular cancers and germ-cell aplasia . Genetic factors including aneuploidies and single-gene mutations are also contributed to the male infertility. Patients with nonobstructive azoospermia or oligozoospermia show microdeletions in the long arm of the Y chromosome and/or chromosomal abnormalities, each with the respective frequency of 9.7% and 13%. A large percentage of human male infertility is estimated to be caused by mutations in genes involved in primary or secondary spermatogenesis and sperm quality and function. Single-gene defects are the focus of most research carried out in this field. [ 1 ] [ 2 ]
NR5A1 mutations are associated with male infertility, suggesting the possibility that these mutations cause the infertility. However, it is possible that these mutations individually have no major effect and only contribute to the male infertility by collaboration with other contributors such as environmental factors and other genomics variants. [ 3 ] Vice versa, existence of the other alleles could reduce the phenotypic effects of impaired NR5A1 proteins and attenuate the expression of abnormal phenotypes and manifest male infertility solely.
Nuclear receptor subfamily 5 group A member 1 (NR5A1), also known as SF1 or Ad4BP ( MIM 184757), is located on the long arm of chromosome 9 (9q33.3). The NR5A1 is an orphan nuclear receptor that was first identified following the search for a common regulator of the cytochrome P450 steroid hydroxylase enzyme family. This receptor is a pivotal transcriptional regulator of an array of genes involved in reproduction, steroidogenesis and male sexual differentiation and also plays a crucial role in adrenal gland formation in both sexes. NR5A1 regulates the Müllerian inhibitory substance by binding to a conserved upstream regulatory element and directly participates in the process of mammalian sex determination through Müllerian duct regression. Targeted disruption of NR5A1 (Ftzf1) in mice results in gonadal and adrenal agenesis, persistence of Müllerian structures and abnormalities of the hypothalamus and pituitary gonadotropes. Heterozygous animals demonstrate a milder phenotype including an impaired adrenal stress response and reduced testicular size. In humans, NR5A1 mutations were first described in patients with 46, XY karyotype and disorders of sex development (DSD), Müllerian structures and primary adrenal failure (MIM 612965). After that, heterozygous NR5A1 mutations were described in seven patients showing 46, XY karyotype and ambiguous genitalia, gonadal dysgenesis , but no adrenal insufficiency. Since then, studies have confirmed that mutations in NR5A1 in patients with 46, XY karyotype cause severe underandrogenisation, but no adrenal insufficiency, establishing dynamic and dosage-dependent actions for NR5A1. Subsequent studies revealed that NR5A1 heterozygous mutations cause primary ovarian insufficiency (MIM 612964). [ 4 ] [ 5 ] [ 6 ] [ 7 ]
Recently, NR5A1 mutations have been related to human male infertility (MIM 613957). These findings substantially increase the number of NR5A1 mutations reported in humans and show that mutations in NR5A1 can be found in patients with a wide range of phenotypic features, ranging from 46,XY sex reversal with primary adrenal failure to male infertility. For the first time, Bashamboo et al. (2010) conducted a study on the nonobstructive infertile men (a non-Caucasian mixed ancestry n = 315), which resulted in the report of all missense mutations in the NR5A1 gene with 4% frequency. Functional studies of the missense mutations revealed impaired transcriptional activation of NR5A1-responsive target genes. Subsequently, three missense mutations were identified as associated with and most likely the cause of the male infertility, according to computational analyses. [ 8 ] The study indicated that the mutation frequency is below 1% ( Caucasian German origin, n = 488). [ 8 ] In another study the coding sequence of NR5A1 has been analysed in a cohort of 90 well-characterised idiopathic Iranian azoospermic infertile men versus 112 fertile men. [ 9 ] Heterozygous NR5A1 mutations were found in 2 of 90 (2.2%) of cases. [ 9 ] These two patients harboured missense mutations within the hinge region (p.P97T) and ligand-binding domain (p.E237K) of the NR5A1 protein. [ 9 ]
Small supernumerary marker chromosome (sSMCs) are extra chromosomes consisting of parts of virtually any other chromosome(s). By definition, they are smaller than one of the smaller chromosomes, chromosome 20. sSMCs typically develop in individuals as a result of abnormal chromosomal events occurring in one of their parent's eggs, sperms, or zygotes but in less common cases are directly inherited from a parent carrier of the sSMC. [ 10 ] sSMCs occur in 0.125% of all infertility cases, [ 11 ] are 7.5-fold more common in men, [ 11 ] and in women are often associated with ovarian failure . [ 12 ] The sSMCs associated with infertility can consist of parts of virtually any other chromosome. While only a small percentage of these sSMCs have had their genetic material defined, those that have include sSMCs containing: a) band 11.1 from the short arm of chromosome 15 (notated as (15)q11.1)(this sSMC is associated with premature ovarian failure); b) band ll.2 from the short arm of chromosome 13 (notated as (13)q11.2)(this sSMC is associated with oligoasthenoteratozoospermia, i.e. oligozoospermia [low sperm count], teratozoospermia [presence of sperm with abnormal shapes], and asthenozoospermia [sperm with reduced motility]); [ 12 ] c) band 11 from the short arm of chromosome 14 (notated as (14)q11.1)(this sCMC is associated with otherwise uncharacterized infertility; and d) band 11 on the short arm of chromosome 22 notated as (22)q11)(this sSMC is associated with repeated abortions). [ 13 ] | https://en.wikipedia.org/wiki/Genetics_of_infertility |
The genetic influences of post-traumatic stress disorder ( PTSD ) are not understood well due to the limitations of any genetic study of mental illness; in that, it cannot be ethically induced in selected groups. Because of this, all studies must use naturally occurring groups with genetic similarities and differences, thus the amount of data is limited. Still, genetics play some role in the development of PTSD.
Approximately 30% of the variance in PTSD is caused by genetics alone. [ 1 ] For twins exposed to combat in the Vietnam War , a monozygotic (identical) twin with PTSD was associated with an increased risk of the co-twin having PTSD, as compared to dizygotic (non-identical) twins; [ 2 ] additionally, assaultive trauma (compared to non-assaultive trauma) was more likely to exacerbate these effects. [ 3 ]
There is also evidence that those with a genetically smaller hippocampus are more likely to develop PTSD following a traumatic event. [ citation needed ]
Research has also found that PTSD shares many genetic influences common to other psychiatric disorders. Panic and generalized anxiety disorders and PTSD share 60% of the same genetic variance. Alcohol, nicotine, and drug dependence share greater than 40% genetic similarities. [ 1 ] Additional disorders—such as depression , schizophrenia , and bipolar disorder —share the same fundamental genetic phenotypes as PTSD.
An individual's potential for onset of many psychological disorders is heavily affected by genetic phenotypes , yet this is not the only contributing factor. Environment plays an important role as well, especially for trauma-based disorders such as PTSD, considering that certain life experiences can trigger the activation of an underlying genetic phenotype which might have been previously dormant. [ 4 ] This can be further understood by examining the diathesis-stress model for the onset of psychological disorders, which explains that certain individuals, due to their genetic phenotypes, are more susceptible to psychological disorders when encountering the same stressful life situations or stimuli as other individuals without these same underlying genetic phenotypes. [ 5 ]
Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the brain. A 2009 study [ 6 ] reported a significant interaction between three single nucleotide polymorphisms (SNP) in the GABA alpha-2 receptor gene and the severity of childhood trauma in predicting PTSD in adults. [ 1 ] Another study [ 7 ] found an association between a specific SNP of the RGS2 gene [ note 1 ] and PTSD symptoms in adults who experienced high environmental stress (hurricane exposure) and low social support. [ 1 ]
Studies in 2008 found that several SNPs in the FKBP5 (FK506 binding protein 5) gene interact with childhood trauma to predict severity of adult PTSD. [ 8 ] [ 9 ] These findings suggest that individuals with these SNPs who are abused as children are more susceptible to PTSD as adults. This is particularly important given that FKBP5 SNPs have previously been associated with peritraumatic dissociation in medically injured children (that is, dissociation at the time of the childhood trauma), [ 10 ] [ 11 ] which has itself been shown to be predictive of PTSD. [ 12 ] [ 13 ] Furthermore, FKBP5 may be less expressed in those with current PTSD. [ 14 ]
In 2011, another study found that a single SNP in a putative estrogen response element on the ADCYAP1R1 gene [ note 2 ] predicts PTSD diagnosis and symptoms in females. [ 15 ] Incidentally, this SNP is also associated with fear discrimination. The study suggests that perturbations in the PACAP /PAC1 pathway are involved in abnormal stress responses underlying PTSD.
PTSD is a psychiatric disorder that requires an environmental event that individuals may variously respond to. Because of this, gene-environment studies tend to be the most indicative of their effect on the probability of PTSD than studies of the main effect of the gene. Studies have demonstrated the interaction between the FKBP5 gene and childhood environment to predict the severity of PTSD. Polymorphisms in FKBP5 have been associated with peritraumatic dissociation in mentally ill children. [ 1 ]
A 2008 study of highly traumatized, inner city African Americans demonstrated that four polymorphisms of the FKBP5 gene interacted with severity of childhood abuse to predict severity of adult PTSD symptoms. This finding was partially replicated in a 2010 study, which reported that within the African American population, the TT genotype of the FKBP5 gene is associated with the highest risk of PTSD among those having experienced childhood adversity, while those with this genotype that experienced no childhood adversity had the lowest risk of PTSD. [ 1 ] In addition, alcohol dependence interacts with the FKBP5 polymorphisms and childhood adversity to increase the risk of PTSD in these populations.
A 2005 study found that FKPB5 mRNA was differentially expressed in emergency room trauma patients who were later diagnosed with PTSD. However, a 2009 study found FKPB5 mRNA expression was reduced in 9/11 survivors diagnosed with PTSD. [ 1 ]
Catechol-O-methyl transferase (COMT) is an enzyme that catalyzes the extraneuronal breakdown of catecholamines . The gene that codes for COMT has a functional polymorphism in which a valine has been replaced with a methionine at codon 158. This polymorphism has lower enzyme activity and has been tied to a slower breakdown of the catecholamines. A study of Rwandan genocide survivors indicated that carriers of the Val allele demonstrated the expected response relationship between the higher number of lifetime traumatic events and a lifetime diagnosis of PTSD. However, those with homozygotes for the Met/Met genotype demonstrated a high risk of lifetime PTSD independent of the number of traumatic experiences. Those with Met/Met genotype also demonstrated a reduced extinction of conditioned fear responses which may account for the high risk for PTSD experienced by this genotype. [ 1 ]
Many genes impact the limbic-frontal neurocircuitry as a result of its complexity. The main effect of the D2A1 allele of the dopamine receptor D2 ( DRD2 ) gene has a strong association with the diagnosis of PTSD. The D2A1 allele has also shown a significant association to PTSD in those having engaged in harmful drinking. In addition, a polymorphism in the dopamine transporter SLC6A3 gene has a significant association with chronic PTSD. A polymorphism of the serotonin receptor 2A gene has been associated with PTSD in Korean women. The short allele of the promoter region of the serotonin transporter (5-HTTLPR) has been shown to be less efficient than the long allele and is associated with the amygdala response for the extinction of fear conditioning. However, the short allele is associated with a decreased risk of PTSD in a low-risk environment, but a high risk of PTSD in a high-risk environment. The s/s genotype demonstrated a high risk for the development of PTSD even in response to a small number of traumatic events, but those with the l allele demonstrate increased rates of PTSD with increasing traumatic experiences. [ 1 ]
A genome-wide association study (GWAS) offers an opportunity to identify novel risk variants for PTSD that will in turn inform our understanding of the etiology of the disorder. Early results indicate the feasibility and potential power of GWAS to identify biomarkers for anxiety-related behaviors that suggest a future of PTSD. These studies will lead to the discovery of novel loci for the susceptibility and symptomatology of anxiety disorders including PTSD. [ dubious – discuss ] [ 1 ]
Epigenetic modification is an environmentally induced change in DNA that alters a gene's function rather than its structure. Its biological mechanism typically involves the methylation of cytosine within a gene, which leads to decreased transcription and thus reduced expression of the gene. Epigenetic modification can offer insight into the importance of developmental timing of stressor exposure in producing the phenotypic changes associated with PTSD. [ 1 ]
Neuroendocrine alterations seen in animal models parallel those of PTSD in humans, where low basal cortisol and enhanced suppression of cortisol in response to synthetic glucocorticoid becomes hereditary . Lower levels of glucocorticoid receptor (GR) mRNA have been demonstrated in the hippocampus of suicide victims with histories of childhood abuse. Although it has not been possible to monitor the state of methylation over time, the interpretation is that early developmental methylation changes are long-lasting and enduring. It is hypothesized that epigenetic-mediated changes in the HPA axis could be associated with an increased vulnerability to PTSD following traumatic events. These findings support the mechanism in which early life trauma strongly validates as a risk factor for PTSD development in adulthood by recalibrating the set point and stress-responsivity of the HPA axis. [ 1 ]
Epigenetic mechanisms may also be relevant to the intrauterine environment. Pregnant mothers who developed PTSD from the 9/11 attacks produced infants with lower salivary cortisol levels, but only if the traumatic exposure occurred during the third trimester of gestation. These changes occur via transmission of hormonal responses to the fetus, leading to a reprogramming of the glucocorticoid responsivity in the offspring. [ 1 ] Separate studies have reported an increased risk for PTSD and low cortisol levels in the offspring of female Holocaust survivors with PTSD. [ 1 ]
Evolutionary psychology interprets fear responses as adaptations that may have been useful in the ancestral environment to avoid or cope with various threats. In general, mammals display several defensive behaviors roughly dependent on how close the threat is: avoidance, vigilant immobility, withdrawal, aggressive defense, appeasement, and finally complete frozen immobility (the last possibly to confuse a predator's attack reflex or to simulate a dead and contaminated body). PTSD may correspond to and be caused by overactivation of such fear circuits. Thus, PTSD avoidance behaviors may correspond to mammal avoidance of and withdrawal from threats. Heightened memory of past threats may increase avoidance of similar situations in the future as well as be a prerequisite for analyzing the past threat and develop better defensive behaviors if the threat should recur. PTSD hyperarousal may correspond to vigilant immobility and aggressive defense. Complex post-traumatic stress disorder (and phenomena such as the Stockholm syndrome ) may in part correspond to the appeasement stage and possibly the frozen immobility stage. [ 16 ] [ 17 ]
There may be evolutionary explanations for differences in resilience to traumatic events. For instance, PTSD is five to ten times less common following traumatic fires than physical abuse or combat. This may be explained by events such as forest fires long being part of the evolutionary history of mammals. [ 18 ] In contrast, PTSD is much more common following modern warfare, perhaps because prolonged modern combat is an evolutionarily new development and very unlike the quick inter-group raids that are argued to have characterized the Paleolithic . [ 19 ] [ 20 ] | https://en.wikipedia.org/wiki/Genetics_of_post-traumatic_stress_disorder |
Synesthesia is a neurological condition where activating one sense unintentionally triggers a response in another. [ 1 ] For example, hearing sounds may evoke the perception of colors. While the phenomenon has intrigued researchers for decades, its genetic foundations are still not fully understood. Initial theories suggested straightforward inheritance patterns, such as X-linked dominance, based on familial trends and the apparent gender bias in reported cases. However, further studies have challenged these early models, revealing a far more intricate and varied genetic picture. Advances in genetic research, including genome-wide analyses and twin studies, point to multiple contributing factors, ranging from rare genetic mutations to early brain development and environmental influences. The understanding of synesthesia inheritance has shifted from basic genetic assumptions to more complex, multifactorial models supported by recent scientific discoveries.
The genetic mechanism of synesthesia has long been debated, with researchers initially proposing that it followed a simple X-linked inheritance pattern , largely due to the observed higher prevalence in women and the apparent absence of male-to-male transmission in early family studies. [ 2 ] In an X-linked model, a male with synesthesia would not pass the condition to his sons, as they inherit his Y chromosome—not his X—making the lack of male-male transmission seemingly supportive of this hypothesis. However, subsequent documented cases of male synesthetes passing the condition to their sons directly contradicted this assumption. [ 3 ] [ 4 ] These findings suggest that synesthesia cannot be solely linked to the X chromosome, indicating that a non-X-linked, autosomal, or more complex mode of inheritance must be involved.
Recent research by Tilot et. al (2018) challenges the previous assumption that synesthesia is simply an X-linked trait, instead providing strong evidence that it is genetically heterogeneous and influenced by multiple rare genetic variants. [ 5 ] For example, an analysis of three multigenerational families with sound–color synesthesia revealed 37 rare genetic variants associated with the condition, none of which were common across all families. This finding supports the idea that synesthesia emerges from different genetic factors unique to each individual. Notably, six key genes identified, COL4A1 , ITGA2 , MYO10 , ROBO3 , SLC9A6 , and SLIT2 are involved in axonogenesis, the developmental process by which neurons form connections in the brain. These results indicate that synesthesia might originate from variations in neural pathway formation and maintenance during early brain development, highlighting how the brain's structural wiring can affect sensory experiences.
The idea that synesthesia follows a simple Mendelian or X-linked pattern of inheritance has been increasingly challenged by failure to explain the wide variation in synesthetic experience types, intensities, and age of onset, even among members of the same family. This variability suggested that the condition could not be explained by a single gene or inheritance pattern. Further evidence came from case studies of monozygotic (genetically identical) twins, where only one twin exhibited synesthesia despite both sharing the same genome. [ 2 ] This finding emphasized that genetic similarity alone is insufficient to ensure the trait’s expression and pointed toward a more complex interplay between genetic, epigenetic , and environmental factors.
As a result, researchers have shifted their focus toward more complex models of inheritance. Synesthesia is now considered to be an oligogenic condition, meaning a primary mutation may predispose an individual to the condition, but additional mutations in other genes are required for the phenotype to be expressed. [ 6 ] Moreover, synesthesia exhibits locus heterogeneity , where different genes — and different locations within those genes — may contribute to similar synesthetic traits in different individuals. These patterns help explain the phenotypic diversity seen both within and across families.
To investigate the genetic basis of synesthesia, researchers have conducted genome-wide linkage studies, which analyze how traits are inherited within families. These studies often use a statistical measure called the LOD score (logarithm of the odds), which assesses the likelihood that two loci—such as a genetic marker and a trait—are located near each other on a chromosome and therefore inherited together. A high LOD score indicates a strong likelihood of genetic linkage, suggesting that a particular region of the genome may contain genes associated with the trait. Several studies have identified regions of suggestive or significant linkage with synesthesia using this method. [ 7 ]
Supporting this, there is no single genetic variant shared across all synesthetes, further reinforcing the concept of locus heterogeneity, where different genetic factors can lead to the same phenotype. [ 5 ] Multiple synesthetic families revealed distinct sets of rare variants in each family, suggesting that synesthesia arises from diverse genetic mechanisms rather than a single, uniform mutation. These findings align with broader research pointing to the role of early-life developmental processes, particularly in how neural connections are formed and maintained, in shaping synesthetic experiences.
Notably, one of the genomic regions with the highest LOD score in an individual with auditory-visual synesthesia has also been linked to autism spectrum disorders —a condition that similarly involves atypical sensory and perceptual processing. Based on the twin study by Taylor et al., there is compelling evidence for a genetic connection between synesthesia and autism spectrum disorder (ASD), particularly through shared perceptual processing traits and overlapping non-social autistic traits. The study found that individuals who reported synesthesia also tended to score higher on autistic trait measures, especially in the domains of repetitive behaviours, restricted interests, and attention to detail (RRBI-D). This association was predominantly explained by shared genetic factors rather than shared environments, suggesting a genetic overlap between the two conditions. [ 8 ]
The study estimated that 46% of the variance in synesthesia could be attributed to additive genetic factors, while the remaining 54% was due to non-shared environmental factors (i.e., factors unique to each individual, such as personal experiences or minor developmental differences). When examining the overlap between synesthesia and ASD traits, genetic factors accounted for over 70% of their phenotypic correlation, particularly with RRBI-D traits. These findings support the hypothesis that atypical sensory processing, which is characteristic of both conditions, may stem from shared biological mechanisms, potentially involving genes related to perceptual processing, axonogenesis, and synaptic connectivity. [ 9 ]
The Universal Neonatal Synesthesia Hypothesis suggests that synesthesia is a default state of the infant brain, with excessive or non-specific neural connectivity between sensory regions. According to this view, infants may begin life with cross-activation between sensory modalities, meaning that all humans may be born with the potential for synesthetic experiences. However, in most individuals, these connections are eliminated through a process known as synaptic pruning, which refines and specializes neural circuits during early development. [ 10 ]
Evidence supporting this hypothesis includes neurobiological findings showing that the number of synaptic connections in the human brain peaks shortly after birth and then declines rapidly due to pruning mechanisms. Some white matter tracts connecting sensory areas, such as those linking auditory and visual cortices, have been shown to diminish in early childhood, aligning with the idea that synesthetic pathways are originally present but later removed in most individuals. In synesthetes, it is thought that this pruning process may be incomplete or altered, allowing these early cross-sensory connections to persist into adulthood. This would explain the presence of stable and involuntary inducer-concurrent pairings (e.g., seeing colors when hearing music) in synesthetes. [ 11 ]
A genome scan of an individual with colored sequence synesthesia—a form in which elements such as days of the week are associated with specific colors—identified a unique region of linkage containing several genes involved in various aspects of neurodevelopment and brain function. [ 13 ] These genes are categorized below according to their biological roles:
Specific Genomic Regions
Earlier studies proposed specific genomic regions, 5q33, 6p12, 12p12, and 2q24 being linked to synesthesia based on family linkage analyses. [ 14 ] However, whole-exome sequencing (WES) in three synesthetic families uncovered rare genetic variants not present in those previously identified regions. [ 5 ] These findings provide support for genetic heterogeneity in synesthesia, indicating that different families may inherit the trait through distinct genetic pathways.
While synesthesia is traditionally viewed as a congenital condition, emerging evidence suggests that associative learning and environmental exposure play a significant role in its development. In a landmark study, Bor et al. (2014) demonstrated that non-synesthetic adults can be trained to develop synesthesia-like experiences through an extensive, adaptive nine-week training program. Participants repeatedly practiced grapheme-color pairings using memory tasks, reading activities, and exposure to colored letters, mimicking the natural learning processes of childhood. [ 15 ]
Following training, most participants exhibited behavioral and physiological markers consistent with genuine synesthesia, such as enhanced Stroop effects , color consistency, and even skin conductance responses to trained stimuli. Importantly, nine out of fourteen participants also reported vivid phenomenological experiences, including seeing colors "in the mind’s eye" or as visual overlays on letters—hallmarks of true grapheme-color synesthesia. These effects were stronger when letter-color pairings had semantic associations (e.g., “r” for red), suggesting a key role for conceptual connections in synesthesia formation. Although these abilities tended to fade after training ceased, the findings support the idea that synesthetic experiences can be acquired in adulthood under the right conditions. [ 16 ]
Recent studies have compared the perceptual and cognitive profiles of individuals with synesthesia and those with schizophrenia, identifying both distinct and overlapping characteristics. Synesthetes often display heightened perceptual integration, particularly in tasks involving multisensory associations. This phenomenon is linked to increased reliance on top-down processing , where prior knowledge and internal expectations influence perception. Conversely, individuals with schizophrenia tend to rely more heavily on bottom-up sensory input, often resulting in reduced perceptual stability and difficulties in integrating context with raw stimuli. [ 17 ]
Behavioral experiments using visibility threshold tasks have demonstrated that synesthetes can identify stimuli with weaker sensory input if the stimuli align with prior associations, such as color-letter pairings. In contrast, individuals with schizophrenia required stronger sensory input to perceive the same stimuli, indicating an impaired use of prior perceptual knowledge. [ 17 ] These findings suggest divergent strategies in perceptual inference, potentially arising from differences in neural prediction mechanisms.
On the genetic level, recent research has explored whether synesthesia and schizophrenia share overlapping risk profiles. One genome-wide association study examined polygenic risk scores (PRS) for schizophrenia in individuals with grapheme–color synesthesia. Results showed a small but statistically significant correlation (Nagelkerke's R² = 0.0047, empirical p = 0.0027), indicating minimal genetic overlap between the two conditions. [ 18 ] The study concluded that while some commonalities may exist in genes associated with sensory processing, synesthesia is not strongly predicted by the same genetic architecture that underlies schizophrenia.
Furthermore, structural and functional neuroimaging studies suggest that synesthesia is associated with increased local connectivity, particularly between sensory cortical areas, whereas schizophrenia often involves reduced long-range connectivity, especially within fronto-temporal and fronto-parietal networks. [ 18 ] These findings support the hypothesis that synesthesia and schizophrenia may reflect opposite ends of a spectrum in neural organization related to sensory integration. | https://en.wikipedia.org/wiki/Genetics_of_synesthesia |
Genetypes is a taxonomic concept proposed in 2010 to describe any genetic sequences from type specimens . [ 1 ] [ 2 ] This nomenclature integrates molecular systematics and terms used in biological taxonomy . This nomenclature is designed to label, or flag, genetic sequences that were sampled from type specimens. The nomenclature of genetypes proposes that genetic sequences from a holotype should be referred to as a “hologenetype” (from “holotype” and “genetype”), sequences from a topotype should be a “topogenetype”, and so forth. In addition, the genetic marker (s) used should be incorporated into the nomenclature (e.g. paragenetype ND2).
The genetypes nomenclatural system could be used to flag “gold standard” sequences that due to their direct link to type specimens will be more credible than standard sequences whose species identification may be problematic. Misidentifications plague many sequences on GenBank [ citation needed ] and having some sequences that are linked to type specimens will help locate and manage misidentifications and to create positively identified "gold standard" sequences available for comparison. It is suggested that this nomenclature be used in publications and databases that display or discuss sequences from type specimens. [ 3 ] [ 2 ]
Examples of genetypes include:
The genetypes concept was superseded by the GenSeq concept, proposed in 2013 due to some confusion among researchers that genetypes were equivalent to name-bearing types . [ 6 ] [ clarification needed ] | https://en.wikipedia.org/wiki/Genetypes |
The Protocol for the Prohibition of the Use in War of Asphyxiating, Poisonous or other Gases, and of Bacteriological Methods of Warfare , usually called the Geneva Protocol , is a treaty prohibiting the use of chemical and biological weapons in international armed conflicts . It was signed at Geneva on 17 June 1925 and entered into force on 8 February 1928. It was registered in League of Nations Treaty Series on 7 September 1929. [ 4 ] The Geneva Protocol is a protocol to the Convention for the Supervision of the International Trade in Arms and Ammunition and in Implements of War signed on the same date, and followed the Hague Conventions of 1899 and 1907 .
It prohibits the use of "asphyxiating, poisonous or other gases, and of all analogous liquids, materials or devices" and "bacteriological methods of warfare". This is now understood to be a general prohibition on chemical weapons and biological weapons between state parties, but has nothing to say about production, storage or transfer. Later treaties did cover these aspects – the 1972 Biological Weapons Convention (BWC) and the 1993 Chemical Weapons Convention (CWC).
A number of countries submitted reservations when becoming parties to the Geneva Protocol, declaring that they only regarded the non-use obligations as applying to other parties and that these obligations would cease to apply if the prohibited weapons were used against them. [ 5 ] [ 6 ]
In the Hague Conventions of 1899 and 1907 , the use of dangerous chemical agents was outlawed. In spite of this, the First World War saw large-scale chemical warfare . France used tear gas in 1914, but the first large-scale successful deployment of chemical weapons was by the German Empire in Ypres , Belgium in 1915, when chlorine gas was released as part of a German attack at the Battle of Gravenstafel . Following this, a chemical arms race began, with the United Kingdom , Russia , Austria-Hungary , the United States , and Italy joining France and Germany in the use of chemical weapons. [ citation needed ]
This resulted in the development of a range of horrific chemicals affecting lungs, skin, or eyes. Some were intended to be lethal on the battlefield, like hydrogen cyanide , and efficient methods of deploying agents were invented. At least 124,000 tons were produced during the war. In 1918, about one grenade out of three was filled with dangerous chemical agents. [ citation needed ] Around 500k-1.3 million casualties of the conflict were attributed to the use of gas, and the psychological effect on troops may have had a much greater effect. A few thousand civilians also became casualties as collateral damage or due to production accidents. [ 7 ]
The Treaty of Versailles included some provisions that banned Germany from either manufacturing or importing chemical weapons. Similar treaties banned the First Austrian Republic , the Kingdom of Bulgaria , and the Kingdom of Hungary from chemical weapons, all belonging to the losing side, the Central powers . Russian bolsheviks and Britain continued the use of chemical weapons in the Russian Civil War and possibly in the Middle East in 1920.
Three years after World War I, the Allies wanted to reaffirm the Treaty of Versailles, and in 1922 the United States introduced the Treaty relating to the Use of Submarines and Noxious Gases in Warfare at the Washington Naval Conference . [ 8 ] Four of the war victors, the United States , the United Kingdom , the Kingdom of Italy and the Empire of Japan , gave consent for ratification , but it failed to enter into force as the French Third Republic objected to the submarine provisions of the treaty. [ 8 ]
At the 1925 Geneva Conference for the Supervision of the International Traffic in Arms the French suggested a protocol for non-use of poisonous gases. The Second Polish Republic suggested the addition of bacteriological weapons. [ 9 ] It was signed on 17 June. [ 10 ]
Eric Croddy, assessing the Protocol in 2005, took the view that the historic record showed it had been largely ineffectual. Specifically it does not prohibit: [ 10 ]
In light of these shortcomings, Jack Beard notes that "the Protocol (...) resulted in a legal framework that allowed states to conduct [biological weapons] research, develop new biological weapons, and ultimately engage in [biological weapons] arms races". [ 6 ]
As such, the use of chemical weapons inside the nation's own territory against its citizens or subjects employed by Spain in the Rif War until 1927, [ 11 ] [ 12 ] Japan against Seediq indigenous rebels in Taiwan (then part of the Japanese colonial empire ) in 1930 during the Musha Incident , Iraq against ethnic Kurdish civilians in the 1988 attack on Halabja during the Iran–Iraq War , and Syria or Syrian opposition forces during the Syrian civil war . [ 13 ]
Despite the U.S. having been a proponent of the protocol, the U.S. military and American Chemical Society lobbied against it, causing the U.S. Senate not to ratify the protocol until 1975, the same year when the United States ratified the Biological Weapons Convention . [ 10 ] [ 14 ]
Several state parties have deployed chemical weapons for combat in spite of the treaty. Italy used mustard gas against the Ethiopian Empire in the Second Italo-Ethiopian War . In World War II , Germany employed chemical weapons in combat on several occasions along the Black Sea , notably in Sevastopol , where they used toxic smoke to force Soviet resistance fighters out of caverns below the city. They also used asphyxiating gas in the catacombs of Odesa in November 1941, following their capture of the city , and in late May 1942 during the Battle of the Kerch Peninsula in eastern Crimea , perpetrated by the Wehrmacht's Chemical Forces and organized by a special detail of SS troops with the help of a field engineer battalion. [ 15 ] After the battle in mid-May 1942, the Germans gassed and killed almost 3,000 of the besieged and non-evacuated Red Army soldiers and Soviet civilians hiding in a series of caves and tunnels in the nearby Adzhimushkay quarry . [ 16 ]
During the 1980-1988 Iran-Iraq War, Iraq is known to have employed a variety of chemical weapons against Iranian forces. Some 100,000 Iranian troops were casualties of Iraqi chemical weapons during the war. [ 17 ] [ 18 ] [ 19 ]
In 1966, United Nations General Assembly resolution 2162B called for, without any dissent, all states to strictly observe the protocol. In 1969, United Nations General Assembly resolution 2603 (XXIV) declared that the prohibition on use of chemical and biological weapons in international armed conflicts, as embodied in the protocol (though restated in a more general form), were generally recognized rules of international law. [ 20 ] Following this, there was discussion of whether the main elements of the protocol now form part of customary international law , and now this is widely accepted to be the case. [ 14 ] [ 21 ]
There have been differing interpretations over whether the protocol covers the use of harassing agents, such as adamsite and tear gas , and defoliants and herbicides , such as Agent Orange , in warfare. [ 14 ] [ 22 ] The 1977 Environmental Modification Convention prohibits the military use of environmental modification techniques having widespread, long-lasting or severe effects. Many states do not regard this as a complete ban on the use of herbicides in warfare, but it does require case-by-case consideration. [ 23 ] The 1993 Chemical Weapons Convention effectively banned riot control agents from being used as a method of warfare, though still permitting it for riot control . [ 24 ]
In recent times, the protocol had been interpreted to cover non-international armed conflicts as well international ones. In 1995, an appellate chamber in the International Criminal Tribunal for the former Yugoslavia stated that "there had undisputedly emerged a general consensus in the international community on the principle that the use of chemical weapons is also prohibited in internal armed conflicts." In 2005, the International Committee of the Red Cross concluded that customary international law includes a ban on the use of chemical weapons in internal as well as international conflicts. [ 25 ]
However, such views drew general criticism from legal authors. They noted that much of the chemical arms control agreements stems from the context of international conflicts. Furthermore, the application of customary international law to banning chemical warfare in non-international conflicts fails to meet two requirements: state practice and opinio juris . Jillian Blake & Aqsa Mahmud cited the periodic use of chemical weapons in non-international conflicts since the end of WWI (as stated above ) as well as the lack of existing international humanitarian law (such as the Geneva Conventions ) and national legislation and manuals prohibiting using them in such conflicts. [ 26 ] Anne Lorenzat stated the 2005 ICRC study was rooted in "'political and operational issues rather than legal ones". [ 27 ]
To become party to the Protocol, states must deposit an instrument with the government of France (the depositary power). Thirty-eight states originally signed the Protocol. France was the first signatory to ratify the Protocol on 10 May 1926. El Salvador, the final signatory to ratify the Protocol, did so on 26 February 2008. As of April 2021, 146 states have ratified, acceded to, or succeeded to the Protocol, [ 3 ] most recently Colombia on 24 November 2015.
