Category Archives: Genome

Rebecca Summers, reporter

(Image: Tracey Haynes Photographs)

When hibernating, western painted turtles can freeze solid and stop breathing. After a long winter without oxygen, submerged in ice-covered ponds, they just wake and pick up where they left off.

(Image: Tracey Haynes Photographs)

An international team of researchers have sequenced the turtle genome looking for novel genes to explain these unique physiological adaptations. However, the turtles don't rely on unique mutations for their superpowers. Instead, they find new ways of activating commonplace gene networks.

For example, the researchers identified 19 genes in the brain and 23 in the heart that are activated in low-oxygen conditions, including one gene, APOLD1, which was expressed nearly 130 times as much as normal. These genes also are present in humans, so they are good candidates to explore for treatments for tissue damage due to oxygen deprivation.

"This is a back-door route for turtles to evolve," says co-author Patrick Minxof The Genome Institute at Washington University in St Louis. "Rather than evolve new genes, they adapted existing genes for new uses."

Link:
First turtle genome shows beauty more than shell-deep

Apr. 2, 2013 Children with autism have increased levels of genetic change in regions of the genome prone to DNA rearrangements, so called "hotspots," according to a research discovery to be published in the print edition of the journal Human Molecular Genetics. The research indicates that these genetic changes come in the form of an excess of duplicated DNA segments in hotspot regions and may affect the chances that a child will develop autism -- a behavioral disorder that affects about 1 of every 88 children in the United States, according to the Centers for Disease Control.

Earlier work had identified, in children with autism, a greater frequency of rare DNA deletions or duplications, known as DNA copy number changes. These rare and harmful events are found in approximately 5 to 10 percent of cases, raising the question as to what other genetic changes might contribute to the disorders known as autism spectrum disorders.

The new research shows that children with autism have -- in addition to these rare events -- an excess of duplicated DNA including more common variants not exclusively found in children with autism, but are found at elevated levels compared to typically developing children.

The research collaboration includes groups led at Penn State by Scott Selleck; at the University of California Davis/MIND Institute by Isaac Pessah, Irva Hertz-Picciotto, Flora Tassone, and Robin Hansen; and at the University of Washington by Evan Eichler.

The investigators also found that the balance of DNA duplications and deletions in children with autism was different from that found in more severe developmental disorders, such as intellectual disability or multiple congenital anomalies, where the levels of both deletions and duplications are increased compared to controls, and are even higher than in children with autism.

They also found that children who had more difficulty with daily living skills also had the greatest level of copy number change throughout their genome. "These measures of adaptive behavior provide an indication of the severity of the impairment in the children with autism. These behaviors were significantly correlated with the amount of DNA copy number change," Selleck said, emphasizing that the research revealed "clear and graded effects of the genetic change."

"These results beg the question as to the origin of this genetic change," Selleck said. "The increased levels of both rare and common variants suggests the possibility that these individuals are predisposed to genetic alteration."

A vigorous debate is ongoing in the research community about the degree of genetic versus environmental contributions to autism. Selleck said the finding of an overall increase in genetic change in children with autism heightens the need to search for the basis of this variation. "We know that environmental factors can affect the stability of the genome, but we don't know if the DNA copy number change we detect in these children is a result of environmental exposures, nutrition, medical factors, lifestyle, genetic susceptibility, or combinations of many elements together," Selleck said. "The elevated levels of common variants is telling us something. It suggests that pure selection of randomly generated variants may not be the whole story."

The Penn State team includes Department of Biochemistry and Molecular Biology Associate Professor Marylyn Ritchie and Assistant Professor Santhosh Girirajan. "The relationship between the level of copy number change and the degree of neurodevelopmental disability is something we have noted previously for large, rare variants" says Girirajan, "but this work extends those observations to common copy number variants, suggesting the level of copy number change in children with autism is larger than we had appreciated." Girirajan, the first author of the study, coordinated the effort between the Penn State and University of Washington researchers.

The research collaboration began with studies supported by the Minnesota Medical Foundation and the Martin Lenz Harrison Endowed Chair in Pediatrics when Selleck was Director of the Autism Initiative at the University of Minnesota. When Selleck arrived at Penn State in 2009, he began a new phase of the analysis with replication studies of early findings conducted with the help and expertise of Evan Eichler and colleagues at the University of Washington using the clinical data and DNA collected by Isaac Pessah, Irva Hertz-Picciotto, Flora Tassone, and Robin Hansen at the University of California Davis/MIND Institute group, which directs a large population-based case-control study of autism called CHARGE (Childhood Autism Risks from Genetics and Environment). In this multiyear study, clinical history, environmental, nutritional, family, and medical data are collected from the families of children with autism and other developmental disorders, as well as from randomly selected control children from the general population. The research took advantage of the CHARGE study, supported by the National Institute of Environmental Health Sciences and the Environmental Protection Agency.

