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Monday, March 30, 2015

Genetically modified crops


From Wikipedia, the free encyclopedia

Genetically modified crops (GMCs, GM crops, or biotech crops) are plants used in agriculture, the DNA of which has been modified using genetic engineering techniques. 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, or environmental conditions, reduction of spoilage, or 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.

Farmers have widely adopted GM technology. Between 1996 and 2011, the total surface area of land cultivated with GM crops had increased by a factor of 94, from 17,000 square kilometers (4,200,000 acres) to 1,600,000 km2 (395 million acres). 10% of the world's crop lands were planted with GM crops in 2010. As of 2011, 11 different transgenic crops were grown commercially on 395 million acres (160 million hectares) in 29 countries.

There is broad scientific consensus that food on the market derived from GM crops poses no greater risk to human health than conventional food.[1][2][3][4][5] GM crops also provide a number of ecological benefits.[6] However, opponents have objected to GM crops per se on several grounds, including environmental concerns, whether food produced from GM crops is safe, whether GM crops are needed to address the world's food needs, and economic concerns raised by the fact these organisms are subject to intellectual property law.

Gene transfer in nature and traditional agriculture

DNA transfers naturally between organisms.[7] Several natural mechanisms allow gene flow across species. These occur in nature on a large scale – for example, it is one mechanism for the development of antibiotic resistance in bacteria.[8] This is facilitated by transposons, retrotransposons, proviruses and other mobile genetic elements that naturally translocate DNA to new loci in a genome.[9][10] Movement occurs over an evolutionary time scale[11][12][13]

The introduction of foreign germplasm into crops has been achieved by traditional crop breeders by overcoming species barriers. A hybrid cereal grain was created in 1875, by crossing wheat and rye.[14] Since then important traits including dwarfing genes and rust resistance have been introduced.[15] Plant tissue culture and deliberate mutations have enabled humans to alter the makeup of plant genomes.[16][17]

History

The first genetically modified plant was produced in 1982, an antibiotic-resistant tobacco plant.[18] The first field trials occurred in France and the USA in 1986, when tobacco plants were engineered for herbicide resistance.[19] In 1987, Plant Genetic Systems (Ghent, Belgium), founded by Marc Van Montagu and Jeff Schell, was the first company to genetically engineer insect-resistant (tobacco) plants by incorporating genes that produced insecticidal proteins from Bacillus thuringiensis (Bt).[20]
The People’s Republic of China was the first country to allow commercialized transgenic plants, introducing a virus-resistant tobacco in 1992,[21] which was withdrawn in 1997.[22]:3 The first genetically modified crop approved for sale in the U.S., in 1994, was the FlavrSavr tomato. It had a longer shelf life, because it took longer to soften after ripening.[23] In 1994, the European Union approved tobacco engineered to be resistant to the herbicide bromoxynil, making it the first commercially genetically engineered crop marketed in Europe.[24]

In 1995, Bt Potato was approved by the US Environmental Protection Agency, making it the country's first pesticide producing crop.[25] In 1995 canola with modified oil composition (Calgene), Bt maize (Ciba-Geigy), bromoxynil-resistant cotton (Calgene), Bt cotton (Monsanto), glyphosate-resistant soybeans (Monsanto), virus-resistant squash (Asgrow), and additional delayed ripening tomatoes (DNAP, Zeneca/Peto, and Monsanto) were approved.[19] As of mid-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.[19] In 2000, Vitamin A-enriched golden rice, was the first food with increased nutrient value.

Methods

Plants (Solanum chacoense) being transformed using agrobacterium

Genetically engineered crops have genes added or removed using genetic engineering techniques,[26] originally including gene guns, electroporaton, microinjection and agrobacterium. More recently, CRISPR and TALEN offered much more precise and convenient editing techniques.

Gene guns (a.k.a. biolistic) "shoot" (direct high energy particles or radiations against[27]) 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.[28] 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, and 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 tumour 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 directly injects the gene into the DNA.[29]

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.[30][31]

In research tobacco and Arabidopsis thaliana are the most frequently modified plants, due to well-developed transformation methods, easy propagation and well studied genomes.[32][33] 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 gene products should be able to be denatured by heat so that they are destroyed during cooking.

Types of modifications


Transgenic maize containing a gene from the bacteria Bacillus thuringiensis

Transgenic

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 correctly and efficiently express in the host organism. Transgenic plants are used to express proteins like the cry toxins from B. thuringiensis, herbicide resistant genes, antibodies[34] and antigens for vaccinations[35]

Transgenic carrots have been used to produce the drug Taliglucerase alfa which is used to treat Gaucher's disease.[36] In the laboratory, transgenic plants have been modified to increase photosynthesis (currently about 2% at most plants to the theoretic potential of 9–10%.[37] This is possible by changing the rubisco enzyme (i.e. changing C3 plants into C4 plants[38]), by placing the rubisco in a carboxysome, by adding CO2 pumps in the cell wall,[39][40] by changing the leaf form/size.[41][42][43][44] Plants have been engineered to exhibit bioluminescence that may become a sustainable alternative to electric lighting.[45] Still other transgenic plants have been modified to fix ambient nitrogen.[46]

Cisgenic

Cisgenic plants are made using genes found within the same species or a closely related one, where conventional plant breeding can occur. 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.[47]

Subgenic

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. The strain promises to reduce or eliminate the heavy use of fungicides to control the disease. Gao used the TALENs and CRISPR gene editing tools without adding or changing any other genes. No field trials were immediately planned.[48][49]

Business impact

The global value of biotech seed alone was US$13.2 billion in 2011, with the end product of commercial grain from biotech maize, soybean grain and cotton valued at approximately US$160 billion or more per year.[50]

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.

