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Friday, November 30, 2018

Genetics in fiction

From Wikipedia, the free encyclopedia

Boris Karloff in James Whale's 1931 film Frankenstein, based on Mary Shelley's 1818 novel. The monster is created by an unorthodox scientific experiment.

Aspects of genetics including mutation, hybridisation, cloning, genetic engineering, and eugenics have appeared in fiction since the 19th century.

Genetics is a young science, having started in 1900 with the rediscovery of Gregor Mendel's study on the inheritance of traits in pea plants. During the 20th century it developed to create new sciences and technologies including molecular biology, DNA sequencing, cloning, and genetic engineering. The ethical implications were brought into focus with the eugenics movement.

Since then, many science fiction novels and films have used aspects of genetics as plot devices, often taking one of two routes: a genetic accident with disastrous consequences; or, the feasibility and desirability of a planned genetic alteration. The treatment of science in these stories has been uneven and often unrealistic. The film Gattaca did attempt to portray science accurately but was criticised by scientists.

Background

The 1953 discovery of the double helix chemical structure of DNA transformed genetics and launched the science of molecular biology.

Modern genetics began with the work of the monk Gregor Mendel in the 19th century, on the inheritance of traits in pea plants. Mendel found that visible traits, such as whether peas were round or wrinkled, were inherited discretely, rather than by blending the attributes of the two parents. In 1900, Hugo de Vries and other scientists rediscovered Mendel's research; William Bateson coined the term "genetics" for the new science, which soon investigated a wide range of phenomena including mutation (inherited changes caused by damage to the genetic material), genetic linkage (when some traits are to some extent inherited together), and hybridisation (crosses of different species).

Eugenics, the production of better human beings by selective breeding, was named and advocated by Charles Darwin's cousin, the scientist Francis Galton, in 1883. It had both a positive aspect, the breeding of more children with high intelligence and good health; and a negative aspect, aiming to suppress "race degeneration" by preventing supposedly "defective" families with attributes such as profligacy, laziness, immoral behaviour and a tendency to criminality from having children.

Molecular biology, the interactions and regulation of genetic materials, began with the identification in 1944 of DNA as the main genetic material; the genetic code and the double helix structure of DNA was determined by James Watson and Francis Crick in 1953. DNA sequencing, the identification of an exact sequence of genetic information in an organism, was developed in 1977 by Frederick Sanger.

Genetic engineering, the modification of the genetic material of a live organism, became possible in 1972 when Paul Berg created the first recombinant DNA molecules (artificially assembled genetic material) using viruses.

Cloning, the production of genetically identical organisms from some chosen starting point, was shown to be practicable with the creation of Dolly the sheep from an ordinary body cell in 1996 at the Roslin Institute.

Genetics themes

Mutants and hybrids


Mutation and hybridisation are widely used in fiction, starting in the 19th century with science fiction works such as Mary Shelley's 1818 novel Frankenstein and H. G. Wells's 1896 The Island of Dr Moreau.

In her 1977 Biological Themes in Modern Science Fiction, Helen Parker identified two major types of story: "genetic accident", the uncontrolled, unexpected and disastrous alteration of a species; and "planned genetic alteration", whether controlled by humans or aliens, and the question of whether that would be either feasible or desirable. In science fiction up to the 1970s, the genetic changes were brought about by radiation, breeding programmes, or manipulation with chemicals or surgery (and thus, notes Lars Schmeink, not necessarily by strictly genetic means). Examples include The Island of Dr Moreau with its horrible manipulations; Aldous Huxley's 1932 Brave New World with a breeding programme; and John Taine's 1951 Seeds of Life, using radiation to create supermen. After the discovery of the double helix and then recombinant DNA, genetic engineering became the focus for genetics in fiction, as in books like Brian Stableford's tale of a genetically modified society in his 1998 Inherit the Earth, or Michael Marshall Smith's story of organ farming in his 1997 Spares.

Comic books have imagined mutated superhumans with extraordinary powers. The DC Universe (from 1939) imagines "metahumans"; the Marvel Universe (from 1961) calls them "mutants", while the Wildstorm (from 1992) and Ultimate Marvel (2000–2015) Universes name them "posthumans". Stan Lee introduced the concept of mutants in the Marvel X-Men books in 1963; the villain Magneto declares his plan to "make Homo sapiens bow to Homo superior!", implying that mutants will be an evolutionary step up from current humanity. Later, the books speak of an X-gene that confers powers from puberty onwards. X-men powers include telepathy, telekinesis, healing, strength, flight, time travel, and the ability to emit blasts of energy. Marvel's god-like Celestials are later (1999) said to have visited Earth long ago and to have modified human DNA to enable mutant powers.

