Gene flow

From Wikipedia, the free encyclopedia

Gene flow is the transfer of alleles from one population to another population through immigration of individuals.

 

In population genetics, gene flow (also known as gene migration or allele flow) is the transfer of genetic variation from one population to another. If the rate of gene flow is high enough, then two populations are considered to have equivalent allele frequencies and therefore effectively be a single population. It has been shown that it takes only "One migrant per generation" to prevent populations from diverging due to drift. Gene flow is an important mechanism for transferring genetic diversity among populations. Migrants change the distribution of genetic diversity within the populations, by modifying the allele frequencies (the proportion of members carrying a particular variant of a gene). High rates of gene flow can reduce the genetic differentiation between the two groups, increasing homogeneity. For this reason, gene flow has been thought to constrain speciation by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to full speciation. In some cases migration may also result in the addition of novel genetic variants to the gene pool of a species or population. 

There are a number of factors that affect the rate of gene flow between different populations. Gene flow is expected to be lower in species that have low dispersal or mobility, that occur in fragmented habitats, where there is long distances between populations, and when there are small population sizes. Mobility plays an important role in the migration rate, as highly mobile individuals tend to have greater migratory prospects. Although animals are thought to be more mobile than plants, pollen and seeds may be carried great distances by animals or wind. When gene flow is impeded, there can be an increase in inbreeding, measured by the inbreeding coefficient (F) within a population. For example, many island populations have low rates of gene flow due to geographic isolation and small population sizes. The Black Footed Rock Wallaby has several inbred populations that live on various islands off the coast of Australia. The population is so strongly isolated that lack of gene flow has led to high rates of inbreeding.

Measuring gene flow

Decrease in population size leads to increased divergence due to drift, while migration reduces divergence and inbreeding. Gene flow can be measured by using the effective population size (${\displaystyle N_{e}}$) and the net migration rate per generation (m). Using the approximation based on the Island model, the effect of migration can be calculated for a population in terms of the degree of genetic differentiation(${\displaystyle Fst}$). This formula accounts for the proportion of total molecular marker variation among populations, averaged over loci. When there is one migrant per generation, the inbreeding coefficient (${\displaystyle Fst}$) equals 0.2. However, when there is less than 1 migrant per generation (no migration), the inbreeding coefficient rises rapidly resulting in fixation and complete divergence (${\displaystyle Fst}$ = 1). The most common ${\displaystyle Fst}$ is less than 0.25. This means there is some migration happening. Measures of population structure range from 0 to 1. When gene flow occurs via migration the deleterious effects of inbreeding can be ameliorated.

${\displaystyle Fst=1/(4N_{e}m+1)}$

The formula can be modified to solve for the migration rate when ${\displaystyle Fst}$ is known:

${\displaystyle Nm=(1/Fst-1)/4}$, Nm = number of migrants.

Barriers to gene flow

Allopatric speciation

Examples of speciation affecting gene flow.

 

When gene flow is blocked by physical barriers, this results in Allopatric speciation or a geographical isolation that does not allow populations of the same species to exchange genetic material. Physical barriers to gene flow are usually, but not always, natural. They may include impassable mountain ranges, oceans, or vast deserts. In some cases, they can be artificial, man-made barriers, such as the Great Wall of China, which has hindered the gene flow of native plant populations. One of these native plants, Ulmus pumila, demonstrated a lower prevalence of genetic differentiation than the plants Vitex negundo, Ziziphus jujuba, Heteropappus hispidus, and Prunus armeniaca whose habitat is located on the opposite side of the Great Wall of China where Ulmus pumila grows. This is because Ulmus pumila has wind-pollination as its primary means of propagation and the latter-plants carry out pollination through insects. Samples of the same species which grow on either side have been shown to have developed genetic differences, because there is little to no gene flow to provide recombination of the gene pools.

Sympatric speciation

Barriers to gene flow need not always be physical. Sympatric speciation happens when new species from the same ancestral species arise along the same range. This is often a result of a reproductive barrier. For example, two palm species of Howea found on Lord Howe Island were found to have substantially different flowering times correlated with soil preference, resulting in a reproductive barrier inhibiting gene flow. Species can live in the same environment, yet show very limited gene flow due to reproductive barriers, fragmentation, specialist pollinators, or limited hybridization or hybridization yielding unfit hybrids. A cryptic species is a species that humans cannot tell is different without the use of genetics. Moreover, gene flow between hybrid and wild populations can result in loss of genetic diversity via genetic pollution, assortative mating and outbreeding. In human populations, genetic differentiation can also result from endogamy, due to differences in caste, ethnicity, customs and religion.

Human assisted gene-flow

Genetic rescue

Gene flow can also be used to assist species which are threatened with extinction. When a species exist in small populations there is an increased risk of inbreeding and greater susceptibility to loss of diversity due to drift. These populations can benefit greatly from the introduction of unrelated individuals who can increase diversity and reduce the amount of inbreeding, and thus increase overall fitness. This was demonstrated in the lab with two bottleneck strains of drosophila melanogaster, in which crosses between the two populations reversed the effects of inbreeding and led to greater chances of survival in not only one generation but two.

Genetic pollution

Human activities such as movement of species and modification of landscape can result in genetic pollution, hybridization, introgression and genetic swamping. These processes can lead to homogenization or replacement of local genotypes as a result of either a numerical and/or fitness advantage of introduced plant or animal. Nonnative species can threaten native plants and animals with extinction by hybridization and introgression either through purposeful introduction by humans or through habitat modification, bringing previously isolated species into contact. These phenomena can be especially detrimental for rare species coming into contact with more abundant ones which can occur between island and mainland species. Interbreeding between the species can cause a 'swamping' of the rarer species' gene pool, creating hybrids that supplant the native stock. This is a direct result of evolutionary forces such as natural selection, as well as genetic drift, which lead to the increasing prevalence of advantageous traits and homogenization. The extent of this phenomenon is not always apparent from outward appearance alone. While some degree of gene flow occurs in the course of normal evolution, hybridization with or without introgression may threaten a rare species' existence. For example, the Mallard is an abundant species of duck that interbreeds readily with a wide range of other ducks and poses a threat to the integrity of some species.

