Living Modified Organism

A genetically modified organism (GMO) is any organism whose genetic material has been altered using genetic engineering techniques. The exact definition of a genetically modified organism and what constitutes genetic engineering varies, with the most common being an organism altered in a way that "does not occur naturally by mating and/or natural recombination". A wide variety of organisms have been genetically modified (GM), from animals to plants and microorganisms. Genes have been transferred within the same species, across species (creating transgenic organisms), and even across kingdoms. New genes can be introduced, or endogenous genes can be enhanced, altered, or knocked out.

Creating a genetically modified organism is a multi-step process. Genetic engineers must isolate the gene they wish to insert into the host organism and combine it with other genetic elements, including a promoter and terminator region and often a selectable marker. A number of techniques are available for inserting the isolated gene into the host genome. Recent advancements using genome editing techniques, notably CRISPR, have made the production of GMOs much simpler. Herbert Boyer and Stanley Cohen made the first genetically modified organism in 1973, a bacterium resistant to the antibiotic kanamycin. The first genetically modified animal, a mouse, was created in 1974 by Rudolf Jaenisch, and the first plant was produced in 1983. In 1994, the Flavr Savr tomato was released, the first commercialized genetically modified food. The first genetically modified animal to be commercialized was the GloFish (2003) and the first genetically modified animal to be approved for food use was the AquAdvantage salmon in 2015.

Bacteria are the easiest organisms to engineer and have been used for research, food production, industrial protein purification (including drugs), agriculture, and art. There is potential to use them for environmental purposes or as medicine. Fungi have been engineered with much the same goals. Viruses play an important role as vectors for inserting genetic information into other organisms. This use is especially relevant to human gene therapy. There are proposals to remove the virulent genes from viruses to create vaccines. Plants have been engineered for scientific research, to create new colors in plants, deliver vaccines, and to create enhanced crops. Genetically modified crops are publicly the most controversial GMOs, in spite of having the most human health and environmental benefits. The majority are engineered for herbicide tolerance or insect resistance. Golden rice has been engineered with three genes that increase its nutritional value. Other prospects for GM crops are as bioreactors for the production of biopharmaceuticals, biofuels, or medicines.

Animals are generally much harder to transform and the vast majority are still at the research stage. Mammals are the best model organisms for humans, making ones genetically engineered to resemble serious human diseases important to the discovery and development of treatments. Human proteins expressed in mammals are more likely to be similar to their natural counterparts than those expressed in plants or microorganisms. Livestock is modified with the intention of improving economically important traits such as growth rate, quality of meat, milk composition, disease resistance, and survival. Genetically modified fish are used for scientific research, as pets, and as a food source. Genetic engineering has been proposed as a way to control mosquitos, a vector for many deadly diseases. Although human gene therapy is still relatively new, it has been used to treat genetic disorders such as severe combined immunodeficiency and Leber's congenital amaurosis.

Many objections have been raised over the development of GMOs, particularly their commercialization. Many of these involve GM crops and whether food produced from them is safe and what impact growing them will have on the environment. Other concerns are the objectivity and rigor of regulatory authorities, contamination of non-genetically modified food, control of the food supply, patenting of life, and the use of intellectual property rights. Although there is a scientific consensus that currently available food derived from GM crops poses no greater risk to human health than conventional food, GM food safety is a leading issue with critics. Gene flow, impact on non-target organisms, and escape are the major environmental concerns. Countries have adopted regulatory measures to deal with these concerns. There are differences in the regulation for the release of GMOs between countries, with some of the most marked differences occurring between the US and Europe. Key issues concerning regulators include whether GM food should be labeled and the status of gene-edited organisms.