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.[51]

As of 2009, the overall Roundup line of products including the GM seeds represented about 50% of Monsanto's business.[52] The patent on the first type of Roundup Ready crop that Monsanto produced (soybeans) expired in 2014[53] and the first harvest of off-patent soybeans occurs in the spring of 2015.[54] Monsanto has broadly licensed the patent to other seed companies that include the glyphosate resistance trait in their seed products.[55] About 150 companies have licensed the technology,[56] including Syngenta[57] and DuPont Pioneer.[58]

Monsanto's triple-stack corn—a combination of Roundup Ready 2-weed control technology with YieldGard (Bt) Corn Borer and YieldGard Rootworm insect control—is the US market leader. U.S. corn farmers planted more than 32 million acres (130,000 km2) of triple-stack corn in 2008.[59] It is estimated that it could be planted on 56 million acres (230,000 km2) in 2014–2015. Bollgard II cotton with Roundup Ready Flex was planted on approximately 5 million acres (20,000 km2) of U.S. cotton in 2008.[60]

According to the International Service for the Acquisition of Agri-Biotech Applications (ISAAA), in 2010 approximately 15 million farmers grew biotech crops in 29 countries. Over 90% of the farmers were resource-poor in developing countries.[61] 6.5 million farmers in China and 6.3 million small farmers in India grew biotech crops (mostly Bt cotton). The Philippines, South Africa (biotech cotton, maize, and soybeans often grown by subsistence women farmers) and another twelve developing countries also grew biotech crops in 2009.[62] 10 million more small and resource-poor farmers may have been secondary beneficiaries of Bt cotton in China.

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 will lead to increased demand for GM feedbcrops.[63] 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.[63]

Yield

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. 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.[64][65]

Yields increased 9% for herbicide tolerance and 25% for insect resistance. 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.[64]

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 fertiliser use. Separately, they concluded that the funding source did not influence study results.[64]

Traits

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[66] and insect-resistant brinjal (eggplant) for India.[67]

Lifetime

The first genetically modified crop approved for sale in the U.S. was the FlavrSavr tomato, which had a longer shelf life.[23] It is no longer on the market.

In November 2014, the USDA approved a GM potato that prevents bruising.[68][69]

In February 2015 Arctic Apples were approved by the USDA,[70] becoming the first genetically modified apple approved for US sale.[71] Gene silencing is used to reduce the expression of polyphenol oxidase (PPO), thus preventing enzymatic browning of the exposed fruit after it has been sliced open. The trait was added to Granny Smith and Golden Delicious varieties.[70][72] The trait also includes a bacterial antibiotic gene that provides resistance to the antibiotic kanamycin. The modification process affected only a small fraction of processed cells. The cells were then cultivated in the presence of kanamycin, which allows only resistant cultivars to survive. Consuming resistant apples does not provide kanamycin resistance.[73] As of the announcement, the FDA continued to review the strains.[71]

Nutrition

Edible oils

Some GM soybeans offer improved oil profiles for processing or healthier eating.[74][75] Camelina sativa has been modified to produce plants that accumulate high levels of oils similar to fish oils.[76][77]

Vitamin enrichment

Golden rice, developed by the International Rice Research Institute (IRRI), provides greater amounts of Vitamin A targeted at reducing Vitamin A deficiency.[78][79]

Researchers vitamin-enriched corn derived from South African white corn variety M37W, producing a 169-fold increase in Vitamin A, 6-fold increase in Vitamin C and doubled concentrations of folate.[80] Modified Cavendish bananas express 10-fold the amount of Vitamin A as unmodified varieties.[81]

Toxin reduction

A genetically modified cassava under development offers lower cyanogen glucosides and enhanced protein and other nutrients (called BioCassava).[82]

In November 2014, the USDA approved a potato, developed by J.R. Simplot Company, that prevents bruising and produces less acrylamide when fried. The modifications prevent natural, harmful proteins from being made via RNA interference.[68][69] They do not employ genes from non-potato species. The trait was added to the Russet Burbank, Ranger Russet and Atlantic varieties.[68]

Stress resistance

Plants engineered to tolerate non-biological stressors such as drought,[68][69][83][84] frost,[85][86] high soil salinity,[87][88] and nitrogen starvation[89] were in development. In 2011, Monsanto's DroughtGard maize became the first drought-resistant GM crop to receive US marketing approval.[90]

Herbicides

Glyphosate
As of 1999 the most prevalent GM trait was glyphosate-resistance.[91] 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.[91]

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.[92][93] 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.
Bromoxynil
Tobacco plants have been engineered to be resistant to the herbicide bromoxynil.[24]
Glufosinate
Crops have been commercialized that are resistant to the herbicide glufosinate, as well.[94] 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.[95][96]
2-4D
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.[97][98] The genetic modification providing resistance to 2,4-D is insertiion of a bacterial aryloxyalkanoate dioxygenase gene, aad1.[97][99] The USDA had approved maize and soybeans with the mutation in September 2014.[100]
Dicamba
Monsanto has requested approval for a stacked strain that is tolerant of both glyphosate and dicamba.[101]

Pest resistance

Insects

Tobacco, corn, rice and many other crops have been engineered to express genes encoding for insecticidal proteins from Bacillus thuringiensis (Bt).[25][102] 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.[103]

In the late 1990s, a GM potato that was resistant to the Colorado potato beetle was withdrawn because major buyers rejected it, fearing consumer opposition.[68]

