Researchers work to save endangered New England cottontail

Scientists with the NH Agricultural Experiment Station are working to restore New Hampshire and Maine’s only native rabbit after new research based on genetic monitoring has found that in the last decade, cottontail populations in northern New England have become more isolated and seen a 50 percent contraction of their range.The endangered New England cottontail is now is at risk of becoming extinct in the region, according to NH Agricultural Experiment Station researchers at the University of New Hampshire College of Life Sciences and Agriculture who believe that restoring habitats is the key to saving the species.”The New England cottontail is a species of great conservation concern in the Northeast. This is our only native rabbit and is an integral component of the native New England wildlife. Maintaining biodiversity gives resilience to our landscape and ecosystems,” said NHAES researcher Adrienne Kovach, research associate professor of natural resources at UNH.New England cottontails have been declining for decades. However, NHAES researchers have found that in the last decade, the New England cottontail population in New Hampshire and Maine has contracted by 50 percent; a decade ago, cottontails were found as far north as Cumberland, Maine.The majority of research on New England cottontails has come out of UNH, much of it under the leadership of John Litvaitis, professor of wildlife ecology, who has studied the New England cottontail for three decades. Kovach’s research expands on this knowledge by using DNA analysis to provide new information on the cottontail’s status, distribution, genetic diversity, and dispersal ecology.The greatest threat and cause of the decline of the New England cottontail is the reduction and fragmentation of their habitat, Kovach said. Fragmentation of habitats occurs when the cottontail’s habitat is reduced or eliminated due to the maturing of forests or land development. Habitats also can become fragmented by roads or natural landscape features, such as bodies of water.”Cottontails require thicketed habitats, which progress from old fields to young forests. Once you have a more mature forest, the cottontail habitat is reduced. A lot of other species rely on these thicket habitats, including bobcats, birds, and reptiles. Many thicket-dependent species are on decline, and the New England cottontail is a representative species for this kind of habitat and its conservation,” Kovach said.Kovach explained that for cottontail and most animal populations to be healthy and grow, it is important for adult animals to leave the place where they were born and relocate to a new habitat, which is known as dispersal. …

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Epigenetic changes can drive cancer, study shows

Cancer has long been thought to be primarily a genetic disease, but in recent decades scientists have come to believe that epigenetic changes — which don’t change the DNA sequence but how it is ‘read’ — also play a role in cancer. In particular DNA methylation, the addition of a methyl group (or molecule), is an epigenetic switch that can stably turn off genes, suggesting the potential to cause cancer just as a genetic mutation can. Until now, however, direct evidence that DNA methylation drives cancer formation was lacking.Researchers at the USDA/ARS Children’s Nutrition Research Center at Baylor College of Medicine and Texas Children’s Hospital have now created a mouse model providing the first in vivo evidence that epigenetic alterations alone can cause cancer. Their report appears in the Journal of Clinical Investigation.”We knew that epigenetic changes are associated with cancer, but didn’t know whether these were a cause or consequence of cancer. Developing this new approach for ‘epigenetic engineering’ allowed us to test whether DNA methylation changes alone can drive cancer,” said Dr. Lanlan Shen, associate professor of pediatrics at Baylor and senior author of the study.Shen and colleagues focused on p16, a gene that normally functions to prevent cancer but is commonly methylated in a broad spectrum of human cancers. They devised an approach to engineer DNA methylation specifically to the mouse p16 regulatory region (promoter). As intended, the engineered p16 promoter acted as a ‘methylation magnet’. As the mice reached adulthood, gradually increasing p16 methylation led to a higher incidence of spontaneous cancers, and reduced survival.”This is not only the first in vivo evidence that epigenetic alteration alone can cause cancer,” said Shen. “This also has profound implications for future studies, because epigenetic changes are potentially reversible. …

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Novel drug cocktail may improve clinical treatment for pancreatic cancer

Pancreatic cancer is the fourth leading cause of cancer deaths in the U.S. and has the lowest overall survival rate of all major cancers (~6%). With current treatment options being met with limited success it is anticipated that pancreatic cancer will move up to the second leading cause of cancer deaths by as early as 2015. Surgical removal of the tumor presents the best chance of survival, however only 15% of patients are eligible due to the late stage of diagnosis common with this disease. With very limited improvements in patient outcome over the last two decades there remains an enormous need for new therapies and treatment options.David Durrant, a Ph.D. student in the laboratory of Dr. Rakesh Kukreja from the Pauley Heart Center at Virginia Commonwealth University’s School of Medicine, is studying a novel combination therapy for the treatment of pancreatic cancer. The traditional chemotherapy drug, doxorubicin (DOX), has long been used in the treatment of several cancers. However, patients commonly acquire resistance to DOX because of increased activation of specific survival proteins or through increased expression of drug transporters which reduce cellular levels of the drug. This is especially true for pancreatic cancer, which does not respond to multiple treatment strategies, including those that contain DOX. …