James Blish's 1952 novel Titan's Daughter (in Kendell Foster Crossen's Future Tense collection) featured stimulated polyploidy (giving organisms multiple sets of genetic material, something that can create new species in a single step), based on spontaneous polyploidy in flowering plants, to create humans with more than normal height, strength, and lifespans.

Cloning

Steven Spielberg's 1993 film Jurassic Park portrayed the recreation of dinosaurs from cloned fossil DNA.

Cloning, too, is a familiar plot device. In his 1990 novel Jurassic Park, Michael Crichton imagined the recovery of the complete genome of a dinosaur from fossil remains, followed by its use to recreate living animals of an extinct species. Aldous Huxley's 1931 dystopian novel Brave New World imagines the in vitro cloning of fertilised human eggs. Huxley was influenced by J. B. S. Haldane's 1924 non-fiction book Daedalus; or, Science and the Future, which used the Greek myth of Daedalus to symbolise the coming revolution in genetics; Haldane predicted that humans would control their own evolution through directed mutation and in vitro fertilisation. Cloning was explored further in stories such as Poul Anderson's 1953 UN-Man.

Cloning is a recurring theme in science fiction films like Jurassic Park (1993), Alien Resurrection (1997), The 6th Day (2000), Resident Evil (2002), Star Wars: Episode II (2002) and The Island (2005). The process of cloning is represented variously in fiction. Many works depict the artificial creation of humans by a method of growing cells from a tissue or DNA sample; the replication may be instantaneous, or take place through slow growth of human embryos in artificial wombs. In the long-running British television series Doctor Who, the Fourth Doctor and his companion Leela were cloned in a matter of seconds from DNA samples ("The Invisible Enemy", 1977) and then—in an apparent homage to the 1966 film Fantastic Voyage—shrunk to microscopic size in order to enter the Doctor's body to combat an alien virus. The clones in this story are short-lived, and can only survive a matter of minutes before they expire. Films such as The Matrix and Star Wars: Episode II – Attack of the Clones have featured human foetuses being cultured on an industrial scale in enormous tanks.

Cloning humans from body parts is a common science fiction trope, one of several genetics themes parodied in Woody Allen's 1973 comedy Sleeper, where an attempt is made to clone an assassinated dictator from his disembodied nose.

Genetic engineering

Genetic engineering features in many science fiction stories. Films such as The Island and Blade Runner (1982) bring the engineered creature to confront the person who created it or the being it was cloned from, a theme seen in some film versions of Frankenstein. Few films have informed audiences about genetic engineering as such, with the exception of the 1978 The Boys from Brazil and the 1993 Jurassic Park, both of which made use of a lesson, a demonstration, and a clip of scientific film. In 1982, Frank Herbert's novel The White Plague described the deliberate use of genetic engineering to create a pathogen which specifically killed women. Another of Herbert's creations, the Dune series of novels, starting with Dune in 1965, emphasises genetics. It combines selective breeding by a powerful sisterhood, the Bene Gesserit, to produce a supernormal male being, the Kwisatz Haderach, with the genetic engineering of the powerful but despised Tleilaxu.

1921 conference logo, depicting eugenics as a tree uniting many fields

Genetic engineering methods are weakly represented in film; Michael Clark, writing for The Wellcome Trust, calls the portrayal of genetic engineering and biotechnology "seriously distorted" in films such as Roger Spottiswoode's 2000 The 6th Day, which makes use of the trope of a "vast clandestine laboratory ... filled with row upon row of 'blank' human bodies kept floating in tanks of nutrient liquid or in suspended animation". In Clark's view, the biotechnology is typically "given fantastic but visually arresting forms" while the science is either relegated to the background or fictionalised to suit a young audience.