Viruses

Virus resistant papaya were developed In response to a papaya ringspot virus (PRV) outbreak in Hawaii in the late 1990s. . They incorporate PRV DNA.[104][105] By 2010, 80% of Hawaiian papaya plants were genetically modified.[106][107]

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.[108]

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.[109]

By-products

Drugs

In 2012, the FDA approved the first plant-produced pharmaceutical, a treatment for Gaucher's Disease.[110] Tobacco plants have been modified to produce therapeutic antibodies.[111]

Biofuel

Algae is under development for use in biofuels.[112] Modified jatropha offers improved qualities for fuel. Syngenta has USDA approval to market a maize trademarked Enogen that has been genetically modified to convert its starch to sugar for ethanol.[113] In 2013, the Flemish Institute for Biotechnology was investigating poplar trees genetically engineered to contain less lignin to ease conversion into ethanol.[114] 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.[115]

Materials

Companies and labs are working on plants that can be used to make bioplastics.[116] Potatoes that produce industrially useful starches have been developed as well.[117] Oilseed can be modified to produce fatty acids for detergents, substitute fuels and petrochemicals.

Bioremediation

Scientists at the University of York developed a weed (Arabidopsis thaliana) that contains genes from bacteria that can clean TNT and RDX-explosive soil contaminants.[118] 16 million hectares in the USA (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.[119]

Genetically modified plants have been used for bioremediation of contaminated soils. Mercury, selenium and organic pollutants such as polychlorinated biphenyls (PCBs).[119][120]

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.[121]

Asexual reproduction

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.[122]

Crops

As of 2010 food species for which a genetically modified version is being commercially grown (percent modified in the table below are mostly 2009/2010 data) include:[123][124][125][126][127][128]
Crop Traits Modification[specify] Percent modified in US Percent modified in world
Alfalfa Tolerance of glyphosate or glufosinate Genes added Planted in the US from 2005–2007; 2007–2010 court injunction; 2011 approved for sale
Apples Delayed browning [72] Genes added for reduced polyphenol oxidase (PPO production from other apples[72] 2015 approved for sale[70]
Canola/ Rapeseed Tolerance of glyphosate or glufosinate High laurate canola,[129] Oleic acid canola[130] Genes added 87% (2005)[128] 21%
Corn Tolerance of herbicides glyphosate glufosinate, and 2,4-D. Insect resistance. Added enzyme, alpha amylase, that converts starch into sugar to facilitate ethanol production.[131] Genes, some from Bt, added.[132] Herbicide-resistant: 2013, 85%[133] Bt: 2013, 76%[133] Stacked: 2013, 71% 26%
Cotton (cottonseed oil) Insect resistance Gene, some from Bt, added Herbicide-resistant: 2013, 82%[133] Bt: 2013, 75%[133] Stacked: 2013, 71%[133] 49%
Papaya (Hawaiian) Resistance to the papaya ringspot virus.[134] Gene added 80%
Potato (food) Resistance to Colorado beetle Resistance to potato leaf roll virus and Potato virus Y[117]
Reduced acrylamide when fried and reduced bruising[68]
Bt cry3A, coat protein from PVY[135] "Innate" potatoes added genetic material coding for mRNA for RNA interference[68] 0% 0%
Potato (starch) Antibiotic resistance gene, used for selection
Better starch production[136]
Antibiotic resistance gene from bacteria
Modifications to endogenous starch-producing enzymes
0% 0%
Rice Enriched with beta-carotene (a source of vitamin A) Genes from maize and a common soil microorganism.[137][138] Forecast to be on the market in 2015 or 2016[139]
Soybeans Tolerance of glyphosate or glufosinate
Reduced saturated fats (high oleic acid);[140]
Kills susceptible insect pests
Herbicide resistant gene taken from bacteria added
Knocked out native genes that catalyze saturation
Gene for one or more Bt crystal proteins added
2013: 93%[133] 77%
Squash (Zucchini/Courgette) Resistance to watermelon, cucumber and zucchini/courgette yellow mosaic viruses[130][141][142] Viral coat protein genes 13% (figure is from 2005)[128]
Sugar beet Tolerance of glyphosate, glufosinate Genes added 95% (2010); regulated 2011; deregulated 2012 9%
Sugarcane Pesticide tolerance
High sucrose content.
Genes added
Sweet peppers Resistance to cucumber mosaic virus[143][144] Viral coat protein genes Small quantities grown in China
Tomatoes Suppression of the enzyme polygalacturonase (PG), retarding fruit softening after harvesting,[145] while at the same time retaining both the natural color and flavor of the fruit Antisense gene of the gene responsible for PG enzyme production added Taken off the market due to commercial failure. Small quantities grown in China
Wheat Tolerance of glyphosate Genes added unknown unknown

Development

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.[133]

Farming practices

Resistance

Constant exposure to a toxin creates evolutionary pressure for pests resistant to that toxin. Overreliance on glyphosate and a reduction in the diversity of weed management practices allowed the spread of glyphosate resistance in 14 weed species/biotypes in the US.[133]

One method of reducing resistance is the creation of refuges to allow nonresistant organisms to survive and maintain a susceptible population.