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Autism linked to increased genetic change in regions of genome instability

(Charles Dharapak/AP)

Every dollar we spent to map the human genome has returned $140 to our economy -- $1 of investment, $140 in return.

--President Obama, Remarks by the President on the BRAIN Initiative and American Innovation, April 2, 2013

Every dollar we invested to map the human genome returned $140 to our economy.

--Obama, 2013 State of the Union address, Feb. 12, 2013

In announcing a new government initiative to map the brain Tuesday, President Obama repeated a statistic he had used in the State of the Union addressone that we had been meaning to examine more closely.

Certainly, the presidents broader point is correctfederal government investment in research is often an important factor in innovations and scientific achievements that have enhanced Americans lives. But 140 times return on investment? That sounded a bit too good to be true.

Lets dig deeper into the data.

The Facts

The presidents factoidwhich he has asserted without citing a sourcecomes from a 2011 study by the Battelle Memorial Institute titled Economic Impact of the Human Genome Project: How a $3.8 billion investment drove $796 billion in economic impact, created 310,000 jobs and launched a genomic revolution.

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A 1 to 140 ‘return’ from the Human Genome Project?

Public release date: 2-Apr-2013 [ | E-mail | Share ]

Contact: Steve Yozwiak syozwiak@tgen.org 602-343-8704 The Translational Genomics Research Institute

KYOTO, Japan April 2, 2013 The scientific benefits of whole genome sequencing at the Translational Genomics Research Institute (TGen) will be presented at the 14th International Myeloma Workshop, April 3-7 at the Kyoto International Conference Center.

Dr. Jonathan Keats, head of TGen's Multiple Myeloma Research Laboratory, will present Discovering the Underlying Genetics of Multiple Myeloma Through Whole Genome Sequencing at 8:15 a.m. (Kyoto time) April 4, following the conference opening talk.

Multiple myeloma is a pathological description of a disease characterized by the accumulation of plasma cells in the bone marrow. Dr. Keats' lab at TGen is focused on using new methods to investigate the genomic features of this disease with the goal of identifying genetic events that drive the development, progression, and mediate therapeutic resistance.

"We will show for the first time the integration of DNA and RNA sequencing in multiple myeloma, and how TGen's comprehensive approach to this research has begun to uncover possible genetic changes that could lead to the underlying causes of this cancer," Dr. Keats said.

Previous studies have identified as many as 10 distinct biological subgroups of multiple myeloma, highlighting the need to identify distinct genetic defects to address each subtype of this disease.

Recent advances in next generation sequencing can now identify nearly all genetics events existing in an individual tumor. Initial studies have focused on whole genome sequencing or exome sequencing and confirmed genetic mutations (TP53, NRAS, KRAS) as well as identified novel mutations (FAM46C and DIS3). In addition, identification of recurrent BRAF mutations and the availability of targeted BRAF inhibitors provide an opportunity to translate research findings into clinical practice to benefit patients.

Dr. Keats is one of the key researchers in TGen's Multiple Myeloma Genomics Initiative, funded by the Multiple Myeloma Research Foundation.

"We will present results from the multiple myeloma genomics initiative using paired whole genome and transcriptome sequencing on 84 patient samples and 68 cell lines. The combination of DNA and RNA based sequencing approaches has improved our ability to identify biologically relevant alterations within each sample," Dr. Keats said.

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TGen professor discusses benefits of whole genome sequencing in study of multiple myeloma

Emily Jane McTavish, a doctoral student in the lab of UT Biology professor David Hillis, hanging out with some of the Longhorns at Hillis's Double Helix Ranch. Credit: Photo by Liz Milano

Texas Longhorn cattle have a hybrid global ancestry, according to a study by University of Texas at Austin researchers published this week in the Proceedings of the National Academy of Sciences.

The study of the genome of the Longhorn and related breeds tells a fascinating global history of human and cattle migration. It traces back through Christopher Columbus' second voyage to the New World, the Moorish invasion of Spain and the ancient domestication of the aurochs in the Middle East and India.

"It's a real Texas story, an American story," said Emily Jane McTavish, a doctoral student in the lab of biology professor David Hillis. "For a long time people thought these New World cattle were domesticated from a pure European lineage. But it turns out they have a more complex, more hybrid, more global ancestry, and there's evidence that this genetic diversity is partially responsible for their greater resilience to harsh climatic conditions."