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Bamboo-loving giant pandas also have a sweet tooth

Despite the popular conception of giant pandas as continually chomping on bamboo to fulfill a voracious appetite for this reedy grass, new research from the Monell Center reveals that this highly endangered species also has a sweet tooth. A combination of behavioral and molecular genetic studies demonstrated that the giant panda both possesses functional sweet taste receptors and also shows a strong preference for some natural sweeteners, including fructose and sucrose.”Examining an animal’s taste DNA can give us clues to their past diet, knowledge that is particularly important for endangered animals in captivity,” said study author Danielle Reed, PhD, a behavioral geneticist at Monell. “This process can provide information on approaches to keep such animals healthy.”The Monell researchers studied the giant pandas as part of a long-term project focused on understanding how taste preferences and diet selection are shaped by taste receptor genes.One previous study found that cats, which must eat meat in order to survive, had lost the ability to taste sweets due to a genetic defect that deactivates the sweet taste receptor.Although giant pandas and cats belong to the same taxonomic order, Carnivora, the giant pandas have a very different diet, as they feed almost exclusively on bamboo.Noting that bamboo is a grass-like plant that contains very small amounts of sugars and does not taste sweet to humans, the researchers wondered whether giant pandas, like their Carnivora cat relatives, had lost sweet taste perception. An alternate possibility was that the panda maintain a functional sweet taste receptor, similar to other plant-eating mammals.In this study, published online in the open-access journal PLOS ONE, eight giant pandas between three and 22 years of age were studied at the Shaanxi Wild Animal Rescue and Research Center in China over a six-month period.For taste preference tests, the animals were given two bowls of liquid and allowed to drink for five minutes. One bowl contained water and the other contained a solution of water mixed with one of six different natural sugars: fructose, galactose, glucose, lactose, maltose, and sucrose. Each sugar was presented at a low and a high concentration.The pandas preferred all the sugar solutions to plain water. This was especially evident for fructose and sucrose, as the animals avidly consumed a full liter of these sugary solutions within the respective five-minute test periods.”Pandas love sugar,” said Reed. “Our results can explain why Bao Bao, the six-month-old giant panda cub at the National Zoo in Washington, DC, is apparently relishing sweet potato as a first food during weaning.”Another series of preference tests explored the giant panda’s response to five artificial sweeteners. There was little to no preference for most artificial sweetener solutions, suggesting that giant pandas cannot taste or do not strongly perceive these compounds as being sweet.Parallel cell-based studies showed a relationship between the pandas’ behavior and how panda taste receptor cells respond to sweeteners in vitro. Using DNA collected from the giant pandas during routine health examinations, genes that code for the panda sweet taste receptor were isolated and then inserted into human host cells grown in culture. …

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DNA from fossils reveal origin of Norwegian lemmings

A new ancient DNA study shows that the Norwegian lemming has a unique history. In contrast to other mammals in Fennoscandia, the Norwegian lemming may have survived the last Ice Age in the far north, sealed off from the rest of the world by gigantic ice sheets. This conclusion is drawn by an international team of researchers in an article published this week in the journal Molecular Ecology.The Norwegian lemming is an iconic small mammal that is unique to the Fennoscandian mountain tundra. Known for its dramatic fluctuations in population size, it is a keystone species in the mountain tundra ecosystem. But its origin has until now remained somewhat of a mystery.Twenty thousand years ago, Fennoscandia was covered by a thick ice sheet. Animals and plants in the region are therefore thought to originate from populations that lived to the south or east of the ice sheet, and colonised Fennoscandia as the ice melted. With this in mind, and international team of scientists, led by researchers at the Swedish Museum of Natural History, set out to investigate from where the Norwegian lemming originated at the end of the last Ice Age. To do this, the researchers retrieved and analysed ancient DNA from lemming populations that surrounded the ice sheet during the last Ice Age.- “We found that even though the populations surrounding the ice sheet were closely related to modern day lemmings, none of them were similar enough to be the direct ancestor of the Norwegian lemming,” says Love Daln, Associate Professor at the Swedish Museum of Natural History.After eliminating these populations as potential sources, the researchers concluded that the only remaining explanation was that the Norwegian lemming originates from a population that survived the last glaciation somewhere locally in Fennoscandia. The exact location where the Norwegian lemming could have survived the last glaciation is not clear, but likely places include coastal areas or mountain plateaus sticking out from the ice sheet.”The Norwegian lemming is the only endemic mammal in Fennoscandia, and its unusual origin is probably the reason why,” says Vendela Lagerholm, lead author on the study.Story Source:The above story is based on materials provided by Expertsvar. Note: Materials may be edited for content and length.