To reduce resistance to 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.[146]

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.[147] 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.[148] 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.[149]

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.[133]

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.[150]

Plant protection

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.[133]

Tillage

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.[151]

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.[151]

Regulation

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 USA 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.[152][153]

Production[edit]

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.[154]

Country 2013– GM planted area (million hectares)[155] Biotech crops
USA 70.1 Maize, Soybean, Cotton, Canola, Sugarbeet, Alfalfa, Papaya, Squash
Brazil 40.3 Soybean, Maize, Cotton
Argentina 24.4 Soybean, Maize, Cotton
India 11.0 Cotton
Canada 10.8 Canola, Maize, Soybean, Sugarbeet
Total 175.2 ----

The United States Department of Agriculture (USDA) reports every year on the total area of GMO varieties planted in the United States.[156][157] 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".[154][158]

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 km2 (432 million acres).[154] 10% of the world's croplands were planted with GM crops in 2010.[50] As of 2011, 11 different transgenic crops were grown commercially on 395 million acres (160 million hectares) in 29 countries such as the USA, Brazil, Argentina, India, Canada, China, Paraguay, Pakistan, South Africa, Uruguay, Bolivia, Australia, Philippines, Myanmar, Burkina Faso, Mexico and Spain.[50] 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.[159] 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.

Land area used for genetically modified crops by country (1996–2009), in millions of hectares. In 2011, the land area used was 160 million hectares, or 1.6 million square kilometers.[50]

In the US, by 2014, 94% of the planted area of soybeans, 96% of cotton and 93% of corn were genetically modified varieties.[123][124][160] 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).[161] 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.[162]

Europe grows relatively few genetically engineered crops[163] with the exception of Spain, where one fifth of maize is genetically engineered,[164] and smaller amounts in five other countries.[165] The EU had a 'de facto' ban on the approval of new GM crops, from 1999 until 2004.[166][167] GM crops are now regulated by the EU.[168] Developing countries grew 54 percent of genetically engineered crops in 2013.[154]

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.[154] 2013's largest increase was in Brazil (403,000 km2 versus 368,000 km2 in 2012). GM cotton began growing in India in 2002, reaching 110,000 km2 in 2013.[154]

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).[154]

Controversy

GM foods are controversial and the subject of protests, vandalism, referenda, legislation, court action and scientific disputes. The controversies involve consumers, biotechnology companies, governmental regulators, non-governmental organizations and scientists. The key areas are whether GM food should be labeled, the role of government regulators, the effect of GM crops on health and the environment, the effects of pesticide use and resistance, the impact on farmers, and their roles in feeding the world and energy production.
Broad scientific consensus states that currently marketed GM food poses no greater risk than conventionally produced food.[1][3][169] No reports of ill effects have been documented in the human population from GM food.[4][170][171] Although GMO labeling is required in many countries, the United States Food and Drug Administration does not require labeling, nor does it recognize a distinction between approved GMO and non-GMO foods.[172]

Advocacy groups such as Greenpeace and the World Wildlife Fund claim that risks related to GM food have not been adequately examined and managed, and have questioned the objectivity of regulatory authorities and scientific bodies.

Genetic engineering


From Wikipedia, the free encyclopedia

Genetic engineering, also called genetic modification, is the direct manipulation of an organism's genome using biotechnology. New DNA may be inserted in the host genome by first isolating and copying the genetic material of interest using molecular cloning methods to generate a DNA sequence, or by synthesizing the DNA, and then inserting this construct into the host organism. Genes may be removed, or "knocked out", using a nuclease. Gene targeting is a different technique that uses homologous recombination to change an endogenous gene, and can be used to delete a gene, remove exons, add a gene, or introduce point mutations.

An organism that is generated through genetic engineering is considered to be a genetically modified organism (GMO). The first GMOs were bacteria in 1973 and GM mice were generated in 1974. Insulin-producing bacteria were commercialized in 1982 and genetically modified food has been sold since 1994. Glofish, the first GMO designed as a pet, was first sold in the United States December in 2003.[1]

Genetic engineering techniques have been applied in numerous fields including research, agriculture, industrial biotechnology, and medicine. Enzymes used in laundry detergent and medicines such as insulin and human growth hormone are now manufactured in GM cells, experimental GM cell lines and GM animals such as mice or zebrafish are being used for research purposes, and genetically modified crops have been commercialized.

Definition


Comparison of conventional plant breeding with transgenic and cisgenic genetic modification.

Genetic engineering alters the genetic make-up of an organism using techniques that remove heritable material or that introduce DNA prepared outside the organism either directly into the host or into a cell that is then fused or hybridized with the host.[4] This involves using recombinant nucleic acid (DNA or RNA) techniques to form new combinations of heritable genetic material followed by the incorporation of that material either indirectly through a vector system or directly through micro-injection, macro-injection and micro-encapsulation techniques.

Genetic engineering does not normally include traditional animal and plant breeding, in vitro fertilisation, induction of polyploidy, mutagenesis and cell fusion techniques that do not use recombinant nucleic acids or a genetically modified organism in the process.[4] However the European Commission has also defined genetic engineering broadly as including selective breeding and other means of artificial selection.[5] Cloning and stem cell research, although not considered genetic engineering,[6] are closely related and genetic engineering can be used within them.[7] Synthetic biology is an emerging discipline that takes genetic engineering a step further by introducing artificially synthesized material from raw materials into an organism.[8]

If genetic material from another species is added to the host, the resulting organism is called transgenic. If genetic material from the same species or a species that can naturally breed with the host is used the resulting organism is called cisgenic.[9] Genetic engineering can also be used to remove genetic material from the target organism, creating a gene knockout organism.[10] In Europe genetic modification is synonymous with genetic engineering while within the United States of America it can also refer to conventional breeding methods.[11][12] The Canadian regulatory system is based on whether a product has novel features regardless of method of origin. In other words, a product is regulated as genetically modified if it carries some trait not previously found in the species whether it was generated using traditional breeding methods (e.g., selective breeding, cell fusion, mutation breeding) or genetic engineering.[13][14][15] Within the scientific community, the term genetic engineering is not commonly used; more specific terms such as transgenic are preferred.