Definition

The definition of a genetically modified organism (GMO) is not clear and varies widely between countries, international bodies, and other communities. At its broadest, the definition of a GMO can include anything that has had its genes altered, including by nature. Taking a less broad view, it can encompass every organism that has had its genes altered by humans, which would include all crops and livestock. In 1993, the ''Encyclopedia Britannica'' defined genetic engineering as "any of a wide range of techniques ... among them artificial insemination, ''in vitro'' fertilization (''e.g.'', 'test-tube' babies), sperm banks, cloning, and gene manipulation." The European Union (EU) included a similarly broad definition in early reviews, specifically mentioning GMOs being produced by "selective breeding and other means of artificial selection"Staf
Economic Impacts of Genetically Modified Crops on the Agri-Food Sector; p. 42 Glossary – Term and Definitions
The European Commission Directorate-General for Agriculture, "Genetic engineering: The manipulation of an organism's genetic endowment by introducing or eliminating specific genes through modern molecular biology techniques. A broad definition of genetic engineering also includes selective breeding and other means of artificial selection", Retrieved 5 November 2012 These definitions were promptly adjusted with a number of exceptions added as the result of pressure from scientific and farming communities, as well as developments in science. The EU definition later excluded traditional breeding, in vitro fertilization, induction of polyploidy, mutation breeding, and cell fusion techniques that do not use recombinant nucleic acids or a genetically modified organism in the process.

Another approach was the definition provided by the Food and Agriculture Organization, the World Health Organization, and the European Commission, stating that the organisms must be altered in a way that does "not occur naturally by mating and/or natural recombination". Progress in science, such as the discovery of horizontal gene transfer being a relatively common natural phenomenon, further added to the confusion on what "occurs naturally", which led to further adjustments and exceptions. There are examples of crops that fit this definition, but are not normally considered GMOs. For example, the grain crop triticale was fully developed in a laboratory in 1930 using various techniques to alter its genome.

Genetically engineered organism (GEO) can be considered a more precise term compared to GMO when describing organisms' genomes that have been directly manipulated with biotechnology. The Cartagena Protocol on Biosafety used the synonym ''living modified organism'' (''LMO'') in 2000 and defined it as "any living organism that possesses a novel combination of genetic material obtained through the use of modern biotechnology." Modern biotechnology is further defined as "In vitro nucleic acid techniques, including recombinant deoxyribonucleic acid (DNA) and direct injection of nucleic acid into cells or organelles, or fusion of cells beyond the taxonomic family."

The term GMO originally was not typically used by scientists to describe genetically engineered organisms until after usage of GMO became common in popular media. The United States Department of Agriculture (USDA) considers GMOs to be plants or animals with heritable changes introduced by genetic engineering or traditional methods, while GEO specifically refers to organisms with genes introduced, eliminated, or rearranged using molecular biology, particularly recombinant DNA techniques, such as transgenesis.

The definitions focus on the process more than the product, which means there could be GMOS and non-GMOs with very similar genotypes and phenotypes. This has led scientists to label it as a scientifically meaningless category, saying that it is impossible to group all the different types of GMOs under one common definition. It has also caused issues for organic institutions and groups looking to ban GMOs. It also poses problems as new processes are developed. The current definitions came in before genome editing became popular and there is some confusion as to whether they are GMOs. The EU has adjudged that they are changing their GMO definition to include "organisms obtained by mutagenesis", but has excluded them from regulation based on their "long safety record" and that they have been "conventionally been used in a number of applications". In contrast the USDA has ruled that gene edited organisms are not considered GMOs.

Even greater inconsistency and confusion is associated with various "Non-GMO" or "GMO-free" labelling schemes in food marketing, where even products such as water or salt, which do not contain any organic substances and genetic material (and thus cannot be genetically modified by definition), are being labelled to create an impression of being "more healthy".

Production

Creating a genetically modified organism (GMO) is a multi-step process. Genetic engineers must isolate the gene they wish to insert into the host organism. This gene can be taken from a cell or artificially synthesized. 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 a selectable marker.

A number of techniques are available for inserting the isolated gene into the host genome. Bacteria can be induced to take up foreign DNA, usually by exposed heat shock or electroporation. 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. In plants the DNA is often inserted using ''Agrobacterium''-mediated recombination, biolistics or electroporation.

As only a single cell is transformed with genetic material, the organism must be regenerated from that single cell. In plants this is accomplished through tissue culture. In animals it is necessary to ensure that the inserted DNA is present in the embryonic stem cells. Further testing using PCR, Southern hybridization, and DNA sequencing is conducted to confirm that an organism contains the new gene.