A number of countries submitted reservations when becoming parties to the Geneva Protocol, declaring that they only regarded the non-use obligations as applying with respect to other parties to the Protocol and/or that these obligations would cease to apply with respect to any state, or its allies, which used the prohibited weapons. Several Arab states also declared that their ratification did not constitute recognition of, or diplomatic relations with, Israel , or that the provision of the Protocol were not binding with respect to Israel.
Generally, reservations not only modify treaty provisions for the reserving party, but also symmetrically modify the provisions for previously ratifying parties in dealing with the reserving party. [ 14 ] : 394 Subsequently, numerous states have withdrawn their reservations, including the former Czechoslovakia in 1990 prior to its dissolution , [ 28 ] or the Russian reservation on biological weapons that "preserved the right to retaliate in kind if attacked" with them, which was dissolved by President Yeltsin . [ 29 ]
According to the Vienna Convention on Succession of States in respect of Treaties , states which succeed to a treaty after gaining independence from a state party "shall be considered as maintaining any reservation to that treaty which was applicable at the date of the succession of States in respect of the territory to which the succession of States relates unless, when making the notification of succession, it expresses a contrary intention or formulates a reservation which relates to the same subject matter as that reservation." While some states have explicitly either retained or renounced their reservations inherited on succession, states which have not clarified their position on their inherited reservations are listed as "implicit" reservations.
The remaining UN member states and UN observers that have not acceded or succeeded to the Protocol are: | https://en.wikipedia.org/wiki/Geneva_Protocol |
The Geneva Rules are the rules established by the International Chemistry Committee in 1892. These rules were the beginning of international cooperation for organic chemistry nomenclature . [ 1 ] They were decided upon by a group of 34 of leading chemists from 9 different European nations. Their goal was to provide rules for the naming of aliphatic compounds, some of which are still in place today such as the longest chain provides the parent name and a functional group is indicated by a suffix. They also intended to extend the rules to include naming schemes for cyclic compounds however this did not occur.
The Geneva rules for nomenclature were described in 62 paragraphs. [ 2 ] Some of these rules were:
Evieux, E. A. (1954-06-01). "The Geneva Congress on Organic Nomenclature, 1892". Journal of Chemical Education . 31 (6): 326. Bibcode : 1954JChEd..31..326E . doi : 10.1021/ed031p326 . ISSN 0021-9584 .
Hepler-Smith, Evan (2015-02-01). " "Just as the Structural Formula Does": Names, Diagrams, and the Structure of Organic Chemistry at the 1892 Geneva Nomenclature Congress". Ambix . 62 (1): 1– 28. doi : 10.1179/1745823414y.0000000006 . ISSN 0002-6980 . PMID 26173340 . S2CID 910247 .
This organic chemistry article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Geneva_Rules |
Genevac Ltd is a company which was founded in 1990 by Michael Cole. It used to specialize in the manufacture of vacuum pumps and centrifugal evaporators , but has since directed its attention to equipment designed for combinatorial chemistry . Following a series of mergers, it is currently a subsidiary of SP Industries. [ 1 ]
This article about a manufacturing company in the United Kingdom is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genevac |
Genevestigator is an application consisting of a gene expression database and tools to analyse the data. It exists in two versions, biomedical and plant, depending on the species of the underlying microarray and RNAseq as well as single-cell RNA-sequencing data. It was started in January 2004 by scientists from ETH Zurich and is currently developed and commercialized by Nebion AG.
Researchers and scientists from academia and industry use it to identify, characterize and validate novel drug targets and biomarkers, identify appropriate research models and in general to understand how gene expression changes with different treatments.
The Genevestigator database comprises transciptomic data from numerous public repositories including GEO , Array Express and renowned cancer research projects as TCGA . Depending on the license agreement, it may also contain data from private gene expression studies. All data are manually curated, quality-controlled and enriched for sample and experiment descriptions derived from corresponding scientific publications.
The number of species from where the samples are derived is constantly increasing. Currently, the biomedical version contains data from human , mouse , and rat used in biomedical research. Gene expression studies are from various research areas including oncology, immunology, neurology, dermatology and cardiovascular diseases. Samples comprise tissue biopsies and cell lines.
The plant version (no longer available) contained both, widely used model species such as arabidopsis and medicago as well as major crop species such as maize , rice , wheat and soybean . After the acquisition of Nebion AG by Immunai Inc. in July 2021, plant data began to be phased out as the biotech company prioritized their focus on biopharma data. As of 2023, the plant data is being maintained on a separate server for remaining users with a license to the plant version of Genevestigator.
More than 60,000 scientists from academia and industry use Genevestigator for their work in molecular biology , toxicogenomics , biomarker discovery and target validation. The original scientific publication has been cited over 3,500 times.
The analysis tools are divided into three major sets: | https://en.wikipedia.org/wiki/Genevestigator |
Genic capture is a hypothesis explaining the maintenance of genetic variance in traits under sexual selection . A classic problem in sexual selection is the fixation of alleles that are beneficial under strong selection, thereby eliminating the benefits of mate choice . Genic capture resolves this paradox by suggesting that additive genetic variance of sexually selected traits reflects the genetic variance in total condition. [ 1 ] A deleterious mutation anywhere in the genome will adversely affect condition, and thereby adversely affect a condition-dependent sexually selected trait. Genic capture therefore resolves the lek paradox by proposing that recurrent deleterious mutation maintains additive genetic variance in fitness by incorporating the entire mutation load of an individual. Thus any condition-dependent trait "captures" the overall genetic variance in condition. Rowe and Houle argued that genic capture ensures that good genes will become a central feature of the evolution of any sexually selected trait.
The key quantity for genic capture is vaguely defined as "condition." The hypothesis only defines condition as a quantity that correlates tightly with overall fitness , such that directional selection will always increase average condition over time. Condition should, in general, reflect overall energy acquisition, such that life-history variation reflects differential allocation to survival and sexual signalling. Genetic variation in condition should be very broadly affected by any changes in the genome. Close to equilibrium any mutation should be deleterious , thereby leading to non-zero overall mutation rate, maintaining variance in fitness.
Rowe and Houle's simple model defines a trait as the result of three heritable components, a condition-independent component a {\displaystyle a} , epistatic modification b {\displaystyle b} and condition, suggesting the following function for a trait:
T = a + b C {\displaystyle T=a+bC}
where C {\displaystyle C} is the condition of an individual. Loci contributing to C {\displaystyle C} are loosely linked and independent of loci contributing to a {\displaystyle a} and b {\displaystyle b} . Rowe and Houle then find the expected variance of T {\displaystyle T} and ignored higher-order terms (i.e. products of variances):
G T ≈ G a + b ¯ 2 G C + C ¯ 2 G b {\displaystyle G_{T}\approx G_{a}+{\bar {b}}^{2}G_{C}+{\bar {C}}^{2}G_{b}}
where G T {\displaystyle G_{T}} represents the genetic variance in the signal and analogously for other traits. Under directional selection on T {\displaystyle T} , the loci underlying a {\displaystyle a} and b {\displaystyle b} may lose all genetic variance. However, there is no qualitative difference in directional selection on C {\displaystyle C} between stabilizing selection (i.e. no sexual selection) and directional selection on T {\displaystyle T} . Therefore, the second term b ¯ 2 G C {\displaystyle {\bar {b}}^{2}G_{C}} will remain positive (due to biased mutation) and dominate G T {\displaystyle G_{T}} under sexual selection.
Genic capture can also play a role in accelerating adaptation to new environments. [ 2 ]
Genic capture was proposed as a simpler alternative to another theory explaining the lek paradox [ 3 ] that proposed that sexual selection creates disruptive selection , i.e. positive selection for genetic variance. Genic capture does not require any particular fitness function. | https://en.wikipedia.org/wiki/Genic_capture |
A geniculum is a small genu , or angular knee -like structure. The term is often used in anatomical nomenclature to designate a sharp knee-like bend in a small structure or organ. [ 1 ] [ 2 ]
For example, in the facial canal , the genicular ganglion is situated on the geniculum of the facial nerve , the point where the nerve changes its direction. [ 3 ]
This anatomy article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Geniculum |
Gennaro Maria D'Afflitto OP (1618 – 1673) was an Italian Dominican friar and military engineer who worked under Philip IV and Charles II of Spain .
Gennaro Maria D'Afflitto was born into a noble family in Naples in 1618. On 16 September 1633, he entered the Dominican convent of Santa Maria della Sanità, Naples . [ 1 ] He received a good scientific and humanistic education, and developed a keen interest in mathematics . In 1647 he met Don John Joseph of Austria , who had been sent to Naples to quell the rebellion of Masaniello . [ 1 ] He followed him in the campaign to recapture Orbetello and Porto Longone (1650) and later served as military engineer in the Spanish Army in Catalonia , Portugal and the Southern Netherlands . [ 1 ] In 1663 the Supreme Council of War appointed him as professor of mathematics in the Real Academia de Matemáticas, Artillería y Fortificación of Madrid. [ 2 ] He was in charge of the chair until 1665. In the following years, he came under the service of Ferdinando II of Tuscany again as a teacher of mathematics and military engineer. At the end of 1667 he became an advisor to the Republic of Genoa on engineering matters, and worked on the fortifications of Savona and Vado Ligure . [ 1 ] D'Afflitto is also credited with fortification works in Cuneo and Nizza Marittima on behalf of the House of Savoy . [ 1 ] He died at Naples in 1673. [ 3 ]
Around 1647 D'Afflitto entered the service as military engineer to Philip IV of Spain natural son John Joseph of Austria , who was in Naples between 1647 and 1648 to suppress Masaniello revolt. [ 4 ] Don John wanted him with him during his many military campaigns. D'Afflitto participated in the campaign to recapture Orbetello and Porto Azzurro and followed Don Giovanni to the Netherlands and Catalonia, where he took part in the siege and bombardment of Tortosa . He also worked at the fort of Peñíscola in Valencia, the fort of Santa Caterina in Cadiz, and the fort of Sanlúcar de Barrameda on the Guadalquivir. D'Afflitto was then called to Madrid to teach mathematics at the Royal Palace. From Madrid he moved on to Zaragoza around 1661, still in the service of the Spanish court, so much so that he earned the title of mathematician of His Catholic Majesty. Following the fall from grace of Don Juan Joseph, D'Afflitto entered the service of Ferdinando II de' Medici . [ 5 ] He did not remain in Florence for long: in 1667 he was in Rome (as deduced from a letter to Antonio Magliabechi ), and then moved on to Genoa where he remained until 1671. On behalf of the Republic of Genoa D'Afflitto inspected the walls of Savona and concurred with Guerrini in fortifying Vado Ligure . He passed into the service of Savoy, working on the fortifications of Cuneo and Nice. [ 6 ] Finally returning to Naples, he died in the Sanità convent in 1673.
D'Afflitto published at Madrid a treatise on fortifications in two volumes, De Munitione et Fortificatione, Libri duo . The first volume is dedicated to Don John Joseph of Austria. [ 7 ] Abstracts of this work were published at Florence in 1665, by Captain Giovanni Battista Sergiuliani, and in 1667 by Filippo Domenico Mazzenghi. Likewise, he is the author of Compendio de modernas fortificaciones (Compendium of Modern Fortifications), translated into Spanish in 1657 by Baltasar Siscara. [ 8 ] D'Afflitto wrote also a treatise on fire and explosive weapons , De igne et ignivomis (Zaragoza, 1661). The work is divided into two parts: the first deals with the nature of fire and the different kinds of fuels; the second describes various types of explosives . [ 9 ] He left in manuscript Terra seu quadripartites orbis, Compendio della Sfera universale , and a number of poems and miscellaneous tracts on philosophical and theological topics. Jonas Moore considered D'Afflitto, together with Francesco Tensini and Pietro Sardi, one of Italy's foremost experts on fortification. [ 10 ] | https://en.wikipedia.org/wiki/Gennaro_Maria_D'Afflitto |
GenoCAD is one of the earliest computer assisted design tools for synthetic biology . [ 1 ] The software is a bioinformatics tool developed and maintained by GenoFAB, Inc.. GenoCAD facilitates the design of protein expression vectors, artificial gene networks and other genetic constructs for genetic engineering and is based on the theory of formal languages . [ 2 ]
GenoCAD originated as an offshoot of an attempt to formalize functional constraints of genetic constructs using the theory of formal languages . In 2007, the website genocad.org (now retired) was set up as a proof of concept by researchers at Virginia Bioinformatics Institute , Virginia Tech . Using the website, users could design genes by repeatedly replacing high-level genetic constructs with lower level genetic constructs, and eventually with actual DNA sequences. [ 2 ]
On August 31, 2009, the National Science Foundation granted a three-year $1,421,725 grant to Dr. Jean Peccoud, an associate professor at the Virginia Bioinformatics Institute at Virginia Tech , for the development of GenoCAD. [ 3 ] GenoCAD was and continues to be developed by GenoFAB, Inc. , a company founded by Peccoud (currently CSO and acting CEO ), who was also one of the authors of the originating study. [ 2 ]
Source code for GenoCAD was originally released on SourceForge in December 2009. [ 4 ]
GenoCAD version 2.0 was released in November 2011 and included the ability to simulate the behavior of the designed genetic code. This feature was a result of a collaboration with the team behind COPASI . [ 5 ]
In April, 2015, Peccoud and colleagues published a library of biological parts, called GenoLIB, [ 6 ] that can be incorporated into the GenoCAD platform. [ 7 ]
The four aims of the project are to develop a: [ 8 ]
The main features of GenoCAD can be organized into three main categories. [ 9 ]
GenoCAD is rooted in the theory of formal languages ; in particular, the design rules describing how to combine different kinds of parts and form context-free grammars . [ 2 ]
A context free grammar can be defined by its terminals, variables, start variable and substitution rules. [ 11 ] In GenoCAD, the terminals of the grammar are sequences of DNA that perform a particular biological purpose (e.g. a promoter ). The variables are less homogeneous: they can represent longer sequences that have multiple functions or can represent a section of DNA that can contain one of multiple different sequences of DNA but perform the same function (e.g. a variable represents the set of promoters). GenoCAD includes built in substitution rules to ensure that the DNA sequence is biologically viable. Users can also define their own sets of rules for other purposes.
Designing a sequence of DNA in GenoCAD is much like creating a derivation in a context free grammar. The user starts with the start variable and repeatedly selects a variable and a substitution for it until only terminals are left. [ 2 ]
The most common alternatives to GenoCAD are Proto, GEC and EuGene [ 12 ] | https://en.wikipedia.org/wiki/GenoCAD |
Genoeconomics is an interdisciplinary field of protoscience that aims to combine molecular genetics and economics . [ 1 ]
Genoeconomics is based on the idea that economic indicators have a genetic basis — that a person's financial behaviour can be traced to their DNA and that genes are related to economic behaviour . As of 2023, the results have been inconclusive. Some minor correlations may have been identified between genetics and economic preferences. [ 2 ]
The word genoeconomics was coined in 2007. [ 3 ]
The field of economics and the economic indicators used by economists predate the Empiricist Age . [ 4 ] Genoeconomics adds biological foundations to these traditional economic indicators. [ 4 ]
Quantitative genetic data was not available to researchers until the year 2000, when the human genome was sequenced as part of the Human Genome Project . [ 3 ] Genetic milestones of the late 20th and early 21st century, such as the sequencing of the human genome, has spurred interest in research combining economics and genetics. [ citation needed ]
Genoeconomics involves the study of single-nucleotide polymorphisms (SNPs). [ 3 ] The field of genoeconomics uses genetic data to infer economic preferences such as time preference , risk aversion , and educational attainment, [ 3 ] as well as macroeconomic data such as per-capita income. [ 5 ] For example, genoeconomic methodology was used in a 2012 study of tobacco taxes in the United States , where such taxes vary across jurisdictions, to look at "the interaction of a single nicotinic receptor and state-level tobacco taxes to predict tobacco use". [ 3 ] Additionally, genoeconomic research in 2013 found that two-fifths of the "variance of educational attainment is explained by genetic factors". [ 6 ]
Some genoeconomic researchers claim that the economic success of a country can be predicted by its genetic diversity . [ 5 ] The American economist Enrico Spolaore says that genoeconomic work could "reduce barriers to the flows of ideas and innovations across populations". [ 5 ]
Genoeconomic research is prone to the public misconception that genetically-influenced behaviours are separate from environmental factors. [ 7 ] The authors of a 2012 paper said that their work "is not about a nature or nurture debate". [ 5 ]
Nature published an online article written in 2012 about the various reactions on the subject. [ 8 ] The field is criticized by biologists for lacking methodological rigour, [ 5 ] drawing conclusions about causation based on causal correlation , [ 3 ] and working with small sample sizes. [ 5 ] The political implications of the field are also a concern for some scientists; anticipating the publication of a genoeconomics article in the journal American Economic Review , a group of scientists and social scientists wrote an open letter which said that "the suggestion that an ideal level of genetic variation could foster economic growth and could even be engineered has the potential to be misused with frightening consequences to justify indefensible practices such as ethnic cleansing or genocide". [ 5 ]
As with other genetic-association research , [ 9 ] the reproducibility of genoeconomic experiments is troublesome to the field. [ 10 ] The small sample sizes used in genoeconomic research are also a problem. [ 11 ] Commonly cited by scientists as a way to improve genoeconomic research is the use of more statistically homogeneous samples. [ 12 ] | https://en.wikipedia.org/wiki/Genoeconomics |
Genomatica is a San Diego–based biotechnology company that develops and licenses biological manufacturing processes for the production of intermediate and basic chemicals. [ 1 ] [ 2 ] Genomatica’s process technology for the chemical 1,4-Butanediol (BDO) is now commercial. Genomatica produced 5 million pounds of renewable BDO in five weeks at a DuPont Tate & Lyle plant in Tennessee. [ 3 ] Its GENO BDO process has been licensed by BASF [ 4 ] and by Novamont. [ 5 ]
Genomatica was founded in San Diego in 1998 by Christophe Schilling and Bernhard Palsson. [ 6 ] Schilling's goal was to use biotechnology to make more sustainable choices in manufacturing. [ 7 ] In 2021, Lululemon partnered with Genomatica to create a plant-based nylon material, which was launched in 2023. [ 7 ]
In 2023, L'Oréal along with Unilever and Kao Corporation invested in Genomatica. [ 8 ] The investment will go toward developing plant-based personal care and cosmetics products. [ 9 ]
This biotechnology article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genomatica |
A genome is all the genetic information of an organism. [ 1 ] It consists of nucleotide sequences of DNA (or RNA in RNA viruses ). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA ), and often a substantial fraction of junk DNA with no evident function. [ 2 ] [ 3 ] Almost all eukaryotes have mitochondria and a small mitochondrial genome . [ 2 ] Algae and plants also contain chloroplasts with a chloroplast genome.
The study of the genome is called genomics . The genomes of many organisms have been sequenced and various regions have been annotated. The first genome to be sequenced was that of the virus φX174 in 1977; [ 4 ] the first genome sequence of a prokaryote ( Haemophilus influenzae ) was published in 1995; [ 5 ] the yeast ( Saccharomyces cerevisiae ) genome was the first eukaryotic genome to be sequenced in 1996. [ 6 ] The Human Genome Project was started in October 1990, and the first draft sequences of the human genome were reported in February 2001. [ 7 ]
The term genome was created in 1920 by Hans Winkler , [ 8 ] professor of botany at the University of Hamburg , Germany. The website Oxford Dictionaries and the Online Etymology Dictionary suggest the name is a blend of the words gene and chromosome . [ 9 ] [ 10 ] [ 11 ] [ 12 ] However, see omics for a more thorough discussion. A few related -ome words already existed, such as biome and rhizome , forming a vocabulary into which genome fits systematically. [ 13 ]
The term "genome" usually refers to the DNA (or sometimes RNA) molecules that carry the genetic information in an organism, but sometimes it is uncertain which molecules to include; for example, bacteria usually have one or two large DNA molecules ( chromosomes ) that contain all of the essential genetic material but they also contain smaller extrachromosomal plasmid molecules that carry important genetic information. In the scientific literature, the term 'genome' usually refers to the large chromosomal DNA molecules in bacteria. [ 14 ]
Eukaryotic genomes are even more difficult to define because almost all eukaryotic species contain nuclear chromosomes plus extra DNA molecules in the mitochondria . In addition, algae and plants have chloroplast DNA. Most textbooks make a distinction between the nuclear genome and the organelle (mitochondria and chloroplast) genomes so when they speak of, say, the human genome, they are only referring to the genetic material in the nucleus. [ 2 ] [ 15 ] This is the most common use of 'genome' in the scientific literature.
Most eukaryotes are diploid , meaning that there are two of each chromosome in the nucleus but the 'genome' refers to only one copy of each chromosome. Some eukaryotes have distinctive sex chromosomes, such as the X and Y chromosomes of mammals, so the technical definition of the genome must include both copies of the sex chromosomes. For example, the standard reference genome of humans consists of one copy of each of the 22 autosomes plus one X chromosome and one Y chromosome. [ 16 ]
A genome sequence is the complete list of the nucleotides (A, C, G, and T for DNA genomes) that make up all the chromosomes of an individual or a species. Within a species, the vast majority of nucleotides are identical between individuals, but sequencing multiple individuals is necessary to understand the genetic diversity.
In 1976, Walter Fiers at the University of Ghent (Belgium) was the first to establish the complete nucleotide sequence of a viral RNA-genome ( Bacteriophage MS2 ). The next year, Fred Sanger completed the first DNA-genome sequence: Phage X174 , of 5386 base pairs. [ 17 ] The first bacterial genome to be sequenced was that of Haemophilus influenzae , completed by a team at The Institute for Genomic Research in 1995. A few months later, the first eukaryotic genome was completed, with sequences of the 16 chromosomes of budding yeast Saccharomyces cerevisiae published as the result of a European-led effort begun in the mid-1980s. The first genome sequence for an archaeon , Methanococcus jannaschii , was completed in 1996, again by The Institute for Genomic Research. [ citation needed ]
The development of new technologies has made genome sequencing dramatically cheaper and easier, and the number of complete genome sequences is growing rapidly. The US National Institutes of Health maintains one of several comprehensive databases of genomic information. [ 18 ] Among the thousands of completed genome sequencing projects include those for rice , a mouse , the plant Arabidopsis thaliana , the puffer fish , and the bacteria E. coli . In December 2013, scientists first sequenced the entire genome of a Neanderthal , an extinct species of humans . The genome was extracted from the toe bone of a 130,000-year-old Neanderthal found in a Siberian cave . [ 19 ] [ 20 ]
Viral genomes can be composed of either RNA or DNA. The genomes of RNA viruses can be either single-stranded RNA or double-stranded RNA , and may contain one or more separate RNA molecules (segments: monopartit or multipartit genome). DNA viruses can have either single-stranded or double-stranded genomes. Most DNA virus genomes are composed of a single, linear molecule of DNA, but some are made up of a circular DNA molecule. [ 21 ]
Prokaryotes and eukaryotes have DNA genomes. Archaea and most bacteria have a single circular chromosome , [ 22 ] however, some bacterial species have linear or multiple chromosomes. [ 23 ] [ 24 ] If the DNA is replicated faster than the bacterial cells divide, multiple copies of the chromosome can be present in a single cell, and if the cells divide faster than the DNA can be replicated, multiple replication of the chromosome is initiated before the division occurs, allowing daughter cells to inherit complete genomes and already partially replicated chromosomes. Most prokaryotes have very little repetitive DNA in their genomes. [ 25 ] However, some symbiotic bacteria (e.g. Serratia symbiotica ) have reduced genomes and a high fraction of pseudogenes: only ~40% of their DNA encodes proteins. [ 26 ] [ 27 ]
Some bacteria have auxiliary genetic material, also part of their genome, which is carried in plasmids . For this, the word genome should not be used as a synonym of chromosome .
Eukaryotic genomes are composed of one or more linear DNA chromosomes. The number of chromosomes varies widely from Jack jumper ants and an asexual nemotode , [ 28 ] which each have only one pair, to a fern species that has 720 pairs. [ 29 ] It is surprising the amount of DNA that eukaryotic genomes contain compared to other genomes. The amount is even more than what is necessary for DNA protein-coding and noncoding genes because eukaryotic genomes show as much as 64,000-fold variation in their sizes. [ 30 ] However, this special characteristic is caused by the presence of repetitive DNA, and transposable elements (TEs).
A typical human cell has two copies of each of 22 autosomes , one inherited from each parent, plus two sex chromosomes , making it diploid. Gametes , such as ova, sperm, spores, and pollen, are haploid, meaning they carry only one copy of each chromosome. In addition to the chromosomes in the nucleus, organelles such as the chloroplasts and mitochondria have their own DNA. Mitochondria are sometimes said to have their own genome often referred to as the " mitochondrial genome ". The DNA found within the chloroplast may be referred to as the " plastome ". Like the bacteria they originated from, mitochondria and chloroplasts have a circular chromosome.
Unlike prokaryotes where exon-intron organization of protein coding genes exists but is rather exceptional, eukaryotes generally have these features in their genes and their genomes contain variable amounts of repetitive DNA. In mammals and plants, the majority of the genome is composed of repetitive DNA. [ 31 ]
High-throughput technology makes sequencing to assemble new genomes accessible to everyone. Sequence polymorphisms are typically discovered by comparing resequenced isolates to a reference, whereas analyses of coverage depth and mapping topology can provide details regarding structural variations such as chromosomal translocations and segmental duplications.
DNA sequences that carry the instructions to make proteins are referred to as coding sequences. The proportion of the genome occupied by coding sequences varies widely. A larger genome does not necessarily contain more genes, and the proportion of non-repetitive DNA decreases along with increasing genome size in complex eukaryotes. [ 31 ]
Noncoding sequences include introns , sequences for non-coding RNAs, regulatory regions, and repetitive DNA. Noncoding sequences make up 98% of the human genome. There are two categories of repetitive DNA in the genome: tandem repeats and interspersed repeats. [ 32 ]
Short, non-coding sequences that are repeated head-to-tail are called tandem repeats . Microsatellites consisting of 2–5 basepair repeats, while minisatellite repeats are 30–35 bp. Tandem repeats make up about 4% of the human genome and 9% of the fruit fly genome. [ 33 ] Tandem repeats can be functional. For example, telomeres are composed of the tandem repeat TTAGGG in mammals, and they play an important role in protecting the ends of the chromosome.
In other cases, expansions in the number of tandem repeats in exons or introns can cause disease . [ 34 ] For example, the human gene huntingtin (Htt) typically contains 6–29 tandem repeats of the nucleotides CAG (encoding a polyglutamine tract). An expansion to over 36 repeats results in Huntington's disease , a neurodegenerative disease. Twenty human disorders are known to result from similar tandem repeat expansions in various genes. The mechanism by which proteins with expanded polygulatamine tracts cause death of neurons is not fully understood. One possibility is that the proteins fail to fold properly and avoid degradation, instead accumulating in aggregates that also sequester important transcription factors, thereby altering gene expression. [ 34 ]
Tandem repeats are usually caused by slippage during replication, unequal crossing-over and gene conversion. [ 35 ]
Transposable elements (TEs) are sequences of DNA with a defined structure that are able to change their location in the genome. [ 33 ] [ 25 ] [ 36 ] TEs are categorized as either as a mechanism that replicates by copy-and-paste or as a mechanism that can be excised from the genome and inserted at a new location. In the human genome, there are three important classes of TEs that make up more than 45% of the human DNA; these classes are The long interspersed nuclear elements (LINEs), The interspersed nuclear elements (SINEs), and endogenous retroviruses. These elements have a big potential to modify the genetic control in a host organism. [ 30 ]
The movement of TEs is a driving force of genome evolution in eukaryotes because their insertion can disrupt gene functions, homologous recombination between TEs can produce duplications, and TE can shuffle exons and regulatory sequences to new locations. [ 37 ]
Retrotransposons [ 38 ] are found mostly in eukaryotes but not found in prokaryotes. Retrotransposons form a large portion of the genomes of many eukaryotes. A retrotransposon is a transposable element that transposes through an RNA intermediate. Retrotransposons [ 39 ] are composed of DNA , but are transcribed into RNA for transposition, then the RNA transcript is copied back to DNA formation with the help of a specific enzyme called reverse transcriptase. A retrotransposon that carries reverse transcriptase in its sequence can trigger its own transposition but retrotransposons that lack a reverse transcriptase must use reverse transcriptase synthesized by another retrotransposon. Retrotransposons can be transcribed into RNA, which are then duplicated at another site into the genome. [ 40 ] Retrotransposons can be divided into long terminal repeats (LTRs) and non-long terminal repeats (Non-LTRs). [ 37 ]
Long terminal repeats (LTRs) are derived from ancient retroviral infections, so they encode proteins related to retroviral proteins including gag (structural proteins of the virus), pol (reverse transcriptase and integrase), pro (protease), and in some cases env (envelope) genes. [ 36 ] These genes are flanked by long repeats at both 5' and 3' ends. It has been reported that LTRs consist of the largest fraction in most plant genome and might account for the huge variation in genome size. [ 41 ]
Non-long terminal repeats (Non-LTRs) are classified as long interspersed nuclear elements (LINEs), short interspersed nuclear elements (SINEs), and Penelope-like elements (PLEs). In Dictyostelium discoideum , there is another DIRS-like elements belong to Non-LTRs. Non-LTRs are widely spread in eukaryotic genomes. [ 42 ]
Long interspersed elements (LINEs) encode genes for reverse transcriptase and endonuclease, making them autonomous transposable elements. The human genome has around 500,000 LINEs, taking around 17% of the genome. [ 43 ]
Short interspersed elements (SINEs) are usually less than 500 base pairs and are non-autonomous, so they rely on the proteins encoded by LINEs for transposition. [ 44 ] The Alu element is the most common SINE found in primates. It is about 350 base pairs and occupies about 11% of the human genome with around 1,500,000 copies. [ 37 ]
DNA transposons encode a transposase enzyme between inverted terminal repeats. When expressed, the transposase recognizes the terminal inverted repeats that flank the transposon and catalyzes its excision and reinsertion in a new site. [ 33 ] This cut-and-paste mechanism typically reinserts transposons near their original location (within 100 kb). [ 37 ] DNA transposons are found in bacteria and make up 3% of the human genome and 12% of the genome of the roundworm C. elegans . [ 37 ]
Genome size is the total number of the DNA base pairs in one copy of a haploid genome. Genome size varies widely across species. Invertebrates have small genomes, this is also correlated to a small number of transposable elements. Fish and Amphibians have intermediate-size genomes, and birds have relatively small genomes but it has been suggested that birds lost a substantial portion of their genomes during the phase of transition to flight. Before this loss, DNA methylation allows the adequate expansion of the genome. [ 30 ]
In humans, the nuclear genome comprises approximately 3.1 billion nucleotides of DNA, divided into 24 linear molecules, the shortest 45 000 000 nucleotides in length and the longest 248 000 000 nucleotides, each contained in a different chromosome. [ 45 ] There is no clear and consistent correlation between morphological complexity and genome size in either prokaryotes or lower eukaryotes . [ 31 ] [ 46 ] Genome size is largely a function of the expansion and contraction of repetitive DNA elements.