Gene flow between species

Horizontal gene transfer

Horizontal gene transfer (HGT) refers to the transfer of genes between organisms in a manner other than traditional reproduction, either through transformation (direct uptake of genetic material by a cell from its surroundings), conjugation (transfer of genetic material between two bacterial cells in direct contact), transduction (injection of foreign DNA by a bacteriophage virus into the host cell) or GTA-mediated transduction (transfer by a virus-like element produced by a bacterium).

Viruses can transfer genes between species. Bacteria can incorporate genes from dead bacteria, exchange genes with living bacteria, and can exchange plasmids across species boundaries. "Sequence comparisons suggest recent horizontal transfer of many genes among diverse species including across the boundaries of phylogenetic 'domains'. Thus determining the phylogenetic history of a species can not be done conclusively by determining evolutionary trees for single genes."

Biologist Gogarten suggests "the original metaphor of a tree no longer fits the data from recent genome research". Biologists [should] instead use the metaphor of a mosaic to describe the different histories combined in individual genomes and use the metaphor of an intertwined net to visualize the rich exchange and cooperative effects of horizontal gene transfer.

"Using single genes as phylogenetic markers, it is difficult to trace organismal phylogeny in the presence of HGT. Combining the simple coalescence model of cladogenesis with rare HGT events suggest there was no single last common ancestor that contained all of the genes ancestral to those shared among the three domains of life. Each contemporary molecule has its own history and traces back to an individual molecule cenancestor. However, these molecular ancestors were likely to be present in different organisms at different times."

Hybridization

In some instances, when a species has a sister species and breeding capabilities are possible due to the removal of previous barriers or through introduction due to human intervention, species can hybridize and exchange genes and corresponding traits. This exchange is not always clear-cut, for sometimes the hybrids may look identical to the original species phenotypically but upon testing the mtDNA it is apparent that hybridization has occurred. Differential hybridization also occurs because some traits and DNA are more readily exchanged than others, and this is a result of selective pressure or the absence thereof that allows for easier transaction. In instances in which the introduced species begins to replace the native species, the native species becomes threatened and the biodiversity is reduced, thus making this phenomenon negative rather than a positive case of gene flow that augments genetic diversity. Introgression is the replacement of the native species genes with that of the invader species. It is important to note that hybrids are generally deemed less "fit" than their parental generation, and as a result is a closely monitored genetic issue as the ultimate goal in conservation genetics is to maintain the genetic integrity of a species and preserve biodiversity.

Examples

Marine iguana of the Galapagos Islands evolved via allopatric speciation, through limited gene flow and geographic isolation.

 

While gene flow can greatly enhance the fitness of a population, it can also have negative consequences depending on the population and the environment in which they reside. The effects of gene flow are context-dependent.

• Fragmented Population: fragmented landscapes such as the Galapagos Islands are an ideal place for adaptive radiation to occur as a result of differing geography. Darwin's Finches likely experienced allopatric speciation in some part due to differing geography, but that doesn't explain why we see so many different kinds of finches on the same island. This is due to adaptive radiation, or the evolution of varying traits in light of competition for resources. Gene flow moves in the direction of what resources are abundant at a given time.
• Island Population: The Marine Iguana is an endemic species of the Galapagos Islands, but it evolved from a mainland ancestor of land iguana. Due to geographic isolation gene flow between the two species was limited and differing environments caused the Marine Iguana to evolve in order to adapt to the island environment. For instance, they are the only iguana that has evolved the ability to swim.

• Human Populations: Two theories exist for the human evolution throughout the world. The first is known as the multiregional model in which modern human variation is seen as a product of radiation of Homo erectus out of Africa after which local differentiation led to the establishment of regional population as we see them now. Gene flow plays an important role in maintaining a grade of similarities and preventing speciation. In contrast the single origin theory assumes that there was a common ancestral population originating in Africa of Homo sapiens which already displayed the anatomical characteristics we see today. This theory minimizes the amount of parallel evolution that is needed.

• Butterflies: Comparisons between sympatric and allopatric populations of Heliconius melpomene, H. cydno, and H. timareta revealed a genome-wide trend of increased shared variation in sympatry, indicative of pervasive interspecific gene flow.
• Human-mediated gene flow: The captive genetic management of threatened species is the only way in which humans attempt to induce gene flow in ex situ situation. One example is the Giant Panda which is part of an international breeding program in which genetic materials are shared between zoological organizations in order to increase genetic diversity in the small populations. As a result of low reproductive success, artificial insemination with fresh/frozen-thawed sperm was developed which increased cub survival rate. A 2014 study found that high levels of genetic diversity and low levels of inbreeding were estimated in the breeding centers.

• Plants: Two species of Monkeyflowers, mimulus lewsii and mimulus cardinalis, were found to have highly specialized pollinators that acted on major genes resulting in a contribution to the floral evolution and reproductive isolation of these two species. The specialized pollination limited gene flow between the two species, eventually resulting in two different species.
• Sika deer: Sika deer were introduced into Western Europe, and they reproduce easily with the native red deer. This translocation of Sika deer has led to introgression and there are no longer "pure" red deer in the region, and all can be classified as hybrids.
• Bobwhite quail: Bobwhite quail were translocated from the southern part of the United States to Ontario in order to increase population numbers and game for hunting.The hybrids that resulted from this translocation was less fit than the native population and were not adapted to survived the Northern Winters.

Persistent organic pollutant

From Wikipedia, the free encyclopedia

Persistent organic pollutants (POPs) are organic compounds that are resistant to environmental degradation through chemical, biological, and photolytic processes. Because of their persistence, POPs bioaccumulate with potential adverse impacts on human health and the environment. The effect of POPs on human and environmental health was discussed, with intention to eliminate or severely restrict their production, by the international community at the Stockholm Convention on Persistent Organic Pollutants in 2001.