Traditionally the new genetic material was inserted randomly within the host genome. 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, zinc finger nucleases, transcription activator-like effector nucleases (TALENs), and the Cas9-guideRNA system (adapted from CRISPR). TALEN and CRISPR are the two most commonly used and each has its own advantages. TALENs have greater target specificity, while CRISPR is easier to design and more efficient.

History

Humans have domesticated plants and 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. 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.

Herbert Boyer and Stanley Cohen made the first genetically modified organism in 1973. They took a gene from a bacterium that provided resistance to the antibiotic kanamycin, inserted it into a plasmid and then induced other bacteria to incorporate the plasmid. The bacteria that had successfully incorporated the plasmid was then able to survive in the presence of kanamycin. Boyer and Cohen expressed other genes in bacteria. This included genes from the toad ''Xenopus laevis'' in 1974, creating the first GMO expressing a gene from an organism of a different kingdom.

In 1974, Rudolf Jaenisch created a transgenic mouse by introducing foreign DNA into its embryo, making it the world's first transgenic animal. However it took another eight years before transgenic mice were developed that passed the transgene to their offspring. Genetically modified mice were created in 1984 that carried cloned oncogenes, predisposing them to developing cancer. Mice with genes removed (termed a knockout mouse) were created in 1989. The first transgenic livestock were produced in 1985 and the first animal to synthesize transgenic proteins in their milk were mice in 1987. The mice were engineered to produce human tissue plasminogen activator, a protein involved in breaking down blood clots.

In 1983, the first genetically engineered plant was developed by Michael W. Bevan, Richard B. Flavell and Mary-Dell Chilton. They infected tobacco with ''Agrobacterium'' transformed with an antibiotic resistance gene and through tissue culture techniques were able to grow a new plant containing the resistance gene. The gene gun was invented in 1987, allowing transformation of plants not susceptible to ''Agrobacterium'' infection. In 2000, Vitamin A-enriched golden rice was the first plant developed with increased nutrient value.

In 1976, Genentech, the first genetic engineering company was founded by Herbert Boyer and Robert Swanson; a year later, the company produced a human protein (somatostatin) in '' E. coli''. Genentech announced the production of genetically engineered human insulin in 1978. The insulin produced by bacteria, branded Humulin, was approved for release by the Food and Drug Administration in 1982. In 1988, the first human antibodies were produced in plants. In 1987, a strain of ''Pseudomonas syringae'' became the first genetically modified organism to be released into the environmentBBC News 14 June 200
GM crops: A bitter harvest?
/ref> when a strawberry and potato field in California were sprayed with it.

The first genetically modified crop, an antibiotic-resistant tobacco plant, was produced in 1982. China was the first country to commercialize transgenic plants, introducing a virus-resistant tobacco in 1992. In 1994, Calgene attained approval to commercially release the Flavr Savr tomato, the first genetically modified food. Also 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. An insect resistant Potato was approved for release in the US in 1995, and by 1996 approval had been granted to commercially grow 8 transgenic crops and one flower crop (carnation) in 6 countries plus the EU.

In 2010, scientists at the J. Craig Venter Institute announced that they had created the first synthetic bacterial genome. They named it Synthia and it was the world's first synthetic life form.

The first genetically modified animal to be commercialized was the GloFish, a Zebra fish with a fluorescent gene added that allows it to glow in the dark under ultraviolet light. It was released to the US market in 2003. In 2015, AquAdvantage salmon became the first genetically modified animal to be approved for food use. Approval is for fish raised in Panama and sold in the US. 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.

Bacteria

Bacteria were the first organisms to be genetically modified in the laboratory, due to the relative ease of modifying their chromosomes. 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 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. A large number of custom plasmids make manipulating DNA extracted from bacteria relatively easy.

Their ease of use has made them great tools for scientists looking to study gene function and evolution. The simplest model organisms come from bacteria, with most of our early understanding of molecular biology coming from studying ''Escherichia coli''. 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. In the field of synthetic biology, they have been used to test various synthetic approaches, from synthesising genomes to creating novel nucleotides.