Since genomes are very complex, one research strategy is to reduce the number of genes in a genome to the bare minimum and still have the organism in question survive. There is experimental work being done on minimal genomes for single cell organisms as well as minimal genomes for multi-cellular organisms (see developmental biology ). The work is both in vivo and in silico . [ 47 ] [ 48 ]
There are many enormous differences in size in genomes, specially mentioned before in the multicellular eukaryotic genomes. Much of this is due to the differing abundances of transposable elements, which evolve by creating new copies of themselves in the chromosomes. [ 30 ] Eukaryote genomes often contain many thousands of copies of these elements, most of which have acquired mutations that make them defective.
All the cells of an organism originate from a single cell, so they are expected to have identical genomes; however, in some cases, differences arise. Both the process of copying DNA during cell division and exposure to environmental mutagens can result in mutations in somatic cells. In some cases, such mutations lead to cancer because they cause cells to divide more quickly and invade surrounding tissues. [ 49 ] In certain lymphocytes in the human immune system, V(D)J recombination generates different genomic sequences such that each cell produces a unique antibody or T cell receptors.
During meiosis , diploid cells divide twice to produce haploid germ cells. During this process, recombination results in a reshuffling of the genetic material from homologous chromosomes so each gamete has a unique genome.
Genome-wide reprogramming in mouse primordial germ cells involves epigenetic imprint erasure leading to totipotency . Reprogramming is facilitated by active DNA demethylation , a process that entails the DNA base excision repair pathway. [ 50 ] This pathway is employed in the erasure of CpG methylation (5mC) in primordial germ cells. The erasure of 5mC occurs via its conversion to 5-hydroxymethylcytosine (5hmC) driven by high levels of the ten-eleven dioxygenase enzymes TET1 and TET2 . [ 51 ]
Genomes are more than the sum of an organism's genes and have traits that may be measured and studied without reference to the details of any particular genes and their products. Researchers compare traits such as karyotype (chromosome number), genome size , gene order, codon usage bias , and GC-content to determine what mechanisms could have produced the great variety of genomes that exist today (for recent overviews, see Brown 2002; Saccone and Pesole 2003; Benfey and Protopapas 2004; Gibson and Muse 2004; Reese 2004; Gregory 2005).
Duplications play a major role in shaping the genome. Duplication may range from extension of short tandem repeats , to duplication of a cluster of genes, and all the way to duplication of entire chromosomes or even entire genomes . Such duplications are probably fundamental to the creation of genetic novelty.
Horizontal gene transfer is invoked to explain how there is often an extreme similarity between small portions of the genomes of two organisms that are otherwise very distantly related. Horizontal gene transfer seems to be common among many microbes . Also, eukaryotic cells seem to have experienced a transfer of some genetic material from their chloroplast and mitochondrial genomes to their nuclear chromosomes. Recent empirical data suggest an important role of viruses and sub-viral RNA-networks to represent a main driving role to generate genetic novelty and natural genome editing.
Works of science fiction illustrate concerns about the availability of genome sequences.
Michael Crichton's 1990 novel Jurassic Park and the subsequent film tell the story of a billionaire who creates a theme park of cloned dinosaurs on a remote island, with disastrous outcomes. A geneticist extracts dinosaur DNA from the blood of ancient mosquitoes and fills in the gaps with DNA from modern species to create several species of dinosaurs. A chaos theorist is asked to give his expert opinion on the safety of engineering an ecosystem with the dinosaurs, and he repeatedly warns that the outcomes of the project will be unpredictable and ultimately uncontrollable. These warnings about the perils of using genomic information are a major theme of the book.
The 1997 film Gattaca is set in a futurist society where genomes of children are engineered to contain the most ideal combination of their parents' traits, and metrics such as risk of heart disease and predicted life expectancy are documented for each person based on their genome. People conceived outside of the eugenics program, known as "In-Valids" suffer discrimination and are relegated to menial occupations. The protagonist of the film is an In-Valid who works to defy the supposed genetic odds and achieve his dream of working as a space navigator. The film warns against a future where genomic information fuels prejudice and extreme class differences between those who can and cannot afford genetically engineered children. [ 52 ] | https://en.wikipedia.org/wiki/Genome |
Genome-based peptide fingerprint scanning (GFS) is a system in bioinformatics analysis that attempts to identify the genomic origin (that is, what species they come from) of sample proteins by scanning their peptide-mass fingerprint against the theoretical translation and proteolytic digest of an entire genome. [ 1 ] This method is an improvement from previous methods because it compares the peptide fingerprints to an entire genome instead of comparing it to an already annotated genome. [ 2 ] This improvement has the potential to improve genome annotation and identify proteins with incorrect or missing annotations.
GFS was designed by Michael C. Giddings (University of North Carolina, Chapel Hill) et al., and released in 2003. Giddings expanded the algorithms for GFS from earlier ideas. Two papers were published in 1993 explaining the techniques used to identify proteins in sequence databases. These methods determined the mass of peptides using mass spectrometry , and then used the mass to search protein databases to identify the proteins [ 3 ] [ 4 ] In 1999 a more complex program was released called Mascot that integrated three types of protein/database searches: peptide molecular weights, tandem mass spectrometry from one or more peptide, and combination mass data with amino acid sequence. [ 5 ] The fallback with this widely used program is that it is unable to detect alternative splice sites that are not currently annotated, and it not usually able to find proteins that have not been annotated. Giddings built upon these sources to create GFS which would compare peptide mass data to entire genomes to identify the proteins. Giddings system is able to find new annotations of genes that have not been found, such as undocumented genes and undocumented alternative splice sites.
In 2012 research was published where genes and proteins were found in a model organism that could not have been found without GFS because they had not been previously annotated. The planarian Schmidtea mediterranea has been used in research for over 100 years. This planarian is capable of regenerating missing body parts and is therefore emerging as potential model organism for stem cell research. Planarians are covered in mucus which aids in locomotion, in protecting them from predation, and in helping their immune system. The genome of Schmidtea mediterranea is sequenced but mostly un-annotated making it a prime candidate for genome-based peptide fingerprint scanning. When the proteins were analyzed with GFS 1,604 proteins were identified. These proteins had mostly not been annotated before they were found with GFS They were also able to find the mucous subproteome (all the genes associated with mucus production). They found that this proteome was conserved in the sister species Schmidtea mansoni . The mucous subproteome is so conserved that 119 orthologs of planarians are found in humans. Due to the similarity in these genes the planarian can now be used as a model to study mucous protein function in humans. This is relevant for infections and diseases related to mucous aberrancies such as cystic fibrosis , asthma , and other lung diseases. These genes could not have been found without GFS because they had not been previously annotated. [ 6 ]
In February 2013, proteogenomic mapping research was done with ENCODE to identify translational regions in the human genome. They applied peptide fingerprint scanning and MASCOT to the protein data to find regions that may not have been previously annotated as translated in the human genome. This search against the whole genome revealed that approximately 4% of unique peptide that they found were outside of previously annotated regions. Also the comparison of the whole genome revealed 15% more hits than from a protein database search (such as MASCOT) alone. GFS can be used as a complementary method for annotation due to the fact that you can find new genes or splice sites that have not been annotated before. However it is important to remember that the whole genome approach used by GFS can be less sensitive than programs that look only at annotated regions. [ 7 ] | https://en.wikipedia.org/wiki/Genome-based_peptide_fingerprint_scanning |
Genome-wide CRISPR-Cas9 knockout screens aim to elucidate the relationship between genotype and phenotype by ablating gene expression on a genome-wide scale and studying the resulting phenotypic alterations. The approach utilises the CRISPR-Cas9 gene editing system, coupled with libraries of single guide RNAs (sgRNAs) , which are designed to target every gene in the genome. Over recent years, the genome-wide CRISPR screen has emerged as a powerful tool for performing large-scale loss-of-function screens, with low noise, high knockout efficiency and minimal off-target effects.
Early studies in Caenorhabditis elegans [ 1 ] and Drosophila melanogaster [ 2 ] [ 3 ] saw large-scale, systematic loss of function (LOF) screens performed through saturation mutagenesis , demonstrating the potential of this approach to characterise genetic pathways and identify genes with unique and essential functions. The saturation mutagenesis technique was later applied in other organisms, for example zebrafish [ 4 ] [ 5 ] and mice. [ 6 ] [ 7 ]
Targeted approaches for gene knockdown emerged in the 1980s with techniques such as homologous recombination , [ 8 ] [ 9 ] trans-cleaving ribozymes , [ 10 ] [ 11 ] and antisense technologies . [ 12 ] [ 13 ]
By the year 2000, RNA interference (RNAi) technology had emerged as a fast, simple, and inexpensive technique for targeted gene knockdown , and was routinely being used to study in vivo gene function in C. elegans . [ 14 ] [ 15 ] [ 16 ] [ 17 ] Indeed, in the span of only a few years following its discovery by Fire et al . (1998), [ 18 ] almost all of the ~19,000 genes in C. elegans had been analysed using RNAi-based knockdown . [ 19 ]
The production of RNAi libraries facilitated the application of this technology on a genome-wide scale, and RNAi-based methods became the predominant approach for genome-wide knockdown screens. [ citation needed ]
Nevertheless, RNAi-based approaches to genome-wide knockdown screens have their limitations. For one, the high off-target effects cause issues with false-positive observations. [ 20 ] [ 21 ] Additionally, because RNAi reduces gene expression at the post-transcriptional level by targeting RNA, RNAi-based screens only result in partial and short-term suppression of genes. Whilst partial knockdown may be desirable in certain situations, a technology with improved targeting efficiency and fewer off-target effects was needed. [ citation needed ]
Since initial identification as a prokaryotic adaptive immune system, [ 22 ] the bacterial type II clustered regularly interspaced short palindrome repeats (CRISPR) / Cas9 system has become a simple and efficient tool for generating targeted LOF mutations. [ 23 ] It has been successfully applied to edit human genomes, and has started to displace RNAi as the dominant tool in mammalian studies. [ 24 ] In the context of genome-wide knockout screens, recent studies have demonstrated that CRISPR/Cas9 screens are able to achieve highly efficient and complete protein depletion, and overcome the off-target issues seen with RNAi screens. [ 25 ] [ 26 ] In summary, the recent emergence of CRISPR-Cas9 has dramatically increased our ability to perform large-scale LOF screens. The versatility and programmability of Cas9, coupled with the low noise, high knockout efficiency and minimal off-target effects, have made CRISPR the platform of choice for many researchers engaging in gene targeting and editing. [ 24 ] [ 27 ]
The clustered regularly interspaced short palindrome repeats (CRISPR) / Cas9 system is a gene-editing technology that can introduce double-strand breaks (DSBs) at a target genomic locus. By using a single guide RNA (sgRNA) , the endonuclease Cas9 can be delivered to a specific DNA sequence where it cleaves the nucleotide chain. [ 28 ] The specificity of the sgRNA is determined by a 20-nt sequence, homologous to the genomic locus of interest, and the binding to Cas9 is mediated by a constant scaffold region of the sgRNA. The desired target site must be immediately followed (5’ to 3’) by a conserved 3 nucleotide protospacer adjacent motif (PAM). [ 29 ] [ 30 ] In order to repair the DSBs, the cell may use the highly error prone non-homologous end joining , or homologous recombination . By designing suitable sgRNAs, planned insertions or deletions can be introduced into the genome. In the context of genome-wide LOF screens, the aim is to cause gene disruption and knockout. [ citation needed ]
To perform CRISPR knockouts on a genome-wide scale, collections of sgRNAs known as sgRNA libraries, or CRISPR knockout libraries, must be generated. The first step in creating a sgRNA library is to identify genomic regions of interest based on known sgRNA targeting rules. [ 31 ] For example, sgRNAs are most efficient when targeting the coding regions of genes and not the 5’ and 3’ UTRs . Conserved exons present as attractive targets, and position relative to the transcription start site should be considered. [ 31 ] Secondly, all the possible PAM sites are identified and selected for. [ 31 ] On- and off-target activity should be analysed, as should GC content, and homopolymer stretches should be avoided. [ 31 ] The most commonly used Cas9 endonuclease, derived from Streptococcus pyogenes , recognises a PAM sequence of NGG. [ 32 ]
Furthermore, specific nucleotides appear to be favoured at specific locations. Guanine is strongly favoured over cytosine on position 20 right next to the PAM motif, and on position 16 cytosine is preferred over guanine. [ 33 ] For the variable nucleotide in the NGG PAM motif, it has been shown that cytosine is preferred and thymine disfavoured. [ 33 ] With such criteria taken into account, the sgRNA library is computationally designed around the selected PAM sites. [ 31 ] [ 33 ] [ 34 ]
Multiple sgRNAs (at least 4–6) should be created against every single gene to limit false-positive detection, and negative control sgRNAs with no known targets should be included. [ 31 ] [ 33 ] The sgRNAs are then created by in situ synthesis, amplified by PCR, and cloned into a vector delivery system.
Developing a new sgRNA library is a laborious and time-consuming process. In practice, researchers may select an existing library depending on their experimental purpose and cell lines of interest.
As of February 2020, the most widely used resources for genome-wide CRISPR knockout screens have been the two Genome-Scale CRISPR Knock-Out (GeCKO) libraries created by the Zhang lab. [ 35 ] Available through Addgene, these lentiviral libraries respectively target human and mouse exons, and both are available as a one-vector system (where the sgRNAs and Cas9 are present on the same plasmid) or as a two-vector system (where the sgRNAs and Cas9 are present on separate plasmids). Each library is delivered as two half-libraries, allowing researchers to screen with 3 or 6 sgRNAs/gene. [ 36 ]
Aside from GeCKO, a number of other CRISPR libraries have been generated and made available through Addgene. The Sabatini & Lander labs currently have 7 separate human and mouse libraries, including targeted sublibraries for distinct subpools such as kinases and ribosomal genes (Addgene #51043–51048). Further, improvements to the specificity of sgRNAs have resulted in ‘second generation’ libraries, such as the Brie (Addgene #73632) and Brunello (Addgene #73178) libraries generated by the Doench and Root labs, and the Toronto knockout (TKO) library (Addgene #1000000069) generated by the Moffat lab. [ 36 ]
Targeted gene knockout using CRISPR/Cas9 requires the use of a delivery system to introduce the sgRNA and Cas9 into the cell. Although a number of different delivery systems are potentially available for CRISPR, [ 37 ] [ 38 ] genome-wide loss-of-function screens are predominantly carried out using third generation lentiviral vectors. [ 35 ] [ 39 ] [ 40 ] These lentiviral vectors are able to efficiently transduce a broad range of cell types and stably integrate into the genome of dividing and non-dividing cells. [ 41 ] [ 42 ] Third generation lentiviral particles are produced by co-transfecting 293T human embryonic kidney (HEK) cells with:
The lentiviral particle-containing supernatant is harvested, concentrated and subsequently used to infect the target cells. [ 45 ] The exact protocol for lentiviral production will vary depending on the research aim and applied library. [ 35 ] [ 43 ] [ 44 ] If a two vector-system is used, for example, cells are sequentially transduced with Cas9 and sgRNA in a two-step procedure. [ 35 ] [ 44 ] Although more complex, this has the advantage of a higher titre for the sgRNA library virus. [ 35 ]
In general, there are two different formats of genome-wide CRISPR knockout screens: arrayed and pooled. In an arrayed screen, each well contains a specific and known sgRNA targeting a specific gene. [ 46 ] Since the sgRNA responsible for each phenotype is known based on well location, phenotypes can be identified and analysed without requiring genetic sequencing. This format allows for the measurement of more specific cellular phenotypes, perhaps by fluorescence or luminescence, and allows researchers to use more library types and delivery methods. [ 46 ] For large-scale LOF screens, however, arrayed formats are considered low-efficiency, and expensive in terms of financial and material resources because cell populations have to be isolated and cultured individually. [ 46 ]
In a pooled screen, cells grown in a single vessel are transduced in bulk with viral vectors collectively containing the entire sgRNA library. To ensure that the amount of cells infected by more than one sgRNA-containing particle is limited, a low multiplicity of infection (MOI) (typically 0.3-0.6) is used. [ 46 ] [ 47 ] Evidence so far has suggested that each sgRNA should be represented in a minimum of 200 cells. [ 48 ] [ 23 ] Transduced cells will be selected for, followed by positive or negative selection for the phenotype of interest, and genetic sequencing will be necessary to identify the integrated sgRNAs. [ 46 ]
Following phenotypic selection, genomic DNA is extracted from the selected clones, alongside a control cell population. [ 23 ] [ 46 ] [ 49 ] In the most common protocols for genome-wide knockouts, a 'Next-generation sequencing (NGS) library' is created by a two step polymerase chain reaction (PCR). [ 23 ] [ 46 ] The first step amplifies the sgRNA region, using primers specific to the lentiviral integration sequence, and the second step adds Illumina i5 and i7 sequences. [ 23 ] NGS of the PCR products allows the recovered sgRNAs to be identified, and a quantification step can be used to determine the relative abundance of each sgRNA. [ 23 ]
The final step in the screen is to computationally evaluate the significantly enriched or depleted sgRNAs, trace them back to their corresponding genes, and in turn determine which genes and pathways could be responsible for the observed phenotype. Several algorithms are currently available for this purpose, with the most popular being the Model-based Analysis of Genome-wide CRISPR/Cas9 Knockout (MAGeCK) method. [ 50 ] Developed specifically for CRISPR/Cas9 knockout screens in 2014, MAGeCK demonstrated better performance compared with alternative algorithms at the time, [ 50 ] and has since demonstrated robust results and high sensitivity across different experimental conditions. [ 51 ] As of 2015, the MAGeCK algorithm has been extended to introduce quality control measurements, and account for the previously overlooked sgRNA knockout efficiency. [ 51 ] A web-based visualisation tool (VISPR) was also integrated, allowing users to interactively explore the results, analysis, and quality controls. [ 51 ]
Over recent years, the genome-wide CRISPR screen has emerged as a powerful tool for studying the intricate networks of cellular signaling. [ 52 ] Cellular signaling is essential for a number of fundamental biological processes, including cell growth, proliferation, differentiation, and apoptosis .
One practical example is the identification of genes required for proliferative signaling in cancer cells. Cells are transduced with a CRISPR sgRNA library, and studied for growth over time. By comparing sgRNA abundance in selected cells to a control, one can identify which sgRNAs become depleted and in turn which genes may be responsible for the proliferation defect. Such screens have been used to identify cancer-essential genes in acute myeloid leukemia [ 53 ] and neuroblastoma , [ 54 ] and to describe tumor-specific differences between cancer cell lines. [ 55 ]
Targeted cancer therapies are designed to target the specific genes, proteins, or environments contributing to tumor cell growth or survival. After a period of prolonged treatment with these therapies, however, tumor cells may develop resistance. Although the mechanisms behind cancer drug resistance are poorly understood, potential causes include: target alteration, drug degradation, apoptosis escape, and epigenetic alterations. [ 56 ] Resistance is well-recognised and poses a serious problem in cancer management. [ citation needed ]
To overcome this problem, a synthetic lethal partner can be identified. Genome-wide LOF screens using CRISPR-Cas9 can be used to screen for synthetic lethal partners. [ 57 ] For this, a wild-type cell line and a tumor cell line containing the resistance-causing mutation are transduced with a CRISPR sgRNA library. The two cell lines are cultivated, and any under-represented or dead cells are analyzed to identify potential synthetic lethal partner genes. A recent study by Hinze et al. (2019) [ 58 ] used this method to identify a synthetic lethal interaction between the chemotherapy drug asparaginase and two genes in the Wnt signalling pathway NKD2 and LGR6.
Due to their small genomes and limited number of encoded proteins, viruses exploit host proteins for entry, replication, and transmission. Identification of such host proteins, also termed host dependency factors (HDFs), is particularly important for identifying therapeutic targets. Over recent years, many groups have successfully used genome-wide CRISPR/Cas9 as a screening strategy for HDFs in viral infections. [ 59 ]
One example is provided by Marceau et al. (2017), [ 60 ] who aimed to dissect the host factors associated with dengue and hepatitis C (HCV) infection (two viruses in family Flaviviridae ). ELAVL1 , an RNA-binding protein encoded by the ELAVL1 gene, was found to be a critical receptor for HCV entry, and a remarkable divergence in host dependency factors was demonstrated between the two flaviviridae. [ 60 ]
Additional reported applications of genome-wide CRISPR screens include the study of: mitochondrial metabolism, [ 61 ] bacterial toxin resistance, [ 62 ] genetic drivers of metastasis, [ 63 ] cancer drug resistance, [ 64 ] West Nile virus-induced cell death, [ 65 ] and immune cell gene networks. [ 66 ] [ 67 ]
This section will specifically address genome-wide CRISPR screens. For a review of CRISPR limitations see Lino et al. (2018) [ 38 ]
Genome-wide CRISPR screens will ultimately be limited by the properties of the chosen sgRNA library. Each library will contain a different set of sgRNAs, and average coverage per gene may vary. Currently available libraries tend to be biased towards sgRNAs targeting early (5’) protein-coding exons, rather than those targeting the more functional protein domains. [ 58 ] This problem was highlighted by Hinze et al. (2019), [ 58 ] who noted that genes associated with asparaginase sensitivity failed to score in their genome-wide screen of asparaginase-resistant leukemia cells.
If an appropriate library is not available, creating and amplifying a new sgRNA library is a lengthy process which may take many months. Potential challenges include: (i) effective sgRNA design; (ii) ensuring comprehensive sgRNA coverage throughout the genome; (iii) lentiviral vector backbone design; (iv) producing sufficient amounts of high-quality lentivirus; (v) overcoming low transformation efficiency; (vi) proper scaling of the bacterial culture. [ 68 ]
One of the largest hurdles for genome-wide CRISPR screening is ensuring adequate coverage of the sgRNA library across the cell population. [ 23 ] Evidence so far has suggested that each sgRNA should be represented and maintained in a minimum of 200-300 cells. [ 23 ] [ 48 ]
Considering that the standard protocol uses a multiplicity of infection of ~0.3, and a transduction efficiency of 30-40% [ 44 ] [ 23 ] the number of cells required to produce and maintain suitable coverage becomes very large. By way of example, the most popular human sgRNA library is the GeCKO v2 library created by the Zhang lab; [ 30 ] it contains 123,411 sgRNAs. Studies using this library commonly transduce more than 1x10 8 cells [ 58 ] [ 59 ] [ 69 ]
As CRISPR continues to exhibit low noise and minimal off-target effects, an alternative strategy is to reduce the number of sgRNAs per gene for a primary screen. Less stringent cut-offs are used for hit selection, and additional sgRNAs are later used in a more specific secondary screen. This approach is demonstrated by Doench et al . (2016), [ 33 ] who found that >92% of genes recovered using the standard protocol were also recovered using fewer sgRNAs per gene. They suggest that this strategy could be useful in studies where scale-up is prohibitively costly. [ citation needed ]
Lentiviral vectors have certain general limitations. For one, it is impossible to control where the viral genome integrates into the host genome, and this may affect important functions of the cell. Vannucci et al. [ 70 ] provide an excellent review of viral vectors along with their general advantages and disadvantages. In the specific context of genome-wide CRISPR screens, producing and transducing the lentiviral particles is relatively laborious and time-consuming, taking about two weeks in total. [ 44 ] Additionally, because the DNA integrates into the host genome, lentiviral delivery leads to long-term expression of Cas9, potentially leading to off-target effects. [ citation needed ]
In an arrayed screen, each well contains a specific and known sgRNA targeting a specific gene. Arrayed screens therefore allow for detailed profiling of a single cell, but are limited by high costs and the labour required to isolate and culture the high number of individual cell populations. [ 46 ] Conventional pooled CRISPR screens are relatively simple and cost effective to perform, but are limited to the study of the entire cell population. This means that rare phenotypes may be more difficult to identify, and only crude phenotypes can be selected for e.g. cell survival, proliferation, or reporter gene expression. [ citation needed ]
The choice of culture medium might affect the physiological relevance of findings from cell culture experiments due to the differences in the nutrient composition and concentrations. [ 71 ] A systematic bias in generated datasets was recently shown for CRISPR and RNAi gene silencing screens (especially for metabolic genes), [ 72 ] and for metabolic profiling of cancer cell lines . [ 71 ] For example, a stronger dependence on ASNS (asparagine synthetase) was found in cell lines cultured in DMEM , which lacks asparagine, compared to cell lines cultured in RPMI or F12 (containing asparagine). [ 72 ] Avoiding such bias might be achieved by using a uniform media for all screened cell lines, and ideally, using a growth medium that better represents the physiological levels of nutrients. Recently, such media types, as Plasmax [ 73 ] and Human Plasma Like Medium (HPLM), [ 74 ] were developed.
Emerging technologies are aiming to combine pooled CRISPR screens with the detailed resolution of massively parallel single-cell RNA-sequencing (RNA-seq) . Studies utilising “CRISP-seq”, [ 75 ] “CROP-seq”, [ 76 ] and “PERTURB-seq” [ 77 ] have demonstrated rich genomic readouts, accurately identifying gene expression signatures for individual gene knockouts in a complex pool of cells. These methods have the added benefit of producing transcriptional profiles of the sgRNA-induced cells. [ 78 ] | https://en.wikipedia.org/wiki/Genome-wide_CRISPR-Cas9_knockout_screens |
Genome-wide complex trait analysis ( GCTA ) Genome-based restricted maximum likelihood ( GREML ) is a statistical method for heritability estimation in genetics, which quantifies the total additive contribution of a set of genetic variants to a trait. GCTA is typically applied to common single nucleotide polymorphisms ( SNPs ) on a genotyping array (or "chip") and thus termed "chip" or "SNP" heritability.
GCTA operates by directly quantifying the chance genetic similarity of unrelated individuals and comparing it to their measured similarity on a trait; if two unrelated individuals are relatively similar genetically and also have similar trait measurements, then the measured genetics are likely to causally influence that trait, and the correlation can to some degree tell how much. This can be illustrated by plotting the squared pairwise trait differences between individuals against their estimated degree of relatedness. [ 1 ] GCTA makes a number of modeling assumptions and whether/when these assumptions are satisfied continues to be debated.
The GCTA framework has also been extended in a number of ways: quantifying the contribution from multiple SNP categories (i.e. functional partitioning); quantifying the contribution of Gene-Environment interactions; quantifying the contribution of non-additive/non-linear effects of SNPs; and bivariate analyses of multiple phenotypes to quantify their genetic covariance (co-heritability or genetic correlation ).
GCTA estimates have implications for the potential for discovery from Genome-wide Association Studies (GWAS) as well as the design and accuracy of polygenic scores . GCTA estimates from common variants are typically substantially lower than other estimates of total or narrow-sense heritability (such as from twin or kinship studies), which has contributed to the debate over the Missing heritability problem .
Estimation in biology/animal breeding using standard ANOVA / REML methods of variance components such as heritability, shared-environment, maternal effects etc. typically requires individuals of known relatedness such as parent/child; this is often unavailable or the pedigree data unreliable, leading to inability to apply the methods or requiring strict laboratory control of all breeding (which threatens the external validity of all estimates), and several authors have noted that relatedness could be measured directly from genetic markers (and if individuals were reasonably related, economically few markers would have to be obtained for statistical power), leading Kermit Ritland to propose in 1996 that directly measured pairwise relatedness could be compared to pairwise phenotype measurements (Ritland 1996, "A Marker-based Method for Inferences About Quantitative Inheritance in Natural Populations" Archived 2009-06-11 at the Wayback Machine [ 2 ] ).
As genome sequencing costs dropped steeply over the 2000s, acquiring enough markers on enough subjects for reliable estimates using very distantly related individuals became possible. An early application of the method to humans came with Visscher et al. 2006 [ 3 ] /2007, [ 4 ] which used SNP markers to estimate the actual relatedness of siblings and estimate heritability from the direct genetics. In humans, unlike the original animal/plant applications, relatedness is usually known with high confidence in the 'wild population', and the benefit of GCTA is connected more to avoiding assumptions of classic behavioral genetics designs and verifying their results, and partitioning heritability by SNP class and chromosomes. The first use of GCTA proper in humans was published in 2010, finding 45% of variance in human height can be explained by the included SNPs. [ 5 ] [ 6 ] (Large GWASes on height have since confirmed the estimate. [ 7 ] ) The GCTA algorithm was then described and a software implementation published in 2011. [ 8 ] It has since been used to study a wide variety of biological, medical, psychiatric, and psychological traits in humans, and inspired many variant approaches.
Twin and family studies have long been used to estimate variance explained by particular categories of genetic and environmental causes. Across a wide variety of human traits studied, there is typically minimal shared-environment influence, considerable non-shared environment influence, and a large genetic component (mostly additive), which is on average ~50% and sometimes much higher for some traits such as height or intelligence. [ 9 ] However, the twin and family studies have been criticized for their reliance on a number of assumptions that are difficult or impossible to verify, such as the equal environments assumption (that the environments of monozygotic and dizygotic twins are equally similar), that there is no misclassification of zygosity (mistaking identical for fraternal & vice versa), that twins are unrepresentative of the general population, and that there is no assortative mating . Violations of these assumptions can result in both upwards and downwards bias of the parameter estimates. [ 10 ] (This debate & criticism have particularly focused on the heritability of IQ .)
The use of SNP or whole-genome data from unrelated subject participants (with participants too related, typically >0.025 or ~fourth cousins levels of similarity, being removed, and several principal components included in the regression to avoid & control for population stratification ) bypasses many heritability criticisms: twins are often entirely uninvolved, there are no questions of equal treatment, relatedness is estimated precisely, and the samples are drawn from a broad variety of subjects.
In addition to being more robust to violations of the twin study assumptions, SNP data can be easier to collect since it does not require rare twins and thus also heritability for rare traits can be estimated (with due correction for ascertainment bias ).
GCTA estimates can be used to resolve the missing heritability problem and design GWASes which will yield genome-wide statistically-significant hits. This is done by comparing the GCTA estimate with the results of smaller GWASes. If a GWAS of n=10k using SNP data fails to turn up any hits, but the GCTA indicates a high heritability accounted for by SNPs, then that implies that a large number of variants are involved ( polygenicity ) and thus that much larger GWASes will be required to accurately estimate each SNP's effect and directly account for a fraction of the GCTA heritability.