 

Many POPs are currently or were in the past used as pesticides, solvents, pharmaceuticals, and industrial chemicals. Although some POPs arise naturally, for example volcanoes and various biosynthetic pathways, most are man-made via total synthesis.

Consequences of persistence

POPs typically are halogenated organic compounds (see lists below) and as such exhibit high lipid solubility. For this reason, they bioaccumulate in fatty tissues. Halogenated compounds also exhibit great stability reflecting the nonreactivity of C-Cl bonds toward hydrolysis and photolytic degradation. The stability and lipophilicity of organic compounds often correlates with their halogen content, thus polyhalogenated organic compounds are of particular concern. They exert their negative effects on the environment through two processes, long range transport, which allows them to travel far from their source, and bioaccumulation, which reconcentrates these chemical compounds to potentially dangerous levels. Compounds that make up POPs are also classed as PBTs (Persistent, Bioaccumulative and Toxic) or TOMPs (Toxic Organic Micro Pollutants).

Long-range transport

POPs enter the gas phase under certain environmental temperatures and volatize from soils, vegetation, and bodies of water into the atmosphere, resisting breakdown reactions in the air, to travel long distances before being re-deposited. This results in accumulation of POPs in areas far from where they were used or emitted, specifically environments where POPs have never been introduced such as Antarctica, and the Arctic circle. POPs can be present as vapors in the atmosphere or bound to the surface of solid particles. POPs have low solubility in water but are easily captured by solid particles, and are soluble in organic fluids (oils, fats, and liquid fuels). POPs are not easily degraded in the environment due to their stability and low decomposition rates. Due to this capacity for long-range transport, POP environmental contamination is extensive, even in areas where POPs have never been used, and will remain in these environments years after restrictions implemented due to their resistance to degradation.

Bioaccumulation

Bioaccumulation of POPs is typically associated with the compounds high lipid solubility and ability to accumulate in the fatty tissues of living organisms for long periods of time. Persistent chemicals tend to have higher concentrations and are eliminated more slowly. Dietary accumulation or bioaccumulation is another hallmark characteristic of POPs, as POPs move up the food chain, they increase in concentration as they are processed and metabolized in certain tissues of organisms. The natural capacity for animals gastrointestinal tract concentrate ingested chemicals, along with poorly metabolized and hydrophobic nature of POPs makes such compounds highly susceptible to bioaccumulation. Thus POPs not only persist in the environment, but also as they are taken in by animals they bioaccumulate, increasing their concentration and toxicity in the environment.

Stockholm Convention on Persistent Organic Pollutants

State parties to the Stockholm Convention on Persistent Organic Pollutants

The Stockholm Convention was adopted and put into practice by the United Nations Environment Programme (UNEP) on May 22, 2001. The UNEP decided that POP regulation needed to be addressed globally for the future. The purpose statement of the agreement is "to protect human health and the environment from persistent organic pollutants." As of 2014, there are 179 countries in compliance with the Stockholm convention. The convention and its participants have recognized the potential human and environmental toxicity of POPs. They recognize that POPs have the potential for long range transport and bioaccumulation and biomagnification. The convention seeks to study and then judge whether or not a number of chemicals that have been developed with advances in technology and science can be categorized as POPs or not. The initial meeting in 2001 made a preliminary list, termed the "dirty dozen," of chemicals that are classified as POPs. As of 2014, the United States of America has signed the Stockholm Convention but has not ratified it. There are a handful of other countries that have not ratified the convention but most countries in the world have ratified the convention.

Compounds on the Stockholm Convention list

In May 1995, the United Nations Environment Programme Governing Council investigated POPs. Initially the Convention recognized only twelve POPs for their adverse effects on human health and the environment, placing a global ban on these particularly harmful and toxic compounds and requiring its parties to take measures to eliminate or reduce the release of POPs in the environment. 