Eugenics

Eugenics plays a central role in films such as Andrew Niccol's 1997 Gattaca, the title alluding to the letters G, A, T, C for guanine, adenine, thymine, and cytosine, the four nucleobases of DNA. Genetic engineering of humans is unrestricted, resulting in genetic discrimination, loss of diversity, and adverse effects on society. The film explores the ethical implications; the production company, Sony Pictures, consulted with a gene therapy researcher, French Anderson, to ensure that the portrayal of science was realistic, and test-screened the film with the Society of Mammalian Cell Biologists and the American National Human Genome Research Institute before its release. This care did not prevent researchers from attacking the film after its release. Philim Yam of Scientific American called it "science bashing"; in Nature Kevin Davies called it a ""surprisingly pedestrian affair"; and the molecular biologist Lee Silver described the film's extreme genetic determinism as "a straw man".

Myth and oversimplification

The geneticist Dan Koboldt observes that while science and technology play major roles in fiction, from fantasy and science fiction to thrillers, the representation of science in both literature and film is often unrealistic. In Koboldt's view, genetics in fiction is frequently oversimplified, and some myths are common and need to be debunked. For example, the Human Genome Project has not (he states) immediately led to a Gattaca world, as the relationship between genotype and phenotype is not straightforward. People do differ genetically, but only very rarely because they are missing a gene that other people have: people have different alleles of the same genes. Eye and hair colour are controlled not by one gene each, but by multiple genes. Mutations do occur, but they are rare: people are 99.99% identical genetically, the 3 million differences between any two people being dwarfed by the hundreds of millions of DNA bases which are identical; nearly all DNA variants are inherited, not acquired afresh by mutation. And, Koboldt writes, believable scientists in fiction should know their knowledge is limited.

A new way to watch brain activity in action

A mouse’s hippocampal brain 
A mouse’s hippocampal brain neurons flash on and off as the animal walks around with a microlens array on its head.

It’s a neuroscientist’s dream: being able to track the millions of interactions among brain cells in animals that move about freely, behaving as they would under natural circumstances. New technology developed at The Rockefeller University represents a big step toward realizing that goal.

The invention, reported today in Nature Methods, is expected to give researchers a dynamic tool to study the brain’s role in various behaviors. Although designed for use on mice, information gleaned from it could someday shed light on neuronal activity in humans as well, says Alipasha Vaziri, who led the technology’s development as head of the Laboratory of Neurotechnology and Biophysics. For example, it might allow us to better understand the neuronal basis of brain disorders such as autism and schizophrenia.

Vaziri says the tool provides an opening to an exciting range of discoveries. As an animal moves about its environment, for instance, some neurons direct spatial navigation while others receive sensory feedback from changes to the body’s position or the visual system. “Until now, no one has been able to detect how these different neurons, which can be located at different depths within a volume of brain tissue, dynamically interact with each other in a freely moving rodent,” says Vaziri, an associate professor at Rockefeller. Similarly, the tool can be used to record the interplay among neurons when two animals meet and interact socially.

High-tech headgear

The technology consists of a tiny microscope attached to a mouse’s head and outfitted with a specialized group of lenses called a microlens array. These lenses enable the microscope to capture images from multiple angles and depths on a sensor chip, producing a three-dimensional record of neurons blinking on and off as they communicate with each other through electrochemical impulses. (In the experiments, the mouse neurons are genetically modified to light up when they become activated.) A coaxial cable attached to the top of the microscope transmits the data for recording. The head-mounted gear weighs only four grams, but Vaziri expects that planned modifications will make it even lighter.

Once the microlens array has captured sensor images from within a volume of brain tissue, the next challenge is to process this raw data. Brain tissue is opaque, making it difficult to pinpoint the source of each neuronal light flash. Vaziri’s team solved this problem, which is the result of so-called scattering, by developing a new computer algorithm. “The algorithm utilizes the statistical properties of neurons’ distribution in space and in activity,” Vaziri explains, “while extracting additional information from the scattered emission light. This enables their activity to be simultaneously and faithfully recorded within a volume despite the highly scattering tissue properties.”

The result is a clear image that shows individual neurons flashing in sequence.

Faster, more effective imaging

Vaziri’s lab has previously applied this algorithm, known by the acronym SID, in studies in which the heads of the mice were secured in a fixed position. Their latest research is the first to demonstrate that these inventions can be used together with a tiny microscope called the Miniscope, developed by a collaborating team at the University of California Los Angeles, to measure neuronal activity volumetrically in unconstrained animals.

The technology, if widely adopted, could offer several advantages over two-photon microscopy, a broadly used neuroscience tool. For example, two-photon microscopy records neuronal activity within individual focal planes—thin, virtual “slices” of the sample—that then are combined to create a three-dimensional image. In contrast, Vaziri’s method immediately captures data in three dimensions over an entire volume of tissue, making it faster and more effective.