GCTA provides an unbiased estimate of the total variance in phenotype explained by all variants included in the relatedness matrix (and any variation correlated with those SNPs). This estimate can also be interpreted as the maximum prediction accuracy (R^2) that could be achieved from a linear predictor using all SNPs in the relatedness matrix. The latter interpretation is particularly relevant to the development of Polygenic Risk Scores, as it defines their maximum accuracy. GCTA estimates are sometimes misinterpreted as estimates of total (or narrow-sense, i.e. additive) heritability, but this is not a guarantee of the method. GCTA estimates are likewise sometimes misinterpreted as "lower bounds" on the narrow-sense heritability but this is also incorrect: first because GCTA estimates can be biased (including biased upwards) if the model assumptions are violated, and second because, by definition (and when model assumptions are met), GCTA can provide an unbiased estimate of the narrow-sense heritability if all causal variants are included in the relatedness matrix. The interpretation of the GCTA estimate in relation to the narrow-sense heritability thus depends on the variants used to construct the relatedness matrix.
Most frequently, GCTA is run with a single relatedness matrix constructed from common SNPs and will not capture (or not fully capture) the contribution of the following factors:
GCTA makes several model assumptions and may produce biased estimates under the following conditions:
The original "GCTA" software package is the most widely used; its primary functionality covers the GREML estimation of SNP heritability, but includes other functionality:
Other implementations and variant algorithms include: | https://en.wikipedia.org/wiki/Genome-wide_complex_trait_analysis |
Genome@home was a volunteer computing project run by Stefan Larson of Stanford University , and a sister project to Folding@home . Its goal was protein design and its applications, which had implications in many fields including medicine . Genome@home was run by the Pande Lab. [ 1 ]
Following the Human Genome Project , scientists needed to know the biological and medical implications of the resulting wealth of genetic information. Genome@home used spare processing power on personal computers to virtually design genes that match existing proteins , although it can also design new proteins that have not been found in nature. [ 2 ] This process is computationally demanding, so distributed computing is a viable option. Researchers can use the results from the project to gain a better understanding of the evolution of natural genomes and proteins, and their functionality. This project had applications in medical therapy , new pharmaceuticals , and assigning functions to newly sequenced genes. [ 2 ]
Genome@home directly studied genomes and proteins by virtually designing new sequences for existing 3-D protein structures, which other scientists obtained through X-ray crystallography or NMR techniques. By understanding the relationship between the sequences and specific protein structures, the Pande lab tackled contemporary issues in structural biology , genetics , and medicine . [ 1 ]
Specifically, the Genome@home project aided the understanding of why thousands of different amino acid sequences all form the same structures and assisted the fields of proteomics and structural genomics by predicting the functions of newly discovered genes and proteins. It also had implications in medical therapy by designing and virtually creating new versions of existing proteins. [ 1 ] Genome@home's software was designed for uniprocessor systems. It begins with a large set of potential sequences, and repeatedly searches through and refines these sequences until a well-designed sequence is found. It then sends this sequence to the server, and repeats the process. [ 1 ]
For financial reasons, the project was officially concluded on March 8, 2004, although data was still collected until April 15. Following its completion, users were asked to donate to Folding@home instead. [ 1 ] [ 3 ]
It accumulated a large database of protein sequences, which will be used for important scientific purposes for years by the Pande Lab and other scientists across the world. [ 1 ] [ 3 ]
Four peer-reviewed scientific publications have resulted from Genome@home. [ 4 ] | https://en.wikipedia.org/wiki/Genome@home |
The Genome Project–Write (also known as GP-Write ) is a large-scale collaborative research project (an extension of Genome Projects , aimed at reading genomes since 1984) that focuses on the development of technologies for the synthesis and testing of genomes of many different species of microbes, plants, and animals, including the human genome in a sub-project known as Human Genome Project–Write ( HGP-Write ). [ 1 ] [ 2 ] [ 3 ] [ 4 ] [ 5 ] [ 6 ] Formally announced on 2 June 2016, the project leverages two decades of work on synthetic biology and artificial gene synthesis .
The newly created GP-Write project will be managed by the Center of Excellence for Engineering Biology, [ 7 ] an American nonprofit organization. Researchers expect that the ability to artificially synthesize large portions of many genomes will result in many scientific and medical advances. [ 1 ] [ 2 ] [ 3 ] [ 4 ] [ 5 ] [ 6 ]
In May 2021, GP-Write and Twist Bioscience launched a new CAD platform for whole genome design. The GP-Write CAD will automate workflows to enable collaborative efforts critical for scale-up from designing plasmids to megabases across entire genomes. [ 8 ]
Technologies for constructing and testing yeast artificial chromosomes (YACs), synthetic yeast genomes (Sc2.0), [ 9 ] and virus/phage-resistant bacterial genomes have industrial, agricultural, and medical applications. [ 2 ]
A complete haploid copy of the human genome consists of at least three billion DNA nucleotide base pairs , which have been described in the Human Genome Project - Read program (95% completed as of 2004). Among the many goals of GP-Write are the making of cell lines resistant to all viruses and synthesis assembly lines to test variants of unknown significance that arise in research and diagnostic sequencing of human genomes (which has been exponentially improving in cost, quality, and interpretation). [ 2 ] | https://en.wikipedia.org/wiki/Genome_Project–Write |
The Genome Reference Consortium ( GRC ) is an international collective of academic and research institutes with expertise in genome mapping, sequencing, and informatics, formed to improve the representation of reference genomes . At the time the human reference was initially described, it was clear that some regions were recalcitrant to analysis with existing technology, leaving gaps in the known sequence. The main reason for improving the reference assemblies are that they are the cornerstones upon which all whole genome studies are based (e.g. the 1000 Genomes Project ).
The GRC is a collaborative effort which interacts with various groups in the scientific community. [ 1 ] The primary member institutes are:
The goal of the Consortium is to correct the small number of regions in the reference that are currently misrepresented, to close as many remaining gaps as possible and to produce alternative assemblies of structurally variant loci when necessary. Initially the focus was on the human and mouse reference genomes, but in expansions new organisms were added to the consortium. In October 2010 full maintenance and improvement of the zebrafish genome sequence was added to the GRC; [ 2 ] in 2015, after the release of the chicken genome assembly Gallus_gallus-5.0, GRC added the chicken reference genome, [ 3 ] and in November 2020 the rat genome assembly was added. [ 4 ]
As of September 2019, the major assembly releases for human, mouse, zebrafish, and chicken are GRCh38, GRCm38, GRCz11, and GRCg6a, respectively. Major assembly releases do not follow a fixed cycle; however, there are minor assembly updates in the form of genome patches which either correct errors in the assembly or add additional alternate loci. [ 5 ] These assemblies are represented in various genome browsers and databases including Ensembl , those in NCBI and UCSC Genome Browser .
Institute Homepages
Genome assemblies | https://en.wikipedia.org/wiki/Genome_Reference_Consortium |
Genome Valley is an Indian high-technology business district spread across 2,000-acre (8.1 km 2 )/(3.1 sq mi) in Hyderabad , India. [ 1 ] [ 2 ] It is located across the suburbs, Turakapally , Shamirpet , Medchal , Uppal , Patancheru , Jeedimetla , Gachibowli and Keesara . The Genome Valley has developed as a cluster for Biomedical research , training and manufacturing. [ 3 ] [ 4 ] [ 5 ] Genome Valley is now into its Phase III, which is about 11 kms from the Phase I and II with the total area approximately 2,000-acre (8.1 km 2 ). [ 6 ]
The concept of Genome Valley was envisioned by Dr. Krishna Ella , the founder of Bharat Biotech. He proposed the idea of creating a dedicated biotech hub that would bring together research, development, and manufacturing facilities in the life sciences sector. The realization of Genome Valley as a world-class biotech hub was driven by the efforts of N. Chandrababu Naidu , the then Chief Minister of Andhra Pradesh (before the bifurcation of the state into Andhra Pradesh and Telangana).
Genome Valley was commissioned by the then combined Government Andhra Pradesh in 1999 as S. P. Biotech Park in a public-private partnership with Bharat Biotech International , and its founder Krishna Ella , alongside private infrastructure companies such as Shapoorji Pallonji Group and ICICI Bank . [ 7 ]
In 2009, U.S.-based infrastructure giant Alexandria Real Estate Equities has announced its plans to invest in the bio-cluster, which led to the Alexandria Knowledge Park SEZ. [ 8 ] The bio-cluster at Shamirpet holds Certification mark by the United States Patent and Trademark Office and the European Union . [ 9 ]
The IKP Knowledge Park is spread over 200 acres in Turakapally , is an initiative of ICICI Bank with five "innovation corridors" - a first of its kind knowledge-nurturing centre for Indian companies and a knowledge gateway for multinational companies". [ 10 ] The first phase of Innovation Corridor I, comprising 10 laboratories, around 3,000 ft² (300 m²) each, is operational and fully occupied. The second phase of Innovation Corridor I, comprising 16 laboratory modules of 1,700 ft² (170 m²) each, is ready for operation.
In 2016, Mission Neutral Park acquired specialized R&D assets in Genome Valley from U.S.-based Alexandria REIT and rechristened it as MN Park. It was later rebranded as Neovantage Innovation Parks in 2023. Neovantage Innovation Parks is a collaborative life sciences ecosystem in Genome Valley, Hyderabad consisting of Grade A R&D facilities.
Neovantage Innovation Parks is spread over 1,000,000 sq ft of space, including built-up facilities of around 850,000 sq.ft. provided to global tenants like Novartis , GlaxoSmithKline , Mylan and Ashland Inc. The campuses consist of pre-leased industrial assets and specialized office spaces to sectors including specialized warehousing, vaccine development, CROs, Bio-Pharma Production, pharmaceutical R&D, biotechnology , etc. | https://en.wikipedia.org/wiki/Genome_Valley |
The 2000s witnessed an explosion of genome sequencing and mapping in evolutionarily diverse species. While full genome sequencing of mammals is rapidly progressing, the ability to assemble and align orthologous whole chromosomal regions from more than a few species is not yet possible. The intense focus on the building of comparative maps for domestic (dogs and cats), laboratory (mice and rats) and agricultural (cattle) animals has traditionally been used to understand the underlying basis of disease-related and healthy phenotypes .
These maps also provide an unprecedented opportunity to use multispecies analysis as a tool to infer karyotype evolution. Comparative chromosome painting and related techniques are very powerful approaches in comparative genome studies. Homologies can be identified with high accuracy using molecularly defined DNA probes for fluorescence in situ hybridization (FISH) on chromosomes of different species. Chromosome painting data are now available for members of nearly all mammalian orders.
It was found that in most orders, there are species with rates of chromosome evolution that can be considered as 'default' rates. It needs to be noted that the number of rearrangements that have become fixed in evolutionary history seems relatively low, due to 180 million years of the mammalian radiation. Thus a record of the history of karyotype changes that have occurred during evolution have been attained through comparative chromosome maps.
Modern mammals (class Mammalia ) are divided into Monotremes , Marsupials , and Placentals . The subclass Prototheria ( Monotremes ) comprises the five species of egg-laying mammals: platypus and four echidna species. The infraclasses Metatheria ( Marsupials ) and Eutheria ( Placentals ) together form the subclass Theria . [ 4 ]
In the 2000s understanding of the relationships among eutherian mammals has experienced a virtual revolution. Molecular phylogenomics, new fossil finds and innovative morphological interpretations now group the more than 4600 extant species of eutherians into four major super-ordinal clades : Euarchontoglires (including Primates , Dermoptera , Scandentia , Rodentia , and Lagomorpha ), Laurasiatheria ( Cetartiodactyla , Perissodactyla , Carnivora , Chiroptera , Pholidota , and Eulipotyphla ), Xenarthra , and Afrotheria ( Proboscidea , Sirenia , Hyracoidea , Afrosoricida , Tubulidentata , and Macroscelidea ). [ 4 ] This tree is very useful in unifying the parts of a puzzle in comparative mammalian cytogenetics.
Each gene maps to the same chromosome in every cell. Linkage is determined by the presence of two or more loci on the same chromosome. The entire chromosomal set of a species is known as a karyotype.
A seemingly logical consequence of descent from common ancestors is that more closely related species should have more chromosomes in common. However, it is now widely thought that species may have phenetically similar karyotypes due to genomic conservation. Therefore, in comparative cytogenetics, phylogenetic relationships should be determined on the basis of the polarity of chromosomal differences (derived traits).
Mammalian comparative cytogenetics, an indispensable part of phylogenomics , has evolved in a series of steps from pure description to the more heuristic science of the genomic era. Technical advances have marked the various developmental steps of cytogenetics.
The first step of the Human Genome Project took place when Tjio and Levan , in 1956, reported the accurate diploid number of human chromosomes as 2n = 46. [ 6 ]
During this phase, data on the karyotypes of hundreds of mammalian species (including information on diploid numbers, relative length and morphology of chromosomes, presence of B chromosomes ) were described. Diploid numbers (2n) were found to vary from 2n = 6–7 in the Indian muntjac [ 7 ] to over 100 in some rodents. [ 8 ]
The second step derived from the invention of C-, G-, R- and other banding techniques and was marked by the Paris Conference (1971), which led to a standard nomenclature to recognize and classify each human chromosome. [ 9 ]
The most widely used banding methods are G-banding (Giemsa-banding) and R-banding (reverse-banding). These techniques produce a characteristic pattern of contrasting dark and light transverse bands on the chromosomes. Banding makes it possible to identify homologous chromosomes and construct chromosomal nomenclatures for many species. Banding of homologous chromosomes allows chromosome segments and rearrangements to be identified. The banded karyotypes of 850 mammalian species were summarized in the Atlas of Mammalian Chromosomes . [ 10 ]
Karyotype variability in mammals is mainly due to the varying amount of heterochromatin in each mammal. Once the amount of heterochromatin is subtracted from total genome content, all mammals have very similar genome sizes.
Mammalian species differ considerably in heterochromatin content and location. Heterochromatin is most often detected using C-banding. [ 12 ] Early studies using C-banding showed that differences in the fundamental number (i.e., the number of chromosome arms) could be entirely due to the addition of heterochromatic chromosome arms. Heterochromatin consists of different types of repetitive DNA, not all seen with C-banding that can vary greatly between karyotypes of even closely related species. The differences of the amount of heterochromatin among congeneric rodent species may reach 33% of nuclear DNA in Dipodomys species, [ 13 ] 36% in Peromyscus species, [ 14 ] 42% in Ammospermophilus [ 15 ] and 60% in Thomomys species where C-value (haploid DNA content) ranges between 2.1 and 5.6 pg. [ 16 ] [ 17 ]
The red viscacha rat ( Tympanoctomys barrerae ) has a record C-value among mammals—9.2 pg. [ 18 ] Although tetrapoidy was first proposed to be a reason for its high genome size and diploid chromosome number, Svartman et al. [ 19 ] showed that the high genome size was due to the enormous amplification of heterochromatin. Although one single copy gene was found to be duplicated in its genome, [ 20 ] data on absence of large genome segment duplications (single paints of most Octodon degu probes) and repetitive DNA hybridization evidence rules against tetraploidy. The study of heterochromatin composition, repeated DNA amount and its distribution on chromosomes of octodontids is absolutely necessary to define exactly what heterochromatin fraction is responsible for the large genomes of the red viscacha rat. [ 21 ]
In comparative cytogenetics, chromosome homology between species was proposed on the basis of similarities in banding patterns. Closely related species often had very similar banding pattern and after 40 years of comparing bands it seems safe to generalize that karyotype divergence in most taxonomic groups follows their phylogenetic relationship, despite notable exceptions. [ 10 ] [ 22 ]
The conservation of large chromosomal segments makes comparison between species worthwhile. Chromosome banding has been a reliable indicator of chromosome homology overall, i.e. that the chromosome identified on the basis of banding actually carries the same genes. This relationship may fail for phylogenetically distant species or species that have experienced extremely rapid chromosome evolution. Banding is still morphological and is not always a foolproof indicator of DNA content. [ 21 ]
The third step occurred when molecular techniques were incorporated into cytogenetics. These techniques use DNA probes of diverse sizes to compare chromosomes at the DNA level. Homology can be confidently compared even between phylogenetically distant species or highly rearranged species (e.g., gibbons ). Using cladistic analysis rearrangements that have diversified the mammalian karyotype are more precisely mapped and placed in a phylogenomic perspective. "Comparative chromosomics" defines the field of cytogenetics dealing with molecular approaches, [ 30 ] although "chromosomics" was originally introduced to define the research of chromatin dynamics and morphological changes in interphase chromosome structures. [ 31 ]
Chromosome painting or Zoo-FISH was the first technique to have a wide-ranging impact. [ 32 ] [ 33 ] [ 34 ] [ 35 ] [ 36 ] With this method the homology of chromosome regions between different species are identified by hybridizing DNA probes of an individual, whole chromosomes of one species to metaphase chromosomes of another species. Comparative chromosome painting allows a rapid and efficient comparison of many species and the distribution of homologous regions makes it possible to track the translocation of chromosomal evolution. When many species covering different mammalian orders are compared, this analysis can provide information on trends and rates of chromosomal evolution in different branches.
However, homology is only detected qualitatively, and resolution is limited by the size of visualized regions. Thus, the method does not detect all minuscule homologous regions from multiple rearrangements (as between mouse and human). The method also fails to report internal inversions within large segments. Another limitation is that painting across great phylogenetic distance often results in a decreased efficiency. Nevertheless, the use of painting probes derived from different species combined with comparative sequencing projects help to increase the resolution of the method. [ 21 ]
In addition to sorting, microdissection of chromosomes and chromosome regions was also used to obtain probes for chromosome painting. Best results were obtained when a series of microdissection probes covering the total human genome were localized on anthropoid primate chromosomes via multicolor banding (MCB). [ 37 ] [ 38 ] However a limitation of MCB is that it can only be used within a group of closely related species ("phylogenetic" resolution is too low). Spectral karyotyping (SKY) and MFISH—the ratio labeling and simultaneous hybridization of a complete chromosomal set have similar drawbacks and little application outside of clinical studies. [ 21 ]
Comparative genomics data including chromosome painting confirmed the substantial conservation of mammalian chromosomes. [ 36 ] Total human chromosomes or their arms can efficiently paint extended chromosome regions in many placentals down to Afrotheria and Xenarthra . Gene localization data on human chromosomes can be extrapolated to the homologous chromosome regions of other species with high reliability. Usefully, humans express conserved syntenic chromosome organization similar to the ancestral condition of all placental mammals.
After the Human Genome Project researchers focused on evolutionary comparisons of the genome structures of different species. The whole genome of any species can be sequenced completely and repeatedly to obtain a comprehensive single-nucleotide map. This method makes it possible to compare genomes for any two species regardless of their taxonomic distance.
Sequencing efforts provided a variety of products useful in molecular cytogenetics. Fluorescence in situ hybridization (FISH) with DNA clones ( BAC and YAC clones, cosmids ) allowed the construction of chromosome maps at a resolution of several megabases that could detect relatively small chromosome rearrangements. A resolution of several kilobases can be achieved on interphase chromatin. A limitation is that hybridization efficiencies decrease with increasing phylogenetic distance.
Radiation hybrid (RH) genome mapping is another efficient approach. This method includes the irradiation of cells to disrupt the genome into the desired number of fragments that are subsequently fused with Chinese hamster cells. The resulting somatic cell hybrids contain individual fragments of the relevant genome. Then, 90–100 (sometimes, more) clones covering the total genome are selected, and the sequences of interest are localized on the cloned fragments via the polymerase chain reaction (PCR) or direct DNA–DNA hybridization. To compare the genomes and chromosomes of two species, RHs should be obtained for both species. [ 21 ]
In contrast to many other taxa, therian mammals and birds are characterized by highly conserved systems of genetic sex determination that lead to special chromosomes, i.e. the sex chromosomes . Although the XX/XY sex chromosome system is the most common among eutherian species, it is not universal. In some species X-autosomal translocations result in the appearance of "additional Y" chromosomes (for example, XX/XY1Y2Y3 systems in black muntjac ). [ 39 ] [ 40 ]
In other species Y-autosomal translocations lead to appearance of additional X chromosomes (for example, in some New World primates such as howler monkeys ). Regarding this aspect, rodents again represent a peculiar derived group, comprising the record number of species with non-classical sex chromosomes such as the wood lemming , the collared lemming , the creep vole, the spinous country rat, the Akodon and the bandicoot rat . [ 41 ] | https://en.wikipedia.org/wiki/Genome_diversity_and_karyotype_evolution_of_mammals |
Genome Informatics (also genoinformatics or genetic information processing ) [ 1 ] is a scientific study of information processing in genomes .
Information processing and information flow occur in the course of an organism's development and throughout its lifespan. [ 2 ] The essence of computation is information processing, and the essence of biological information processing is control of the molecular events inside a cell. [ 3 ] Genome informatics introduces computational techniques and applies them to derive information from genome sequences. [ 4 ] Genome informatics includes methods to analyze DNA sequence information and to predict protein sequence and structure. [ 4 ] Methods of studying a large genomic data include variant-calling, transcriptomic analysis, and variant interpretation. [ 5 ] Genome informatics can analyze DNA sequence information and to predict protein sequence and structure. [ 4 ] Genome informatics dealing with [ 6 ] microbial and metagenomics, sequencing algorithms , variant discovery and genome assembly, evolution, complex traits and phylogenetics, personal and medical genomics, transcriptomics, genome structure and function. [ 6 ] Genoinformatics refers to genome and chromosome dynamics, quantitative biology and modeling, molecular and cellular pathologies. [ 7 ] Genome informatics also includes the field of genome design. There still a lot more we can do and develop in Genome Informatics. Find a potential disease, searching a solution for a disease, or proving why people get sick for no reason. For genomic informatics there are several main applications for it, including:
Biomolecular systems that can process information are sought for computational applications, because of their potential for parallelism and miniaturization and because their biocompatibility also makes them suitable for future biomedical applications. DNA has been used to design machines, motors, finite automata, logic gates, reaction networks and logic programs, amongst many other structures and dynamic behaviours. [ 10 ]
This computer science article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genome_informatics |
Genome mining describes the exploitation of genomic information for the discovery of biosynthetic pathways of natural products and their possible interactions. [ 1 ] It depends on computational technology and bioinformatics tools. The mining process relies on a huge amount of data (represented by DNA sequences and annotations) accessible in genomic databases . By applying data mining algorithms , the data can be used to generate new knowledge in several areas of medicinal chemistry , [ 2 ] [ 3 ] such as discovering novel natural products . [ 4 ]
In the mid- to late 1980s, researchers have increasingly focused on genetic studies with the advancing sequencing technologies . [ 5 ] The GenBank database was established in 1982 for the collection, management, storage, and distribution of DNA sequence data due to the increasing availability of DNA sequences. With the increasing number of genetic data, biotechnological companies have been able to use human DNA sequence to develop protein and antibody drugs through genome mining since 1992. [ 6 ] In the late 1990s, many companies, such as Amgen, Immunec, Genentech were able to develop drugs that progressed to the clinical stage by adopting genome mining. [ 7 ] Since the Human Genome Project was completed in the early 2000, researchers have been sequencing the genomes of many microorganisms . [ 8 ] Subsequently, many of these genomes have been carefully studied to identify new genes and biosynthetic pathways. [ 9 ]
As large quantities of genomic sequence data began to accumulate in public databases, genetic algorithms became important to decipher the enormous collection of genomic data. They are commonly used to generate high-quality solutions to optimization and search problems by relying on bio-inspired operators such as mutation, crossover and selection. [ 10 ] The followings are commonly used genetic algorithms:
Genome mining applies on the discovery of natural product by facilitating the characterization of novel molecules and biosynthetic pathways. [ 4 ] [ 17 ]
The production of natural products is regulated by the biosynthetic gene clusters (BGCs) encoded in the microorganism. [ 18 ] By adopting genome mining, the BGCs that produce the target natural product can be predicted. [ 19 ] Some important enzymes responsible for the formation of natural products are polyketide synthases (PKS), non-ribosomal peptide synthases (NRPS), ribosomally and post-translationally modified peptides (RiPPs), and terpenoids , and many more. [ 20 ] Mining for enzymes, researchers can figure out the classes that BGCs encode and compare target gene clusters to known gene clusters. [ 21 ] To verify the relation between the BGCs and natural products, the target BGCs can be expressed by suitable host through the use of molecular cloning . [ 22 ]
Genetic data has been accumulated in databases. Researchers are able to utilize algorithms to decipher the data accessible from databases for the discovery of new processes, targets, and products. [ 10 ] The following are databases and tools: | https://en.wikipedia.org/wiki/Genome_mining |
Genome projects are scientific endeavours that ultimately aim to determine the complete genome sequence of an organism (be it an animal , a plant , a fungus , a bacterium , an archaean , a protist or a virus ) and to annotate protein-coding genes and other important genome-encoded features. [ 1 ] The genome sequence of an organism includes the collective DNA sequences of each chromosome in the organism. For a bacterium containing a single chromosome, a genome project will aim to map the sequence of that chromosome. For the human species, whose genome includes 22 pairs of autosomes and 2 sex chromosomes, a complete genome sequence will involve 46 separate chromosome sequences.
The Human Genome Project is a well known example of a genome project. [ 2 ]
Genome assembly refers to the process of taking a large number of short DNA sequences and reassembling them to create a representation of the original chromosomes from which the DNA originated. In a shotgun sequencing project, all the DNA from a source (usually a single organism , anything from a bacterium to a mammal ) is first fractured into millions of small pieces. These pieces are then "read" by automated sequencing machines. A genome assembly algorithm works by taking all the pieces and aligning them to one another, and detecting all places where two of the short sequences, or reads , overlap. These overlapping reads can be merged, and the process continues.
Genome assembly is a very difficult computational problem, made more difficult because many genomes contain large numbers of identical sequences, known as repeats . These repeats can be thousands of nucleotides long, and occur different locations, especially in the large genomes of plants and animals .
The resulting (draft) genome sequence is produced by combining the information sequenced contigs and then employing linking information to create scaffolds. Scaffolds are positioned along the physical map of the chromosomes creating a "golden path".
Originally, most large-scale DNA sequencing centers developed their own software for assembling the sequences that they produced. However, this has changed as the software has grown more complex and as the number of sequencing centers has increased. An example of such assembler Short Oligonucleotide Analysis Package developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis. [ 3 ] [ 4 ] [ 5 ]
Since the 1980s, molecular biology and bioinformatics have created the need for DNA annotation . DNA annotation or genome annotation is the process of identifying attaching biological information to sequences , and particularly in identifying the locations of genes and determining what those genes do.
When sequencing a genome, there are usually regions that are difficult to sequence (often regions with highly repetitive DNA ). Thus, 'completed' genome sequences are rarely ever complete, and terms such as 'working draft' or 'essentially complete' have been used to more accurately describe the status of such genome projects. Even when every base pair of a genome sequence has been determined, there are still likely to be errors present because DNA sequencing is not a completely accurate process. It could also be argued that a complete genome project should include the sequences of mitochondria and (for plants) chloroplasts as these organelles have their own genomes.
It is often reported that the goal of sequencing a genome is to obtain information about the complete set of genes in that particular genome sequence. The proportion of a genome that encodes for genes may be very small (particularly in eukaryotes such as humans, where coding DNA may only account for a few percent of the entire sequence). However, it is not always possible (or desirable) to only sequence the coding regions separately. Also, as scientists understand more about the role of this noncoding DNA (often referred to as junk DNA ), it will become more important to have a complete genome sequence as a background to understanding the genetics and biology of any given organism.
In many ways genome projects do not confine themselves to only determining a DNA sequence of an organism. Such projects may also include gene prediction to find out where the genes are in a genome, and what those genes do. There may also be related projects to sequence ESTs or mRNAs to help find out where the genes actually are.
Historically, when sequencing eukaryotic genomes (such as the worm Caenorhabditis elegans ) it was common to first map the genome to provide a series of landmarks across the genome. Rather than sequence a chromosome in one go, it would be sequenced piece by piece (with the prior knowledge of approximately where that piece is located on the larger chromosome). Changes in technology and in particular improvements to the processing power of computers, means that genomes can now be ' shotgun sequenced ' in one go (there are caveats to this approach though when compared to the traditional approach).
Improvements in DNA sequencing technology have meant that the cost of sequencing a new genome sequence has steadily fallen (in terms of cost per base pair ) and newer technology has also meant that genomes can be sequenced far more quickly.
When research agencies decide what new genomes to sequence, the emphasis has been on species which are either high importance as model organism or have a relevance to human health (e.g. pathogenic bacteria or vectors of disease such as mosquitos ) or species which have commercial importance (e.g. livestock and crop plants). Secondary emphasis is placed on species whose genomes will help answer important questions in molecular evolution (e.g. the common chimpanzee ).
In the future, it is likely that it will become even cheaper and quicker to sequence a genome. This will allow for complete genome sequences to be determined from many different individuals of the same species. For humans, this will allow us to better understand aspects of human genetic diversity .
Many organisms have genome projects that have either been completed or will be completed shortly, including: | https://en.wikipedia.org/wiki/Genome_project |
Genome sequencing of endangered species is the application of Next Generation Sequencing (NGS) technologies in the field of conservation biology, with the aim of generating life history , demographic and phylogenetic data of relevance to the management of endangered wildlife . [ 1 ]
In the context of conservation biology , genomic technologies such as the production of large-scale sequencing data sets via DNA sequencing can be used to highlight the relevant aspects of the biology of wildlife species for which management actions may be required. This may involve the estimation of recent demographic events, genetic variations , divergence between species and population structure. Genome-wide association studies (GWAS) are useful to examine the role of natural selection at the genome level, to identify the loci associated with fitness, local adaptation, inbreeding, depression or disease susceptibility. The access to all these data and the interrogation of genome-wide variation of SNP markers can help the identification of the genetic changes that influence the fitness of wild species and are also important to evaluate the potential respond to changing environments. NGS projects are expected to rapidly increase the number of threatened species for which assembled genomes and detailed information on sequence variation are available and the data will advance investigations relevant to the conservation of biological diversity. [ 1 ]
The traditional approaches in the preservation of endangered species are captive breeding and the private farming . In some cases those methods led to great results, but some problems still remain. For example, by inbreeding only few individuals, the genetic pool of a subpopulation remains limited or may decrease. [ citation needed ]
Genetic analyses can remove subjective elements from the determination of the phylogenetic relationship between organisms. Considering the great variety of information provided by living organisms, it is clear that the type of data will affect both the method of treatment and validity of the results: the higher the correlation of data and genotype, the greater is the validity likely to be. The data analysis can be used to compared different sequencing database and find similar sequences, or similar protein in different species. The comparison can be done using informatic software based on alignment to know the divergence between different species and evaluate the similarities. [ 2 ] [ better source needed ]
Since whole-genome sequencing is generally very data-intensive, techniques for reduced representation genomic approaches are sometimes used for practical applications. For example, restriction site-associated DNA sequencing ( RADseq ) and double digest RADseq are being developed. With those techniques researchers can target different numbers of loci. With a statistical and bioinformatic approach scientists can make considerations about big genomes, by just focusing on a small representative part of it. [ 3 ]
While solving biological problems, one encounters multiple types of genomic data or sometimes an aggregate of same type of data across multiple studies and decoding such huge amount of data manually is unfeasible and tedious. Therefore, integrated analysis of genomic data using statistical methods has become popular. The rapid advancement in high throughput technologies allows researchers to answer more complex biological questions enabling the development of statistical methods in integrated genomics to establish more effective therapeutic strategies for human disease. [ 4 ]
While studying the genome, there are some crucial aspects that should be taken in consideration. Gene prediction is the identification of genetic elements in a genomic sequence. This study is based on a combination of approaches: de novo, homology prediction, and transcription. Tools such as EvidenceModeler are used to merge the different results. [ 5 ] Gene structure also have been compared, including mRNA length, exon length, intron length, exon number, and non-coding RNA . [ citation needed ]
Analysis of repeated sequences has been found useful in reconstructing species divergence timelines. [ 6 ]
In order to preserve a specie, knowledge of the mating system is crucial: scientists can stabilize wild populations through captive breeding, followed by the release in the environment of new individuals. [ 3 ] This task is particularly difficult by considering the species with homomorphic sex chromosomes and a large genome. [ 3 ] For example, in the case of amphibians , there are multiple transitions among male and/or female heterogamety . Sometimes even variation of sex chromosomes within amphibian populations of the same specie were reported. [ 3 ]
The multiple transitions among XY and ZW systems that occur in amphibians determine the sex chromosome systems to be labile in salamanders populations. By understanding the chromosomal basis of sex of those species, it is possible to reconstruct the phylogenetic history of those families and use more efficient strategies in their conservation.