1. Aldrin, an insecticide used in soils to kill termites, grasshoppers, Western corn rootworm, and others, is also known to kill birds, fish, and humans. Humans are primarily exposed to aldrin through dairy products and animal meats.
2. Chlordane, an insecticide used to control termites and on a range of agricultural crops, is known to be lethal in various species of birds, including mallard ducks, bobwhite quail, and pink shrimp; it is a chemical that remains in the soil with a reported half-life of one year. Chlordane has been postulated to affect the human immune system and is classified as a possible human carcinogen. Chlordane air pollution is believed the primary route of humane exposure.
3. Dieldrin, a pesticide used to control termites, textile pests, insect-borne diseases and insects living in agricultural soils. In soil and insects, aldrin can be oxidized, resulting in rapid conversion to dieldrin. Dieldrin’s half-life is approximately five years. Dieldrin is highly toxic to fish and other aquatic animals, particularly frogs, whose embryos can develop spinal deformities after exposure to low levels. Dieldrin has been linked to Parkinson's disease, breast cancer, and classified as immunotoxic, neurotoxic, with endocrine disrupting capacity. Dieldrin residues have been found in air, water, soil, fish, birds, and mammals. Human exposure to dieldrin primarily derives from food.
4. Endrin, an insecticide sprayed on the leaves of crops, and used to control rodents. Animals can metabolize endrin, so fatty tissue accumulation is not an issue, however the chemical has a long half-life in soil for up to 12 years. Endrin is highly toxic to aquatic animals and humans as a neurotoxin. Human exposure results primarily through food.
5. Heptachlor, a pesticide primarily used to kill soil insects and termites, along with cotton insects, grasshoppers, other crop pests, and malaria-carrying mosquitoes. Heptachlor, even at every low doses has been associated with the decline of several wild bird populations – Canada geese and American kestrels. In laboratory tests have shown high-dose heptachlor as lethal, with adverse behavioral changes and reduced reproductive success at low-doses, and is classified as a possible human carcinogen. Human exposure primarily results from food.
6. Hexachlorobenzene (HCB), was first introduced in 1945–59 to treat seeds because it can kill fungi on food crops. HCB-treated seed grain consumption is associated with photosensitive skin lesions, colic, debilitation, and a metabolic disorder called porphyria turcica, which can be lethal. Mothers who pass HCB to their infants through the placenta and breast milk had limited reproductive success including infant death. Human exposure is primarily from food.
7. Mirex, an insecticide used against ants and termites or as a flame retardant in plastics, rubber, and electrical goods. Mirex is one of the most stable and persistent pesticides, with a half-life of up to 10 years. Mirex is toxic to several plant, fish and crustacean species, with suggested carcinogenic capacity in humans. Humans are exposed primarily through animal meat, fish, and wild game.
8. Toxaphene, an insecticide used on cotton, cereal, grain, fruits, nuts, and vegetables, as well as for tick and mite control in livestock. Widespread toxaphene use in the US and chemical persistence, with a half-life of up to 12 years in soil, results in residual toxaphene in the environment. Toxaphene is highly toxic to fish, inducing dramatic weight loss and reduced egg viability. Human exposure primarily results from food. While human toxicity to direct toxaphene exposure is low, the compound is classified as a possible human carcinogen.
9. Polychlorinated biphenyls (PCBs), used as heat exchange fluids, in electrical transformers, and capacitors, and as additives in paint, carbonless copy paper, and plastics. Persistence varies with degree of halogenation, an estimated half-life of 10 years. PCBs are toxic to fish at high doses, and associated with spawning failure at low doses. Human exposure occurs through food, and is associated with reproductive failure and immune suppression. Immediate effects of PCB exposure include pigmentation of nails and mucous membranes and swelling of the eyelids, along with fatigue, nausea, and vomiting. Effects are transgenerational, as the chemical can persist in a mother’s body for up to 7 years, resulting in developmental delays and behavioral problems in her children. Food contamination has led to large scale PCB exposure.
10. Dichlorodiphenyltrichloroethane (DDT) is probably the most infamous POP. It was widely used as insecticide during WWII to protect against malaria and typhus. After the war, DDT was used as an agricultural insecticide. In 1962, the American biologist Rachel Carson published Silent Spring, describing the impact of DDT spraying on the US environment and human health. DDT’s persistence in the soil for up to 10–15 years after application has resulted in widespread and persistent DDT residues throughout the world including the arctic, even though it has been banned or severely restricted in most of the world. DDT is toxic to many organisms including birds where it is detrimental to reproduction due to eggshell thinning. DDT can be detected in foods from all over the world and food-borne DDT remains the greatest source of human exposure. Short-term acute effects of DDT on humans are limited, however long-term exposure has been associated with chronic health effects including increased risk of cancer and diabetes, reduced reproductive success, and neurological disease.
11. Dioxins are unintentional by-products of high-temperature processes, such as incomplete combustion and pesticide production. Dioxins are typically emitted from the burning of hospital waste, municipal waste, and hazardous waste, along with automobile emissions, peat, coal, and wood. Dioxins have been associated with several adverse effects in humans, including immune and enzyme disorders, chloracne, and are classified as a possible human carcinogen. In laboratory studies of dioxin effects an increase in birth defects and stillbirths, and lethal exposure have been associated with the substances. Food, particularly from animals, is the principal source of human exposure to dioxins.
12. Polychlorinated dibenzofurans are by-products of high-temperature processes, such as incomplete combustion after waste incineration or in automobiles, pesticide production, and polychlorinated biphenyl production. Structurally similar to dioxins, the two compounds share toxic effects. Furans persist in the environment and classified as possible human carcinogens. Human exposure to furans primarily results from food, particularly animal products.

New POPs on the Stockholm Convention list

Since 2001, this list has been expanded to include some polycyclic aromatic hydrocarbons (PAHs), brominated flame retardants, and other compounds. Additions to the initial 2001 Stockholm Convention list are as following POPs:

• Chlordecone, a synthetic chlorinated organic compound,is primarily used as an agricultural pesticide, related to DDT and Mirex. Chlordecone is toxic to aquatic organisms, and classified as a possible human carcinogen. Many countries have banned chlordecone sale and use, or intend to phase out stockpiles and wastes.
• α-Hexachlorocyclohexane (α-HCH) and β-Hexachlorocyclohexane (β-HCH) are insecticides as well as by-products in the production of lindane. Large stockpiles of HCH isomers exist in the environment. α-HCH and β-HCH are highly persistent in the water of colder regions. α-HCH and β-HCH has been linked Parkinson's and Alzheimer's disease.
• Hexabromodiphenyl ether (hexaBDE) and heptabromodiphenyl ether (heptaBDE) are main components of commercial octabromodiphenyl ether (octaBDE). Commercial octaBDE is highly persistent in the environment, whose only degradation pathway is through debromination and the production of bromodiphenyl ethers, which can increase toxicity.
• Lindane (γ-hexachlorocyclohexane), a pesticide used as a broad spectrum insecticide for seed, soil, leaf, tree and wood treatment, and against ectoparasites in animals and humans (head lice and scabies). Lindane rapidly bioconcentrates. It is immunotoxic, neurotoxic, carcinogenic, linked to liver and kidney damage as well as adverse reproductive and developmental effects in laboratory animals and aquatic organisms. Production of lindane unintentionally produces two other POPs α-HCH and β-HCH.^{[citation needed]}
• Pentachlorobenzene (PeCB), is a pesticide and unintentional byproduct. PeCB has also been used in PCB products, dyestuff carriers, as a fungicide, a flame retardant, and a chemical intermediate. PeCB is moderately toxic to humane, while highly toxic to aquatic organisms.
• Tetrabromodiphenyl ether (tetraBDE) and pentabromodiphenyl ether (pentaBDE) are industrial chemicals and the main components of commercial pentabromodiphenyl ether (pentaBDE). PentaBDE has been detected in humans in all regions of the world.
• Perfluorooctanesulfonic acid (PFOS) and its salts are used in the production of fluoropolymers. PFOS and related compounds are extremely persistent, bioaccumulating and biomagnifying. The negative effects of trace levels of PFOS have not been established.
• Endosulfans are insecticides to control pests on crops such coffee, cotton, rice and sorghum and soybeans, tsetse flies, ectoparasites of cattle. They are used as a wood preservative. Global use and manufacturing of endosulfan has been banned under the Stockholm convention in 2011, although many countries had previously banned or introduced phase-outs of the chemical when the ban was announced. Toxic to humans and aquatic and terrestrial organisms, linked to congenital physical disorders, mental retardation, and death. Endosulfans' negative health effects are primarily liked to its endocrine disrupting capacity acting as an antiandrogen.
• Hexabromocyclododecane (HBCD) is a brominated flame retardant primarily used in thermal insulation in the building industry. HBCD is persistent, toxic and ecotoxic, with bioaccumulative and long-range transport properties.