Vaziri plans to continue developing tools to record neuronal activity in even larger portions of the brain than currently possible, and at higher speeds and resolution. “We hope this work will ultimately lead to a deeper understanding of how the brain processes information underlying the generation of behavior,” he says.

Genetic engineering (updated)

From Wikipedia, the free encyclopedia

Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism's genes using biotechnology. It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms. New DNA is obtained by either isolating and copying the genetic material of interest using recombinant DNA methods or by artificially synthesising the DNA. A construct is usually created and used to insert this DNA into the host organism. The first recombinant DNA molecule was made by Paul Berg in 1972 by combining DNA from the monkey virus SV40 with the lambda virus. As well as inserting genes, the process can be used to remove, or "knock out", genes. The new DNA can be inserted randomly, or targeted to a specific part of the genome.

An organism that is generated through genetic engineering is considered to be genetically modified (GM) and the resulting entity is a genetically modified organism (GMO). The first GMO was a bacterium generated by Herbert Boyer and Stanley Cohen in 1973. Rudolf Jaenisch created the first GM animal when he inserted foreign DNA into a mouse in 1974. The first company to focus on genetic engineering, Genentech, was founded in 1976 and started the production of human proteins. Genetically engineered human insulin was produced in 1978 and insulin-producing bacteria were commercialised in 1982. Genetically modified food has been sold since 1994, with the release of the Flavr Savr tomato. The Flavr Savr was engineered to have a longer shelf life, but most current GM crops are modified to increase resistance to insects and herbicides. GloFish, the first GMO designed as a pet, was sold in the United States in December 2003. In 2016 salmon modified with a growth hormone were sold.

Genetic engineering has been applied in numerous fields including research, medicine, industrial biotechnology and agriculture. In research GMOs are used to study gene function and expression through loss of function, gain of function, tracking and expression experiments. By knocking out genes responsible for certain conditions it is possible to create animal model organisms of human diseases. As well as producing hormones, vaccines and other drugs genetic engineering has the potential to cure genetic diseases through gene therapy. The same techniques that are used to produce drugs can also have industrial applications such as producing enzymes for laundry detergent, cheeses and other products.

The rise of commercialised genetically modified crops has provided economic benefit to farmers in many different countries, but has also been the source of most of the controversy surrounding the technology. This has been present since its early use, the first field trials were destroyed by anti-GM activists. 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 concern with critics. Gene flow, impact on non-target organisms, control of the food supply and intellectual property rights have also been raised as potential issues. These concerns have led to the development of a regulatory framework, which started in 1975. It has led to an international treaty, the Cartagena Protocol on Biosafety, that was adopted in 2000. Individual countries have developed their own regulatory systems regarding GMOs, with the most marked differences occurring between the USA and Europe.

Overview

Comparison of conventional plant breeding with transgenic and cisgenic genetic modification

Genetic engineering is a process that alters the genetic structure of an organism by either removing or introducing DNA. Unlike traditional animal and plant breeding, which involves doing multiple crosses and then selecting for the organism with the desired phenotype, genetic engineering takes the gene directly from one organism and inserts it in the other. This is much faster, can be used to insert any genes from any organism (even ones from different domains) and prevents other undesirable genes from also being added.

Genetic engineering could potentially fix severe genetic disorders in humans by replacing the defective gene with a functioning one. It is an important tool in research that allows the function of specific genes to be studied. Drugs, vaccines and other products have been harvested from organisms engineered to produce them. Crops have been developed that aid food security by increasing yield, nutritional value and tolerance to environmental stresses.

The DNA can be introduced directly into the host organism or into a cell that is then fused or hybridised with the host. This relies on recombinant nucleic acid 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 or micro-encapsulation.

Genetic engineering does not normally include traditional 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. However, some broad definitions of genetic engineering include selective breeding. Cloning and stem cell research, although not considered genetic engineering, are closely related and genetic engineering can be used within them. Synthetic biology is an emerging discipline that takes genetic engineering a step further by introducing artificially synthesised material into an organism.

Plants, animals or micro organisms that have been changed through genetic engineering are termed genetically modified organisms or GMOs. 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. If genetic engineering is used to remove genetic material from the target organism the resulting organism is termed a knockout organism. In Europe genetic modification is synonymous with genetic engineering while within the United States of America and Canada genetic modification can also be used to refer to more conventional breeding methods.