By using the ddRADseq method scientists found new sex-related loci in a 56 Gb genome of the family Cryptobranchidae. Their results support the hypothesis of female heterogamety of this species. These loci were confirmed through the bioinformatic analysis of presence/absence of that genetic locus in sex-determined individuals. Their sex was established previously by ultrasound, laparoscopy and measuring serum calcium level differences. The determination of those candidate sexual loci was performed so as to test hypotheses of both female heterogamety and male heterogamety. Finally to evaluate the validity of those loci, they were amplified through PCR directly from samples of known-sex individuals. This final step led to the demonstration of female heterogamety of several divergent populations of the family Cryptobranchidae. [ 3 ]
A recent study used whole-genome sequencing data to demonstrate the sister lineage between the Dryas monkey and vervet monkey and their divergence with additional bidirectional gene flow approximately 750,000 to approximately 500,000 years ago. With <250 remaining adult individuals, the study showed high genetic diversity and low levels of inbreeding and genetic load in the studied Dryas monkey individuals. [ 7 ]
Another study used several techniques such as single-molecule real time sequencing , paired-end sequencing , optical maps , and high-throughput chromosome conformation capture to obtain a high quality chromosome assembly from already constructed incomplete and fragmented genome assembly for the golden snub-nosed monkey . The modern techniques used in this study represented 100-fold improvement in the genome with 22,497 protein-coding genes, of which majority were functionally annotated. The reconstructed genome showed a close relationship between the species and the Rhesus macaque , indicating a divergence approximately 13.4 million years ago. [ 8 ]
Plants species identified as PSESP ("plant species with extremely small population") have been the focus of genomic studies, with the aim of determining the most endangered populations. [ 9 ] [ 10 ] The DNA genome can be sequenced starting from the fresh leaves by doing a DNA extraction. The combination of different sequencing techniques together can be used to obtain a high quality data that can be used to assembly the genome. The RNA extraction is essential for the transcriptome assembly and the extraction process start from stem, roots, fruits, buds and leaves. The de novo genome assembly can be performed using software to optimize assembly and scaffolding. The software can also be used to fill the gaps and reduce the interaction between chromosome. The combination of different data can be used for the identification of orthologous gene with different species, phylogenetic tree construction, and interspecific genome comparisons. [ 9 ]
The development of indirect sequencing methods has to some degree mitigated the lack of efficient DNA sequencing technologies. These techniques allowed researchers to increase scientific knowledge in fields like ecology and evolution. Several genetic markers , more or less well suited for the purpose, were developed helping researchers to address many issues among which demography and mating systems, population structures and phylogeography, speciational processes and species differences, hybridization and introgression, phylogenetics at many temporal scales. However, all these approaches had a primary deficiency: they were all limited only to a fraction of the entire genome so that genome-wide parameters were inferred from a tiny amount of genetic material. [ 11 ]
The invention and rising of DNA sequencing methods brought a huge contribution in increasing available data potentially useful to improve the field of conservation biology . The ongoing development of cheaper and high throughput allowed the production of a wide array of information in several disciplines providing conservation biologists a very powerful databank from which was possible to extrapolate useful information about, for example, population structure, genetic connections, identification of potential risks due to demographic changes and inbreeding processes through population-genomic approaches that rely on the detection of SNPs, indel or CNV. From one side of the coin, data derived from high throughput sequencing of whole genomes were potentially a massive advance in the field of species conservation, opening wide doors for future challenges and opportunities. On the other side all these data brought researchers to face two main issues. First, how to process all these information. Second, how to translate all the available information into conservation's strategies and practice or, in other words, how to fill the gap between genomic researches and conservation application. [ 12 ] [ 13 ] [ 14 ]
Unfortunately, there are many analytical and practical problems to consider using approaches involving genome-wide sequencing. Availability of samples is a major limiting factor: sampling procedures may disturb an already fragile population or may have a big impact in individual animals itself putting limitations to samples' collection. For these reasons several alternative strategies where developed: constant monitoring, for example with radio collars, allow us to understand the behavior and develop strategies to obtain genetic samples and management of the endangered populations. The samples taken from those species are then used to produce primary cell culture from biopsies. Indeed, this kind of material allow us to grow in vitro cells, and allow us to extract and study genetic material without constantly sampling the endangered populations. Despite a faster and easier data production and a continuous improvement of sequencing technologies, there is still a marked delay of data analysis and processing techniques. Genome-wide analysis and big genomes studies require advances in bioinformatics and computational biology . At the same time improvements in the statistical programs and in the population genetics are required to make better conservation strategies. This last aspect work in parallel with prediction strategies which should take in consideration all features that determine fitness of a species. [ 1 ] | https://en.wikipedia.org/wiki/Genome_sequencing_of_endangered_species |
In the fields of bioinformatics and computational biology , Genome survey sequences (GSS) are nucleotide sequences similar to expressed sequence tags (ESTs) that the only difference is that most of them are genomic in origin, rather than mRNA . [ 1 ]
Genome survey sequences are typically generated and submitted to NCBI by labs performing genome sequencing and are used, amongst other things, as a framework for the mapping and sequencing of genome size pieces included in the standard GenBank divisions. [ 1 ]
Genome survey sequencing is a new way to map the genome sequences since it is not dependent on mRNA . Current genome sequencing approaches are mostly high-throughput shotgun methods, and GSS is often used on the first step of sequencing. GSSs can provide an initial global view of a genome, which includes both coding and non-coding DNA and contain repetitive section of the genome unlike ESTs . For the estimation of repetitive sequences, GSS plays an important role in the early assessment of a sequencing project since these data can affect the assessment of sequences coverage, library quality and the construction process. [ 2 ] For example, in the estimation of dog genome, it can estimate the global parameters, such as neutral mutation rate and repeat content. [ 3 ]
GSS is also an effective way to large-scale and rapidly characterizing genomes of related species where there is only little gene sequences or maps. [ 4 ] GSS with low coverage can generate abundant information of gene content and putative regulatory elements of comparative species. [ 5 ] It can compare these genes of related species to find out relatively expanded or contracted families. And combined with physical clone coverage, researchers can navigate the genome easily and characterize the specific genomic section by more extensive sequencing. [ 3 ]
The limitation of genomic survey sequence is that it lacks long-range continuity because of its fragmentary nature, which makes it harder to forecast gene and marker order. For example, to detect repetitive sequences in GSS data, it may not be possible to find out all the repeats since the repetitive genome may be longer than the reads, which is difficult to recognize. [ 2 ]
The GSS division contains (but is not limited to) the following types of data:
Random “single pass read” genome survey sequences is GSSs that generated along single pass read by random selection. Single-pass sequencing with lower fidelity can be used on the rapid accumulation of genomic data but with a lower accuracy. [ 6 ] It includes RAPD , RFLP , AFLP and so on. [ 7 ]
Cosmid/BAC/YAC end sequences use Cosmid / Bacterial artificial chromosome / Yeast artificial chromosome to sequence the genome from the end side. These sequences act like very low copy plasmids that there is only one copy per cell sometimes. To get enough chromosome, they need a large number of E. coli culture that 2.5 - 5 litres may be a reasonable amount. [ 8 ]
Cosmid/BAC/YAC can also be used to get bigger clone of DNA fragment than vectors like plasmid and phagemid. A larger insert is often helpful for the sequence project in organizing clones. [ 9 ]
Eukaryotic proteins can be expressed by using YAC with posttranslational modification. [ 10 ] BAC can’t do that, but BACs can reliably represent human DNA much better than YAC or cosmid. [ 11 ]
Exon trapped sequence is used to identify genes in cloned DNA, and this is achieved by recognizing and trapping carrier containing exon sequence of DNA. Exon trapping has two main features: First, it is independent of availability of the RNA expressing target DNA. Second, isolated sequences can be derived directly from clone without knowing tissues expressing the gene which needs to be identified. [ 12 ] During slicing, exon can be remained in mRNA and information carried by exon can be contained in the protein. Since fragment of DNA can be inserted into sequences, if an exon is inserted into intron, the transcript will be longer than usual and this transcript can be trapped by analysis.
Alu repetitive element is member of Short Interspersed Elements (SINE) in mammalian genome. There are about 300 to 500 thousand copies of Alu repetitive element in human genome, which means one Alu element exists in 4 to 6 kb averagely. Alu elements are distributed widely in mammalian genome, and repeatability is one of the characteristics, that is why it is called Alu repetitive element. By using special Alu sequence as target locus, specific human DNA can be obtained from clone of TAC, BAC, PAC or human-mouse cell hybrid.
PCR is an approach used to clone a small piece of fragment of DNA. The fragment could be one gene or just a part of gene. PCR can only clone very small fragment of DNA, which generally does not exceed 10kbp.
Alu PCR is a "DNA fingerprinting" technique. This approach is rapid and easy to use. It is obtained from analysis of many genomic loci flanked by Alu repetitive elements, which are non-autonomous retrotransposons present in high number of copies in primate genomes. [ 13 ] Alu element can be used for genome fingerprinting based on PCR, which is also called Alu PCR.
There are several ways to analyze the function of a particular gene sequence, the most direct method is to replace it or cause a mutation and then to analyze the results and effects. There are three method are developed for this purpose: gene replacement, sense and anti-sense suppression, and insertional mutagenesis . Among these methods, insertional mutagenesis was proved to be very good and successful approach.
At first, T-DNA was applied for insertional mutagenesis. However, using transposable element can bring more advantages. Transposable elements were first discovered by Barbara McClintock in maize plants. She identified the first transposable genetic element, which she called the Dissociation (Ds) locus. [ 14 ] The size of transposable element is between 750 and 40000bp. Transposable element can be mainly classified as two classes: One class is very simple, called insertion sequence (IS), the other class is complicated, called transposon. Transposon has one or several characterized genes, which can be easily identified. IS has the gene of transposase.
Transposon can be used as tag for a DNA with a know sequence. Transposon can appear at other locus through transcription or reverse transcription by the effect of nuclease. This appearance of transposon proved that genome is not statistical, but always changing the structure of itself.
There are two advantages by using transposon tagging. First, if a transposon is inserted into a gene sequence, this insertion is single and intact. The intactness can make tagged sequence easily to molecular analysis. The other advantage is that, many transposons can be found eliminated from tagged gene sequence when transposase is analyzed. This provides confirmation that the inserted gene sequence was really tagged by transposon. [ 15 ]
The following is an example of GSS file that can be submitted to GenBank: [ 16 ] | https://en.wikipedia.org/wiki/Genome_survey_sequence |
The Genomes OnLine Database (GOLD) is a web-based resource for comprehensive information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. [ 1 ] Since 2011, the GOLD database has been run by the DOE Joint Genome Institute
The GOLD database was created in 1997; the first version of the database contained information for 350 sequencing projects, of which 48 had been completely sequenced with their analyses published. [ 1 ]
GOLD v.5 was released on 28 May 2014. As of 5 August 2015 [update] , the GOLD database contains information for 67,879 genome sequencing projects, of which 7,210 have been completed. [ 2 ]
In order to facilitate comparative analysis between the information in GOLD and other databases (for example, GenBank and the EMBL ), GOLD supports the minimum information standards metadata specifications recommended by the Genomic Standards Consortium , in particular, the MIxS (Minimum Information about any (x) Sequence) specification. [ 2 ] GOLD also allows the annotation of genomes or metagenomes using the DOE JGI Integrated Microbial Genomes System and has links to the BioMed Central journal Standards in Genomic Sciences , allowing (meta)genomic data to be published. [ 2 ] [ 3 ] | https://en.wikipedia.org/wiki/Genomes_OnLine_Database |
Genomic convergence is a multifactor approach used in genetic research that combines different kinds of genetic data analysis to identify and prioritize susceptibility genes for a complex disease .
In January 2003, Michael Hauser along with fellow researchers at the Duke Center for Human Genetics (CHG) coined the term “genomic convergence” to describe their endeavor to identify genes affecting the expression of Parkinson disease (PD) . Their work successfully combined serial analysis of gene expression (SAGE) with genetic linkage analysis. The authors explain, “While both linkage and expression analyses are powerful on their own, the number of possible genes they present as candidates for PD or any complex disorder remains extremely large”. [ 1 ] The convergence of the two methods allowed researchers to decrease the number of possible PD genes to consider for further study.
Their success prompted further use of the genomic convergence method at the CHG, and in July 2003 Yi-Ju Li, et al. published a paper revealing that glutathione S-transferase omega-1 (GSTO1) modifies the age-at-onset (AAO) of Alzheimer disease (AD) and PD. [ 2 ]
In May 2004, Dr. Margaret Pericak-Vance , currently the director of the John P. Hussman Institute for Human Genomics at the University of Miami Miller School of Medicine and then the director of the CHG, articulated the value of the genomic convergence method at a New York Academy of Sciences (NYAS) keynote address entitled "Novel Methods in Genetic Exploration of Neurodegenerative Disease." She stated, "No single method is going to get us where we need to be with these complex traits . It is going to take a combination of methods to dissect the underlying etiology of these disorders". [ 3 ]
Genomic convergence has a countless number of creative applications that combine the strengths of different analyses and studies. Maher Noureddine et al., note in their 2005 paper, “One of the growing problems in the study of complex diseases is how to prioritize research and make sense of the immense amount of data now readily available at the click of a computer mouse...The best approach may be to take advantage of the strengths of both…SAGE …and microarrays ”. [ 4 ]
The results of combining methods of analysis have continued to be promising. Sofia Oliveira et al. (2005) combined gene expression, linkage data, and “iterative association mapping” to identify several genes associated with PD AAO . [ 5 ]
Future studies will continue to apply genomic convergence to elucidate the etiology of complex diseases. Dr. Jeff Vance, Director of the Morris K. Udall PD Research Center of Excellence, notes, “Genomic convergence is really no different from mathematical convergence – the more angles from which you can come at a problem, the better chance you have of solving it”. [ 6 ] | https://en.wikipedia.org/wiki/Genomic_convergence |
The genomic evolution of birds has come under scrutiny since the advent of rapid DNA sequencing , as birds have the smallest genomes of the amniotes despite acquiring highly derived phenotypic traits. Whereas mammalian and reptilian genomes range between 1.0 and 8.2 giga base pairs (Gb), avian genomes have sizes between 0.91 Gb (black-chinned hummingbird, Archilochus alexandri ) and 1.3 Gb (common ostrich, Struthio camelus ). [ 1 ] Avian genomes reflect the action of natural selection and are the basis of their phenotypes, reflected in their morphology and behaviour , which have evolved significantly since their divergence from other archosaurian , diapsid , and amniotic lineages.
Compared to other tetrapod lineages, birds have fewer repeated elements in their genomes, comprising only 4–10% of its extent, compared to 34–52% in mammals. The total size of avian short interspersed nuclear elements (SINEs) has been drastically reduced, averaging only 1.3 mega base pairs (Mb), compared to animals in similar lineages: The American alligator ( Alligator mississippiensis ), a fellow archosaur, averages 12.6 Mb SINEs, and the green sea turtle ( Chelonia mydas ), a non-archosaur diapsid, averages 34.9 Mb. These data suggest that the last common ancestor of modern birds already had a reduced number of SINEs. [ 1 ]
The mean size of introns , intergenic sequences , and even exons is significantly reduced. Mammalian and reptilian introns have an average size of 4.3 kb and 3.1 kb respectively, whereas those of birds are only 2.1 kb long. Likewise, gene spacing averages 91 kb for mammals and 61 kb for reptiles, but only 49 kb in birds. Similar reductions have occurred in bats, suggesting that genome-size reduction is advantageous to flying animals , allowing, for example, the rapid regulation of gene expression required for powered flight . To rule out the possibility of genomic expansion in mammals and reptiles, Zhang et al. (2014) reconstructed successive deletion events in the avian ancestral genome compared to the reptilian. [ 1 ]
Birds have experienced the most genomic reductions of any vertebrate group. The early chromosomic fragmentation event that led to the appearance of microchromosomes in birds possibly contributed to this gene loss. [ 1 ] These fragmentation events must have taken place in a common ancestor of most birds, since approximately every two out of three species studied have at least 30 pairs of microchromosomes , 2n = 80 being the size of the average karyotype of birds (with the only exception the family Falconidae , which are 2n = 6–12). [ 2 ]
Macrosynteny studies have determined that, in vocal learner birds , genes have undergone a deeper rearrangement along their corresponding chromosomes than those of non-vocal learner birds . In addition to that, microsynteny studies revealed that birds possess a higher number of orthologous genes that maintain synteny . This proves that gene order along chromosomes is more conserved in birds than in other animal groups. A clear example are genes coding for haemoglobin subunits . These genes are easily duplicated and lost. As a consequence, there are huge differences regarding the number and relative position of the genes of alpha-hemoglobins and beta-hemoglobins in mammals. In birds, that is not the case. Both position and number of these genes are highly conserved among them.
Birds' point mutation rate (1.9 × 10 −3 mutations per site per Ma) is smaller than that of mammals (2.7 × 10 −3 mutations per site per Ma). This rate is also smaller among aequornithes (water birds) than that of telluraves (land birds). In this last group, birds of prey have the smallest mutation rate, and songbirds have the highest. These rates are consistent with the broad distribution of birds in different environments and the phenotypic changes in response to selective pressures exerted by the ecological niches they occupy. [ 1 ]
The presence of functional restrictions in genome self-regulation can be studied by comparing the genomes of species whose last common ancestor is more ancient. It is known that, approximately, 7.5% of bird genome is comprised by highly conserved elements (HCEs). Of those HCEs, 12.6% are directly involved in protein coding genes functionality. Non-coding HCEs that are bird specific (not found in mammals) happen to be related with the regulation of the activity of transcription factors related to metabolism . In comparison, mammal HCEs are related to controlling cell signalling , development, and response to stimuli .
The rate of genetic variation is not homogeneous across the genome. This can be assayed using K a /K s ratio studies (also known as d N /d S ) to estimate the balance between neutral mutations, purifying mutations, and beneficial mutations.
In birds, Z-chromosome genes have the highest variability, perhaps due to the low gene density in the Z-chromosome. Genetic variability is higher in macrochromosomes than in microchromosomes , perhaps related to the lower recombination frequency of the latter.
While genes that mediate the development of the central nervous system vary most rapidly in mammals, the genes that mediate morphological development experience the most rapid change in avian genomes.
The avian ability to learn songs has appeared independently at least twice: once in the ancestor of hummingbirds and another in the common ancestor of songbirds and parrots . These lineages possess a number of neuronal circuits not found in lineages unable to learn songs. A d N /d S analysis showed conserved evolution in 227 genes, most of which are highly expressed in the regions of the brain that control singing. Furthermore, 20% of them seemed to be regulated by singing.
To fly , bird ancestors had to undergo a series of changes at the molecular level that translate into changes at morphological level . Approximately half of the genes involved in ossification are known to have been positively selected. Some relevant examples are AHSG , that controls bone mineralization density, and P2RX7 , which is associated to bone homeostasis . Their action would be responsible for the differences observed between mammal and bird bones .
Something similar occurs with the respiratory system . In mammals, the total inner volume of lungs changes during ventilation . However, this does not happen in birds. They make the air circulate through their lungs by contracting and expanding their air sacs . Five genes are involved in this process in mammals and birds.
Feathers are one of the most characteristic features of birds, along with the beak . Feathers are formed of α- and β- keratins . Compared to reptiles and mammals, α-keratin protein family has been reduced in birds, whereas β-keratins has expanded enormously. Since every major bird lineage possess at least one protein of each of the six β-keratin groups, it can be said that their last common ancestor already possessed a large diversity of this kind of protein. 56% of β-keratins are feather-specific and can only be found in birds, whereas those that make up scales and claws can also be found in reptiles. The variety and number of copies of these genes seems to correlate with the bird's lifestyle, land birds having a larger variety, and the variety being larger still in domestic birds .
Birds are also known for being toothless. This feature seems to be a consequence of several modifications and deletions which occurred in the exons of the genes implicated in the formation of enamel and dentine . It is thought that the common ancestor of birds already lacked mineralized teeth , and that later genome changes pushed the situation to the current status.
Also, birds have the best vision system known in vertebrates. They have a higher number of photoreceptors , and most birds are tetrachromats . [ 3 ] The only exception are penguins, which have only three functional opsin genes (and hence are trichromats ). This exception could be related to the aquatic lifestyle, since marine mammals have also lost either one or two cone opsin genes.
In many birds the right ovary has become non-functional. [ 4 ] There are two ovary development-related genes, MMP19 and AKR1C3 , that have disappeared in birds. The fact that a high number of genes related to spermatogenesis are evolving fast (which does not happen in those related to ovogenensis) suggest that males undergo a stronger selective pressure .
Rapid genomic sequencing data enabled research into the early evolution and divergence of bird groups and produced a more detailed phylogenetic tree . Earlier phylogenetic reconstructions based on single genes proved inadequate due to incomplete lineage sorting .
The low resolution of single-gene phylogenies, scarcity of coding DNA data, and convergent evolution confused early attempts to reconstruct avian phylogeny. For example, when base pairing errors occur, DNA repair mechanisms favor GC pairs .
Genomic analysis suggests 36 bird lineages arose in a period of 10–15 My, relatively quickly on an evolutionary timescale. That period includes the massive K-Pg extinction event that freed many niches, allowing for the adaptive radiation and diversification of surviving species. The genomic analysis accords with fossil record data and with mammal evolution estimates. [ 5 ]
The cladogram from this analysis recovers Accipitriformes as a separate clade from Falconiformes , which traditionally subsumed it.
Zebra finch
Medium ground finch
American crow
Golden-collared manakin
Rifleman
Budgerigar
Kea
Peregrine falcon
Red-legged seriema
Carmine Bee-eater
Downy Woodpecker
Rhinoceros hornbill
Bar-tailed trogon
Cuckoo roller
Speckled mousebird
Barn Owl
Bald eagle
White-tailed eagle
Turkey vulture
Dalmatian pelican
Little egret
Ibis
Great cormorant
Northern fulmar
Adelie penguin
Emperor penguin
Red-throated loon
White-tailed tropicbird
Sunbittern
Killdeer
Grey-crowned crane
Hoatzin
Hummingbirds
Common swift
Chuck-will's-widow
Bustard
Red-crested turaco
Common cuckoo
Brown mesite
Yellow-throated sandgrouse
Pigeon
American flamingo
Great crested grebe
Mallard
Tufted duck
Turkey
Chicken
White-throated tinamou
Common ostrich
Phylogenetic tree of birds according to Jarvis et al. 2014 [ 5 ] In the present representation, due to format restrictions, evolutive distances between different taxa are not directly presented. | https://en.wikipedia.org/wiki/Genomic_evolution_of_birds |
Genomic imprinting is an epigenetic phenomenon that causes genes to be expressed or not, depending on whether they are inherited from the female or male parent. [ 1 ] [ 2 ] [ 3 ] [ 4 ] [ 5 ] Genes can also be partially imprinted. Partial imprinting occurs when alleles from both parents are differently expressed rather than complete expression and complete suppression of one parent's allele. [ 6 ] Forms of genomic imprinting have been demonstrated in fungi, plants and animals. [ 7 ] [ 8 ] In 2014, there were about 150 imprinted genes known in mice and about half that in humans. [ 9 ] As of 2019, 260 imprinted genes have been reported in mice and 228 in humans. [ 10 ]
Genomic imprinting is an inheritance process independent of the classical Mendelian inheritance . [ 11 ] It is an epigenetic process that involves DNA methylation and histone methylation without altering the genetic sequence. These epigenetic marks are established ("imprinted") in the germline (sperm or egg cells) of the parents and are maintained through mitotic cell divisions in the somatic cells of an organism. [ 12 ]
Appropriate imprinting of certain genes is important for normal development. Human diseases involving genomic imprinting include Angelman , Prader–Willi , and Beckwith–Wiedemann syndromes. [ 13 ] Methylation defects have also been associated with male infertility . [ 3 ]
In diploid organisms (like humans), the somatic cells possess two copies of the genome , one inherited from the male and one from the female. Each autosomal gene is therefore represented by two copies, or alleles, with one copy inherited from each parent at fertilization . The expressed allele is dependent upon its parental origin. For example, the gene encoding insulin-like growth factor 2 (IGF2/Igf2) is only expressed from the allele inherited from the male. Although imprinting accounts for a small proportion of mammalian genes, they play an important role in embryogenesis particularly in the formation of visceral structures and the nervous system. [ 14 ]
The term "imprinting" was first used to describe events in the insect Pseudococcus nipae . [ 15 ] In Pseudococcids ( mealybugs ) ( Hemiptera , Coccoidea ) both the male and female develop from a fertilised egg. In females, all chromosomes remain euchromatic and functional. In embryos destined to become males, one haploid set of chromosomes becomes heterochromatinised after the sixth cleavage division and remains so in most tissues; males are thus functionally haploid. [ 16 ] [ 17 ] [ 18 ]
That imprinting might be a feature of mammalian development was suggested in breeding experiments in mice carrying reciprocal chromosomal translocations . [ 19 ] Nucleus transplantation experiments in mouse zygotes in the early 1980s confirmed that normal development requires the contribution of both the maternal and paternal genomes. The vast majority of mouse embryos derived from parthenogenesis (called parthenogenones, with two maternal or egg genomes) and androgenesis (called androgenones, with two paternal or sperm genomes) die at or before the blastocyst/implantation stage. In the rare instances that they develop to postimplantation stages, gynogenetic embryos show better embryonic development relative to placental development, while for androgenones, the reverse is true. Nevertheless, for the latter, only a few have been described (in a 1984 paper). [ 20 ] [ 21 ] [ 22 ] Nevertheless, in 2018 genome editing allowed for bipaternal and viable bimaternal [ 23 ] [ 24 ] mouse and even (in 2022) parthenogenesis, still this is far from full reimprinting. [ 25 ] Finally in March 2023 viable bipaternal embryos were created. [ 26 ]
No naturally occurring cases of parthenogenesis exist in mammals because of imprinted genes. However, in 2004, experimental manipulation by Japanese researchers of a paternal methylation imprint controlling the Igf2 gene led to the birth of a mouse (named Kaguya ) with two maternal sets of chromosomes, though it is not a true parthenogenone since cells from two different female mice were used. The researchers were able to succeed by using one egg from an immature parent, thus reducing maternal imprinting, and modifying it to express the gene Igf2, which is normally only expressed by the paternal copy of the gene.
Parthenogenetic/gynogenetic embryos have twice the normal expression level of maternally derived genes, and lack expression of paternally expressed genes, while the reverse is true for androgenetic embryos. It is now known that there are at least 80 imprinted genes in humans and mice, many of which are involved in embryonic and placental growth and development. [ 12 ] [ 27 ] [ 28 ] [ 29 ] Hybrid offspring of two species may exhibit unusual growth due to the novel combination of imprinted genes. [ 30 ]
Various methods have been used to identify imprinted genes. In swine, Bischoff et al. compared transcriptional profiles using DNA microarrays to survey differentially expressed genes between parthenotes (2 maternal genomes) and control fetuses (1 maternal, 1 paternal genome). [ 31 ] An intriguing study surveying the transcriptome of murine brain tissues revealed over 1300 imprinted gene loci (approximately 10-fold more than previously reported) by RNA-sequencing from F1 hybrids resulting from reciprocal crosses. [ 32 ] The result however has been challenged by others who claimed that this is an overestimation by an order of magnitude due to flawed statistical analysis. [ 33 ] [ 34 ]
In domesticated livestock, single-nucleotide polymorphisms in imprinted genes influencing foetal growth and development have been shown to be associated with economically important production traits in cattle, sheep and pigs. [ 35 ] [ 36 ]
At the same time as the generation of the gynogenetic and androgenetic embryos discussed above, mouse embryos were also being generated that contained only small regions that were derived from either a paternal or maternal source. [ 37 ] [ 38 ] The generation of a series of such uniparental disomies , which together span the entire genome, allowed the creation of an imprinting map. [ 39 ] Those regions which when inherited from a single parent result in a discernible phenotype contain imprinted gene(s). Further research showed that within these regions there were often numerous imprinted genes. [ 40 ] Around 80% of imprinted genes are found in clusters such as these, called imprinted domains, suggesting a level of co-ordinated control. [ 5 ] More recently, genome-wide screens to identify imprinted genes have used differential expression of mRNAs from control fetuses and parthenogenetic or androgenetic fetuses hybridized to gene expression profiling microarrays, [ 41 ] allele-specific gene expression using SNP genotyping microarrays, [ 42 ] transcriptome sequencing, [ 43 ] and in silico prediction pipelines. [ 44 ]
Imprinting is a dynamic process. It must be possible to erase and re-establish imprints through each generation so that genes that are imprinted in an adult may still be expressed in that adult's offspring. (For example, the maternal genes that control insulin production will be imprinted in a male but will be expressed in any of the male's offspring that inherit these genes.) The nature of imprinting must therefore be epigenetic rather than DNA sequence dependent. In germline cells the imprint is erased and then re-established according to the sex of the individual, i.e. in the developing sperm (during spermatogenesis ), a paternal imprint is established, whereas in developing oocytes ( oogenesis ), a maternal imprint is established. This process of erasure and reprogramming [ 45 ] is necessary such that the germ cell imprinting status is relevant to the sex of the individual. In both plants and mammals there are two major mechanisms that are involved in establishing the imprint; these are DNA methylation and histone modifications.
Recently, a new study [ 46 ] has suggested a novel inheritable imprinting mechanism in humans that would be specific of placental tissue and that is independent of DNA methylation (the main and classical mechanism for genomic imprinting). This was observed in humans, but not in mice, suggesting development after the evolutionary divergence of humans and mice, ~80 Mya . Among the hypothetical explanations for this novel phenomenon, two possible mechanisms have been proposed: either a histone modification that confers imprinting at novel placental-specific imprinted loci or, alternatively, a recruitment of DNMTs to these loci by a specific and unknown transcription factor that would be expressed during early trophoblast differentiation.