Genetically modified organisms

Plants, animals or micro organisms that have changed through genetic engineering are termed genetically modified organisms or GMOs.[16] Bacteria were the first organisms to be genetically modified. Plasmid DNA containing new genes can be inserted into the bacterial cell and the bacteria will then express those genes. These genes can code for medicines or enzymes that process food and other substrates.[17][18] Plants have been modified for insect protection, herbicide resistance, virus resistance, enhanced nutrition, tolerance to environmental pressures and the production of edible vaccines.[19] Most commercialised GMO's are insect resistant and/or herbicide tolerant crop plants.[20] 
Genetically modified animals have been used for research, model animals and the production of agricultural or pharmaceutical products. They include animals with genes knocked out, increased susceptibility to disease, hormones for extra growth and the ability to express proteins in their milk.[21]

History

Humans have altered the genomes of species for thousands of years through selective breeding, or artificial selection as contrasted with natural selection, and more recently through mutagenesis. Genetic engineering as the direct manipulation of DNA by humans outside breeding and mutations has only existed since the 1970s. The term "genetic engineering" was first coined by Jack Williamson in his science fiction novel Dragon's Island, published in 1951,[22] one year before DNA's role in heredity was confirmed by Alfred Hershey and Martha Chase,[23] and two years before James Watson and Francis Crick showed that the DNA molecule has a double-helix structure.

In 1974 Rudolf Jaenisch created the first GM animal.

In 1972 Paul Berg created the first recombinant DNA molecules by combining DNA from the monkey virus SV40 with that of the lambda virus.[24] In 1973 Herbert Boyer and Stanley Cohen created the first transgenic organism by inserting antibiotic resistance genes into the plasmid of an E. coli bacterium.[25][26] A year later Rudolf Jaenisch created a transgenic mouse by introducing foreign DNA into its embryo, making it the world’s first transgenic animal.[27] These achievements led to concerns in the scientific community about potential risks from genetic engineering, which were first discussed in depth at the Asilomar Conference in 1975. One of the main recommendations from this meeting was that government oversight of recombinant DNA research should be established until the technology was deemed safe.[28][29]

In 1976 Genentech, the first genetic engineering company, was founded by Herbert Boyer and Robert Swanson and a year later the company produced a human protein (somatostatin) in E.coli. Genentech announced the production of genetically engineered human insulin in 1978.[30] In 1980, the U.S. Supreme Court in the Diamond v. Chakrabarty case ruled that genetically altered life could be patented.[31] The insulin produced by bacteria, branded humulin, was approved for release by the Food and Drug Administration in 1982.[32]

In the 1970s graduate student Steven Lindow of the University of Wisconsin–Madison with D.C. Arny and C. Upper found a bacterium he identified as P. syringae that played a role in ice nucleation and in 1977, he discovered a mutant ice-minus strain. Later, he successfully created a recombinant ice-minus strain.[33] In 1983, a biotech company, Advanced Genetic Sciences (AGS) applied for U.S. government authorization to perform field tests with the ice-minus strain of P. syringae to protect crops from frost, but environmental groups and protestors delayed the field tests for four years with legal challenges.[34] In 1987, the ice-minus strain of P. syringae became the first genetically modified organism (GMO) to be released into the environment[35] when a strawberry field and a potato field in California were sprayed with it.[36] Both test fields were attacked by activist groups the night before the tests occurred: "The world's first trial site attracted the world's first field trasher".[35]

The first field trials of genetically engineered plants occurred in France and the USA in 1986, tobacco plants were engineered to be resistant to herbicides.[37] The People’s Republic of China was the first country to commercialize transgenic plants, introducing a virus-resistant tobacco in 1992.[38] In 1994 Calgene attained approval to commercially release the Flavr Savr tomato, a tomato engineered to have a longer shelf life.[39] In 1994, the European Union approved tobacco engineered to be resistant to the herbicide bromoxynil, making it the first genetically engineered crop commercialized in Europe.[40] 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 USA.[41] In 2009 11 transgenic crops were grown commercially in 25 countries, the largest of which by area grown were the USA, Brazil, Argentina, India, Canada, China, Paraguay and South Africa.[42]

In the late 1980s and early 1990s, guidance on assessing the safety of genetically engineered plants and food emerged from organizations including the FAO and WHO.[43][44][45][46]

In 2010, scientists at the J. Craig Venter Institute, announced that they had created the first synthetic bacterial genome. The researchers added the new genome to bacterial cells and selected for cells that contained the new genome. To do this the cells undergoes a process called resolution, where during bacterial cell division one new cell receives the original DNA genome of the bacteria, whilst the other receives the new synthetic genome. When this cell replicates it uses the synthetic genome as its template. The resulting bacterium the researchers developed, named Synthia, was the world's first synthetic life form.[47][48]

On 19 March 2015, scientists, including an inventor of CRISPR, urged a worldwide moratorium on using gene editing methods to genetically engineer the human genome in a way that can be inherited, writing “scientists should avoid even attempting, in lax jurisdictions, germline genome modification for clinical application in humans” until the full implications “are discussed among scientific and governmental organizations.”[49][50][51][52]

Process

The first step is to choose and isolate the gene that will be inserted into the genetically modified organism. As of 2012, most commercialised GM plants have genes transferred into them that provide protection against insects or tolerance to herbicides.[53] The gene can be isolated using restriction enzymes to cut DNA into fragments and gel electrophoresis to separate them out according to length.[54] Polymerase chain reaction (PCR) can also be used to amplify up a gene segment, which can then be isolated through gel electrophoresis.[55] If the chosen gene or the donor organism's genome has been well studied it may be present in a genetic library. If the DNA sequence is known, but no copies of the gene are available, it can be artificially synthesized.[56]
The gene to be inserted into the genetically modified organism must be combined with other genetic elements in order for it to work properly. The gene can also 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. The selectable marker, which in most cases confers antibiotic resistance to the organism it is expressed in, is needed 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.[57] The manipulation of the DNA generally occurs within a plasmid.