To reconstruct the genetic history of Texas Longhorns, McTavish, Hillis and colleagues from the University of Missouri-Columbia analyzed almost 50,000 genetic markers from 58 cattle breeds. The most comprehensive such analysis to date, it was funded in part by the Cattlemen's Texas Longhorn Conservancy, which helped the scientists get access to samples used by ranchers.

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The study of the genome of the Texas Longhorn and related breeds, animated here, tells a fascinating global history of human and cattle migration. It traces back through Christopher Columbus' second voyage to the New World, the Moorish invasion of Spain and the ancient domestication of the aurochs in the Middle East and India. Animation by Marianna Grenadier

Over the next two centuries the Spanish moved the cattle north, arriving in the area that would become Texas near the end of the 17th century. The cattle escaped or were turned loose on the open range, where they remained mostly wild for the next two centuries.

"It was known on some level that Longhorns are descendants from cattle brought over by early Spanish settlers," said Hillis, the Alfred W. Roark Centennial Professor in the College of Natural Sciences, "but they look so different from the cattle you see in Spain and Portugal today. So there was speculation that there had been interbreeding with later imports from Europe. But their genetic signature is co mpletely consistent with being direct descendants of the cattle Columbus brought over."

The study reveals that being a "pure" descendant of cattle from the Iberian peninsula indicates a more complicated ancestry than was understood. Approximately 85 percent of the Longhorn genome is "taurine," descended from the ancient domestication of the wild aurochs that occurred in the Middle East 8,000-10,000 years ago. As a result, Longhorns look similar to purer taurine breeds such as Holstein, Hereford and Angus, which came to Europe from the Middle East.

Excerpt from:
Genome of Texas Longhorn, related breeds tells global history of human, cattle migration

With its close relationship to the poplar genome, the peach genome offers researchers more than just the opportunity to learn more about the basic biology of trees. For example, comparing peach gene families to those of six other fully sequenced diverse plant species is helping to unravel unique metabolic pathways such as those that lead to lignin biosynthesis -- the molecular "glue" that holds the plant cells together -- and a key barrier to deconstructing biomass into fuels. Credit: Jonathan Eisen

Rapidly growing trees like poplars and willows are candidate "biofuel crops" from which it is expected that cellulosic ethanol and higher energy content fuels can be efficiently extracted. Domesticating these as crops requires a deep understanding of the physiology and genetics of trees, and scientists are turning to long-domesticated fruit trees for hints. The relationship between a peach and a poplar may not be obvious at first glance, but to botanists both trees are part of the rosid superfamily, which includes not only fruit crops like apples, strawberries, cherries, and almonds, but many other plants as well, including rose that gives the superfamily its name.

"The close relationship between peach and poplar trees is evident from their DNA sequence," said Jeremy Schmutz, head of the Plant Program at the U.S. Department of Energy Joint Genome Institute (DOE JGI).

In the March 24 edition of Nature Genetics, Schmutz and several colleagues were part of the International Peach Genome Initiative (IPGI) that published the 265-million base genome of the Lovell variety of Prunus persica.

"Using comparative genomics approaches, characterization of the peach sequence can be exploited not only for the improvement and sustainability of peach and other important tree species, but also to enhance our understanding of the basic biology of trees," the team wrote. They compared 141 peach gene families to those of six other fully sequenced diverse plant species to unravel unique metabolic pathways, for instance, those that lead to lignin biosynthesisthe molecular "glue" that holds the plant cells togetherand a key barrier to deconstructing biomass into fuels.

For bioenergy researchers, the size of the peach genome makes it ideal to serve as a plant model for studying genes found in related genomes, such as poplar, one of the DOE JGI's Plant Flagship Genomes, and develop methods for improving plant biomass yield for biofuels.

"One gene we're interested in is the so-called "evergreen" locus in peaches, which extends the growing season," said Daniel Rokhsar, DOE JGI Eukaryotic Program head under whose leadership sequencing of the peach genome began back in 2007. "In theory, it could be manipulated in poplar to increase the accumulation of biomass."

The publication comes three years after the International Peach Genome Consortium publicly released the draft assembly of the annotated peach genome on the DOE JGI Plant portal Phytozome.net and on other websites. The decision to sequence the peach genome was first announced during the 2007 Plant and Animal Genome XI Conference.

In the United States, the Initiative was funded by the U.S. Department of Energy Office of Science and led by researchers at the DOE JGI, The HudsonAlpha Institute for Biotechnology, Clemson University, North Carolina State University, and Washington State University. Additional support was contributed by U.S. Department of Agriculture and by the Energy Biosciences Institute, of the University of California, Berkeley, who supported senior author Therese Mitros. The Italian government also supported this international effort, including the work of first author Ignazio Verde of the Fruit Tree Research Centre/Agricultural Research Council in Rome, Italy. Contributions were also made from research institutes in Chile, Spain, and France.