The grouping of imprinted genes within clusters allows them to share common regulatory elements, such as non-coding RNAs and differentially methylated regions (DMRs) . When these regulatory elements control the imprinting of one or more genes, they are known as imprinting control regions (ICR). The expression of non-coding RNAs , such as antisense Igf2r RNA ( Air ) on mouse chromosome 17 and KCNQ1OT1 on human chromosome 11p15.5, have been shown to be essential for the imprinting of genes in their corresponding regions. [ 47 ]
Differentially methylated regions are generally segments of DNA rich in cytosine and guanine nucleotides, with the cytosine nucleotides methylated on one copy but not on the other. Contrary to expectation, methylation does not necessarily mean silencing; instead, the effect of methylation depends upon the default state of the region. [ 48 ]
The control of expression of specific genes by genomic imprinting is unique to therian mammals ( placental mammals and marsupials ) and flowering plants. Imprinting of whole chromosomes has been reported in mealybugs (Genus: Pseudococcus ) [ 15 ] [ 16 ] [ 17 ] [ 18 ] and a fungus gnat ( Sciara ). [ 49 ] It has also been established that X-chromosome inactivation occurs in an imprinted manner in the extra-embryonic tissues of mice and all tissues in marsupials, where it is always the paternal X-chromosome which is silenced. [ 5 ] [ 50 ]
The majority of imprinted genes in mammals have been found to have roles in the control of embryonic growth and development, including development of the placenta. [ 27 ] [ 51 ] Other imprinted genes are involved in post-natal development, with roles affecting suckling and metabolism. [ 51 ] [ 52 ]
A widely accepted hypothesis for the evolution of genomic imprinting is the "parental conflict hypothesis". [ 53 ] Also known as the kinship theory of genomic imprinting, this hypothesis states that the inequality between parental genomes due to imprinting is a result of the differing interests of each parent in terms of the evolutionary fitness of their genes . [ 54 ] [ 55 ] The father 's genes that encode for imprinting gain greater fitness through the success of the offspring, at the expense of the mother . The mother's evolutionary imperative is often to conserve resources for her own survival while providing sufficient nourishment to current and subsequent litters. Accordingly, paternally expressed genes tend to be growth-promoting whereas maternally expressed genes tend to be growth-limiting. [ 53 ] In support of this hypothesis, genomic imprinting has been found in all placental mammals, where post-fertilisation offspring resource consumption at the expense of the mother is high; although it has also been found in oviparous birds [ 56 ] [ 57 ] where there is relatively little post-fertilisation resource transfer and therefore less parental conflict. A small number of imprinted genes are fast evolving under positive Darwinian selection possibly due to antagonistic co-evolution. [ 58 ] The majority of imprinted genes display high levels of micro- synteny conservation and have undergone very few duplications in placental mammalian lineages. [ 58 ]
However, our understanding of the molecular mechanisms behind genomic imprinting show that it is the maternal genome that controls much of the imprinting of both its own and the paternally-derived genes in the zygote, making it difficult to explain why the maternal genes would willingly relinquish their dominance to that of the paternally-derived genes in light of the conflict hypothesis. [ 59 ]
Another hypothesis proposed is that some imprinted genes act coadaptively to improve both fetal development and maternal provisioning for nutrition and care. [ 9 ] [ 59 ] [ 60 ] In it, a subset of paternally expressed genes are co-expressed in both the placenta and the mother's hypothalamus. This would come about through selective pressure from parent-infant coadaptation to improve infant survival. Paternally expressed 3 ( PEG3 ) is a gene for which this hypothesis may apply. [ 9 ]
Others have approached their study of the origins of genomic imprinting from a different side, arguing that natural selection is operating on the role of epigenetic marks as machinery for homologous chromosome recognition during meiosis, rather than on their role in differential expression. [ 61 ] This argument centers on the existence of epigenetic effects on chromosomes that do not directly affect gene expression, but do depend on which parent the chromosome originated from. [ 62 ] This group of epigenetic changes that depend on the chromosome's parent of origin (including both those that affect gene expression and those that do not) are called parental origin effects, and include phenomena such as paternal X inactivation in the marsupials , nonrandom parental chromatid distribution in the ferns, and even mating type switching in yeast. [ 62 ] This diversity in organisms that show parental origin effects has prompted theorists to place the evolutionary origin of genomic imprinting before the last common ancestor of plants and animals, over a billion years ago. [ 61 ]
Natural selection for genomic imprinting requires genetic variation in a population. A hypothesis for the origin of this genetic variation states that the host-defense system responsible for silencing foreign DNA elements, such as genes of viral origin, mistakenly silenced genes whose silencing turned out to be beneficial for the organism. [ 63 ] There appears to be an over-representation of retrotransposed genes , that is to say genes that are inserted into the genome by viruses , among imprinted genes. It has also been postulated that if the retrotransposed gene is inserted close to another imprinted gene, it may just acquire this imprint. [ 64 ]
Unfortunately, the relationship between the phenotype and genotype of imprinted genes is solely conceptual. The idea is frameworked using two alleles on a single locus and hosts three different possible classes of genotypes. [ 65 ] The reciprocal heterozygotes genotype class contributes to understanding how imprinting will impact genotype to phenotype relationship. Reciprocal heterozygotes have a genetically equivalent, but they are phenotypically nonequivalent. [ 66 ] Their phenotype may not be dependent on the equivalence of the genotype. This can ultimately increase diversity in genetic classes, expanding flexibility of imprinted genes. [ 67 ] This increase will also force a higher degree in testing capabilities and assortment of tests to determine the presences of imprinting.
When a locus is identified as imprinted, two different classes express different alleles. [ 65 ] Inherited imprinted genes of offspring are believed to be monoallelic expressions. A single locus will entirely produce one's phenotype although two alleles are inherited. This genotype class is called parental imprinting, as well as dominant imprinting. [ 68 ] Phenotypic patterns are variant to possible expressions from paternal and maternal genotypes. Different alleles inherited from different parents will host different phenotypic qualities. One allele will have a larger phenotypic value and the other allele will be silenced. [ 65 ] Underdominance of the locus is another possibility of phenotypic expression. Both maternal and paternal phenotypes will have a small value rather than one hosting a large value and silencing the other.
Statistical frameworks and mapping models are used to identify imprinting effects on genes and complex traits. Allelic parent-of-origin influences the vary in phenotype that derive from the imprinting of genotype classes. [ 65 ] These models of mapping and identifying imprinting effects include using unordered genotypes to build mapping models. [ 67 ] These models will show classic quantitative genetics and the effects of dominance of the imprinted genes.
Imprinting may cause problems in cloning , with clones having DNA that is not methylated in the correct positions. It is possible that this is due to a lack of time for reprogramming to be completely achieved. When a nucleus is added to an egg during somatic cell nuclear transfer , the egg starts dividing in minutes, as compared to the days or months it takes for reprogramming during embryonic development. If time is the responsible factor, it may be possible to delay cell division in clones, giving time for proper reprogramming to occur. [ citation needed ]
In vitro fertilisation , including ICSI , is associated with an increased risk of imprinting disorders, with an odds ratio of 3.7 (95% confidence interval 1.4 to 9.7). [ 69 ]
Epigenetic deregulations at H19 imprinted gene in sperm have been observed associated with male infertility . [ 70 ] Indeed, methylation loss at H19 imprinted gene has been observed associated with MTHFR gene promoter hypermethylation in semen samples from infertile males. [ 70 ]
The first imprinted genetic disorders to be described in humans were the reciprocally inherited Prader-Willi syndrome and Angelman syndrome . Both syndromes are associated with loss of the chromosomal region 15q11-13 (band 11 of the long arm of chromosome 15). This region contains the paternally expressed genes SNRPN and NDN and the maternally expressed gene UBE3A .
The imprinted brain hypothesis is an unsubstantiated hypothesis in evolutionary psychology regarding the causes of autism spectrum and schizophrenia spectrum disorders , first presented by Bernard Crespi and Christopher Badcock in 2008. It claims that certain autistic and schizotypal traits are opposites, and that this implies the etiology of the two conditions must be at odds.
The imprinted brain hypothesis is based around genomic imprinting, an epigenetic process through which genes are expressed differently by way of one parent's contribution having more effect than the other. Specifically, proponents of the imprinted brain hypothesis propose that autism spectrum disorders are caused by paternal overimprinting, while schizophrenia spectrum disorders are caused by maternal overimprinting; they point to a number of supposed correlations and anticorrelations seen between the disorders and other traits to support the hypothesis.
DIRAS3 is a paternally expressed and maternally imprinted gene located on chromosome 1 in humans. Reduced DIRAS3 expression is linked to an increased risk of ovarian and breast cancers; in 41% of breast and ovarian cancers the protein encoded by DIRAS3 is not expressed, suggesting that it functions as a tumor suppressor gene . [ 74 ] Therefore, if uniparental disomy occurs and a person inherits both chromosomes from the mother, the gene will not be expressed and the individual is put at a greater risk for breast and ovarian cancer.
Other conditions involving imprinting include Beckwith-Wiedemann syndrome , Silver-Russell syndrome , and pseudohypoparathyroidism . [ 75 ]
Transient neonatal diabetes mellitus can also involve imprinting. [ 76 ]
The " imprinted brain hypothesis " argues that unbalanced imprinting may be a cause of autism and psychosis .
In insects, imprinting affects entire chromosomes. In some insects the entire paternal genome is silenced in male offspring, and thus is involved in sex determination. The imprinting produces effects similar to the mechanisms in other insects that eliminate paternally inherited chromosomes in male offspring, including arrhenotoky . [ 77 ]
In social honey bees, the parent of origin and allele-specific genes has been studied from reciprocal crosses to explore the epigenetic mechanisms underlying aggressive behavior. [ 78 ]
In placental species, parent-offspring conflict can result in the evolution of strategies, such as genomic imprinting, for embryos to subvert maternal nutrient provisioning. Despite several attempts to find it, genomic imprinting has not been found in the platypus, reptiles, birds, or fish. The absence of genomic imprinting in a placental reptile, the Pseudemoia entrecasteauxii , is interesting as genomic imprinting was thought to be associated with the evolution of viviparity and placental nutrient transport. [ 79 ]
Studies in domestic livestock, such as dairy and beef cattle, have implicated imprinted genes (e.g. IGF2) in a range of economic traits, [ 80 ] [ 81 ] [ 35 ] including dairy performance in Holstein-Friesian cattle. [ 82 ]
In sheep, the CLPG gene ("callipyge" from Greek , meaning "beautiful buttocks") produces a large buttocks consisting of muscle with very little fat. The large-buttocked phenotype only occurs when the allele is present on the copy of chromosome 18 inherited from a sheep's father and is not on the copy of chromosome 18 inherited from that sheep's mother. [ 83 ] The CLPG locus is encompassed by Dlk1 -Gtl2, an imprinted region of the mammalian genome, and the atypical presentation of this gene is a result of this imprinting. [ 84 ]
Foraging behavior in mice studied is influenced by a sexually dimorphic allele expression implicating a cross-gender imprinting influence that varies throughout the body and may dominate expression and shape a behavior. [ 85 ] [ 86 ]
A similar imprinting phenomenon has also been described in flowering plants (angiosperms). [ 87 ] During fertilization of the egg cell, a second, separate fertilization event gives rise to the endosperm , an extraembryonic structure that nourishes the embryo in a manner analogous to the mammalian placenta . Unlike the embryo, the endosperm is often formed from the fusion of two maternal cells with a male gamete . This results in a triploid genome. The 2:1 ratio of maternal to paternal genomes appears to be critical for seed development. Some genes are found to be expressed from both maternal genomes while others are expressed exclusively from the lone paternal copy. [ 88 ] It has been suggested that these imprinted genes are responsible for the triploid block effect in flowering plants that prevents hybridization between diploids and autotetraploids. [ 89 ] Several computational methods to detect imprinting genes in plants from reciprocal crosses have been proposed. [ 90 ] [ 91 ] [ 92 ] | https://en.wikipedia.org/wiki/Genomic_imprinting |
A genomic island ( GI ) is part of a genome that has evidence of horizontal origins . [ 1 ] The term is usually used in microbiology , especially with regard to bacteria . A GI can code for many functions, can be involved in symbiosis or pathogenesis , and may help an organism's adaptation. Many sub-classes of GIs exist that are based on the function that they confer. [ 2 ] For example, a GI associated with pathogenesis is often called a pathogenicity island (PAIs), while GIs that contain many antibiotic resistant genes are referred to as antibiotic resistance islands. The same GI can occur in distantly related species as a result of various types of horizontal gene transfer (transformation, conjugation, transduction). This can be determined by base composition analysis, as well as phylogeny estimations.
Various genomic island predictions programs have been developed. These tools can be broadly grouped into sequence based methods and comparative genomics /phylogeny based methods.
Sequence based methods depend on the naturally occurring variation that exists between the genome sequence composition of different species. Genomic regions that show abnormal sequence composition (such as nucleotide bias or codon bias) suggests that these regions may have been horizontally transferred. Two major problems with these methods are that false predictions can occur due to natural variation in the genome (sometimes due to highly expressed genes) and that horizontally transferred DNA will ameliorate (change to the host genome) over time; therefore, limiting predictions to only recently acquired GIs.
Comparative genomics based methods try to identify regions that show signs that they have been horizontally transferred using information from several related species. For example, a genomic region that is present in one species, but is not present in several other related species suggests that the region may have been horizontally transferred. The alternative explanations are (i) that the region was present in the common ancestor but has been lost in all the other species being compared, or (ii) that the region was absent in the common ancestor but was acquired through mutation and selection in the species in which it is still found. The argument for multiple deletions of the region would be strengthened if there is evidence from outgroups that the region was present in the common ancestor, or if the phylogeny implies relatively few actual deletion events would be required. The argument for acquisition via mutation would be strengthened if the species with the region is known to have diverged substantially from the other species, or if the region in question is small. The plausibility of either (i) or (ii) would be modified if taxon sampling omitted many extinct species that may have possessed the region, and particularly if extinction was correlated with the presence of the region.
One example of a method that integrates several of the most accurate GI prediction methods is IslandViewer. [ 3 ]
In bacteria , many type III and type IV secretion systems are located on genomic islands. These "islands" are characterised by their large size(>10 Kb ), their frequent association with tRNA-encoding genes and a different G+C content compared with the rest of the genome. Many genomic islands are flanked by repeat structures and carry fragments of other mobile elements such as phages and plasmids . Some genomic islands, including those adjacent to integrative and conjugative elements (ICEs), can excise themselves spontaneously from the chromosome and can be transferred to other suitable recipients. [ 4 ] While excision is dependent on the ICE machinery present, integration is attributed to integrases present on the genomic islands. | https://en.wikipedia.org/wiki/Genomic_island |
A genomic library is a collection of overlapping DNA fragments that together make up the total genomic DNA of a single organism . The DNA is stored in a population of identical vectors , each containing a different insert of DNA. In order to construct a genomic library, the organism's DNA is extracted from cells and then digested with a restriction enzyme to cut the DNA into fragments of a specific size. The fragments are then inserted into the vector using DNA ligase . [ 1 ] Next, the vector DNA can be taken up by a host organism - commonly a population of Escherichia coli or yeast - with each cell containing only one vector molecule. Using a host cell to carry the vector allows for easy amplification and retrieval of specific clones from the library for analysis. [ 2 ]
There are several kinds of vectors available with various insert capacities. Generally, libraries made from organisms with larger genomes require vectors featuring larger inserts, thereby fewer vector molecules are needed to make the library. Researchers can choose a vector also considering the ideal insert size to find the desired number of clones necessary for full genome coverage. [ 3 ]
Genomic libraries are commonly used for sequencing applications. They have played an important role in the whole genome sequencing of several organisms, including the human genome and several model organisms . [ 4 ] [ 5 ]
The first DNA-based genome ever fully sequenced was achieved by two-time Nobel Prize winner, Frederick Sanger , in 1977. Sanger and his team of scientists created a library of the bacteriophage , phi X 174 , for use in DNA sequencing . [ 6 ] The importance of this success contributed to the ever-increasing demand for sequencing genomes to research gene therapy . Teams are now able to catalog polymorphisms in genomes and investigate those candidate genes contributing to maladies such as Parkinson's disease , Alzheimer's disease , multiple sclerosis , rheumatoid arthritis , and Type 1 diabetes . [ 7 ] These are due to the advance of genome-wide association studies from the ability to create and sequence genomic libraries. Prior, linkage and candidate-gene studies were some of the only approaches. [ 8 ]
Construction of a genomic library involves creating many recombinant DNA molecules. An organism's genomic DNA is extracted and then digested with a restriction enzyme . For organisms with very small genomes (~10 kb) , the digested fragments can be separated by gel electrophoresis . The separated fragments can then be excised and cloned into the vector separately. However, when a large genome is digested with a restriction enzyme, there are far too many fragments to excise individually. The entire set of fragments must be cloned together with the vector, and separation of clones can occur after. In either case, the fragments are ligated into a vector that has been digested with the same restriction enzyme. The vector containing the inserted fragments of genomic DNA can then be introduced into a host organism. [ 1 ]
Below are the steps for creating a genomic library from a large genome.
Below is a diagram of the above outlined steps.
After a genomic library is constructed with a viral vector, such as lambda phage , the titer of the library can be determined. Calculating the titer allows researchers to approximate how many infectious viral particles were successfully created in the library. To do this, dilutions of the library are used to transform cultures of E. coli of known concentrations. The cultures are then plated on agar plates and incubated overnight. The number of viral plaques are counted and can be used to calculate the total number of infectious viral particles in the library. Most viral vectors also carry a marker that allows clones containing an insert to be distinguished from those that do not have an insert. This allows researchers to also determine the percentage of infectious viral particles actually carrying a fragment of the library. [ 11 ]
A similar method can be used to titer genomic libraries made with non-viral vectors, such as plasmids and BACs . A test ligation of the library can be used to transform E. coli. The transformation is then spread on agar plates and incubated overnight. The titer of the transformation is determined by counting the number of colonies present on the plates. These vectors generally have a selectable marker allowing the differentiation of clones containing an insert from those that do not. By doing this test, researchers can also determine the efficiency of the ligation and make adjustments as needed to ensure they get the desired number of clones for the library. [ 12 ]
In order to isolate clones that contain regions of interest from a library, the library must first be screened . One method of screening is hybridization . Each transformed host cell of a library will contain only one vector with one insert of DNA. The whole library can be plated onto a filter over media . The filter and colonies are prepared for hybridization and then labeled with a probe . [ 13 ] The target DNA- insert of interest- can be identified by detection such as autoradiography because of the hybridization with the probe as seen below.
Another method of screening is with polymerase chain reaction (PCR). Some libraries are stored as pools of clones and screening by PCR is an efficient way to identify pools containing specific clones. [ 2 ]
Genome size varies among different organisms and the cloning vector must be selected accordingly. For a large genome, a vector with a large capacity should be chosen so that a relatively small number of clones are sufficient for coverage of the entire genome. However, it is often more difficult to characterize an insert contained in a higher capacity vector. [ 3 ]
Below is a table of several kinds of vectors commonly used for genomic libraries and the insert size that each generally holds.
A plasmid is a double stranded circular DNA molecule commonly used for molecular cloning . Plasmids are generally 2 to 4 kilobase-pairs (kb) in length and are capable of carrying inserts up to 15kb. Plasmids contain an origin of replication allowing them to replicate inside a bacterium independently of the host chromosome . Plasmids commonly carry a gene for antibiotic resistance that allows for the selection of bacterial cells containing the plasmid. Many plasmids also carry a reporter gene that allows researchers to distinguish clones containing an insert from those that do not. [ 3 ]
Phage λ is a double-stranded DNA virus that infects E. coli . The λ chromosome is 48.5kb long and can carry inserts up to 25kb. These inserts replace non-essential viral sequences in the λ chromosome, while the genes required for formation of viral particles and infection remain intact. The insert DNA is replicated with the viral DNA; thus, together they are packaged into viral particles. These particles are very efficient at infection and multiplication leading to a higher production of the recombinant λ chromosomes. [ 3 ] However, due to the smaller insert size, libraries made with λ phage may require many clones for full genome coverage. [ 14 ]
Cosmid vectors are plasmids that contain a small region of bacteriophage λ DNA called the cos sequence. This sequence allows the cosmid to be packaged into bacteriophage λ particles. These particles- containing a linearized cosmid- are introduced into the host cell by transduction . Once inside the host, the cosmids circularize with the aid of the host's DNA ligase and then function as plasmids. Cosmids are capable of carrying inserts up to 40kb in size. [ 2 ]
Bacteriophage P1 vectors can hold inserts 70 – 100kb in size. They begin as linear DNA molecules packaged into bacteriophage P1 particles. These particles are injected into an E. coli strain expressing Cre recombinase . The linear P1 vector becomes circularized by recombination between two loxP sites in the vector. P1 vectors generally contain a gene for antibiotic resistance and a positive selection marker to distinguish clones containing an insert from those that do not. P1 vectors also contain a P1 plasmid replicon , which ensures only one copy of the vector is present in a cell. However, there is a second P1 replicon- called the P1 lytic replicon- that is controlled by an inducible promoter . This promoter allows the amplification of more than one copy of the vector per cell prior to DNA extraction . [ 2 ]
P1 artificial chromosomes (PACs) have features of both P1 vectors and Bacterial Artificial Chromosomes (BACs). Similar to P1 vectors, they contain a plasmid and a lytic replicon as described above. Unlike P1 vectors, they do not need to be packaged into bacteriophage particles for transduction. Instead they are introduced into E. coli as circular DNA molecules through electroporation just as BACs are. [ 2 ] Also similar to BACs, these are relatively harder to prepare due to a single origin of replication. [ 14 ]
Bacterial artificial chromosomes (BACs) are circular DNA molecules, usually about 7kb in length, that are capable of holding inserts up to 300kb in size. BAC vectors contain a replicon derived from E. coli F factor , which ensures they are maintained at one copy per cell. [ 4 ] Once an insert is ligated into a BAC, the BAC is introduced into recombination deficient strains of E. coli by electroporation. Most BAC vectors contain a gene for antibiotic resistance and also a positive selection marker. [ 2 ] The figure to the right depicts a BAC vector being cut with a restriction enzyme, followed by the insertion of foreign DNA that is re-annealed by a ligase. Overall, this is a very stable vector, but they may be hard to prepare due to a single origin of replication just like PACs. [ 14 ]
Yeast artificial chromosomes (YACs) are linear DNA molecules containing the necessary features of an authentic yeast chromosome, including telomeres , a centromere , and an origin of replication . Large inserts of DNA can be ligated into the middle of the YAC so that there is an “arm” of the YAC on either side of the insert. The recombinant YAC is introduced into yeast by transformation; selectable markers present in the YAC allow for the identification of successful transformants. YACs can hold inserts up to 2000kb, but most YAC libraries contain inserts 250-400kb in size. Theoretically there is no upper limit on the size of insert a YAC can hold. It is the quality in the preparation of DNA used for inserts that determines the size limit. [ 2 ] The most challenging aspect of using YAC is the fact they are prone to rearrangement . [ 14 ]
Vector selection requires one to ensure the library made is representative of the entire genome. Any insert of the genome derived from a restriction enzyme should have an equal chance of being in the library compared to any other insert. Furthermore, recombinant molecules should contain large enough inserts ensuring the library size is able to be handled conveniently. [ 14 ] This is particularly determined by the number of clones needed to have in a library. The number of clones to get a sampling of all the genes is determined by the size of the organism's genome as well as the average insert size. This is represented by the formula (also known as the Carbon and Clarke formula): [ 15 ]
N = l n ( 1 − P ) l n ( 1 − f ) {\displaystyle N={\frac {ln(1-P)}{ln(1-f)}}}
where,
N {\displaystyle N} is the necessary number of recombinants [ 16 ]
P {\displaystyle P} is the desired probability that any fragment in the genome will occur at least once in the library created
f {\displaystyle f} is the fractional proportion of the genome in a single recombinant
f {\displaystyle f} can be further shown to be:
f = i g {\displaystyle f={\frac {i}{g}}}
where,
i {\displaystyle i} is the insert size
g {\displaystyle g} is the genome size
Thus, increasing the insert size (by choice of vector) would allow for fewer clones needed to represent a genome. The proportion of the insert size versus the genome size represents the proportion of the respective genome in a single clone. [ 14 ] Here is the equation with all parts considered:
N = l n ( 1 − P ) l n ( 1 − i g ) {\displaystyle N={\frac {ln(1-P)}{ln(1-{\frac {i}{g}})}}}
The above formula can be used to determine the 99% confidence level that all sequences in a genome are represented by using a vector with an insert size of twenty thousand basepairs (such as the phage lambda vector). The genome size of the organism is three billion basepairs in this example.
N = l n ( 1 − 0.99 ) l n [ 1 − 2.0 × 10 4 b a s e p a i r s 3.0 × 10 9 b a s e p a i r s ] {\displaystyle N={\frac {ln(1-0.99)}{ln[1-{\frac {2.0\times 10^{4}basepairs}{3.0\times 10^{9}basepairs}}]}}}
N = − 4.61 − 6.7 × 10 − 6 {\displaystyle N={\frac {-4.61}{-6.7\times 10^{-6}}}}
N = 688 , 060 {\displaystyle N=688,060} clones
Thus, approximately 688,060 clones are required to ensure a 99% probability that a given DNA sequence from this three billion basepair genome will be present in a library using a vector with an insert size of twenty thousand basepairs.
After a library is created, the genome of an organism can be sequenced to elucidate how genes affect an organism or to compare similar organisms at the genome-level. The aforementioned genome-wide association studies can identify candidate genes stemming from many functional traits. Genes can be isolated through genomic libraries and used on human cell lines or animal models to further research. [ 17 ] Furthermore, creating high-fidelity clones with accurate genome representation and no stability issues would contribute well as intermediates for shotgun sequencing or the study of complete genes in functional analysis. [ 10 ]
One major use of genomic libraries is hierarchichal shotgun sequencing , which is also called top-down, map-based or clone-by-clone sequencing. This strategy was developed in the 1980s for sequencing whole genomes before high throughput techniques for sequencing were available. Individual clones from genomic libraries can be sheared into smaller fragments, usually 500bp to 1000bp, which are more manageable for sequencing. [ 4 ] Once a clone from a genomic library is sequenced, the sequence can be used to screen the library for other clones containing inserts which overlap with the sequenced clone. Any new overlapping clones can then be sequenced forming a contig . This technique, called chromosome walking , can be exploited to sequence entire chromosomes. [ 2 ]
Whole genome shotgun sequencing is another method of genome sequencing that does not require a library of high-capacity vectors. Rather, it uses computer algorithms to assemble short sequence reads to cover the entire genome. Genomic libraries are often used in combination with whole genome shotgun sequencing for this reason. A high resolution map can be created by sequencing both ends of inserts from several clones in a genomic library. This map provides sequences of known distances apart, which can be used to help with the assembly of sequence reads acquired through shotgun sequencing. [ 4 ] The human genome sequence, which was declared complete in 2003, was assembled using both a BAC library and shotgun sequencing. [ 18 ] [ 19 ]
Genome-wide association studies are general applications to find specific gene targets and polymorphisms within the human race. In fact, the International HapMap project was created through a partnership of scientists and agencies from several countries to catalog and utilize this data. [ 20 ] The goal of this project is to compare genetic sequences of different individuals to elucidate similarities and differences within chromosomal regions. [ 20 ] Scientists from all of the participating nations are cataloging these attributes with data from populations of African, Asian, and European ancestry. Such genome-wide assessments may lead to further diagnostic and drug therapies while also helping future teams focus on orchestrating therapeutics with genetic features in mind. These concepts are already being exploited in genetic engineering . [ 20 ] For example, a research team has actually constructed a PAC shuttle vector that creates a library representing two-fold coverage of the human genome. [ 17 ] This could serve as an incredible resource to identify genes, or sets of genes, causing disease. Moreover, these studies can serve as a powerful way to investigate transcriptional regulation as it has been seen in the study of baculoviruses. [ 21 ] Overall, advances in genome library construction and DNA sequencing has allowed for efficient discovery of different molecular targets. [ 5 ] Assimilation of these features through such efficient methods can hasten the employment of novel drug candidates.
Klug, Cummings, Spencer, Palladino (2010). Essentials of Genetics . Pearson. pp. 355– 264. ISBN 978-0-321-61869-6 . {{ cite book }} : CS1 maint: multiple names: authors list ( link ) | https://en.wikipedia.org/wiki/Genomic_library |
The genomic signature refers to the characteristic frequency of oligonucleotides in a genome or sequence . [ 1 ] It has been observed that the genomic signature of phylogenetically related genomes is similar. [ 2 ]
This genetics article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genomic_signature |
Genopolitics is the study of the genetic basis of political behavior and attitudes. It combines behavior genetics , psychology , and political science and it is closely related to the emerging fields of neuropolitics (the study of the neural basis of political attitudes and behavior) and political physiology (the study of biophysical correlates of political attitudes and behavior).
In 2008, The Chronicle of Higher Education reported on the increase in academicians' recognition of and engagement in genopolitics as a discrete field of study, [ 1 ] and New York Times Magazine included genopolitics in its "Eighth Annual Year in Ideas" for the same year, noting that the term was originally coined by James Fowler . [ 2 ] Critics of genopolitics have argued that it is "a fundamentally misguided undertaking", and that it is inconsistent with evidence in the fields of genetics , neuroscience , and evolutionary biology . [ 3 ]
Psychologists and behavior geneticists began using twin studies in the 1980s to study variation in social attitudes, and these studies suggested that both genes and environment played a role. In particular, Nick Martin and his colleagues published an influential twin study of social attitudes in Proceedings of the National Academy of Sciences in 1986. [ 4 ]
However, this early work did not specifically analyze whether or not political orientations were heritable, and political scientists remained mostly unaware of the heritability of social attitudes until 2005. In that year, the American Political Science Review published a reanalysis of political questions on Martin's social attitude survey of twins in that the suggested liberal and conservative ideology is heritable. [ 5 ] The article sparked considerable debate between critics, the authors and their defenders. [ 6 ] [ 7 ] [ 8 ] [ 9 ] [ 10 ] [ 11 ]
A more recent analysis of multiple twin studies finds that political views are approximately 40 percent heritable. [ 12 ]
Initial twin studies suggested that predispositions toward espousal of certain political ideas are heritable, but they said little about political behavior (patterns of voting and/or activism) or predispositions toward it. A 2008 article published in the American Political Science Review matched publicly available voter registration records to a twin registry in Los Angeles, analyzed self-reported voter turnout in the National Longitudinal Study of Adolescent Health (Add Health), and studied other forms of political participation . In all three cases, both genes and environment contributed significantly to variation in political behavior. [ 13 ]
However, other studies showed that the decision to affiliate with any political party and the strength of this attachment are significantly influenced by genes. [ 14 ] [ 15 ]
Scholars therefore recently turned their attention to specific genes that might be associated with political behaviors and attitudes. In the first-ever research to link specific genes to political phenotypes, a direct association was established between voter turnout and monoamine oxidase A (MAO-A) and a gene–environment interaction between turnout and the serotonin transporter (5HTT) gene among those who frequently participated in religious activities. [ 16 ] In other research scholars have also found an association between voter turnout and a dopamine receptor (DRD2) gene that is mediated by a significant association between that gene and the tendency to affiliate with a political party. [ 17 ] [ clarification needed ] More recent studies show an interaction between friendships and the dopamine receptor (DRD4) gene that is associated with political ideology. [ 18 ] Although this work is preliminary and needs replication, it suggests that neurotransmitter function has an important effect on political behavior.
The candidate genes approach to genopolitics received substantial criticism in a 2012 article, published in the American Political Science Review , which argued that many of the candidate genes identified in the above research are associated with innumerable traits and behaviors. The degree to which these genes are associated with so many outcomes thus undermines the apparent important of evidence linking a gene to any particular outcome. [ 19 ]
Employing a more general approach, researchers used genome-wide linkage analysis to identify chromosomal regions associated with political attitudes assessed using scores on a liberalism-conservativism scale. [ 20 ] Their analysis identified several significant linkage peaks and the associated chromosomal regions implicate a possible role for NMDA and glutamate related receptors in forming political attitudes. However, this role is speculative as linkage analysis cannot identify the effect of individual genes.