The most common form of genetic engineering involves inserting new genetic material randomly within the host genome.[citation needed] Other techniques allow new genetic material to be inserted at a specific location in the host genome or generate mutations at desired genomic loci capable of knocking out endogenous genes. The technique of gene targeting uses homologous recombination to target desired changes to a specific endogenous gene. This tends to occur at a relatively low frequency in plants and animals and generally requires the use of selectable markers. The frequency of gene targeting can be greatly enhanced with the use of engineered nucleases such as zinc finger nucleases,[58][59] engineered homing endonucleases,[60][61] or nucleases created from TAL effectors.[62][63] In addition to enhancing gene targeting, engineered nucleases can also be used to introduce mutations at endogenous genes that generate a gene knockout.[64][65]

Transformation

A. tumefaciens attaching itself to a carrot cell

Only about 1% of bacteria are naturally capable of taking up foreign DNA. However, this ability can be induced in other bacteria via stress (e.g. thermal or electric shock), thereby increasing the cell membrane's permeability to DNA; up-taken DNA can either integrate with the genome or exist as extrachromosomal DNA. DNA is generally inserted into animal cells using microinjection, where it can be injected through the cell's nuclear envelope directly into the nucleus or through the use of viral vectors.[66] In plants the DNA is generally inserted using Agrobacterium-mediated recombination or biolistics.[67]

In Agrobacterium-mediated recombination, the plasmid construct contains T-DNA, DNA which is responsible for insertion of the DNA into the host plants genome. This plasmid is transformed into Agrobacterium containing no plasmids prior to infecting the plant cells. The Agrobacterium will then naturally insert the genetic material into the plant cells.[68] In biolistics transformation particles of gold or tungsten are coated with DNA and then shot into young plant cells or plant embryos. Some genetic material will enter the cells and transform them. This method can be used on plants that are not susceptible to Agrobacterium infection and also allows transformation of plant plastids. Another transformation method for plant and animal cells is electroporation. Electroporation involves subjecting the plant or animal cell to an electric shock, which can make the cell membrane permeable to plasmid DNA. In some cases the electroporated cells will incorporate the DNA into their genome. Due to the damage caused to the cells and DNA the transformation efficiency of biolistics and electroporation is lower than agrobacterial mediated transformation and microinjection.[69]

As often only a single cell is transformed with genetic material the organism must be regenerated from that single cell. As bacteria consist of a single cell and reproduce clonally regeneration is not necessary. In plants this is accomplished through the use of tissue culture. Each plant species has different requirements for successful regeneration through tissue culture. If successful an adult plant is produced that contains the transgene in every cell. In animals it is necessary to ensure that the inserted DNA is present in the embryonic stem cells. Selectable markers are used to easily differentiate transformed from untransformed cells. 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.[70] When the offspring is produced they can be screened for the presence of the gene. All offspring from the first generation will be heterozygous for the inserted gene and must be mated together to produce a homozygous animal.

Further testing uses PCR, Southern hybridization, and DNA sequencing is conducted to confirm that an organism contains the new gene. These tests can also confirm the chromosomal location and copy number of the inserted gene. The presence of the gene does not guarantee it will be expressed at appropriate levels in the target tissue so methods that look for and measure the gene products (RNA and protein) are also used. These include northern hybridization, quantitative RT-PCR, Western blot, immunofluorescence, ELISA and phenotypic analysis. For stable transformation the gene should be passed to the offspring in a Mendelian inheritance pattern, so the organism's offspring are also studied.

Genome editing

Genome editing is a type of genetic engineering in which DNA is inserted, replaced, or removed from a genome using artificially engineered nucleases, or "molecular scissors." The nucleases create specific double-stranded break (DSBs) at desired locations in the genome, and harness the cell’s endogenous mechanisms to repair the induced break by natural processes of homologous recombination (HR) and nonhomologous end-joining (NHEJ). There are currently four families of engineered nucleases: meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPRs.[71][72]

Applications

Genetic engineering has applications in medicine, research, industry and agriculture and can be used on a wide range of plants, animals and micro organisms.

Medicine

In medicine, genetic engineering has been used to mass-produce insulin, human growth hormones, follistim (for treating infertility), human albumin, monoclonal antibodies, antihemophilic factors, vaccines and many other drugs.[73][74] Vaccination generally involves injecting weak, live, killed or inactivated forms of viruses or their toxins into the person being immunized.[75] Genetically engineered viruses are being developed that can still confer immunity, but lack the infectious sequences.[76] Mouse hybridomas, cells fused together to create monoclonal antibodies, have been humanised through genetic engineering to create human monoclonal antibodies.[77] Genetic engineering has shown promise for treating certain forms of cancer.[78][79]

Genetic engineering is used to create animal models of human diseases. Genetically modified mice are the most common genetically engineered animal model.[80] They have been used to study and model cancer (the oncomouse), obesity, heart disease, diabetes, arthritis, substance abuse, anxiety, aging and Parkinson disease.[81] Potential cures can be tested against these mouse models. Also genetically modified pigs have been bred with the aim of increasing the success of pig to human organ transplantation.[82]

Gene therapy is the genetic engineering of humans by replacing defective human genes with functional copies. This can occur in somatic tissue or germline tissue. If the gene is inserted into the germline tissue it can be passed down to that person's descendants.[83][84] Gene therapy has been successfully used to treat multiple diseases, including X-linked SCID,[85] chronic lymphocytic leukemia (CLL),[86] and Parkinson's disease.[87] In 2012, Glybera became the first gene therapy treatment to be approved for clinical use in either Europe or the United States after its endorsement by the European Commission.[88][89] There are also ethical concerns should the technology be used not just for treatment, but for enhancement, modification or alteration of a human beings' appearance, adaptability, intelligence, character or behavior.[90] The distinction between cure and enhancement can also be difficult to establish.[91] Transhumanists consider the enhancement of humans desirable.