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Braking system for immune responses

For the first time, researchers have identified a receptor on human cells that specifically recognizes crystals. It is found on immune cells and binds uric acid crystals, which trigger gout but also control immune responses. The team, led by researchers from Technische Universitt Mnchen (TUM)’s Klinikum rechts der Isar hospital have published their findings in the Immunity journal.The surface of immune system cells is home to a number of receptors which are able to detect pathogens. As soon as these receptors are activated, inflammation occurs and the body’s defense mechanisms kick in. Immune cells also have receptors that regulate or even suppress immunological responses to prevent damage to individual cells.There are other immune receptors that recognize endogenous substances that are released when tissue damage or cell death occurs. As such, the organism can defend itself even in cases where the damage caused by the pathogen, but not the pathogen itself, is detected.With the discovery of the surface molecule Clec12a from the family of C-type lectin receptors, the team led by Prof. Jrgen Ruland of Klinikum rechts der Isar have found the first known immune receptor for uric acid crystals. Uric acid is a break-down product of nucleic acids like DNA in response to cell damage. Whenever a large number of cells die, for example when a tumor is being medically treated or during an infection, the uric acid becomes more concentrated and the molecules crystallize.Immune responses have to be regulatedUric acid crystals also form when tissue is damaged and they boost the immune response. However, Clec12a limits the immune response instead of increasing it. …

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Stirring the simmering ‘designer baby’ pot

From genetic and genomic testing to new techniques in human assisted reproduction, various technologies are providing parents with more of a say about the children they have and “stirring the pot of ‘designer baby’ concerns,” writes Thomas H. Murray, President Emeritus of The Hastings Center, in a commentary in Science.Murray calls for a national conversation about how much discretion would-be parents should have. “Preventing a lethal disease is one thing; choosing the traits we desire is quite another,” he writes.He discusses public hearings two weeks ago by the United States Food and Drug Administration to consider whether to permit human testing of a new method of assisted reproduction — mitochondrial manipulation — that would prevent the transmission of certain rare diseases and perhaps address some causes of female infertility. At issue is the safety of the technology, as well as its ethical implications.Mitochondrial manipulation creates an embryo with the nuclear DNA from the prospective mother and father (which contains most of the genetic material) and the mitochondrial DNA (containing 37 genes) from a donor without mitochondrial defects. Among the ethical concerns is that daughters produced by this procedure could pass down the mitochondrial DNA to their children. “Up to now, the United States has not allowed such genetic changes across generations,” Murray writes.He says that the FDA’s discussion is the latest development that “tapped into a simmering controversy over what it means to have a child in an era of increasing convergence among genetic, genomic, and reproductive technologies.” Those technologies include preimplantation genetic diagnosis (genetic analysis of embryos before implantation via in vitro fertilization) and prenatal screening to detect health problems in the fetus, including the prospects of a blood test of a pregnant woman to screen fetal DNA in her blood.”Of all the possible choices prospective parents might make, sex selection for non-medical purposes has prompted the strongest policy response, “Murray writes. “It is prohibited in at least 36 countries, but not in the United States.” He notes that “conflicts over the legal and moral status of embryos and fetuses have discouraged American legislators from proposing sensible regulations, lest they be drawn in to the abortion debate.”The absence of federal legislation has left the regulation of sex selection up to professional societies. But they have different guidelines, reflecting “clashing ethical frameworks for thinking about parenthood in the genomic era.”Murray calls for a national conversation about current and emerging technologies shaping the choices that parents have, beginning with an examination by the U.S. Presidential Commission for the Study of Bioethical Issues. “It will not be easy to avoid the quicksand of the abortion debate,” he writes, “but it would be a great public service to provide a sober assessment of the choices that would-be parents increasingly face, and to encourage a respectful dialogue about the meaning of parenthood and the worth of a child so that parents and children can flourish together.”Story Source:The above story is based on materials provided by The Hastings Center. …

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Link between missing DNA, birth defects confirmed

In 2010, scientists in Italy reported that a woman and her daughter showed a puzzling array of disabilities, including epilepsy and cleft palate. The mother had previously lost a 15-day-old son to respiratory failure, and the research team noted that the mother and daughter were missing a large chunk of DNA on their X chromosome. But the researchers were unable to definitively show that the problems were tied to that genetic deletion.Now a team from the University of Pennsylvania and The Children’s Hospital of Philadelphia has confirmed that those patients’ ailments resulted from the genetic anomaly. Creating mice that lacked the same region of DNA, the Penn and CHOP researchers showed that these animals suffered the same problems that afflicted the mother, daughter and son — cleft palate, epilepsy and respiratory difficulties, a condition called human Xq22.1 deletion syndrome. And, by clarifying the syndrome’s genetic basis, the researchers have laid the foundation for identifying the underlying molecular mechanism of these troubles and potentially treating them at their biological root.”This study has demonstrated that deleting this region in mice causes them to respond like humans with the same deletion,” said P. Jeremy Wang, senior author on the study and professor in the Penn School of Veterinary Medicine’s Department of Animal Biology. “Now that we have a mouse model, we can dissect and try to genetically pinpoint which genes are responsible.”Wang co-led the study with his postdoctoral researcher Jian Zhou. Additional coauthors included Penn Vet’s N. Adrian Leu and CHOP’s Ethan Goldberg, Lei Zhou and Douglas Coulter.The study appears in the journal Human Molecular Genetics.To investigate the effects of missing this portion of DNA, more than 1 million base pairs long, the Penn team crossed existing mice that had particular deletions in their DNA to create a mouse that lacked the entire stretch that the human patients were missing. They quickly observed that all male mice died at birth due to respiratory failure. …