Associations between genetic markers and political behavior are often assumed to predict a causal connection between the two. Scholars have little incentive to be skeptical of this presumed causal link. Yet it is possible that a confounding factor exists which makes the genetic relationship with politics purely correlative. For instance work on Irish parties, which shows some evidence of a genetic basis for the otherwise inexplicable distinction between the historically two main parties there, is also and more easily explained by socialization. [ 21 ] | https://en.wikipedia.org/wiki/Genopolitics |
A genosome (also known as a lipoplex ) is a lipid and DNA complex that is used to deliver genes . It can be a form of non-viral gene therapy as the complex does not require any components of a virus in order to transport genetic material. In presence of CT-DNA , genosomes can form through surface electrostatic interaction . [ 1 ]
This biochemistry article is a stub . You can help Wikipedia by expanding it .
This genetics article is a stub . You can help Wikipedia by expanding it . | https://en.wikipedia.org/wiki/Genosome |
Genotropism is defined as the reciprocal attraction between carriers of the same or related latent recessive genes . [ 1 ] Developed by the Hungarian psychiatrist Léopold Szondi in the 1930s, the theory concludes that instinct is biological and genetic in origin. Szondi believed that these genes regulated the "possibilities of fate" and was the working principle of the familial unconscious .
Genotropism consists of the theory that genes influence human behavior . While identified as entities, genes exist in groups because evolution favors cooperation. Within each gene group, it is possible to detect specific needs that function as mechanisms of screening and natural selection .
Szondi arrived a sort of genetic determinism, a philosophical theory of predestination. "The latent hereditary factors in human beings, the recessive genes, do not remain dormant or inactive within the human organism, but exert a very important and even decisive influence upon its behavior. This latent or recessive gene theory claims that these non-dominant hereditary factors determine the Object selection, voluntary and involuntary, of the individual. The drives resulting from these latent genes, therefore, direct the individual's selection of love objects, friendships, occupations, diseases, and forms of death. Hence, from the very beginning of the human's existence there is a hidden plan of life guided by 'Instinctual drives'." [ 2 ]
In Szondi's theory, each "need" (a link between genes and behavior) comprises a polarity of positive and negative tendencies. Needs also group together in polarities to form larger wholes called "instinctual drives." Together, behavior tendencies, needs, and drives combine to form patterned wholes.
Szondi created a drive theory that determines that every drive has at least four genes. "The four Szondian drives are (1) contact, (2) sexual, (3) paroxysmal, and (4) ego. They are implicated in their corresponding psychiatric disorders and equivalents: (1) manic-depression, (2) sexual abnormality, (3) epilepsy and hysteria, and (4) schizophrenia." [ 3 ] By locating mental disorders in biological drives, one can illustrate that illness is a disharmony of basic needs.
Genotropism is the working principle of the familial unconscious, the quantitative sharing of genes across the generations of family. Offspring may inherit several genes from both parents, while others receive fewer genes and exhibit spectrum conditions. (For example, while one child is diagnosed with epilepsy, the other only shows various symptoms over a period of time).
Szondi observed that when families pass down genes for specific diseases, the same family transmits defenses against those disorders. Known to Szondi as heterosis , it is currently known as " balancing selection ."
Szondi concluded that genetic traits confer needs and tendencies that shape decision making. "Genetic tendencies can be decoded by constructing genealogies, indicating recurrent patterns of marriage, friendship, and vocational choices in relation to types of illness and modes of death. Destiny comprises all of the hereditary tendencies in the familial unconscious which are expressed primarily through marriage and vocational selections." [ 1 ] Basically, the needs and tendencies in which humans exhibit will guide similar genes to one another.
While Szondi accepted the Oedipus complex, he found that it existed only under the following conditions: when the mother sees her father or brother represented in her son, or when the father sees his mother or sister in his daughter. Therefore, the son takes after the genes represented in his maternal grandfather or uncles, and the daughter after her paternal grandmother or aunt. [ 4 ]
Although it was mostly abandoned by psychologists in the years after Szondi's death, recent discoveries in evolutionary psychology might be bringing it back in a revised form, through the study of homogamy and psychopathology . | https://en.wikipedia.org/wiki/Genotropism |
The genotype of an organism is its complete set of genetic material. [ 1 ] Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. [ 2 ] The number of alleles an individual can have in a specific gene depends on the number of copies of each chromosome found in that species, also referred to as ploidy . In diploid species like humans, two full sets of chromosomes are present, meaning each individual has two alleles for any given gene. If both alleles are the same, the genotype is referred to as homozygous . If the alleles are different, the genotype is referred to as heterozygous.
Genotype contributes to phenotype , the observable traits and characteristics in an individual or organism. [ 3 ] The degree to which genotype affects phenotype depends on the trait. For example, the petal color in a pea plant is exclusively determined by genotype. The petals can be purple or white depending on the alleles present in the pea plant. [ 4 ] However, other traits are only partially influenced by genotype. These traits are often called complex traits because they are influenced by additional factors, such as environmental and epigenetic factors. Not all individuals with the same genotype look or act the same way because appearance and behavior are modified by environmental and growing conditions. Likewise, not all organisms that look alike necessarily have the same genotype.
The term genotype was coined by the Danish botanist Wilhelm Johannsen in 1903. [ 5 ]
Any given gene will usually cause an observable change in an organism, known as the phenotype. The terms genotype and phenotype are distinct for at least two reasons:
A simple example to illustrate genotype as distinct from phenotype is the flower colour in pea plants (see Gregor Mendel ). There are three available genotypes, PP ( homozygous dominant ), Pp (heterozygous), and pp (homozygous recessive). All three have different genotypes but the first two have the same phenotype (purple) as distinct from the third (white).
A more technical example to illustrate genotype is the single-nucleotide polymorphism or SNP. A SNP occurs when corresponding sequences of DNA from different individuals differ at one DNA base, for example where the sequence AAGCCTA changes to AAGCTTA. [ 6 ] This contains two alleles : C and T. SNPs typically have three genotypes, denoted generically AA Aa and aa. In the example above, the three genotypes would be CC, CT and TT. Other types of genetic marker , such as microsatellites , can have more than two alleles, and thus many different genotypes.
Penetrance is the proportion of individuals showing a specified genotype in their phenotype under a given set of environmental conditions. [ 7 ]
Traits that are determined exclusively by genotype are typically inherited in a Mendelian pattern. These laws of inheritance were described extensively by Gregor Mendel , who performed experiments with pea plants to determine how traits were passed on from generation to generation. [ 8 ] He studied phenotypes that were easily observed, such as plant height, petal color, or seed shape. [ 8 ] He was able to observe that if he crossed two true-breeding plants with distinct phenotypes, all the offspring would have the same phenotype. For example, when he crossed a tall plant with a short plant, all the resulting plants would be tall. However, when he self-fertilized the plants that resulted, about 1/4 of the second generation would be short. He concluded that some traits were dominant , such as tall height, and others were recessive, like short height. Though Mendel was not aware at the time, each phenotype he studied was controlled by a single gene with two alleles. In the case of plant height, one allele caused the plants to be tall, and the other caused plants to be short. When the tall allele was present, the plant would be tall, even if the plant was heterozygous. In order for the plant to be short, it had to be homozygous for the recessive allele. [ 8 ] [ 9 ]
One way this can be illustrated is using a Punnett square . In a Punnett square, the genotypes of the parents are placed on the outside. An uppercase letter is typically used to represent the dominant allele, and a lowercase letter is used to represent the recessive allele. The possible genotypes of the offspring can then be determined by combining the parent genotypes. [ 10 ] In the example on the right, both parents are heterozygous, with a genotype of Bb. The offspring can inherit a dominant allele from each parent, making them homozygous with a genotype of BB. The offspring can inherit a dominant allele from one parent and a recessive allele from the other parent, making them heterozygous with a genotype of Bb. Finally, the offspring could inherit a recessive allele from each parent, making them homozygous with a genotype of bb. Plants with the BB and Bb genotypes will look the same, since the B allele is dominant. The plant with the bb genotype will have the recessive trait.
These inheritance patterns can also be applied to hereditary diseases or conditions in humans or animals. [ 11 ] [ 12 ] [ 13 ] Some conditions are inherited in an autosomal dominant pattern, meaning individuals with the condition typically have an affected parent as well. A classic pedigree for an autosomal dominant condition shows affected individuals in every generation. [ 11 ] [ 12 ] [ 13 ]
Other conditions are inherited in an autosomal recessive pattern, where affected individuals do not typically have an affected parent. Since each parent must have a copy of the recessive allele in order to have an affected offspring, the parents are referred to as carriers of the condition. [ 11 ] [ 12 ] [ 13 ] In autosomal conditions, the sex of the offspring does not play a role in their risk of being affected. In sex-linked conditions, the sex of the offspring affects their chances of having the condition. In humans, females inherit two X chromosomes , one from each parent, while males inherit an X chromosome from their mother and a Y chromosome from their father. X-linked dominant conditions can be distinguished from autosomal dominant conditions in pedigrees by the lack of transmission from fathers to sons, since affected fathers only pass their X chromosome to their daughters. [ 13 ] [ 11 ] [ 14 ] In X-linked recessive conditions, males are typically affected more commonly because they are hemizygous, with only one X chromosome. In females, the presence of a second X chromosome will prevent the condition from appearing. Females are therefore carriers of the condition and can pass the trait on to their sons. [ 13 ] [ 11 ] [ 14 ]
Mendelian patterns of inheritance can be complicated by additional factors. Some diseases show incomplete penetrance , meaning not all individuals with the disease-causing allele develop signs or symptoms of the disease. [ 13 ] [ 15 ] [ 16 ] Penetrance can also be age-dependent, meaning signs or symptoms of disease are not visible until later in life. For example, Huntington disease is an autosomal dominant condition, but up to 25% of individuals with the affected genotype will not develop symptoms until after age 50. [ 17 ] Another factor that can complicate Mendelian inheritance patterns is variable expressivity , in which individuals with the same genotype show different signs or symptoms of disease. [ 13 ] [ 15 ] [ 16 ] For example, individuals with polydactyly can have a variable number of extra digits. [ 15 ] [ 16 ]
Many traits are not inherited in a Mendelian fashion, but have more complex patterns of inheritance.
For some traits, neither allele is completely dominant. Heterozygotes often have an appearance somewhere in between those of homozygotes. [ 18 ] [ 19 ] For example, a cross between true-breeding red and white Mirabilis jalapa results in pink flowers. [ 19 ]
Codominance refers to traits in which both alleles are expressed in the offspring in approximately equal amounts. [ 20 ] A classic example is the ABO blood group system in humans, where both the A and B alleles are expressed when they are present. Individuals with the AB genotype have both A and B proteins expressed on their red blood cells. [ 20 ] [ 18 ]
Epistasis is when the phenotype of one gene is affected by one or more other genes. [ 21 ] This is often through some sort of masking effect of one gene on the other. [ 22 ] For example, the "A" gene codes for hair color, a dominant "A" allele codes for brown hair, and a recessive "a" allele codes for blonde hair, but a separate "B" gene controls hair growth, and a recessive "b" allele causes baldness. If the individual has the BB or Bb genotype, then they produce hair and the hair color phenotype can be observed, but if the individual has a bb genotype, then the person is bald which masks the A gene entirely.
A polygenic trait is one whose phenotype is dependent on the additive effects of multiple genes. The contributions of each of these genes are typically small and add up to a final phenotype with a large amount of variation. A well studied example of this is the number of sensory bristles on a fly. [ 23 ] These types of additive effects is also the explanation for the amount of variation in human eye color.
Genotyping refers to the method used to determine an individual's genotype. There are a variety of techniques that can be used to assess genotype. The genotyping method typically depends on what information is being sought. Many techniques initially require amplification of the DNA sample, which is commonly done using PCR .
Some techniques are designed to investigate specific SNPs or alleles in a particular gene or set of genes, such as whether an individual is a carrier for a particular condition. This can be done via a variety of techniques, including allele specific oligonucleotide (ASO) probes or DNA sequencing . [ 24 ] [ 25 ] Tools such as multiplex ligation-dependent probe amplification can also be used to look for duplications or deletions of genes or gene sections. [ 25 ] Other techniques are meant to assess a large number of SNPs across the genome, such as SNP arrays . [ 24 ] [ 25 ] This type of technology is commonly used for genome-wide association studies .
Large-scale techniques to assess the entire genome are also available. This includes karyotyping to determine the number of chromosomes an individual has and chromosomal microarrays to assess for large duplications or deletions in the chromosome. [ 24 ] [ 25 ] More detailed information can be determined using exome sequencing , which provides the specific sequence of all DNA in the coding region of the genome, or whole genome sequencing , which sequences the entire genome including non-coding regions. [ 24 ] [ 25 ]
In linear models, the genotypes can be encoded in different manners. Let us consider a biallelic locus with two possible alleles, encoded by A {\textstyle A} and a {\displaystyle a} . We consider A {\displaystyle A} to correspond to the dominant allele to the reference allele a {\textstyle a} . The following table details the different encoding. [ 26 ] | https://en.wikipedia.org/wiki/Genotype |
Genetic variation in populations can be analyzed and quantified by the frequency of alleles . Two fundamental calculations are central to population genetics : allele frequencies and genotype frequencies. [ 1 ] Genotype frequency in a population is the number of individuals with a given genotype divided by the total number of individuals in the population. [ 2 ] In population genetics , the genotype frequency is the frequency or proportion (i.e., 0 < f < 1) of genotypes in a population.
Although allele and genotype frequencies are related, it is important to clearly distinguish them.
Genotype frequency may also be used in the future (for "genomic profiling") to predict someone's having a disease [ 3 ] or even a birth defect. [ 4 ] It can also be used to determine ethnic diversity.
Genotype frequencies may be represented by a De Finetti diagram .
As an example, consider a population of 100 four-o-'clock plants ( Mirabilis jalapa ) with the following genotypes:
When calculating an allele frequency for a diploid species, remember that homozygous individuals have two copies of an allele, whereas heterozygotes have only one. In our example, each of the 42 pink-flowered heterozygotes has one copy of the a allele, and each of the 9 white-flowered homozygotes has two copies. Therefore, the allele frequency for a (the white color allele) equals
This result tells us that the allele frequency of a is 0.3. In other words, 30% of the alleles for this gene in the population are the a allele.
Compare genotype frequency:
let's now calculate the genotype frequency of aa homozygotes (white-flowered plants).
Allele and genotype frequencies always sum to one (100%).
The Hardy–Weinberg law describes the relationship between allele and genotype frequencies when a population is not evolving. Let's examine the Hardy–Weinberg equation using the population of four-o'clock plants that we considered above: if the allele A frequency is denoted by the symbol p and the allele a frequency denoted by q , then p+q=1 .
For example, if p =0.7, then q must be 0.3. In other words, if the allele frequency of A equals 70%, the remaining 30% of the alleles must be a , because together they equal 100%. [ 5 ]
For a gene that exists in two alleles, the Hardy–Weinberg equation states that ( p 2 ) + (2 pq ) + ( q 2 ) = 1 .
If we apply this equation to our flower color gene, then
If p =0.7 and q =0.3, then
This result tells us that, if the allele frequency of A is 70% and the allele frequency of a is 30%, the expected genotype frequency of AA is 49%, Aa is 42%, and aa is 9%. [ 6 ] | https://en.wikipedia.org/wiki/Genotype_frequency |
The genotype–phenotype distinction is drawn in genetics . The " genotype " is an organism's full hereditary information. The " phenotype " is an organism's actual observed properties, such as morphology , development , or behavior . This distinction is fundamental in the study of inheritance of traits and their evolution .
The terms "genotype" and "phenotype" were created by Wilhelm Johannsen in 1911, [ 2 ] although the meaning of the terms and the significance of the distinction have evolved since they were introduced. [ 3 ]
It is the organism's physical properties that directly determine its chances of survival and reproductive output, but the inheritance of physical properties is dependent on the inheritance of genes. Therefore, understanding the theory of evolution via natural selection requires understanding the genotype–phenotype distinction. The genes contribute to a trait, and the phenotype is the observable manifestation of the genes (and therefore the genotype that affects the trait). If a white mouse had recessive genes that caused the genes responsible for color to be inactive, its genotype would be responsible for its phenotype (the white color). [ citation needed ]
The mapping of a set of genotypes to a set of phenotypes is sometimes referred to as the genotype–phenotype map . [ 4 ]
An organism's genotype is a major (the largest by far for morphology ) influencing factor in the development of its phenotype, but it is not the only one. Even two organisms with identical genotypes may differ in their phenotypes, due to phenotypic plasticity . To what extent a particular genotype influences a phenotype depends on the relative dominance , penetrance , and expresivity of the alleles in question. [ citation needed ]
One experiences this in everyday life with monozygous (i.e. identical) twins . Identical twins share the same genotype, since their genomes are identical; but they never have the same phenotype, although their phenotypes may be very similar. This is apparent in the fact that close relations can always tell them apart, even though others might not be able to see the subtle differences. Further, identical twins can be distinguished by their fingerprints , which are never completely identical. [ citation needed ]
The concept of phenotypic plasticity defines the degree to which an organism's phenotype is determined by its genotype. A high level of plasticity means that environmental factors have a strong influence on the particular phenotype that develops. If there is little plasticity, the phenotype of an organism can be reliably predicted from knowledge of the genotype, regardless of environmental peculiarities during development. An example of high plasticity can be observed in larval newts 1 : when these larvae sense the presence of predators such as dragonflies , they develop larger heads and tails relative to their body size and display darker pigmentation . Larvae with these traits have a higher chance of survival when exposed to the predators, but grow more slowly than other phenotypes. [ citation needed ]
In contrast to phenotypic plasticity, the concept of genetic canalization addresses the extent to which an organism's phenotype allows conclusions about its genotype. A phenotype is said to be canalized if mutations (changes in the genome) do not noticeably affect the physical properties of the organism. This means that a canalized phenotype may form from a large variety of different genotypes, in which case it is not possible to exactly predict the genotype from knowledge of the phenotype (i.e. the genotype–phenotype map is not invertible). If canalization is not present, small changes in the genome have an immediate effect on the phenotype that develops. [ citation needed ]
According to Lewontin , [ 5 ] the theoretical task for population genetics is a process in two spaces: a "genotypic space" and a "phenotypic space". The challenge of a complete theory of population genetics is to provide a set of laws that predictably map a population of genotypes ( G 1 ) to a phenotype space ( P 1 ), where selection takes place, and another set of laws that map the resulting population ( P 2 ) back to genotype space ( G 2 ) where Mendelian genetics can predict the next generation of genotypes, thus completing the cycle. Even if non-Mendelian aspects of molecular genetics are ignored, this is a gargantuan task. Visualizing the transformation schematically:
(adapted from Lewontin 1974, p. 12). T 1 represents the genetic and epigenetic laws, the aspects of functional biology, or development , that transform a genotype into phenotype. This is the " genotype–phenotype map ". T 2 is the transformation due to natural selection, T 3 are epigenetic relations that predict genotypes based on the selected phenotypes and finally T 4 the rules of Mendelian genetics.
In practice, there are two bodies of evolutionary theory that exist in parallel, traditional population genetics operating in the genotype space and the biometric theory used in plant and animal breeding , operating in phenotype space. The missing part is the mapping between the genotype and phenotype space. This leads to a "sleight of hand" (as Lewontin terms it) whereby variables in the equations of one domain, are considered parameters or constants , where, in a full-treatment, they would be transformed themselves by the evolutionary process and are functions of the state variables in the other domain. The "sleight of hand" is assuming that the mapping is known. Proceeding as if it is understood is enough to analyze many cases of interest. For example, if the phenotype is almost one-to-one with genotype ( sickle-cell disease ) or the time-scale is sufficiently short, the "constants" can be treated as such; however, there are also many situations where that assumption does not hold. [ citation needed ] | https://en.wikipedia.org/wiki/Genotype–phenotype_distinction |
The genotype–phenotype map is a conceptual model in genetic architecture . Coined in a 1991 paper by Pere Alberch , [ 1 ] it models the interdependency of genotype (an organism's full hereditary information) with phenotype (an organism's actual observed properties).
The map visualises a relationship between genotype & phenotype which, crucially: [ 2 ] | https://en.wikipedia.org/wiki/Genotype–phenotype_map |
Genotyping is the process of determining differences in the genetic make-up ( genotype ) of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence. It reveals the alleles an individual has inherited from their parents. [ 1 ] Traditionally genotyping is the use of DNA sequences to define biological populations by use of molecular tools. It does not usually involve defining the genes of an individual.
A restriction fragment length polymorphism (RFLP) is a variation between different people at sites of the genome recognized by restriction enzymes . DNA containing different restriction sites will be cut by bacterial restriction enzymes differently and this can be seen using gel electrophoresis . When running the sample through, a successfully cleaved sample will contain two bands, while the sample with a different restriction site polymorphism will have one band as it had not been cleaved. A small change is enough to cause that restriction site to deny the restriction enzyme. This method is often used to trace the inheritance of DNA through families. [ 2 ]
The random amplified polymorphic detection (RAPD) method relies on polymerase chain reaction (PCR) methods to amplify and isolate lengths of DNA fragments. Oligonucleotide primers are used which bind to denatured DNA fragments which have been produced through heat treatment. Two primers, one to define the starting point and ending point of PCR DNA synthesis, are used in this process. The fragments of DNA will range from two to three kilo base pairs and different primers are tried until the desired trait is isolated from the genome. This method is useful in locating small differences to differentiate between species . [ 3 ]
The amplified fragment length polymorphism (AFLP) detection method is much like RAPD as it also relies on PCR amplification of DNA, with the difference being that this process is more precise but also more time consuming than the RAPD counterpart. [ 4 ] It also does not require random primers, instead the DNA is digested by restriction enzymes and the ends are then ligated to adaptors which allow for specification of strands when performing PCR amplification, this is where the improved precision of this method comes from. [ 5 ]
This process uses specific oligonucleotides which are placed on a DNA microarray which bind to complementary strands of DNA. This method is optimal for detecting single nucleotide polymorphisms (SNPs) in the DNA. The DNA will bind to the oligonucleotide bead up until one base pair before the SNP , where a single labeled nucleotide will be incorporated. This will be seen through dyes and fluorescently labeled proteins which indicate which SNP can be found at the locus of interest. [ 6 ] [ 7 ]
This is a method which takes the sequenced genome and compares different genomes to find genomic variants correlated with different traits or diseases. [ 8 ] In this method, thousands of SNPs are studied and compared in sample sizes ranging up to millions of genomes. If certain SNPs are found to be statistically significant over the sample, the genes are identified which contain those SNPs and that gene is then correlated with the trait of interest. [ 9 ] This method can be useful implications in the future for personalized medicine. [ 9 ]
Genotyping applies to a broad range of individuals, including microorganisms. For example, viruses and bacteria can be genotyped. Genotyping in this context may help in controlling the spreading of pathogens, by tracing the origin of outbreaks. This area is often referred to as molecular epidemiology or forensic microbiology . [ citation needed ]
Humans can also be genotyped. For example, when testing fatherhood or motherhood, scientists typically only need to examine 10 or 20 genomic regions (like SNPs).
When genotyping transgenic organisms, a single genomic region may be all that needs to be examined to determine the genotype. A single PCR assay is typically enough to genotype a transgenic mouse .
Ancient DNA (aDNA) studies have been very important in understanding human evolution , but the samples are often highly degraded. This means there are certain steps and techniques required to ensure accuracy and readability of ancient genomes. To begin the researchers must ensure the DNA being studied is not contaminated with any recent DNA and only contains aDNA. To do this researchers will often look for terminal deamination as this is typically seen in aDNA. They will also often compare the sample with moderns human DNA to see if it is similar. Since aDNA can be sparse, certain techniques involve a targeted enrichment of the area of interest in the aDNA which can increase the resolution of these regions. [ 10 ]
They also must work around the various DNA changes that can occur after the death of the individual. One very common form of damage is the deamination of cytosines . This causes the genome to be misread with C to T and G to A mistakes. This is often mitigated by treating the DNA with an USER reagent. This is a mix of uracil-DNA glycosylase and endonuclease VIII. This functions by removing the uracil and cleaving the site which it was removed from. [ 10 ]
This genotyping method is often used for aDNA studies when the DNA reads available are low-coverage or when there is a large number of low coverage genomes being studied. This method does not determine the true diploid genotype but instead researchers will specify which SNPs they would like to focus on and read from the genome . Tools that allow this method include programs like pileupCaller and bam-caller. [ 10 ]
Probabilistic genotyping is best used when the aDNA available is of high quality. This method finds the probability that the ancient genotype was present in the aDNA, often using modern DNA genotypes as reference samples. Programs used for this type of genotyping include snpAD, ATLAS, bcftools, GATK, or ANGSD. [ 10 ]
Genotyping is used in the medical field to identify and control the spread of tuberculosis (TB). Originally, genotyping was only used to confirm outbreaks of tuberculosis; but with the evolution of genotyping technology it is now able to do far more. Advances in genotyping technology led to the realization that many cases of tuberculosis, including infected individuals living in the same household, were not actually linked. [ 11 ] This caused the formation of universal genotyping in an attempt to understand transmission dynamics. Universal genotyping revealed complex transmission dynamics based on things like socio-epidemiological factors. This led to the use of polymerase chain reactions which allowed for faster detection of tuberculosis. This rapid detection method is used to prevent TB. [ 11 ] The addition of whole genome sequencing (WGS) allowed for identification of strains of TB which could then be put in a chronological cluster map. These cluster maps show the origin of cases and the time in which those cases arose. This gives a much clearer picture of transmission dynamics and allows for better control and prevention of transmission. All of these different forms of genotyping are used together to detect TB, prevent its spread and trace the origin of infections. This has helped to reduce the number of TB cases. [ 11 ]
Many types of genotyping are used in agriculture . One type that is used is genotyping by sequencing because it aids agriculture with crop breeding. For this purpose, SNPs are used as markers and RNA sequencing is used to look at gene expression in crops. [ 12 ] The knowledge gained from this type of genotyping allows for selective breeding of crops in ways which benefit agriculture. In the case of alfalfa, the cell wall was improved through selective breeding that was made possible by this type of genotyping. [ 12 ] These techniques have also resulted in the discovery of genes that provide resistance to diseases. A gene called Yr15 was discovered in wheat, which protects against a disease called yellow wheat rust. Selective breeding for the Yr15 gene then prevented yellow wheat rust, benefiting agriculture. [ 12 ]
In avian species where external phenotypic sexual dimorphism is absent or subtle, such as monomorphic species in captivity and juveniles in the wild, sexing birds for research purposes can utilize molecular genetic methods. DNA samples be collected from feathers and blood of birds. [ 13 ] Birds possess a ZW sex determination system, in which females are heterogametic (ZW) and males are homogametic (ZZ). [ 13 ] This is in contrast to the XY sex determination system of humans where males are heterogametic (XY) and females are homogametic (XX).
A widely used genetic marker for avian sexing is the CHD1 gene, which exists in slightly different forms on the Z and W chromosomes, called CHD1Z and CHD1W, respectively. These gene variants differ in the number of base pairs , enabling their detection through amplification by PCR followed by gel electrophoresis separation. [ 14 ]
There are many well-developed and validated primers that amplify a certain region of the CHD1 gene that shows a difference in size between the W and Z chromosome variants. [ 13 ] Five sets of two primers for the CHD1 gene, each (166F/279R, 1237L/1272H, 2550F/2718R, P8/P2, P3/P2) have been tested to show different lengths of PCR products in a wide range of roughly 80 bird species ranging from songbirds to chicken. [ 13 ] These sets of primers contain one primer for each of the sex chromosomes . When amplified PCR products are separated via gel electrophoresis, males (ZZ) display a single band (two identical CHD1Z genes), while females (ZW) exhibit two bands corresponding to each gene variant of different sizes (CHD1Z and CHD1W). [ 13 ] Sex can then be determined by identifying the number of bands for each bird being genotyped.
The CHD1 molecular sexing assay can be used in a wide range of applications, from conservation biology to sexing avian models of behaviour. [ 13 ] PCR-based sex determination is of use when morphological indicators are absent or unavailable. Despite its' ease of use and convenience, there are some limitations with using CHD1 as the main marker for determining sex. Because the nucleotide length difference between the CHD1W and CHD1Z gene varies between species, difficulties with genotypic sexing using the P2/P8 and 1237L/1272H CHD1 primers have been reported. [ 14 ] As a result, alternative primers and markers have been provided to obtain more reliable genotyping results between species. These methods utilize different post-PCR modifications, and protocols, including Single Strand Conformation Polymorphism and Restriction Fragment Length Polymorphism that further processes CHD1 PCR products. [ 14 ]
The Chinese soft-shell turtle determines sex genetically rather than through environmental conditions. This species has a ZZ/ZW sex chromosome system, where males have two Z chromosomes and females have one Z and one W chromosome. [ 15 ] [ 16 ] While some earlier studies suggested that incubation temperature could influence the sex of hatchlings, later research using both incubation experiments and chromosome analysis showed that temperature has no effect on sex outcome. [ 15 ] Modern genetic techniques, including whole-genome sequencing and polymerase chain reaction (PCR), have helped identify DNA markers that are specific to females. [ 16 ] These markers allow scientists to determine the sex of turtles at early life stages with high accuracy. [ 16 ] Because juvenile turtles lack obvious physical differences between sexes, these genetic tools are especially useful in farming and conservation . [ 17 ] In adulthood, male turtles typically grow larger and have thicker shells, showing clear physical differences from females. [ 17 ] Understanding how sex is determined in the Chinese softshell turtle is important for managing breeding programs and maintaining healthy populations in aquaculture . [ 16 ]
Genotyping studies in the Chinese softshell turtle have focused on identifying DNA sequences found only in females to enable accurate sex identification . [ 18 ] [ 19 ] One research team used whole-genome sequencing (WGS) to compare male and female genomes and found over 4 megabases of female-specific DNA. [ 18 ] Based on this, they developed seven PCR primers including P44, P45, and PB1 which consistently amplified female-specific DNA bands. [ 18 ] These primers were validated in over 160 turtles across eight populations and correctly identified female individuals at both adult and embryonic stages, even before gonads were visibly developed. [ 18 ] To determine genetic sex , DNA from tissue or blood is extracted and amplified using polymerase chain reaction (PCR). [ 18 ] The resulting DNA is then visualized using gel electrophoresis. In this process, females (ZW) produce two DNA bands resulting from the Z chromosome and the other from the W chromosome, whereas males (ZZ) show only a single Z band. These visible banding patterns provide a fast, accurate, and non-lethal way to determine sex at very early life stages. [ 18 ]
A separate study used restriction site-associated DNA sequencing ( RAD-seq ) to identify genetic markers unique to female Chinese soft-shell turtles in support of early and accurate sex identification. [ 20 ] Researchers analyzed DNA from male and female turtles and discovered two female-specific DNA fragments, from which they designed three primers named ps4085, ps3137s1, and ps3137s2. [ 20 ] These markers were tested on 296 turtles from different populations and showed 100% accuracy in identifying females. [ 20 ] The presence of these sex-specific sequences confirmed that the species follows a ZW-type sex determination system, where females are the heterogametic sex. [ 20 ] The study demonstrated that RAD-seq is a reliable tool for developing molecular markers, offering practical benefits for aquaculture breeding and population monitoring through non-invasive genetic sexing methods. [ 20 ]
These methods confirm that the Chinese soft-shell turtle has a ZW-type sex determination system and demonstrates how genotyping enables early sex identification by detecting W-linked DNA in embryos or hatchlings , before any morphological differences between sexes have developed during the maturation process. This makes these genetic techniques a valuable tool for breeding programs and conservation efforts. [ 18 ] [ 20 ]
In addition to developing reliable sex-specific markers, recent genotyping studies have identified several candidate genes that may be involved in sexual differentiation . Whole-genome sequencing of the Chinese soft-shell turtle revealed over 4 megabases of female-specific DNA, from which seven primer sets were created to amplify W-linked sequences through PCR. [ 18 ] Within these W-specific regions, researchers discovered genes with potential roles in sexual differentiation. [ 18 ] The gene Ran is involved in nuclear transport and cell cycle regulation and may influence androgen signalling pathways important in gonadal development. [ 18 ] Eif4et , a gene associated with the initiation of protein translation , could affect the expression of proteins critical for female differentiation. [ 18 ] Crkl participates in multiple signaling pathways and has been linked to ovarian development, suggesting a role in establishing sexual phenotype. [ 18 ] Moreover, two additional genes called LHX1 and FGF7 were found to be differentially expressed in the brains of males and females, indicating possible involvement in both growth and sex-regulatory pathways. [ 21 ] Ongoing research into these candidate genes continues to progress the study in molecular sexing in the Chinese softshell turtle and contributes to a more detailed understanding of sexual differentiation in this species.