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 – one year before DNA's role in heredity was confirmed by Alfred Hershey and Martha Chase, and two years before James Watson and Francis Crick showed that the DNA molecule has a double-helix structure – though the general concept of direct genetic manipulation was explored in rudimentary form in Stanley G. Weinbaum's 1936 science fiction story Proteus Island.

In 1974 Rudolf Jaenisch created a genetically modified mouse, 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. In 1973 Herbert Boyer and Stanley Cohen created the first transgenic organism by inserting antibiotic resistance genes into the plasmid of an Escherichia coli bacterium. A year later Rudolf Jaenisch created a transgenic mouse by introducing foreign DNA into its embryo, making it the world’s first transgenic animal. 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.

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. In 1980, the U.S. Supreme Court in the Diamond v. Chakrabarty case ruled that genetically altered life could be patented. The insulin produced by bacteria was approved for release by the Food and Drug Administration (FDA) in 1982.

In 1983, a biotech company, Advanced Genetic Sciences (AGS) applied for U.S. government authorisation to perform field tests with the ice-minus strain of Pseudomonas syringae to protect crops from frost, but environmental groups and protestors delayed the field tests for four years with legal challenges. In 1987, the ice-minus strain of P. syringae became the first genetically modified organism (GMO) to be released into the environment when a strawberry field and a potato field in California were sprayed with it. 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".

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. The People’s Republic of China was the first country to commercialise transgenic plants, introducing a virus-resistant tobacco in 1992. In 1994 Calgene attained approval to commercially release the first genetically modified food, the Flavr Savr, a tomato engineered to have a longer shelf life. In 1994, the European Union approved tobacco engineered to be resistant to the herbicide bromoxynil, making it the first genetically engineered crop commercialised in Europe. 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. 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.

In 2010, scientists at the J. Craig Venter Institute created the first synthetic genome and inserted it into an empty bacterial cell. The resulting bacterium, named Mycoplasma laboratorium, could replicate and produce proteins. Four years later this was taken a step further when a bacterium was developed that replicated a plasmid containing a unique base pair, creating the first organism engineered to use an expanded genetic alphabet. In 2012, Jennifer Doudna and Emmanuelle Charpentier collaborated to develop the CRISPR/Cas9 system, a technique which can be used to easily and specifically alter the genome of almost any organism.

Process

Polymerase chain reaction is a powerful tool used in molecular cloning

Creating a GMO is a multi-step process. Genetic engineers must first choose what gene they wish to insert into the organism. This is driven by what the aim is for the resultant organism and is built on earlier research. Genetic screens can be carried out to determine potential genes and further tests then used to identify the best candidates. The development of microarrays, transcriptomics and genome sequencing has made it much easier to find suitable genes. Luck also plays its part; the round-up ready gene was discovered after scientists noticed a bacterium thriving in the presence of the herbicide.

Gene isolation and cloning

The next step is to isolate the candidate gene. The cell containing the gene is opened and the DNA is purified. The gene is separated by using restriction enzymes to cut the DNA into fragments or polymerase chain reaction (PCR) to amplify up the gene segment. These segments can then be extracted through gel electrophoresis. If the chosen gene or the donor organism's genome has been well studied it may already be accessible from a genetic library. If the DNA sequence is known, but no copies of the gene are available, it can also be artificially synthesised. Once isolated the gene is ligated into a plasmid that is then inserted into a bacterium. The plasmid is replicated when the bacteria divide, ensuring unlimited copies of the gene are available.

Before the gene is inserted into the target organism it must be combined with other genetic elements. These include a promoter and terminator region, which initiate and end transcription. A selectable marker gene is added, which in most cases confers antibiotic resistance, so researchers can easily determine which cells have been successfully transformed. The gene can also be modified at this stage for better expression or effectiveness. These manipulations are carried out using recombinant DNA techniques, such as restriction digests, ligations and molecular cloning.

Inserting DNA into the host genome

A gene gun uses biolistics to insert DNA into plant tissue

There are a number of techniques available for inserting the gene into the host genome. Some bacteria can naturally take up foreign DNA. This ability can be induced in other bacteria via stress (e.g. thermal or electric shock), which increases 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.