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After the saffron spice DNA

Researchers at the UPM and the University of Tor Vegata of Roma have proposed a new technique that allows the detection of adulterated saffron spice.A collaborative research between Universidad Politcnica de Madrid (UPM) and the University of de Tor Vegata has studied the DNA of the saffron spice through the analysis of its genetic code. The use of this technique has clarified aspects of the genetic variability of this species, which has allowed the design of a system that can discriminate and certify the authenticity of saffron spice to avoid cases of adulteration.Saffron (Crocus sativus L.) is sterile plant species of bulbous herb with purple colored flowers whose origin is still unknown. The dry stigmas of the Crocus sativus L. are commonly known as saffron, which is a cultivated plant with a gastronomical reputation that dates back from ancient times. In fact, it is only vegetatively propagated by bulbs due to its incapacity of producing fertile pollen and for this reason, seeds.The plant blooms just once a year and the harvest of stigmas are made by manual selection in a very short amount of time. For this reason, saffron spice is the most expensive spice in the world.This research has used a DNA barcode technique to define different species and saffron spice crop fields. For this reason, researchers have analyzed samples of various species of Crocus, both Italians and Spanish ones, including species from different origins of cultivated saffron spice. As a result of this study, researchers found some aspects of the phylogeny of this gender, particularly the genetic drift of Crocus sativus.Numerous morphological studies support the theory that saffron spice was originated from evolution or hybridization of other saffron species, especially C. thomasii, C. hadriaticus and C. …

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Mutations in leukemia gene linked to new childhood growth disorder

Mutations in a gene associated with leukemia cause a newly described condition that affects growth and intellectual development in children, new research reports.A study led by scientists at The Institute of Cancer Research, London, identified mutations in the DNA methyltransferase gene, DNMT3A, in 13 children.All the children were taller than usual for their age, shared similar facial features and had intellectual disabilities. The mutations were not present in their parents, nor in 1,000 controls from the UK population.The new condition has been called ‘DNMT3A overgrowth syndrome’.The research is published today in the journal Nature Genetics and is a part of the Childhood Overgrowth Study, which is funded by the Wellcome Trust, and aims to identify causes of developmental disorders that include increased growth in childhood. The DNMT3A gene is crucial for development because it adds the ‘methylation’ marks to DNA that determine where and when genes are active.Intriguingly, DNMT3A mutations are already known to occur in certain types of leukemia. The mutations that occur in leukemia are different from those in DNMT3A overgrowth syndrome and there is no evidence that children with DNMT3A mutations are at increased risk of cancer.Researchers at The Institute of Cancer Research (ICR), with colleagues at St George’s, University of London, The Royal Marsden NHS Foundation Trust, and genetics centres across Europe and the US, identified the mutations after analysing the genomes of 152 children with overgrowth disorders and their parents.Study leader Professor Nazneen Rahman, Head of Genetics and Epidemiology at The Institute of Cancer Research, London, and Head of Cancer Genetics at The Royal Marsden NHS Foundation Trust, said: “Our findings establish DNMT3A mutations as the cause of a novel human developmental disorder and add to the growing list of genes that appear to have dual, but distinct, roles in human growth disorders and leukemias.”The new discovery is of immediate value to the families in providing a reason for why their child has had problems. Moreover, because the mutations have arisen in the child and have not been inherited from either parent, the risk of another child in the family being similarly affected is very low. This is very welcome news for families.Study co-leader Dr Katrina Tatton-Brown, Clinical Researcher at The Institute of Cancer Research, London, and Consultant Geneticist at St George’s, University of London, said: “Having a diagnosis can make a real difference to families — I recently gave the result back to one of the families in which we identified a DNMT3A mutation and they greatly appreciated having a reason for their daughter’s condition after many years of uncertainty.”Story Source:The above story is based on materials provided by Institute of Cancer Research. Note: Materials may be edited for content and length.