Genotyping techniques have become an important tool in aquaculture and conservation efforts involving the Chinese soft-shelled turtle. [ 22 ] This species exhibits sexual dimorphism in growth, with males typically growing faster and developing larger, thicker carapaces than females. [ 23 ] These traits make male turtles more economically valuable in farming, where faster-growing individuals reduce costs and increase yield. [ 22 ] [ 23 ] Since external sex differences are not visible at the hatchling or juvenile stage, DNA-based sexing methods enable farmers to identify and select male individuals early in development, allowing for the cultivation of all-male populations through selective breeding . [ 22 ] [ 24 ]
In conservation programs, genotyping is used to determine the sex ratios of natural or captive populations, which is critical for population management and long-term viability. [ 22 ] [ 25 ] This is particularly useful in hatchlings or young turtles where morphological sexing is impossible. [ 22 ] PCR-based genotyping allows for non-invasive sex identification using DNA from small tissue or blood samples, making it suitable for use in protected or endangered populations without harming individuals. [ 22 ] [ 25 ] [ 26 ] Moreover, understanding the genetic basis of sex determination in the Chinese softshell turtle helps inform broader research into reptilian sex systems and evolutionary biology .
Genotyping provides a valuable tool for sex identification in the Chinese softshell turtle, especially during early developmental stages when morphological differences between males and females are not yet visible. [ 22 ] The ability to detect W-linked sequences through PCR enables early and accurate sex determination, which is particularly important in aquaculture settings where males are preferred for their larger size and commercial value. [ 22 ] [ 25 ] The identification of female-specific DNA markers allows for the development of molecular assays that can support breeding programs aimed at producing monosexual populations, thereby improving yield and economic efficiency. [ 22 ] [ 24 ] [ 25 ] Genotyping has also enabled the discovery of candidate genes related to sex differentiation, offering new insights into the genetic basis of sex determination in this species. [ 22 ]
While genotyping offers clear advantages, it also has limitations that can affect its generalizability and long-term reliability. In Zhu et al.’s study, the developed sex-specific markers for the Chinese softshell turtle showed 100% accuracy during validation. [ 22 ] However, the genetic diversity across regional populations raises the possibility that markers effective in one group may not perform identically in others. As additional sex-linked markers are discovered, it becomes increasingly important to validate them across different populations to account for potential mismatches between genotype and phenotype. [ 16 ] This highlights the need to confirm marker effectiveness broadly to ensure accurate sex identification in diverse genetic backgrounds.
Another limitation involves the practicality of applying genotyping in field-based conservation settings. Although PCR-based methods are reliable in laboratories, their effectiveness in field environments can be affected by factors such as sample degradation, transportation issues, or limited infrastructure. [ 27 ] These challenges may reduce the feasibility of widespread implementation in conservation programs operating in remote or low-resource areas. [ 27 ]
There is also a need for ongoing updates to marker systems, as future studies may identify more universally effective or higher-resolution markers. Current tools are robust, but continued development is necessary to enhance their scalability and relevance across broader applications. [ 28 ] [ 27 ]
A further limitation of genotyping is that it only assesses DNA-level variation, which does not capture the functional dynamics of gene expression. For example, a separate transcriptome study using Single-Molecule Real-Time (SMRT) sequencing , which allows for the direct reading of full-length RNA transcripts, identified sex-biased genes not detected by genotyping alone. [ 29 ] Female turtles showed higher expression of Smad4 , Wif1 , and 17β-hsd , while males expressed more Nkd2 and Prp18 . [ 29 ] These genes are involved in hormone-regulated pathways such as TGF-β and Wnt , both of which play critical roles in sex differentiation and development. [ 29 ] Thus, integrating transcriptomic data with genotyping enhances the overall understanding of sex determination mechanisms in the Chinese softshell turtle. [ 29 ]
Accurate sex determination is essential in laboratory animal research , especially when studying sex-linked traits, developmental pathways, or biological responses that differ between males and females. In neonatal mice, however, external sexual characteristics are underdeveloped or absent, making early identification challenging. Newborn mice are monomorphic , meaning males and females cannot be distinguished by external features at birth. For this reason, researchers increasingly rely on genotypic methods to determine sex as early as possible. Genotyping approaches, particularly those involving PCR , allow for early, reliable, and objective sex identification. These methods are often integrated into standard genotyping workflows , ensuring efficient and accurate classification of sex alongside other genetic markers. [ 30 ]
One of the most widely used molecular sexing techniques involves PCR amplification of the Sry gene, a sex-determining region located on the Y chromosome . This gene is present only in male mice and serves as a direct indicator of male genotype. DNA is typically extracted from tissue samples such as tail tips or fetal heads, and PCR is performed using Sry-specific primers . A housekeeping gene such as Gapdh is co-amplified to confirm PCR success and ensure accurate interpretation of results. The presence of the Sry gene product, which appears as a band at approximately 273 base pairs , indicates a male genotype, while its absence indicates a female. This method has demonstrated extremely high accuracy and is frequently used as the gold standard for validating other sexing techniques. [ 30 ] Because it provides binary results and is applicable to all developmental stages, Sry genotyping remains a preferred method in both fetal and neonatal mouse research.
Another highly effective genotypic sexing method targets the Rbm31x and Rbm31y genes, which are homologous but differ by an 84-base pair deletion in the Y-linked version. In this assay, a single pair of primers is used to amplify both genes simultaneously. The PCR reaction yields a 269 base pair product in all samples, representing Rbm31x, and an additional 353 base pair product in males, representing Rbm31y. This results in a clear, two-band pattern for males and a single band for females. Developed by Tunster in 2017, the Rbm31x/y simplex PCR method is praised for its speed, efficiency, and low reagent use. The protocol requires only 15 microliter reactions, does not require DNA purification , and can be completed in under two hours. The clarity of results, combined with the ability to use crude lysates and standard gel electrophoresis, makes this method particularly suitable for high-throughput genotyping in early-stage mouse pups. Its reliability and simplicity have made it a valuable alternative to Sry genotyping in many labs. [ 31 ]
Several other PCR-based sexing methods are available, each with unique advantages and limitations. One such method targets the Sly and Xlr genes. The Sly gene is located on the Y chromosome and produces a PCR product of approximately 280 base pairs, while the Xlr gene is located on the X chromosome and produces a much larger product around 685 base pairs. In this assay, males produce two distinct bands, and females produce only the Xlr band. The large size difference makes interpretation straightforward; however, amplification bias and the presence of nonspecific bands can occur in certain genetic backgrounds, which may complicate analysis. [ 31 ]
Another option is the Kdm5c / Kdm5d assay, which targets X- and Y-linked versions of the Kdm5 gene. The Kdm5c gene product is 331 base pairs, while Kdm5d is 302 base pairs. Males produce both bands, and females produce only the Kdm5c band. While this method is fast and easy to perform, the small difference in size between the two products can make the bands difficult to resolve on standard gels. In such cases, higher-resolution agarose gels or longer electrophoresis times are needed to ensure accurate differentiation. Despite these challenges, both the Sly/Xlr and Kdm5c / Kdm5d methods are valid alternatives to Sry or Rbm31x/y-based sexing, particularly when used with optimized protocols. [ 31 ]
Although genotypic sexing provides high accuracy and objectivity, it is not without limitations. The process requires access to specialized equipment, such as thermocyclers , gel electrophoresis systems, and UV imaging stations, as well as the technical skill to extract and handle genomic DNA. While assays like the Rbm31x/y PCR are relatively cost-effective per reaction, the upfront costs of lab infrastructure and reagents can be substantial for smaller facilities or field-based research. Additionally, the processing time—from tissue collection and DNA extraction to PCR and gel interpretation—can span several hours, making it less practical for immediate on-site decisions or large-scale colony assessments without automation. [ 30 ]
There is also a learning curve for researchers unfamiliar with PCR troubleshooting, as non-specific amplification, primer-dimer artifacts, or DNA degradation can all affect result quality. Moreover, genotypic sexing requires careful consideration of strain background and genetic mutations, especially in transgenic lines where Y chromosome rearrangements or deletions might interfere with primer binding. Despite being a robust standard in most cases, genotypic sexing is not completely immune to technical error and should be periodically validated with known control samples. [ 31 ] [ 30 ]
The ethics of genotyping humans have been a topic of discussion. The rise of genotyping technologies will make it possible to screen large populations of people for genetic diseases and predispositions for disease. [ 32 ] The benefits of population wide genotyping have been contended by ethical concerns on consent and general benefit of wide span screening. [ 32 ]
Genotyping identifies mutations that increase susceptibility of a person to develop a disease, but disease development is not guaranteed in most cases, which can cause psychological damage. [ 33 ]
Discrimination can arise from various genetic markers identified by genotyping, such as athletic advantages or disadvantages in professional sports or risk of disease development later in life. [ 34 ] [ 33 ]
Much of the ethical concerns surrounding genotyping arise from information availability, as in who can access the genotype of an individual in various contexts. [ 33 ] | https://en.wikipedia.org/wiki/Genotyping |
In the field of genetic sequencing , genotyping by sequencing , also called GBS , is a method to discover single nucleotide polymorphisms (SNP) in order to perform genotyping studies, such as genome-wide association studies ( GWAS ). [ 1 ] GBS uses restriction enzymes to reduce genome complexity and genotype multiple DNA samples. [ 2 ] After digestion, PCR is performed to increase fragments pool and then GBS libraries are sequenced using next generation sequencing technologies, usually resulting in about 100bp single-end reads. [ 3 ] It is relatively inexpensive and has been used in plant breeding . [ 2 ] Although GBS presents an approach similar to restriction-site-associated DNA sequencing (RAD-seq) method, they differ in some substantial ways. [ 4 ] [ 5 ] [ 6 ]
GBS is a robust, simple, and affordable procedure for SNP discovery and mapping. Overall, this approach reduces genome complexity with restriction enzymes (REs) in high-diversity, large genomes species for efficient high-throughput, highly multiplexed sequencing. By using appropriate REs, repetitive regions of genomes can be avoided and lower copy regions can be targeted, which reduces alignments problems in genetically highly diverse species. The method was first described by Elshire et al. (2011). [ 1 ] In summary, high molecular weight DNAs are extracted and digested using a specific RE previously defined by cutting frequently [ 7 ] in the major repetitive fraction of the genome. ApeKI is the most used RE. Barcode adapters are then ligated to sticky ends and PCR amplification is performed. Next-generation sequencing technology is performed resulting in about 100 bp single-end reads. Raw sequence data are filtered and aligned to a reference genome using usually Burrows–Wheeler alignment tool (BWA) or Bowtie 2 . The next step is to identify SNPs from aligned tags and score all discovered SNPs for various coverage, depth and genotypic statistics. Once a large-scale, species-wide SNP production has been run, it is possible to quickly call known SNPs in newly sequenced samples. [ 8 ]
When initially developed, the GBS approach was tested and validated in recombinant inbred lines (RILs) from a high-resolution maize mapping population (IBM) and doubled haploid (DH) barley lines from the Oregon Wolfe Barley (OWB) mapping population. Up to 96 RE (ApeKI)-digested DNA samples were pooled and processed simultaneously during the GBS library construction, which was checked on a Genome Analyzer II (Illumina, Inc.). Overall, 25,185 biallelic tags were mapped in maize, while 24,186 sequence tags were mapped in barley. Barley GBS marker validation using a single DH line (OWB003) showed 99% agreement between the reference markers and the mapped GBS reads. Although barley lacks a complete genome sequence, GBS does not require a reference genome for sequence tag mapping, the reference is developed during the process of sampling genotyping. Tags can also be treated as dominant markers for alternative genetic analysis in the absence of a reference genome. Other than the multiplex GBS skimming, imputation of missing SNPs has the potential to further reduce GBS costs. GBS is a versatile and cost-effective procedure that will allow
mining genomes of any species without prior knowledge of its genome structure. [ 1 ] | https://en.wikipedia.org/wiki/Genotyping_by_sequencing |
Gentamicin is an aminoglycoside antibiotic used to treat several types of bacterial infections . [ 4 ] This may include bone infections , endocarditis , pelvic inflammatory disease , meningitis , pneumonia , urinary tract infections , and sepsis among others. [ 4 ] It is not effective for gonorrhea or chlamydia infections . [ 4 ] It can be given intravenously , by intramuscular injection , or topically . [ 4 ] Topical formulations may be used in burns or for infections of the outside of the eye. [ 5 ] It is often only used for two days until bacterial cultures determine what specific antibiotics the infection is sensitive to. [ 6 ] The dose required should be monitored by blood testing. [ 4 ]
Gentamicin can cause inner ear problems and kidney problems . [ 4 ] The inner ear problems can include problems with balance and hearing loss . [ 4 ] These problems may be permanent. [ 4 ] If used during pregnancy , it can cause harm to the developing fetus. [ 4 ] However, it appears to be safe for use during breastfeeding . [ 7 ] Gentamicin is a type of aminoglycoside [ 4 ] and works by disrupting the ability of the bacteria to make proteins, which typically kills the bacteria . [ 4 ]
Gentamicin is naturally produced by the bacterium Micromonospora purpurea , [ 8 ] [ 4 ] was patented in 1962, approved for medical use in 1964. [ 9 ] The antibiotic is collected from the culture of the Micromonospora by perforating the cell wall of the bacterium. Current research is underway to understand the biosynthesis of this antibiotic in an attempt to increase expression and force secretion of gentamicin for higher titer . Gentamicin is on the World Health Organization's List of Essential Medicines . [ 10 ] The World Health Organization classifies gentamicin as critically important for human medicine. [ 11 ] It is available as a generic medication . [ 12 ]
Gentamicin is active against a wide range of bacterial infections, mostly Gram-negative bacteria including Pseudomonas , Proteus , Escherichia coli , Klebsiella pneumoniae , Enterobacter aerogenes , Serratia , and the Gram-positive Staphylococcus . [ 13 ] Gentamicin is used in the treatment of respiratory tract infections, urinary tract infections, blood, bone and soft tissue infections of these susceptible bacteria. [ 14 ]
There is insufficient evidence to support gentamicin as the first line treatment of Neisseria gonorrhoeae infection. [ 15 ] Gentamicin is not used for Neisseria meningitidis or Legionella pneumophila bacterial infections (because of the risk of the person going into shock from lipid A endotoxin found in certain Gram-negative organisms). Gentamicin is also useful against Yersinia pestis (responsible for plague ), its relatives, and Francisella tularensis (the organism responsible for tularemia often seen in hunters and trappers). [ 16 ]
Some Enterobacteriaceae , Pseudomonas spp. , Enterococcus spp. , Staphylococcus aureus and other Staphylococcus spp. have varying degrees of resistance to gentamicin. [ 17 ]
Gentamicin is not recommended in pregnancy unless the benefits outweigh the risks for the mother. Gentamicin can cross the placenta and several reports of irreversible bilateral congenital deafness in children have been seen. Intramuscular injection of gentamicin in mothers can cause muscle weakness in the newborn . [ 14 ]
The safety and efficacy for gentamicin in nursing mothers has not been established. Detectable gentamicin levels are found in human breast milk and in nursing babies. [ 14 ]
In the elderly, renal function should be assessed before beginning therapy as well as during treatment due to a decline in glomerular filtration rate. Gentamicin levels in the body can remain higher for a longer period of time in this population. Gentamicin should be used cautiously in persons with renal , auditory , vestibular , or neuromuscular dysfunction. [ 13 ]
Gentamicin may not be appropriate to use in children, including babies. Studies have shown higher serum levels and a longer half-life in this population. [ 18 ] Kidney function should be checked periodically during therapy. Long-term effects of treatment can include hearing loss and balance problems. Hypocalcemia , hypokalemia , and muscle weakness have been reported when used by injection. [ 13 ]
Gentamicin should not be used if a person has a history of hypersensitivity , such as anaphylaxis , or other serious toxic reaction to gentamicin or any other aminoglycosides . [ 14 ] Greater care is required in people with myasthenia gravis and other neuromuscular disorders as there is a risk of worsening weakness. [ 4 ] Gentamicin should also be avoided when prescribing empirical antibiotics in the setting of possible infant botulism (Ampicillin with Gentamicin is commonly used as empiric therapy in infants) also due to worsening of neuromuscular function. [ 19 ]
Adverse effects of gentamicin can range from less severe reactions, such as nausea and vomiting, to more severe reactions including: [ 13 ]
Nephrotoxicity and ototoxicity are thought to be dose related with higher doses causing greater chance of toxicity. [ 13 ] These two toxicities may have delayed presentation, sometimes not appearing until after completing treatment. [ 13 ]
Kidney damage is a problem in 10–25% of people who receive aminoglycosides, and gentamicin is one of the most nephrotoxic drugs of this class. [ 20 ] Oftentimes, acute nephrotoxicity is reversible, but it may be fatal. [ 13 ] The risk of nephrotoxicity can be affected by the dose, frequency, duration of therapy, and concurrent use of certain medications, such as NSAIDs , diuretics , cisplatin , ciclosporin , cephalosporins , amphotericin , iodide contrast media , and vancomycin . [ 20 ]
Factors that increase risk of nephrotoxicity include: [ 20 ]
Kidney dysfunction is monitored by measuring creatinine in the blood, electrolyte levels, urine output , presence of protein in the urine , and concentrations of other chemicals, such as urea, in the blood. [ 20 ]
About 11% of the population who receives aminoglycosides experience damage to their inner ear . [ 21 ] The common symptoms of inner ear damage include tinnitus , hearing loss, vertigo , trouble with coordination , and dizziness. [ 22 ] Chronic use of gentamicin can affect two areas of the ears. First, damage of the inner ear hair cells can result in irreversible hearing loss. Second, damage to the inner ear vestibular apparatus can lead to balance problems. [ 22 ] To reduce the risk of ototoxicity during treatment, it is recommended to stay hydrated. [ 13 ]
Factors that increase the risk of inner ear damage include: [ 13 ] [ 14 ]
Gentamicin is a bactericidal antibiotic that works by binding the 30S subunit of the bacterial ribosome, negatively impacting protein synthesis . The primary mechanism of action is generally accepted to work through ablating the ability of the ribosome to discriminate on proper transfer RNA and messenger RNA interactions. [ 23 ] Typically, if an incorrect tRNA pairs with an mRNA codon at the aminoacyl site of the ribosome, adenosines 1492 and 1493 are excluded from the interaction and retract, signaling the ribosome to reject the aminoacylated tRNA :: Elongation Factor Thermo-Unstable complex. [ 24 ] However, when gentamicin binds at helix 44 of the 16S rRNA , it forces the adenosines to maintain the position they take when there is a correct, or cognate, match between aa-tRNA and mRNA. [ 25 ] This leads to the acceptance of incorrect aa-tRNAs, causing the ribosome to synthesize proteins with wrong amino acids placed throughout (roughly every 1 in 500). [ 26 ] The non-functional, mistranslated proteins misfold and aggregate, eventually leading to death of the bacterium. Moreover, it has been observed that gentamicin can cause a substantial slowdown in the overall elongation rate of peptide chains in live bacterial cells, independent of the misincorporation of amino acids. [ 27 ] This finding indicates that gentamicin not only induces errors in protein synthesis but also broadly hampers the efficiency of the translation process itself. An additional mechanism has been proposed based on crystal structures of gentamicin in a secondary binding site at helix 69 of the 23S rRNA , which interacts with helix 44 and proteins that recognize stop codons . At this secondary site, gentamicin is believed to preclude interactions of the ribosome with ribosome recycling factors, causing the two subunits of the ribosome to stay complexed even after translation completes, creating a pool of inactive ribosomes that can no longer re-initiate and translate new proteins. [ 28 ]
Since gentamicin is derived from the species Micromonospora , the backbone for this antibiotic is the aminocyclitol 2-deoxystreptamine . [ 29 ] [ 30 ] This six carbon ring is substituted at the carbon positions 4 and 6 by the amino sugar molecules cyclic purpurosamine and garosamine , respectively. [ 31 ] [ 29 ] The gentamicin complex, is differentiated into five major components (C 1 , C 1a , C 2 , C 2a , C 2b ) and multiple minor components by substitution at the 6' carbon of the purpurosamine unit indicated in the image to the right by R 1 and R 2 . [ 31 ] [ 29 ] [ 32 ] [ 33 ] The R 1 and R 2 can have the follow substitutions for some of the species in the gentamicin complex. [ 31 ] [ 34 ] [ 30 ]
Gentamicins consist of three hexosamines : gentosamine/garosamine, 2-deoxystreptamine, and purpurosamine (see illustrations, from left to right). [ 35 ] [ 36 ]
Kanamycins and tobramycin exhibit similar structures. Sisomicin is 4,5-dehydrogentamicin-C 1a .
Gentamicin is composed of a number of related gentamicin components and fractions which have varying degrees of antimicrobial potency. [ 37 ] The main components of gentamicin include members of the gentamicin C complex: gentamicin C 1 , gentamicin C 1a , and gentamicin C 2 which compose approximately 80% of gentamicin and have been found to have the highest antibacterial activity. Gentamicin A, B, X, and a few others make up the remaining 20% of gentamicin and have lower antibiotic activity than the gentamicin C complex. [ 33 ] The exact composition of a given sample or lot of gentamicin is not well defined, and the level of gentamicin C components or other components in gentamicin may differ from lot-to-lot depending on the gentamicin manufacturer or manufacturing process. Because of this lot-to-lot variability, it can be difficult to study various properties of gentamicin including pharmacokinetics and microorganism susceptibility if there is an unknown combination of chemically related but different compounds. [ 38 ]
The complete biosynthesis of gentamicin is not entirely elucidated. The genes controlling the biosynthesis of gentamicin are of particular interest due to the difficulty in obtaining the antibiotic after production. [ 33 ] [ 32 ] [ 34 ] [ 39 ] [ 40 ] Since gentamicin is collected at the cell surface and the cell surface must be perforated somehow to obtain the antibiotic. [ 33 ] [ 32 ] [ 34 ] [ 39 ] [ 40 ] Many propose the amount of gentamicin collected after production could increase if the genes are identified and re-directed to secrete the antibiotic instead of collecting gentamicin at the cell surface. [ 33 ] [ 32 ] [ 34 ] [ 39 ] [ 40 ] Literature also agrees with the gentamicin biosynthesis pathway starting with D- Glucose-6-phosphate being dephopsphorylated , transaminated , dehydrogenated and finally glycosylated with D- glucosamine to generate paromamine inside Micromonospora echinospora . [ 31 ] The addition of D- xylose leads to the first intermediate of the gentamicin C complex pathway, gentamicin A2. [ 31 ] [ 41 ] Gentamicin A2 is C-methylated and epimerized into gentamicin X 2 , the first branch point of this biosynthesis pathway [ 41 ]
When X 2 is acted on by the cobalamin -dependent radical S-adenosyl-L-methionine enzyme GenK, the carbon position 6' is methylated to form the pharmacologically active intermediate G418 [ 42 ] [ 41 ] [ 31 ] [ 43 ] G418 then undergoes dehydrogenation and amination at the C6' position by the dehydrogenase gene, GenQ, to generate the pharmacologically active JI-20B, although another intermediate, 6'-dehydro-6'oxo-G418 (6'DOG) is proposed to be in-between this step and for which the gene GenB1 is proposed as the aminating gene. [ 31 ] [ 44 ] JI-20B is dehydroxylated and epimerized to first component of the gentamicin C complex, gentamicin C2a which then undergoes an epimerization by GenB2 and then a N-methylation by an unconfirmed gene to form the final product in this branch point, gentamicin C1. [ 41 ] [ 44 ] [ 31 ] [ 45 ]
When X 2 bypasses GenK and is directly dehydrogenated and aminated by the GenQ enzyme, the other pharmacologically relevant intermediate JI-20A is formed. [ 31 ] [ 44 ] Although, there has been identification of an intermediate for this step, 6'-dehydro-6'-oxo-gentamicin X2 (6'-DOX), for which the enzyme GenB1 is purposed as the aminating enzyme. [ 44 ] JI-20A is then dehydroxylated into the first component of the gentamicin C complex for this branch, gentamicin C1a via a catalytic reaction with GenB4. [ 45 ] C1a then undergoes an N-methylation by an unconfirmed enzyme to form the final component, gentamicin C2b. [ 44 ] [ 41 ] [ 31 ] [ 45 ]
Gentamicin is only synthesized via submerged fermentation and inorganic sources of nutrients have been found to reduce production. [ 31 ] Traditional fermentation used yeast beef broth, [ 32 ] but there has been research into optimizing the growth medium for producing gentamicin C complex due to the C complex currently being the only pharmaceutically relevant component. [ 31 ] The main components of the growth medium are carbon sources, mainly sugars, but several studies found increased gentamicin production by adding vegetable and fish oils and decreased gentamicin production with the addition of glucose , xylose and several carboxylic acids . [ 31 ] Tryptone and various forms of yeast and yeast derivatives are traditionally used as the nitrogen source in the growth medium, but several amino acids , soybean meal , corn steep liquor , ammonium sulfate , and ammonium chloride have proven to be beneficial additives. [ 31 ] [ 34 ] Phosphate ions , metal ions ( cobalt and a few others at low concentration), various vitamins (mostly B vitamins ), purine and pyrimidine bases are also supplemented into the growth medium to increase gentamicin production, but the margin of increase is dependent on the species of Micromonospora and the other components in the growth medium. [ 31 ] [ 39 ] With all of these aforementioned additives, pH and aeration are key determining factors for the amount of gentamicin produced. [ 31 ] [ 34 ] A range of pH from 6.8 to 7.5 is used for gentamicin biosynthesis and the aeration is determined by independent experimentation reliant on type of growth medium and species of Micromonospora . [ 31 ] [ 34 ]
Gentamicin is produced by the fermentation of Micromonospora purpurea . It was discovered in 1963 by Weinstein, Wagman et al. at Schering Corporation in Bloomfield, N.J. while working with source material (soil samples) provided by Rico Woyciesjes. [ 8 ] When M. purpurea grows in culture it is a vivid purple colour similar to the colour of the dye Gentian Violet and hence this was why Gentamicin took then name it did. Subsequently, it was purified and the structures of its three components were determined by Cooper, et al., also at the Schering Corporation. It was initially used as a topical treatment for burns at burn units in Atlanta and San Antonio and was introduced into IV usage in 1971. It remains a mainstay for use in sepsis . [ citation needed ]
It is synthesized by Micromonospora , a genus of Gram-positive bacteria widely present in the environment (water and soil). According to the American Medical Association Committee on Generic Names, antibiotics not produced by Streptomyces should not use y in the ending of the name, and to highlight their specific biological origins, gentamicin and other related antibiotics produced by this genus ( verdamicin , mutamicin , sisomicin , netilmicin , and retymicin ) have their spellings ending in ~micin and not in ~mycin . [ 46 ]
Gentamicin is also used in molecular biology research as an antibacterial agent in tissue and cell culture, to prevent contamination of sterile cultures. Gentamicin is one of the few heat-stable antibiotics that remain active even after autoclaving , which makes it particularly useful in the preparation of some microbiological growth media. [ citation needed ] | https://en.wikipedia.org/wiki/Gentamicin |
The gentamicin protection assay or survival assay or invasion assay is a method used in microbiology . It is used to quantify the ability of pathogenic bacteria to invade eukaryotic cells .
The assay is based on several observations made in the 1970s, in which the ability of internalized bacteria to avoid killing by antibiotics was reported. [ 1 ] [ 2 ] The assay started to be used in biological research in the early 1980s.
Intracellular bacteria need to enter host cells ( cells of the infected organism ) in order to replicate and propagate infection. Many species of Shigella (causes bacillary dysentery ), Salmonella ( typhoid fever ), Mycobacterium ( leprosy and tuberculosis ) and Listeria ( listeriosis ), to name but a few, are intracellular.
Several antibiotics cannot penetrate eukaryotic cells. Therefore, these antibiotics cannot hurt intracellular bacteria that are already internalized. Using such antibiotics enables us to differentiate between bacteria that succeed in penetrating eukaryotic cells and those that do not. Applying such an antibiotic to a culture of eukaryotic cells infected with bacteria would kill the bacteria that remain outside the cells while sparing the ones that penetrated. The antibiotic of choice for this assay is the aminoglycoside gentamicin .
HeLa cells are commonly used as eukaryotic cells in the gentamicin protection assay, but other cells can be used as well. As for bacteria, only species susceptible to gentamicin can be assayed.
The assay is performed in plastic microtiter plates , which are commonly used in laboratories for culturing eukaryotic cells. The cells are allowed to grow in the wells overnight, creating a flat layer. Bacteria are separately grown overnight. On the next day the eukaryotic cells are inoculated with the bacteria and are incubated together for an hour. Centrifuging the plates for a few minutes may help bring cells and bacteria in contact and initiate infection.
After infection gentamicin is added to the plates, and they are incubated for an hour, allowing the antibiotic to kill all bacteria that were not able to penetrate the cells and remained outside. The plates are then washed well to remove the dead bacteria. Next the eukaryotic cells are lysed using a detergent , most commonly Triton X-100 .
The bacteria that penetrated the cells and remained alive are now released, and they are plated on solid medium plates . Counting the colonies formed on the plates on the next day, and knowing how many bacteria were used in the beginning of the assay, enables the researcher to calculate the percentage of bacteria that were able to invade the eukaryotic cells.
The gentamicin protection assay is commonly used in pathogen research. The contribution of specific genes or proteins to the bacteria's ability to invade cells can be easily assayed using this method. The gene in question can be knocked out , and the bacteria's invasiveness compared with that of normal, wild type bacteria. Environmental conditions, such as pH level and temperature , can also be assayed for their effect on invasiveness.
The gentamicin protection assay is very sensitive, as it can detect the internalization of even single bacteria. It has several drawbacks:
To help assess the accuracy of a particular assay, positive and negative controls should be performed. When performing the assay as described above, bacteria that are known to be entirely invasive (positive control) and bacteria that are known as non-invasive (negative control) should be included in the assay.
An alternative invasion assay is the differential immunostaining assay, based on the binding of antibodies to bacteria before and after invasion. The antibodies emit fluorescent , colored light , and the results of this assay are viewed under the microscope . | https://en.wikipedia.org/wiki/Gentamicin_protection_assay |
Gentex is an international standard ( ITU F.20) for the transmission of telegrams over the Telex network. It replaces fixed telegraph connections between stations and means instead that the telegraph station that transmits the telegram connects directly to the receiving station and transmits the telegram with a remote typewriter . [ 1 ]
The first official Gentex traffic was introduced in 1956 between the Netherlands , Switzerland , West Germany and Austria . Sweden introduced in 1960 as a test Gentexexpedition with the Netherlands. In 1963 the Nordic countries decided to introduce Gentexexpedition between their countries. [ 2 ] | https://en.wikipedia.org/wiki/Gentex_(standard) |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.