In plants the DNA is often inserted using Agrobacterium-mediated recombination, taking advantage of the Agrobacteriums T-DNA sequence that allows natural insertion of genetic material into plant cells. Other methods include biolistics, where particles of gold or tungsten are coated with DNA and then shot into young plant cells, and electroporation, which involves using an electric shock to make the cell membrane permeable to plasmid DNA. Due to the damage caused to the cells and DNA the transformation efficiency of biolistics and electroporation is lower than agrobacterial transformation and microinjection.

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 the use of tissue culture. In animals it is necessary to ensure that the inserted DNA is present in the embryonic stem cells. Bacteria consist of a single cell and reproduce clonally so regeneration is not necessary. Selectable markers are used to easily differentiate transformed from untransformed cells. 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.

A. tumefaciens attaching itself to a carrot cell

Further testing using 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 hybridisation, quantitative RT-PCR, Western blot, immunofluorescence, ELISA and phenotypic analysis.

The new genetic material can be inserted randomly within the host genome or targeted to a specific location. The technique of gene targeting uses homologous recombination to make 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 through genome editing. Genome editing uses artificially engineered nucleases that create specific double-stranded breaks at desired locations in the genome, and use the cell’s endogenous mechanisms to repair the induced break by the natural processes of homologous recombination and nonhomologous end-joining. 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. In addition to enhancing gene targeting, engineered nucleases can be used to introduce mutations at endogenous genes that generate a gene knockout.

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. Bacteria, the first organisms to be genetically modified, can have plasmid DNA inserted containing new genes that code for medicines or enzymes that process food and other substrates. Plants have been modified for insect protection, herbicide resistance, virus resistance, enhanced nutrition, tolerance to environmental pressures and the production of edible vaccines. Most commercialised GMOs are insect resistant or herbicide tolerant crop plants. Genetically modified animals have been used for research, model animals and the production of agricultural or pharmaceutical products. The genetically modified animals include animals with genes knocked out, increased susceptibility to disease, hormones for extra growth and the ability to express proteins in their milk.

Medicine

Genetic engineering has many applications to medicine that include the manufacturing of drugs, creation of model animals that mimic human conditions and gene therapy. One of the earliest uses of genetic engineering was to mass-produce human insulin in bacteria. This application has now been applied to, human growth hormones, follicle stimulating hormones (for treating infertility), human albumin, monoclonal antibodies, antihemophilic factors, vaccines and many other drugs. Mouse hybridomas, cells fused together to create monoclonal antibodies, have been adapted through genetic engineering to create human monoclonal antibodies. In 2017, genetic engineering of chimeric antigen receptors on a patient's own T-cells was approved by the U.S. FDA as a treatment for the cancer acute lymphoblastic leukemia. Genetically engineered viruses are being developed that can still confer immunity, but lack the infectious sequences.

Genetic engineering is also used to create animal models of human diseases. Genetically modified mice are the most common genetically engineered animal model. They have been used to study and model cancer (the oncomouse), obesity, heart disease, diabetes, arthritis, substance abuse, anxiety, aging and Parkinson disease. 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.

Gene therapy is the genetic engineering of humans, generally by replacing defective genes with effective ones. Clinical research using somatic gene therapy has been conducted with several diseases, including X-linked SCID, chronic lymphocytic leukemia (CLL), and Parkinson's disease. In 2012, Alipogene tiparvovec became the first gene therapy treatment to be approved for clinical use. In 2015 a virus was used to insert a healthy gene into the skin cells of a boy suffering from a rare skin disease, epidermolysis bullosa, in order to grow, and then graft healthy skin onto 80 percent of the boy's body which was affected by the illness.

Germline gene therapy would result in any change being inheritable, which has raised concerns within the scientific community. In 2015, CRISPR was used to edit the DNA of non-viable human embryos, leading scientists of major world academies to call for a moratorium on inheritable human genome edits. There are also concerns that the technology could be used not just for treatment, but for enhancement, modification or alteration of a human beings' appearance, adaptability, intelligence, character or behavior. The distinction between cure and enhancement can also be difficult to establish. In November 2018, a Chinese scientist reported the birth of twin human girls, Lulu and Nana, who were genetically edited to resist the HIV virus.

Researchers are altering the genome of pigs to induce the growth of human organs to be used in transplants. Scientists are creating "gene drives", changing the genomes of mosquitoes to make them immune to malaria, and then spreading the genetically altered mosquitoes throughout the mosquito population in the hopes of eliminating the disease.