Research


Human cells in which some proteins are fused with green fluorescent protein to allow them to be visualised

Genetic engineering is an important tool for natural scientists. Genes and other genetic information from a wide range of organisms are transformed 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.

Organisms are genetically engineered to discover the functions of certain genes. This could be the effect on the phenotype of the organism, where the gene is expressed or what other genes it interacts with. These experiments generally involve loss of function, gain of function, tracking and expression.
  • Loss of function experiments, such as in a gene knockout experiment, in which an organism is engineered to lack the activity of one or more genes. A knockout experiment involves the creation and manipulation of a DNA construct in vitro, which, in a simple knockout, consists of a copy of the desired gene, which has been altered such that it is non-functional. Embryonic stem cells incorporate the altered gene, which replaces the already present functional copy. These stem cells are injected into blastocysts, which are implanted into surrogate mothers. This allows the experimenter to analyze the defects caused by this mutation and thereby determine the role of particular genes. It is used especially frequently in developmental biology. Another method, useful in organisms such as Drosophila (fruit fly), is to induce mutations in a large population and then screen the progeny for the desired mutation. A similar process can be used in both plants and prokaryotes.
  • Gain of function experiments, the logical counterpart of knockouts. These are sometimes performed in conjunction with knockout experiments to more finely establish the function of the desired gene. The process is much the same as that in knockout engineering, except that the construct is designed to increase the function of the gene, usually by providing extra copies of the gene or inducing synthesis of the protein more frequently.
  • Tracking experiments, which seek to gain information about the localization and interaction of the desired protein. One way to do this is to replace the wild-type gene with a 'fusion' gene, which is a juxtaposition of the wild-type gene with a reporting element such as green fluorescent protein (GFP) that will allow easy visualization of the products of the genetic modification. While this is a useful technique, the manipulation can destroy the function of the gene, creating secondary effects and possibly calling into question the results of the experiment. More sophisticated techniques are now in development that can track protein products without mitigating their function, such as the addition of small sequences that will serve as binding motifs to monoclonal antibodies.
  • Expression studies aim to discover where and when specific proteins are produced. In these experiments, the DNA sequence before the DNA that codes for a protein, known as a gene's promoter, is reintroduced into an organism with the protein coding region replaced by a reporter gene such as GFP or an enzyme that catalyzes the production of a dye. Thus the time and place where a particular protein is produced can be observed. Expression studies can be taken a step further by altering the promoter to find which pieces are crucial for the proper expression of the gene and are actually bound by transcription factor proteins; this process is known as promoter bashing.

Industrial

Using genetic engineering techniques one can transform microorganisms such as bacteria or yeast, or transform cells from multicellular organisms such as insects or mammals, with a gene coding for a useful protein, such as an enzyme, so that the transformed organism will overexpress the desired protein. One can manufacture mass quantities of the protein by growing the transformed organism in bioreactor equipment using techniques of industrial fermentation, and then purifying the protein.[92] Some genes do not work well in bacteria, so yeast, insect cells, or mammalians cells, each a eukaryote, can also be used.[93] These techniques are used to produce medicines such as insulin, human growth hormone, and vaccines, supplements such as tryptophan, aid in the production of food (chymosin in cheese making) and fuels.[94] Other applications involving genetically engineered bacteria being investigated involve making the bacteria perform tasks outside their natural cycle, such as making biofuels,[95] cleaning up oil spills, carbon and other toxic waste[96] and detecting arsenic in drinking water.[97]

Experimental, lab scale industrial applications

In materials science, a genetically modified virus has been used in an academic lab as a scaffold for assembling a more environmentally friendly lithium-ion battery.[98][99]

Bacteria have been engineered to function as sensors by expressing a fluorescent protein under certain environmental conditions.[100]

Agriculture

Bt-toxins present in peanut leaves (bottom image) protect it from extensive damage caused by European corn borer larvae (top image).[101]

One of the best-known and controversial applications of genetic engineering is the creation and use of genetically modified crops or genetically modified organisms, such as genetically modified fish, which are used to produce genetically modified food and materials with diverse uses. There are four main goals in generating genetically modified crops.[102]

One goal, and the first to be realized commercially, is to provide protection from environmental threats, such as cold (in the case of Ice-minus bacteria), or pathogens, such as insects or viruses, and/or resistance to herbicides. There are also fungal and virus resistant crops developed or in development.[103][104] They have been developed to make the insect and weed management of crops easier and can indirectly increase crop yield.[105]

Another goal in generating GMOs is to modify the quality of produce by, for instance, increasing the nutritional value or providing more industrially useful qualities or quantities.[106] The Amflora potato, for example, produces a more industrially useful blend of starches. Cows have been engineered to produce more protein in their milk to facilitate cheese production.[107] Soybeans and canola have been genetically modified to produce more healthy oils.[108][109]

Another goal consists of driving the GMO to produce materials that it does not normally make. One example is "pharming", which uses crops as bioreactors to produce vaccines, drug intermediates, or drug themselves; the useful product is purified from the harvest and then used in the standard pharmaceutical production process.[110] Cows and goats have been engineered to express drugs and other proteins in their milk, and in 2009 the FDA approved a drug produced in goat milk.[111][112]