Health effects

POP exposure may cause developmental defects, chronic illnesses, and death. Some are carcinogens per IARC, possibly including breast cancer. Many POPs are capable of endocrine disruption within the reproductive system, the central nervous system, or the immune system. People and animals are exposed to POPs mostly through their diet, occupationally, or while growing in the womb. For humans not exposed to POPs through accidental or occupational means, over 90% of exposure comes from animal product foods due to bioaccumulation in fat tissues and bioaccumulate through the food chain. In general, POP serum levels increase with age and tend to be higher in females than males.

Studies have investigated the correlation between low level exposure of POPs and various diseases. In order to assess disease risk due to POPs in a particular location, government agencies may produce a human health risk assessment which takes into account the pollutants' bioavailability and their dose-response relationships.

Endocrine disruption

The majority of POPs are known to disrupt normal functioning of the endocrine system. Low level exposure to POPs during critical developmental periods of fetus, newborn and child can have a lasting effect throughout its lifespan. A 2002 study summarizes data on endocrine disruption and health complications from exposure to POPs during critical developmental stages in an organism’s lifespan. The study aimed to answer the question whether or not chronic, low level exposure to POPs can have a health impact on the endocrine system and development of organisms from different species. The study found that exposure of POPs during a critical developmental time frame can produce a permanent changes in the organisms path of development. Exposure of POPs during non-critical developmental time frames may not lead to detectable diseases and health complications later in their life. In wildlife, the critical development time frames are in utero, in ovo, and during reproductive periods. In humans, the critical development timeframe is during fetal development.

Reproductive system

The same study in 2002 with evidence of a link from POPs to endocrine disruption also linked low dose exposure of POPs to reproductive health effects. The study stated that POP exposure can lead to negative health effects especially in the male reproductive system, such as decreased sperm quality and quantity, altered sex ratio and early puberty onset. For females exposed to POPs, altered reproductive tissues and pregnancy outcomes as well as endometriosis have been reported.

Gestational weight gain and newborn head circumference

A Greek study from 2014 investigated the link between maternal weight gain during pregnancy, their PCB-exposure level and PCB level in their newborn infants, their birth weight, gestational age, and head circumference. The lower the birth weight and head circumference of the infants was, the higher POP levels during prenatal development had been, but only if mothers had either excessive or inadequate weight gain during pregnancy. No correlation between POP exposure and gestational age was found. A 2013 case-control study conducted 2009 in Indian mothers and their offspring showed prenatal exposure of two types of organochlorine pesticides (HCH, DDT and DDE) impaired the growth of the fetus, reduced the birth weight, length, head circumference and chest circumference.

Additive and synergistic effects

Evaluation of the effects of POPs on health is very challenging in the laboratory setting. For example, for organisms exposed to a mixture of POPs, the effects are assumed to be additive. Mixtures of POPs can in principle produce synergistic effects. With synergistic effects, the toxicity of each compound is enhanced (or depressed) by the presence of other compounds in the mixture. When put together, the effects can far exceed the approximated additive effects of the POP compound mixture.

In urban areas and indoor environments

Traditionally it was thought that human exposure to POPs occurred primarily through food, however indoor pollution patterns that characterize certain POPs have challenged this notion. Recent studies of indoor dust and air have implicated indoor environments as a major sources for human exposure via inhalation and ingestion. Furthermore, significant indoor POP pollution must be a major route of human POP exposure, considering the modern trend in spending larger proportions of life indoor. Several studies have shown that indoor (air and dust) POP levels to exceed outdoor (air and soil) POP concentrations.

Control and removal in the environment

Current studies aimed at minimizing POPs in the environment are investigating their behavior in photo catalytic oxidation reactions. POPs that are found in humans and in aquatic environments the most are the main subjects of these experiments. Aromatic and aliphatic degradation products have been identified in these reactions. Photochemical degradation is negligible compared to photocatalytic degradation. A method of removal of POPs from marine environments that has been explored is adsorption. It occurs when an absorbable solute comes into contact with a solid with a porous surface structure. This technique was investigated by Mohamed Nageeb Rashed of Aswan University, Egypt. Current efforts are more focused on banning the use and production of POPs worldwide rather than removal of POPs.

Genetically modified plant

From Wikipedia, the free encyclopedia

 

Genetically modified plants have been engineered for scientific research, to create new colours in plants, deliver vaccines, and to create enhanced crops. Many plant cells are pluripotent, meaning that a single cell from a mature plant can be harvested and then under the right conditions form a new plant. This ability can be taken advantage of by genetic engineers; by selecting for cells that have been successfully transformed in an adult plant a new plant can then be grown that contains the transgene in every cell through a process known as tissue culture.

Research

Much of the advances in the field genetic engineering has come from experimentation with tobacco. Major advances in tissue culture and plant cellular mechanisms for a wide range of plants has originated from systems developed in tobacco. It was the first plant to be genetically engineered and is considered a model organism for not only genetic engineering, but a range of other fields. As such the transgenic tools and procedures are well established making it one of the easiest plants to transform. Another major model organism relevant to genetic engineering is Arabidopsis thaliana. Its small genome and short life cycle makes it easy to manipulate and it contains many homolgs to important crop species. It was the first plant sequenced, has abundant bioinformatic resources and can be transformed by simply dipping a flower in a transformed Agrobacterium solution.