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 can be inserted into bacteria for storage and modification, creating genetically modified bacteria in the process. Bacteria are cheap, easy to grow, clonal, multiply quickly, relatively easy to transform and can be stored at -80 °C almost indefinitely. Once a gene is isolated it can be stored inside the bacteria providing an unlimited supply for research.

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. In a simple knockout a copy of the desired gene has been altered to make it 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 analyse the defects caused by this mutation and thereby determine the role of particular genes. It is used especially frequently in developmental biology. When this is done by creating a library of genes with point mutations at every position in the area of interest, or even every position in the whole gene, this is called "scanning mutagenesis". The simplest method, and the first to be used, is "alanine scanning", where every position in turn is mutated to the unreactive amino acid alanine;
  • 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. Gain of function is used to tell whether or not a protein is sufficient for a function, but does not always mean it's required, especially when dealing with genetic or functional redundancy;
  • Tracking experiments, which seek to gain information about the localisation 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 visualisation 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 catalyses 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

Organisms can have their cells transformed with a gene coding for a useful protein, such as an enzyme, so that they will overexpress the desired protein. Mass quantities of the protein can then be manufactured by growing the transformed organism in bioreactor equipment using industrial fermentation, and then purifying the protein. Some genes do not work well in bacteria, so yeast, insect cells or mammalians cells can also be used. 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. Other applications with genetically engineered bacteria could involve making them perform tasks outside their natural cycle, such as making biofuels, cleaning up oil spills, carbon and other toxic waste and detecting arsenic in drinking water. Certain genetically modified microbes can also be used in biomining and bioremediation, due to their ability to extract heavy metals from their environment and incorporate them into compounds that are more easily recoverable.

In materials science, a genetically modified virus has been used in a research laboratory as a scaffold for assembling a more environmentally friendly lithium-ion battery. Bacteria have also been engineered to function as sensors by expressing a fluorescent protein under certain environmental conditions.

Agriculture

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

One of the best-known and controversial applications of genetic engineering is the creation and use of genetically modified crops or genetically modified livestock to produce genetically modified food. Crops have been developed to increase production, increase tolerance to abiotic stresses, alter the composition of the food, or to produce novel products.

The first crops to be realised commercially on a large scale provided protection from insect pests or tolerance to herbicides. Fungal and virus resistant crops have also been developed or are in development. This make the insect and weed management of crops easier and can indirectly increase crop yield. GM crops that directly improve yield by accelerating growth or making the plant more hardy (by improving salt, cold or drought tolerance) are also under development. In 2016 Salmon have been genetically modified with growth hormones to reach normal adult size much faster.

GMOs have been developed that modify the quality of produce by increasing the nutritional value or providing more industrially useful qualities or quantities. The Amflora potato produces a more industrially useful blend of starches. Soybeans and canola have been genetically modified to produce more healthy oils. The first commercialised GM food was a tomato that had delayed ripening, increasing its shelf life.

Plants and animals have been engineered to produce materials they do not normally make. Pharming uses crops and animals as bioreactors to produce vaccines, drug intermediates, or the drugs themselves; the useful product is purified from the harvest and then used in the standard pharmaceutical production process. 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.

Other applications

Genetic engineering has potential applications in conservation and natural area management. Gene transfer through viral vectors has been proposed as a means of controlling invasive species as well as vaccinating threatened fauna from disease. Transgenic trees have been suggested as a way to confer resistance to pathogens in wild populations. With the increasing risks of maladaptation in organisms as a result of climate change and other perturbations, facilitated adaptation through gene tweaking could be one solution to reducing extinction risks. Applications of genetic engineering in conservation are thus far mostly theoretical and have yet to be put into practice.

Genetic engineering is also being used to create microbial art. Some bacteria have been genetically engineered to create black and white photographs. Novelty items such as lavender-colored carnations, blue roses, and glowing fish have also been produced through genetic engineering.

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 GMOs. The development of a regulatory framework began in 1975, at Asilomar, California. The Asilomar meeting recommended a set of voluntary guidelines regarding the use of recombinant technology. As the technology improved USA established a committee at the Office of Science and Technology, which assigned regulatory approval of GM food to the USDA, FDA and EPA. The Cartagena Protocol on Biosafety, an international treaty that governs the transfer, handling, and use of GMOs,[150] was adopted on 29 January 2000. One hundred and fifty-seven countries are members of the Protocol and many use it as a reference point for their own regulations.