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It slices, it dices, and it protects the body from harm: 3-D structure of enzyme that helps defend against bacteria

An essential weapon in the body’s fight against infection has come into sharper view. Researchers at Princeton University have discovered the 3D structure of an enzyme that cuts to ribbons the genetic material of viruses and helps defend against bacteria.The discovery of the structure of this enzyme, a first-responder in the body’s “innate immune system,” could enable new strategies for fighting infectious agents and possibly prostate cancer and obesity. The work was published Feb. 27 in the journal Science.Until now, the research community has lacked a structural model of the human form of this enzyme, known as RNase L, said Alexei Korennykh, an assistant professor of molecular biology and leader of the team that made the discovery.”Now that we have the human RNase L structure, we can begin to understand the effects of carcinogenic mutations in the RNase L gene. For example, families with hereditary prostate cancers often carry genetic mutations in the region, or locus, encoding RNase L,” Korennykh said. The connection is so strong that the RNase L locus also goes by the name “hereditary prostate cancer 1.” The newly found structure reveals the positions of these mutations and explains why some of these mutations could be detrimental, perhaps leading to cancer, Korennykh said. RNase L is also essential for insulin function and has been implicated in obesity.The Princeton team’s work has also led to new insights on the enzyme’s function.The enzyme is an important player in the innate immune system, a rapid and broad response to invaders that includes the production of a molecule called interferon. Interferon relays distress signals from infected cells to neighboring healthy cells, thereby activating RNase L to turn on its ability to slice through RNA, a type of genetic material that is similar to DNA. The result is new cells armed for destruction of the foreign RNA.The 3D structure uncovered by Korennykh and his team consists of two nearly identical subunits called protomers. The researchers found that one protomer finds and attaches to the RNA, while the other protomer snips it.The initial protomer latches onto one of the four “letters” that make up the RNA code, in particular, the “U,” which stands for a component of RNA called uridine. …

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Substance Found in Turmeric Packs Powerful Punch against Mesothelioma

Curcumin,a naturally occurring polyphenol in turmeric, is being studied for its possible application in the treatment and prevention of mesothelioma. Turmeric has long been believed to have anticancer properties due to its antioxidant andanti-inflammatory properties.Researchers at the University of Vermont found that curcumin caused pyroptotic cell death in both mouse and human in vitro models with malignant mesothelioma cell lines. Cell death was induced by the activation of the enzyme caspase-1, and the increased release of high-mobility group box 1 (HMGB1), a nuclear protein responsible for organizing DNA and regulating transcription.Researchers blocked production of pro-inflammatory cytokines IL-1β and IL-18 by inhibiting the NF-κB pathway, a protein responsible for cytokine production and cell survival which has been linked to cancer, …

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Trigger found for most common form of intellectual disability, autism

A new study led by Weill Cornell Medical College scientists shows that the most common genetic form of mental retardation and autism occurs because of a mechanism that shuts off the gene associated with the disease. The findings, published today in Science, also show that a drug that blocks this silencing mechanism can prevent fragile X syndrome — suggesting similar therapy is possible for 20 other diseases that range from mental retardation to multisystem failure.Fragile X syndrome occurs mostly in boys, causing intellectual disability as well as telltale physical, behavioral and emotional traits. While researchers have known for more than two decades that the culprit behind the disease is an unusual mutation characterized by the excess repetition of a particular segment of the genetic code, they weren’t sure why the presence of a large number of these repetitions — 200 or more — sets the disease process in motion.Using stem cells from donated human embryos that tested positive for fragile X syndrome, the scientists discovered that early on in fetal development, messenger RNA — a template for protein production — begins sticking itself onto the fragile X syndrome gene’s DNA. This binding appears to gum up the gene, making it inactive and unable to produce a protein crucial to the transmission of signals between brain cells.”Until 11 weeks of gestation, the fragile X syndrome gene is active — it produces its messenger RNA and protein normally. Then, all of a sudden it turns off, and stays off for the rest of the patient’s lifetime, causing fragile X syndrome. But scientists have not understood why this gene gets shut off,” says senior author Dr. Samie Jaffrey, a professor of pharmacology at Weill Cornell Medical College. “We discovered that the messenger RNA can jam up one strand of the gene’s DNA, shutting down the gene — which was not known before.”This is new biology — an interaction between the RNA and the DNA of the fragile X syndrome gene causes disease,” Dr. Jaffrey says. “We are coming to understand that RNAs are powerful molecules that can regulate gene expression, but this mechanism is completely novel — and very exciting.”The malfunction occurs suddenly — before the end of the first trimester in humans and after 50 days in laboratory embryonic stem cells. …

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Interactive map of human genetic history revealed