In research, plants are engineered to help discover the functions of certain genes. The simplest way to do this is to remove the gene and see what phenotype develops compared to the wild type form. Any differences are possibly the result of the missing gene. Unlike mutagenisis, genetic engineering allows targeted removal without disrupting other genes in the organism. Some genes are only expressed in certain tissue, so reporter genes, like GUS, can be attached to the gene of interest allowing visualisation of the location. Other ways to test a gene is to alter it slightly and then return it to the plant and see if it still has the same effect on phenotype. Other strategies include attaching the gene to a strong promoter and see what happens when it is over expressed, forcing a gene to be expressed in a different location or at different developmental stages.

Ornamental

Suntory "blue" rose

 

Kenyans examining insect-resistant transgenic Bt corn

 

Some genetically modified plants are purely ornamental. They are modified for lower color, fragrance, flower shape and plant architecture. The first genetically modified ornamentals commercialised altered colour. Carnations were released in 1997, with the most popular genetically modified organism, a blue rose (actually lavender or mauve) created in 2004. The roses are sold in Japan, the United States, and Canada. Other genetically modified ornamentals include Chrysanthemum and Petunia. As well as increasing aesthetic value there are plans to develop ornamentals that use less water or are resistant to the cold, which would allow them to be grown outside their natural environments.

Conservation

It has been proposed to genetically modify some plant species threatened by extinction to be resistant invasive plants and diseases, such as the emerald ash borer in North American and the fungal disease, Ceratocystis platani, in European plane trees. The papaya ringspot virus (PRSV) devastated papaya trees in Hawaii in the twentieth century until transgenic papaya plants were given pathogen-derived resistance. However, genetic modification for conservation in plants remains mainly speculative. A unique concern is that a transgenic species may no longer bear enough resemblance to the original species to truly claim that the original species is being conserved. Instead, the transgenic species may be genetically different enough to be considered a new species, thus diminishing the conservation worth of genetic modification.

Crops

Genetically modified crops are genetically modified plants that are used in agriculture. The first crops provided are used for animal or human food and provide resistance to certain pests, diseases, environmental conditions, spoilage or chemical treatments (e.g. resistance to a herbicide). The second generation of crops aimed to improve the quality, often by altering the nutrient profile. Third generation genetically modified crops can be used for non-food purposes, including the production of pharmaceutical agents, biofuels, and other industrially useful goods, as well as for bioremediation.

There are three main aims to agricultural advancement; increased production, improved conditions for agricultural workers and sustainability. GM crops contribute by improving harvests through reducing insect pressure, increasing nutrient value and tolerating different abiotic stresses. Despite this potential, as of 2018, the commercialised crops are limited mostly to cash crops like cotton, soybean, maize and canola and the vast majority of the introduced traits provide either herbicide tolerance or insect resistance. Soybeans accounted for half of all genetically modified crops planted in 2014. Adoption by farmers has been rapid, between 1996 and 2013, the total surface area of land cultivated with GM crops increased by a factor of 100, from 17,000 square kilometers (4,200,000 acres) to 1,750,000 km² (432 million acres). Geographically though the spread has been very uneven, with strong growth in the Americas and parts of Asia and little in Europe and Africa. Its socioeconomic spread has been more even, with approximately 54% of worldwide GM crops grown in developing countries in 2013.

Food

The majority of GM crops have been modified to be resistant to selected herbicides, usually a glyphosate or glufosinate based one. Genetically modified crops engineered to resist herbicides are now more available than conventionally bred resistant varieties; in the USA 93% of soybeans and most of the GM maize grown is glyphosate tolerant. Most currently available genes used to engineer insect resistance come from the Bacillus thuringiensis bacterium. Most are in the form of delta endotoxin genes known as cry proteins, while a few use the genes that encode for vegetative insecticidal proteins. The only gene commercially used to provide insect protection that does not originate from B. thuringiensis is the Cowpea trypsin inhibitor (CpTI). CpTI was first approved for use cotton in 1999 and is currently undergoing trials in rice. Less than one percent of GM crops contained other traits, which include providing virus resistance, delaying senescence, modifying flower colour and altering the plants composition. Golden rice is the most well known GM crop that is aimed at increasing nutrient value. It has been engineered with three genes that biosynthesise beta-carotene, a precursor of vitamin A, in the edible parts of rice. It is intended to produce a fortified food to be grown and consumed in areas with a shortage of dietary vitamin A. a deficiency which each year is estimated to kill 670,000 children under the age of 5 and cause an additional 500,000 cases of irreversible childhood blindness. The original golden rice produced 1.6μg/g of the carotenoids, with further development increasing this 23 times. In 2018 it gained its first approvals for use as food.

Biopharmaceuticals

Plants and plant cells have been genetically engineered for production of biopharmaceuticals in bioreactors, a process known as Pharming. Work has been done with duckweed Lemna minor, the algae Chlamydomonas reinhardtii and the moss Physcomitrella patens. Biopharmaceuticals produced include cytokines, hormones, antibodies, enzymes and vaccines, most of which are accumulated in the plant seeds. Many drugs also contain natural plant ingredients and the pathways that lead to their production have been genetically altered or transferred to other plant species to produce greater volume and better products. Other options for bioreactors are biopolymers and biofuels. Unlike bacteria, plants can modify the proteins post-translationally, allowing them to make more complex molecules.They also pose less risk of being contaminated. Therapeutics have been cultured in transgenic carrot and tobacco cells, including a drug treatment for Gaucher's disease.

Vaccines

Vaccine production and storage has great potential in transgenic plants. Vaccines are expensive to produce, transport and administer, so having a system that could produce them locally would allow greater access to poorer and developing areas. As well as purifying vaccines expressed in plants it is also possible to produce edible vaccines in plants. Edible vaccines stimulate the immune system when ingested to protect against certain diseases. Being stored in plants reduces the long-term cost as they can be disseminated without the need for cold storage, don't need to be purified and have long term stability. Also being housed within plant cells provides some protection from the gut acids upon digestion. However the cost of developing, regulating and containing transgenic plants is high, leading to most current plant-based vaccine development being applied to veterinary medicine, where the controls are not as strict.