Bacteria have been used in the production of food for a 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, flavorings, 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. 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. The majority are produced in the US and even though regulations are in place to allow production in Europe, as of 2015 no food products derived from bacteria are currently available there.

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. The high cost of extraction and purification has meant that only high value products have been produced at an industrial scale. The majority of these products are human proteins for use in medicine. 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. The first medicinal use of GM bacteria was to produce the protein insulin to treat diabetes. Other medicines produced include clotting factors to treat haemophilia, human growth hormone to treat various forms of dwarfism, interferon to treat some cancers, erythropoietin for anemic patients, and tissue plasminogen activator which dissolves blood clots. Outside of medicine they have been used to produce biofuels. There is interest in developing an extracellular expression system within the bacteria to reduce costs and make the production of more products economical.

With a greater understanding of the role that the microbiome plays in human health, there is a 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. 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. 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.

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 colonize 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, which have the ice-forming genes removed. When applied to crops they can compete with the non-modified bacteria and confer some frost resistance.

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. Bioart has also been created using genetically modified bacteria. In the 1980s artist Jon 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''. This was taken a step further in 2012, when a whole book was encoded onto DNA. Paintings have also been produced using bacteria transformed with fluorescent proteins.

Viruses

Viruses are often modified so they can be used as vectors for inserting genetic information into other organisms. This process is called transduction and if successful the recipient of the introduced DNA becomes a GMO. Different viruses have different efficiencies and capabilities. Researchers can use this to control for various factors; including the target location, insert size, and duration of gene expression. Any dangerous sequences inherent in the virus must be removed, while those that allow the gene to be delivered effectively are retained.

While viral vectors can be used to insert DNA into almost any organism it is especially relevant for its potential in treating human disease. Although primarily still at trial stages, there has been some successes using gene therapy to replace defective genes. This is most evident in curing patients with severe combined immunodeficiency rising from adenosine deaminase deficiency (ADA-SCID), although the development of leukemia in some ADA-SCID patients along with the death of Jesse Gelsinger in a 1999 trial set back the development of this approach for many years. In 2009, another breakthrough was achieved when an eight-year-old boy with Leber's congenital amaurosis regained normal eyesight and in 2016 GlaxoSmithKline gained approval to commercialize a gene therapy treatment for ADA-SCID. 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.

The most common virus used for gene delivery comes 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. Herpes simplex viruses make promising vectors, having a carrying capacity of over 30kb and providing long term expression, although they are less efficient at gene delivery than other vectors. 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.

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. This does not affect the viruses infectivity, invokes 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. Another potential approach is to use vectors to create novel vaccines for diseases that have no vaccines available or the vaccines that do not work effectively, such as AIDS, malaria, and tuberculosis. The most effective vaccine against Tuberculosis, the Bacillus Calmette–Guérin (BCG) vaccine, only provides partial protection. A modified vaccine expressing ''a M tuberculosis'' antigen is able to enhance BCG protection. It has been shown to be safe to use at phase II trials, although not as effective as initially hoped. Other vector-based vaccines have already been approved and many more are being developed.

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. Since then, several researchers have developed genetically modified oncolytic viruses that show promise as treatments for various types of cancer. In 2017, researchers genetically modified a virus to express spinach defensin proteins. The virus was injected into orange trees to combat citrus greening disease that had reduced orange production by 70% since 2005.

Natural viral diseases, such as myxomatosis and rabbit haemorrhagic disease, have been used to help control pest populations. Over time the surviving pests become resistant, leading researchers to look at alternative methods. Genetically modified viruses that make the target animals infertile through immunocontraception have been created in the laboratory as well as others that target the developmental stage of the animal. There are concerns with using this approach regarding virus containment and cross species infection. Sometimes the same virus can be modified for contrasting purposes. 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.

Outside of biology scientists have used a genetically modified virus to construct a lithium-ion battery and other nanostructured materials. It is possible to engineer bacteriophages to express modified proteins on their surface and join them up in specific patterns (a technique called phage display). These structures have potential uses for energy storage and generation, biosensing and tissue regeneration with some new materials currently produced including quantum dots, liquid crystals, nanorings and nanofibres. The battery was made by engineering M13 bacteriaophages so they would coat themselves in iron phosphate