The legal and regulatory status of GM foods varies by country, with some nations banning or restricting them, and others permitting them with widely differing degrees of regulation. Some countries allow the import of GM food with authorisation, but either do not allow its cultivation (Russia, Norway, Israel) or have provisions for cultivation even though no GM products are yet produced (Japan, South Korea). Most countries that do not allow GMO cultivation do permit research. Some of the most marked differences occurring between the USA and Europe. The US policy focuses on the product (not the process), only looks at verifiable scientific risks and uses the concept of substantial equivalence. The European Union by contrast has possibly the most stringent GMO regulations in the world. All GMOs, along with irradiated food, are considered "new food" and subject to extensive, case-by-case, science-based food evaluation by the European Food Safety Authority. The criteria for authorisation fall in four broad categories: "safety," "freedom of choice," "labelling," and "traceability." The level of regulation in other countries that cultivate GMOs lie in between Europe and the United States.

Regulatory agencies by geographical region
Region Regulators Notes
USA USDA, FDA and EPA
Europe European Food Safety Authority
Canada Health Canada and the Canadian Food Inspection Agency Regulated products with novel features regardless of method of origin
Africa Common Market for Eastern and Southern Africa Final decision lies with each individual country.
China Office of Agricultural Genetic Engineering Biosafety Administration
India Institutional Biosafety Committee, Review Committee on Genetic Manipulation and Genetic Engineering Approval Committee
Argentina National Agricultural Biotechnology Advisory Committee (environmental impact), the National Service of Health and Agrifood Quality (food safety) and the National Agribusiness Direction (effect on trade) Final decision made by the Secretariat of Agriculture, Livestock, Fishery and Food.
Brazil National Biosafety Technical Commission (environmental and food safety) and the Council of Ministers (commercial and economical issues)
Australia Office of the Gene Technology Regulator (oversees all GM products), Therapeutic Goods Administration (GM medicines) and Food Standards Australia New Zealand (GM food). The individual state governments can then assess the impact of release on markets and trade and apply further legislation to control approved genetically modified products.

One of the key issues concerning regulators is whether GM products should be labeled. The European Commission says that mandatory labeling and traceability are needed to allow for informed choice, avoid potential false advertising and facilitate the withdrawal of products if adverse effects on health or the environment are discovered. The American Medical Association and the American Association for the Advancement of Science say that absent scientific evidence of harm even voluntary labeling is misleading and will falsely alarm consumers. Labeling of GMO products in the marketplace is required in 64 countries. Labeling can be mandatory up to a threshold GM content level (which varies between countries) or voluntary. In Canada and the USA labeling of GM food is voluntary, while in Europe all food (including processed food) or feed which contains greater than 0.9% of approved GMOs must be labelled.

Controversy

Critics have objected to the use of genetic engineering on several grounds, that include ethical, ecological and economic concerns. Many of these concerns involve GM crops and whether food produced from them is safe and what impact growing them will have on the environment. These controversies have led to litigation, international trade disputes, and protests, and to restrictive regulation of commercial products in some countries.

Accusations that scientists are "playing God" and other religious issues have been ascribed to the technology from the beginning. Other ethical issues raised include the patenting of life, the use of intellectual property rights, the level of labeling on products, control of the food supply and the objectivity of the regulatory process. Although doubts have been raised, economically most studies have found growing GM crops to be beneficial to farmers.

Gene flow between GM crops and compatible plants, along with increased use of selective herbicides, can increase the risk of "superweeds" developing. Other environmental concerns involve potential impacts on non-target organisms, including soil microbes, and an increase in secondary and resistant insect pests. Many of the environmental impacts regarding GM crops may take many years to be understood and are also evident in conventional agriculture practices. With the commercialisation of genetically modified fish there are concerns over what the environmental consequences will be if they escape.

There are three main concerns over the safety of genetically modified food: whether they may provoke an allergic reaction; whether the genes could transfer from the food into human cells; and whether the genes not approved for human consumption could outcross to other crops. There is a scientific consensus that currently available food derived from GM crops poses no greater risk to human health than conventional food, but that each GM food needs to be tested on a case-by-case basis before introduction. Nonetheless, members of the public are much less likely than scientists to perceive GM foods as safe.

Operator (computer programming)

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