Transgene

From Wikipedia, the free encyclopedia

 

A transgene is a gene or genetic material that has been transferred naturally, or by any of a number of genetic engineering techniques from one organism to another. The introduction of a transgene (called "transgenesis") has the potential to change the phenotype of an organism. 

In its most precise usage, the term transgene describes a segment of DNA containing a gene sequence that has been isolated from one organism and is introduced into a different organism. This non-native segment of DNA may either retain the ability to produce RNA or protein in the transgenic organism or alter the normal function of the transgenic organism's genetic code. In general, the DNA is incorporated into the organism's germ line. For example, in higher vertebrates this can be accomplished by injecting the foreign DNA into the nucleus of a fertilized ovum. This technique is routinely used to introduce human disease genes or other genes of interest into strains of laboratory mice to study the function or pathology involved with that particular gene.

The construction of a transgene requires the assembly of a few main parts. The transgene must contain a promoter, which is a regulatory sequence that will determine where and when the transgene is active, an exon, a protein coding sequence (usually derived from the cDNA for the protein of interest), and a stop sequence. These are typically combined in a bacterial plasmid and the coding sequences are typically chosen from transgenes with previously known functions.

Transgenic or genetically modified organisms, be they bacteria, viruses or fungi, serve all kinds of research purposes. Transgenic plants, insects, fish and mammals have been bred. Transgenic plants such as corn and soybean have replaced wild strains in agriculture in some countries (e.g. the United States). Transgene escape has been documented for GMO crops since 2001 with persistence and invasiveness. Transgenetic organisms pose ethical questions and may cause biosafety problems.

History

The idea of shaping an organism to fit a specific need isn't a new science; selective breeding of animals and plants started before recorded history. However, until the late 1900s farmers and scientist could breed new strains of a plant or organism only from closely related species, because the DNA had to be compatible for offspring to be able to reproduce another generation.

In the 1970 and 1980s, scientists passed this hurdle by inventing procedures for combining the DNA of two vastly different species with genetic engineering. The organisms produced by these procedures were termed transgenic. Transgenesis is the same as gene therapy in the sense that they both transform cells for a specific purpose. However, they are completely different in their purposes, as gene therapy aims to cure a defect in cells, and transgenesis seeks to produce a genetically modified organism by incorporating the specific transgene into every cell and changing the genome. Transgenesis will therefore change the germ cells, not only the somatic cells, in order to ensure that the transgenes are passed down to the offspring when the organisms reproduce. Transgenes alter the genome by blocking the function of a host gene; they can either replace the host gene with one that codes for a different protein, or introduce an additional gene.

The first transgenic organism was created in 1974 when Annie Chang and Stanley Cohen expressed Staphylococcus aureus genes in Escherichia coli. In 1978, yeast cells were the first eukaryotic organisms to undergo gene transfer. Mouse cells were first transformed in 1979, followed by mouse embryos in 1980. Most of the very first transmutations were performed by microinjection of DNA directly into cells. Scientists were able to develop other methods to perform the transformations, such as incorporating transgenes into retroviruses and then infecting cells, using electroinfusion which takes advantage of an electric current to pass foreign DNA through the cell wall, biolistics which is the procedure of shooting DNA bullets into cells, and also delivering DNA into the egg that has just been fertilized.

The first transgenic animals were only intended for genetic research to study the specific function of a gene, and by 2003, thousands of genes had been studied.

Use in plants

A variety of transgenic plants have been designed for agriculture to produce genetically modified crops, such as corn, soybean, rapeseed oil, cotton, rice and more. As of 2012, these GMO crops were planted on 170 million hectares globally.

Golden rice

One example of a transgenic plant species is golden rice. In 1997,^{[citation needed]} five million children developed xerophthalmia, a medical condition caused by vitamin A deficiency, in Southeast Asia alone. Of those children, a quarter million went blind. To combat this, scientists used biolistics to insert the daffodil phytoene synthase gene into Asia indigenous rice cultivars. The daffodil insertion increased the production of ß-carotene. The product was a transgenic rice species rich in vitamin A, called golden rice. Little is known about the impact of golden rice on xerophthalmia because anti-GMO campaigns have prevented the full commercial release of golden rice into agricultural systems in need.

Transgene escape

The escape of genetically-engineered plant genes via hybridization with wild relatives was first discussed and examined in Mexico and Europe in the mid-1990s. There is agreement that escape of transgenes is inevitable, even "some proof that it is happening". Up until 2008 there were few documented cases.

Corn

Corn sampled in 2000 from the Sierra Juarez, Oaxaca, Mexico contained a transgenic 35S promoter, while a large sample taken by a different method from the same region in 2003 and 2004 did not. A sample from another region from 2002 also did not, but directed samples taken in 2004 did, suggesting transgene persistence or re-introduction. A 2009 study found recombinant proteins in 3.1% and 1.8% of samples, most commonly in southeast Mexico. Seed and grain import from the United States could explain the frequency and distribution of transgenes in west-central Mexico, but not in the southeast. Also, 5.0% of corn seed lots in Mexican corn stocks expressed recombinant proteins despite the moratorium on GM crops.

Cotton

In 2011, transgenic cotton was found in Mexico among wild cotton, after 15 years of GMO cotton cultivation.

Rapeseed (canola)

Transgenic rapeseed Brassicus napus, hybridized with a native Japanese species Brassica rapa, was found in Japan in 2011 after they had been identified 2006 in Québec, Canada. They were persistent over a 6-year study period, without herbicide selection pressure and despite hybridization with the wild form. This was the first report of the introgression—the stable incorporation of genes from one gene pool into another—of an herbicide resistance transgene from Brassica napus into the wild form gene pool.

Creeping bentgrass

Transgenic creeping bentgrass, engineered to be glyphosate-tolerant as "one of the first wind-pollinated, perennial, and highly outcrossing transgenic crops", was planted in 2003 as part of a large (about 160 ha) field trial in central Oregon near Madras, Oregon. In 2004, its pollen was found to have reached wild growing bentgrass populations up to 14 kilometres away. Cross-pollinating Agrostis gigantea was even found at a distance of 21 kilometres. The grower, Scotts Company could not remove all genetically engineered plants, and in 2007, the U.S. Department of Agriculture fined Scotts $500,000 for noncompliance with regulations.