Another goal in generating GMOs, is to directly improve yield by accelerating growth, or making the organism more hardy (for plants, by improving salt, cold or drought tolerance).[106] Some agriculturally important animals have been genetically modified with growth hormones to increase their size.[113]

The genetic engineering of agricultural crops can increase the growth rates and resistance to different diseases caused by pathogens and parasites.[114] This is beneficial as it can greatly increase the production of food sources with the usage of fewer resources that would be required to host the world's growing populations. These modified crops would also reduce the usage of chemicals, such as fertilizers and pesticides, and therefore decrease the severity and frequency of the damages produced by these chemical pollution.[114][115]

Ethical and safety concerns have been raised around the use of genetically modified food.[116] A major safety concern relates to the human health implications of eating genetically modified food, in particular whether toxic or allergic reactions could occur.[117] Gene flow into related non-transgenic crops, off target effects on beneficial organisms and the impact on biodiversity are important environmental issues.[118] Ethical concerns involve religious issues, corporate control of the food supply, intellectual property rights and the level of labeling needed on genetically modified products.

BioArt and entertainment

Genetic engineering is also being used to create BioArt.[119] Some bacteria have been genetically engineered to create black and white photographs.[120]

Genetic engineering has also been used to create novelty items such as lavender-colored carnations,[121] blue roses,[122] and glowing fish.[123][124]

Regulation

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 USA and Europe. Regulation varies in a given country depending on the intended use of the products of the genetic engineering. For example, a crop not intended for food use is generally not reviewed by authorities responsible for food safety.

Controversy

Critics have objected to use of genetic engineering per se on several grounds, including ethical concerns, ecological concerns, and economic concerns raised by the fact GM techniques and GM organisms are subject to intellectual property law. GMOs also are involved in controversies over GM food with respect to whether food produced from GM crops is safe, whether it should be labeled, and whether GM crops are needed to address the world's food needs. See the genetically modified food controversies article for discussion of issues about GM crops and GM food. 
These controversies have led to litigation, international trade disputes, and protests, and to restrictive regulation of commercial products in some countries.

Genetic recombination


From Wikipedia, the free encyclopedia


A current model of meiotic recombination, initiated by a double-strand break or gap, followed by pairing with an homologous chromosome and strand invasion to initiate the recombinational repair process. Repair of the gap can lead to crossover (CO) or non-crossover (NCO) of the flanking regions. CO recombination is thought to occur by the Double Holliday Junction (DHJ) model, illustrated on the right, above. NCO recombinants are thought to occur primarily by the Synthesis Dependent Strand Annealing (SDSA) model, illustrated on the left, above. Most recombination events appear to be the SDSA type.

Genetic recombination is the production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead, through sexual reproduction, to a novel set of genetic information that can be passed on through heredity from the parents to the offspring. Most recombination is naturally occurring. During meiosis in eukaryotes, genetic recombination involves the pairing of homologous chromosomes. This may be followed by information exchange between the chromosomes. The information exchange 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 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 homologous that is similar molecules (homologs) of DNA. 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.
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.

Synapsis

During meiosis, synapsis (the pairing of homologous chromosomes) ordinarily precedes genetic recombination.

Mechanism

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.

Chromosomal crossover

Thomas Hunt Morgan's illustration of crossing over (1916)

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. 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 accumulate genetic deletions in an irreversible manner.

Chromosomal crossover involves recombination between the paired chromosomes inherited from each of one's parents, generally occurring during meiosis. During prophase I (pachytene stage) the four available chromatids are in tight formation with one another. While in this formation, homologous sites on two chromatids can closely pair with one another, and may exchange genetic information.[1]

Because recombination can occur with small probability at any location along chromosome, the frequency of recombination between two locations depends on the distance separating them. Therefore, for genes sufficiently distant on the same chromosome the amount of crossover is high enough to destroy the correlation between alleles.

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. 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 another gene. This is typically used in order to detect the presence of a disease-causing gene.[2]

Gene conversion

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[3] 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).

Nonhomologous recombination

Recombination can occur between DNA sequences that contain no sequence homology. This can cause chromosomal translocations, sometimes leading to cancer.

In B cells

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.

Genetic engineering

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.

Recombinational repair

During both mitosis and meiosis, 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).[4] 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 and rodents, deficiencies in the gene products necessary for HRR during meiosis cause infertility.[4] 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.[5] 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 bacteriophages T4 and lambda,[6] 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.[5]

Meiotic recombination

Molecular models of meiotic recombination have evolved over the years as relevant evidence accumulated. A major incentive for developing a fundamental understanding of the mechanism of meiotic recombination is that such understanding is crucial for solving the problem of the adaptive function of sex, a major unresolved issue in biology. A recent model that reflects current understanding was presented by Anderson and Sekelsky,[7] and is outlined in the first figure in this article. The figure shows that two of the four chromatids present early in meiosis (prophase I) are paired with each other and able to interact. Recombination, in this version of the model, is initiated by a double-strand break (or gap) shown in the DNA molecule (chromatid) at the top of the first figure in this article. However, 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.

As indicated in the first figure, above, 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.[4] 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 and heterochiasmy

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. Heterochiasmy is the term used to describe recombination rates which differ between the sexes of a species.[8] This sexual dimorphic pattern in recombination rate has been observed in many species. In mammals, females most often have higher rates of recombination. The "Haldane-Huxley rule" states that achiasmy usually occurs in the heterogametic sex.[8]

Entropy (statistical thermodynamics)

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