A global map detailing the genetic histories of 95 different populations across the world, showing likely genetic impacts of European colonialism, the Arab slave trade, the Mongol Empire and European traders near the Silk Road mixing with people in China, has been revealed for the first time.The interactive map, produced by researchers from Oxford University and UCL (University College London), details the histories of genetic mixing between each of the 95 populations across Europe, Africa, Asia and South America spanning the last four millennia.It can be accessed at: http://admixturemap.paintmychromosomes.com/The study, published this week in Science, simultaneously identifies, dates and characterises genetic mixing between populations. To do this, the researchers developed sophisticated statistical methods to analyse the DNA of 1490 individuals in 95 populations around the world. The work was chiefly funded by the Wellcome Trust and Royal Society.’DNA really has the power to tell stories and uncover details of humanity’s past.’ said Dr Simon Myers of Oxford University’s Department of Statistics and Wellcome Trust Centre for Human Genetics, co-senior author of the study.’Because our approach uses only genetic data, it provides information independent from other sources. Many of our genetic observations match historical events, and we also see evidence of previously unrecorded genetic mixing. For example, the DNA of the Tu people in modern China suggests that in around 1200CE, Europeans similar to modern Greeks mixed with an otherwise Chinese-like population. Plausibly, the source of this European-like DNA might be merchants travelling the nearby Silk Road.’The powerful technique, christened ‘Globetrotter’, provides insight into past events such as the genetic legacy of the Mongol Empire. Historical records suggest that the Hazara people of Pakistan are partially descended from Mongol warriors, and this study found clear evidence of Mongol DNA entering the population during the period of the Mongol Empire. Six other populations, from as far west as Turkey, showed similar evidence of genetic mixing with Mongols around the same time.’What amazes me most is simply how well our technique works,’ said Dr Garrett Hellenthal of the UCL Genetics Institute, lead author of the study. ‘Although individual mutations carry only weak signals about where a person is from, by adding information across the whole genome we can reconstruct these mixing events. Sometimes individuals sampled from nearby regions can have surprisingly different sources of mixing.’For example, we identify distinct events happening at different times among groups sampled within Pakistan, with some inheriting DNA from sub-Saharan Africa, perhaps related to the Arab Slave Trade, others from East Asia, and yet another from ancient Europe. …

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Genetic chip will help salmon farmers breed better fish

Atlantic salmon production could be boosted by a new technology that will help select the best fish for breeding.The development will enable salmon breeders to improve the quality of their stock and its resistance to disease.A chip loaded with hundreds of thousands of pieces of DNA — each holding a fragment of the salmon’s genetic code — will allow breeders to detect fish with the best genes.It does so by detecting variations in the genetic code of each individual fish — known as single nucleotide polymorphisms (SNPs). These variations make it possible to identify genes that are linked to desirable physical traits, such as growth or resistance to problematic diseases, for example sea lice infestations.Salmon breeders will be able to carry out the test by taking a small sample of fin tissue.The chip carries over twenty times more genetic information than existing tools. Similar chips have already transformed breeding programmes for land-farmed livestock including cattle and pigs.Salmon farming contributes around half a billion pounds to the UK economy each year and provides healthy, high quality food. Worldwide, approximately 1.5 million tonnes of Atlantic salmon are produced every year.Scientists from the University of Edinburgh’s Roslin Institute and Edinburgh Genomics initiative developed the chip with researchers from the Universities of Stirling and Glasgow. They worked with industrial partners Affymetrix UK and Landcatch Natural Selection. The work was funded by the UK’s innovation agency — the Technology Strategy Board — and the Biotechnology and Biological Sciences Research Council.The chip is highlighted in a study published today in the journal BMC Genomics and it will be available to breeders and farmers from March 2014.Dr Ross Houston, of The Roslin Institute, said: “Selective breeding programmes have been used to improve salmon stocks since the 1970s. This new technology will allow the best breeding fish to be selected more efficiently and accurately, particularly those with characteristics that are difficult to measure such as resistance to disease”Dr Alan Tinch, director of genetics at Landcatch Natural Selection, said: “This development takes selective breeding programmes to a whole new level. It is an extension to the selective breeding of salmon allowing more accurate identification of the best fish to create healthier and more robust offspring.”Story Source:The above story is based on materials provided by University of Edinburgh. Note: Materials may be edited for content and length.

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Scientists chip away at mystery of what lives in our mouths