Risk assessment

The long-term monitoring and controlling of a particular transgene has been shown not to be feasible. The European Food Safety Authority published a guidance for risk assessment in 2010.

Use in mice

Genetically modified mice are the most common animal model for transgenic research. Transgenic mice are currently being used to study a variety of diseases including cancer, obesity, heart disease, arthritis, anxiety, and Parkinson’s disease. The two most common types of genetically modified mice are knockout mice and oncomice. Knockout mice are a type of mouse model that uses transgenic insertion to disrupt an existing gene’s expression. In order to create knockout mice, a transgene with the desired sequence is inserted into an isolated mouse blastocyst using electroporation. Then, homologous recombination occurs naturally within some cells, replacing the gene of interest with the designed transgene. Through this process, researchers were able to demonstrate that a transgene can be integrated into the genome of an animal, serve a specific function within the cell, and be passed down to future generations.

Oncomice are another genetically modified mouse species created by inserting transgenes that increase the animal’s vulnerability to cancer. Cancer researchers utilize oncomice to study the profiles of different cancers in order to apply this knowledge to human studies.

Use in Drosophila

Multiple studies have been conducted concerning transgenesis in Drosophila melanogaster, the fruit fly. This organism has been a helpful genetic model for over 100 years, due to its well-understood developmental pattern. The transfer of transgenes into the Drosophila genome has been performed using various techniques, including P element, Cre-loxP, and ΦC31 insertion. The most practiced method used thus far to insert transgenes into the Drosophila genome utilizes P elements. The transposable P elements, also known as transposons, are segments of bacterial DNA that are translocated into the genome, without the presence of a complementary sequence in the host’s genome. P elements are administered in pairs of two, which flank the DNA insertion region of interest. Additionally, P elements often consist of two plasmid components, one known as the P element transposase and the other, the P transposon backbone. The transposase plasmid portion drives the transposition of the P transposon backbone, containing the transgene of interest and often a marker, between the two terminal sites of the transposon. Success of this insertion results in the nonreversible addition of the transgene of interest into the genome. While this method has been proven effective, the insertion sites of the P elements are often uncontrollable, resulting in an unfavorable, random insertion of the transgene into the Drosophila genome.

To improve the location and precision of the transgenic process, an enzyme known as Cre has been introduced. Cre has proven to be a key element in a process known as recombination-mediated cassette exchange (RMCE). While it has shown to have a lower efficiency of transgenic transformation than the P element transposases, Cre greatly lessens the labor-intensive abundance of balancing random P insertions. Cre aids in the targeted transgenesis of the DNA gene segment of interest, as it supports the mapping of the transgene insertion sites, known as loxP sites. These sites, unlike P elements, can be specifically inserted to flank a chromosomal segment of interest, aiding in targeted transgenesis. The Cre transposase is important in the catalytic cleavage of the base pairs present at the carefully positioned loxP sites, permitting more specific insertions of the transgenic donor plasmid of interest.

To overcome the limitations and low yields that transposon-mediated and Cre-loxP transformation methods produce, the bacteriophage ΦC31 has recently been utilized. Recent breakthrough studies involve the microinjection of the bacteriophage ΦC31 integrase, which shows improved transgene insertion of large DNA fragments that are unable to be transposed by P elements alone. This method involves the recombination between an attachment (attP) site in the phage and an attachment site in the bacterial host genome (attB). Compared to usual P element transgene insertion methods, ΦC31 integrates the entire transgene vector, including bacterial sequences and antibiotic resistance genes. Unfortunately, the presence of these additional insertions has been found to affect the level and reproducibility of transgene expression.

Future potential

The study of application of transgenes is a rapidly growing area of molecular biology. In fact, it is predicted that in the next two decades, 300 000 lines of transgenic mice will be generated. Researchers have identified many applications for transgenes, particularly in the medical field. Scientists are focusing on the use of transgenes to study the function of the human genome in order to better understand disease, adapting animal organs for transplantation into humans, and the production of pharmaceutical products such as insulin, growth hormone, and blood anti-clotting factors from the milk of transgenic cows.

There are currently five thousand known genetic diseases, and the potential to treat these diseases using transgenic animals is, perhaps, one of the most promising applications of transgenes. There is a potential to use human gene therapy to replace a mutated gene with an unmutated copy of a transgene in order to treat the genetic disorder. This can be done through the use of Cre-Lox or knockout. Moreover, genetic disorders are being studied through the use of transgenic mice, pigs, rabbits, and rats. More recently, scientists have also begun using transgenic goats to study genetic disorders related to fertility.

Transgenes may soon be used for xenotransplantation from pig organs. Through the study of xeno-organ rejection, it was found that an acute rejection of the transplanted organ occurs upon the organ's contact with blood from the recipient due to the recognition of foreign antibodies on endothelial cells of the transplanted organ. Scientists have identified the antigen in pigs that causes this reaction, and therefore are able to transplant the organ without immediate rejection by removal of the antigen. However, the antigen begins to be expressed later on, and rejection occurs. Therefore, further research is being conducted.

Transgenes are being used by manufactures to produce goods such as milk with high levels of proteins, silk from the milk of goats, and microorganisms that are capable of producing proteins that contain enzymes that increase the rate of industrial reactions. Agricultural applications aim to selectively breed animals for particular traits and animals that are resistant to diseases.

Ethical controversy

Transgene use in humans is currently fraught with issues. Transformation of genes into human cells has not been perfected yet. The most famous example of this involved certain patients developing T-cell leukemia after being treated for X-linked severe combined immunodeficiency (X-SCID). This was attributed to the close proximity of the inserted gene to the LMO2 promoter, which controls the transcription of the LMO2 proto-oncogene. In common with most forms of genetic engineering, the use of transgenes for purposes other than to correct life-threatening genetic abnormalities is a major bioethical issue.