Scientists have pieced together sections of DNA from 12 individual cells to sequence the genome of a bacterium known to live in healthy human mouths.With this new data about a part of the body considered “biological dark matter,” the researchers were able to reinforce a theory that genes in a closely related bacterium could be culprits in its ability to cause severe gum disease.Why the dark matter reference? More than 60 percent of bacteria in the human mouth refuse to grow in a laboratory dish, meaning they have never been classified, named or studied. The newly sequenced bacterium, Tannerella BU063, is among those that to date have not successfully been grown in culture — and its genome is identified as “most wanted” by the Human Microbiome Project.The federal Human Microbiome Project aims to improve research about the microbes that play a role in health and disease. Those 12 cells of BU063 are a good example of the complexity of life in the mouth: They came from a single healthy person but represented eight different strains of the bacterium.BU063 is closely related to the pathogen Tannerella forsythia, a bacterium linked to the gum disease periodontitis. Despite being “cousins,” this research revealed that they have clear differences in their genetic makeup.Those genes lacking in BU063 but present in forsythia — meaning they are a likely secret behind forsythia’s virulence — are now identified as good targets for further study, researchers say.”One of the tantalizing things about this study was the ability to do random searches of other bacteria whose levels are higher in periodontitis,” said Clifford Beall, research assistant professor of oral biology at The Ohio State University and lead author of the study. “We looked for genes that were present in these bacteria and forsythia and not in BU063. There is one particular gene complex in a whole list of these periodontitis-related bacteria that could be involved with virulence.”The research is published in the journal PLOS ONE.Periodontitis results when extensive inflammation or infection of the gums spreads beyond the gums to damage structures that support the teeth, including bone. Pockets that form between the gums and teeth are filled with different kinds of bacteria. Treatment typically involves deep cleaning or surgery to remove these infected pockets. Because multiple bacteria are associated with the disease, antibiotics have not been considered effective for treatment.And though many bacteria in these pockets have been collected and at least partially identified, their characteristics remain a mystery.”We think some of the gene differences we’ve found in this study are important, but it’s still not clear what all these genes do, meaning we still don’t know why certain bacteria in periodontitis are pathogenic in the first place. …

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Mixed genes: Interactive world map of human genetic history reveals likely genetic impacts of historical events

When individuals from different groups interbreed, their offspring’s DNA becomes a mixture of the DNA from each admixing group. Pieces of this DNA are then passed along through subsequent generations, carrying on all the way to the present day. Researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, Oxford University and University College London (UCL) have now produced a global map detailing the genetic histories of 95 different populations across the world, spanning the last four millennia.The interactive world map that is accessible via the internet, details the histories of genetic mixing between each of the 95 populations across Europe, Africa, Asia and South America. It shows likely genetic impacts of historical events including European colonialism, the Mongol Empire, the Arab slave trade and European traders near the Silk Road mixing with people in China.The study, published this week in Science, is the first to simultaneously identify, date and characterise genetic mixing between populations. To do this, the researchers developed sophisticated statistical methods to analyse the DNA of 1490 individuals in 95 populations around the world. “DNA really has the power to tell stories and uncover details of humanity’s past,” said Simon Myers of Oxford University’s Department of Statistics and Wellcome Trust Centre for Human Genetics, co-senior author of the study. “Because our approach uses only genetic data, it provides information independent from other sources. Many of our genetic observations match historical events, and we also see evidence of previously unrecorded genetic mixing. For example, the DNA of the Tu people in modern China suggests that in around 1200CE, Europeans similar to modern Greeks mixed with an otherwise Chinese-like population. Plausibly, the source of this European-like DNA might be merchants travelling the nearby Silk Road.”The powerful technique, christened ‘Globetrotter’, provides insight into past events such as the genetic legacy of the Mongol Empire. …

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Seven new genetic regions linked to type 2 diabetes

Seven new genetic regions associated with type 2 diabetes have been identified in the largest study to date of the genetic basis of the disease.DNA data was brought together from more than 48,000 patients and 139,000 healthy controls from four different ethnic groups. The research was conducted by an international consortium of investigators from 20 countries on four continents, co-led by investigators from Oxford University’s Wellcome Trust Centre for Human Genetics.The majority of such ‘genome-wide association studies’ have been done in populations with European backgrounds. This research is notable for including DNA data from populations of Asian and Hispanic origin as well.The researchers believe that, as more genetic data increasingly become available from populations of South Asian ancestry and, particularly, African descent, it will be possible to map genes implicated in type 2 diabetes ever more closely.’One of the striking features of these data is how much of the genetic variation that influences diabetes is shared between major ethnic groups,’ says Wellcome Trust Senior Investigator Professor Mark McCarthy from the University of Oxford. ‘This has allowed us to combine data from more than 50 studies from across the globe to discover new genetic regions affecting risk of diabetes.’He adds: ‘The overlap in signals between populations of European, Asian and Hispanic origin argues that the risk regions we have found to date do not explain the clear differences in the patterns of diabetes between those groups.’Among the regions identified by the international research team are two, near the genes ARL15 and RREB1, that also show strong links to elevated levels of insulin and glucose in the body — two key characteristics of type 2 diabetes. This finding provides insights into the ways basic biochemical processes are involved in the risk of type 2 diabetes, the scientists say.The genome-wide association study looked at more than 3 million DNA variants to identify those that have a measurable impact on risk of type 2 diabetes. By combining DNA data from many tens of thousands of individuals, the consortium was able to detect, for the first time, regions where the effects on diabetes susceptibility are rather subtle.’Although the genetic effects may be small, each signal tells us something new about the biology of the disease,’ says first author Dr Anubha Mahajan of Oxford University. ‘These findings may lead us to new ways of thinking about the disease, with the aim ultimately of developing novel therapies to treat and prevent diabetes. There’s every reason to expect that drugs acting on these biological processes would have a far larger impact on an individual’s diabetes than the genetic effects we have discovered.’Principal investigator Dr Andrew Morris, also of the Wellcome Trust Centre for Human Genetics at Oxford University, says: ‘The findings of our study should also be relevant to other common human diseases. By combining genetic data from different ethnic groups, we would expect also to be able identify new DNA variants influencing risk of heart disease and some forms of cancer, for example, which are shared across ethnic groups. It has the potential to have a major impact on global public health.’Story Source:The above story is based on materials provided by University of Oxford. …

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Birds of a different color: Three major genes set feather hue in pigeons

Scientists at the University of Utah identified mutations in three key genes that determine feather color in domestic rock pigeons. The same genes control pigmentation of human skin.”Mutations in these genes can be responsible for skin diseases and conditions such as melanoma and albinism,” says Michael Shapiro, associate professor of biology and senior author of the study published online Feb. 6 in the journal Current Biology.”In humans, mutations of these genes often are considered ‘bad’ because they can cause albinism or make cells more susceptible to UV (ultraviolet sunlight) damage and melanoma because the protective pigment is absent or low,” says Eric Domyan, a biology postdoctoral fellow and first author of the study. “In pigeons, mutations of these same genes cause different feather colors, and to pigeon hobbyists that is a very good thing.”Pigeon breeders have drawn on their centuries-long experience to produce about 350 distinct pigeon breeds, focusing particularly on beak shape, plumage color and feather ornaments on the head, feet, beaks and elsewhere. But until this study, the specific mutations that control color in rock pigeons (Columba livia) were unknown.”Across all pigeon breeds, mutations in three major genes explain a huge amount of color variation,” Shapiro says.Various forms of a gene named Tyrp1 make pigeons either blue-black (the grayish color of common city pigeons), red or brown. Mutations of a second gene, named Sox10, makes pigeons red no matter what the first gene does. And different forms of a third gene, named Slc45a2, make the pigeons’ colors either intense or washed out.The scientists discovered how pigeons’ feather color is determined by different versions of these three genes — known as variants or alleles — and by what are called “epistatic” interactions, in which one gene obscures the effects of other genes.”Our work provides new insights about how mutations in these genes affect their functions and how the genes work together,” Shapiro says. “Many traits in animals, including susceptibility to diseases such as cancer, are controlled by more than one gene. To understand how these genes work together to produce a trait, we often have to move beyond studies of humans. It’s difficult to study interactions among the genes in people.””Both Tyrp1 and Sox10 are potential targets for treatment of melanoma,” he adds. …

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Ranking disease-causal mutations within whole genome sequences

Researchers from the University of Washington and the HudsonAlpha Institute for Biotechnology have developed a new method for organizing and prioritizing genetic data. The Combined Annotation-Dependent Depletion, or CADD, method will assist scientists in their search for disease-causing mutation events in human genomes.The new method is the subject of a paper titled “A general framework for estimating the relative pathogenicity of human genetic variants,” published in Nature Genetics.Current methods of organizing human genetic variation look at just one or a few factors and use only a small subset of the information available. For example, the Encyclopedia Of DNA Elements, or ENCODE, catalogs various types of functional elements in human genomes, while sequence conservation looks for similar or identical sequences that have survived across different species through hundreds of millions of years of evolution. CADD brings all of these data together, and more, into one score in order to provide a ranking that helps researchers discern which variants may be linked to disease and which ones may not.”CADD will substantially improve our ability to identify disease-causal mutations, will continue to get better as genomic databases grow, and is an important analytical advance needed to better exploit the information content of whole-genome sequences in both clinical and research settings,” said Gregory M. Cooper, Ph.D., faculty investigator at HudsonAlpha and one of the collaborators on CADD.The goal in developing the new approach was to take the overwhelming amount of data available and distill it down into a single score that can be more easily evaluated by a researcher or clinician. To accomplish that, CADD compares and contrasts the properties of 15 million genetic variants separating humans from chimpanzees with 15 million simulated variants. Variants observed in humans have survived natural selection, which tends to remove harmful, disease-causing variants, while simulated variants are not exposed to selection. Thus, by comparing observed to simulated variants, CADD is able to identify those properties that make a variant harmful or disease-causing. C scores have been pre-computed for all 8.6 billion possible single nucleotide variants and are freely available for researchers.”We didn’t know what to expect,” Cooper said, “but we were pleasantly surprised that CADD was able not only to be applicable to mutations everywhere in the genome but in fact do a substantially better job in nearly every test that we performed than other metrics.”The CADD method is unique from other algorithms in that it assigns scores to mutations anywhere in human genomes, not just the less-than two percent that encode proteins (the “exome”). This unique attribute will be crucial as whole-genome sequencing becomes routine in both clinical and research settings.Story Source:The above story is based on materials provided by HudsonAlpha Institute for Biotechnology. …

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