More information: genome.jgi.doe.gov/programs/plants/flagship_genomes.jsf.

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Peach genome offers insights into breeding strategies for biofuels crops

Gene Details Page Brief With an Issue in the Genome Page

By: ToxoplasmaDreamer

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Gene Details Page Brief With an Issue in the Genome Page - Video

genome 2010-02-12 15-22-38-55

By: psquare12

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genome 2010-02-12 15-22-38-55 - Video

March 28, 2013

Lawrence LeBlond for redOrbit.com Your Universe Online

The western painted turtle (Chrysemys picta bellii) is one of the most widespread species of turtle in North America. This creature is found in fresh, slow-moving waters from southern Canada to northern Mexico and from the Atlantic to the Pacific. And because this species has been widely studied, it only makes sense for researchers to sequence its genome, and that theyve done.

Publishing the work in this weeks Genome Biology, researchers describe that much like the turtle itself, the rate of genome evolution is very slow. Their data show that turtle genomes evolve at a rate that is about a third that of the human genome and a fifth that of the python, the fastest genome analyzed to date.

Through extensive research, scientists have discovered many interesting facts about these abundant North American reptiles. They are long-lived, can withstand low temperatures and can survive long periods with no oxygen. The sex of the turtle is determined by the temperature at which the egg develops rather than through genetics. The painted turtle can survive up to four months under water depending on the temperature.

Previously, analyses of fossils have shown that the painted turtle has existed for more than 15 million years, and four regionally based subspecies have evolved during the last Ice Age. The western painted turtle is by far the largest of the four subspecies and can grow to 10 inches long.

The painted turtle is the first of its genus to have its genome fully sequenced, and only the second non-avian reptile to undergo the analysis. Data has revealed some very interesting insights about the bizarre features and adaptations that exist only in the turtle genome.

Bradley Shaffer, of The Genome Institute at Washington University, St. Louis (WUSTL), and colleagues discovered through genome mapping that turtles are more closely related to birds and crocodilians than to any other vertebrates. They discovered 19 genes in the brain and 23 in the heart whose expression is increased in low oxygen conditions. Furthermore, they found one gene whose expression changes nearly 130 fold. They also discovered through experiments with hatchlings that common microRNA was involved in freeze tolerance adaptation.

Their work indicates clearly that common vertebrate regulatory networks, some of which have analogs in human diseases, are often involved in the western painted turtle achieving its extraordinary physiological capacities.

Shaffer and his team believe that the painted turtle may offer significant insights into human health disorders and the way they are managed and cared for. They particularly see the turtle genome offering important insights into conditions such as anoxia and hypothermia.

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Unraveling The Bizarre Features Of The Turtle Genome

One of the world's most prestigious laboratories is frantically trying to resolve a row over its decision to publish the genome of one of the world's most studied human cell lines a set of cervical cancer cells.

The cells were taken in 1951 from a woman called Henrietta Lacks, without her consent. Her descendants argue that the published genome may reveal genetic traits of family members.

The HeLa cells, as they are dubbed, are exceptionally easy to grow in the lab and have become the cellular equivalent of lab rats. For decades, scientists have worked with these cells to unravel the secrets of cancer and develop new vaccines and treatments.

After publishing the HeLa genome in the online journal G3: Genes, Genomes and Genetics, researchers led by Lars Steinmetz at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany, withdrew the data following a barrage of objections.

"It shouldn't have been published without our consent That is private family information," said Lacks' granddaughter Jeri Lacks-Whye, quoted in The New York Times in a commentary on the dispute by Rebecca Skloot, whose biography of Lacks, The Immortal Life of Henrietta Lacks, appeared in 2011.

EMBL has apologised to the family and is in talks with them to try to resolve the situation.

"As soon as we learned of this we removed our data from the internet out of respect for the family," says EMBL spokeswoman Raeka Aiyar. "We take their concerns very seriously and have reached out to them with our apologies, and to express our determination to work with them towards an appropriate course of action for handling the availability of this data. We are currently awaiting their response."

EMBL also gave the G3 journal a statement on why the researchers withdrew the data.

The paper revealed that the genome of HeLa cells is chaotic. That is as might be expected in cancer cells, which undergo abnormal genetic reorganisation.

Steinmetz found numerous regions where chromosomes are arranged in the wrong order, for example, as well as missing genes and surplus copies of others.

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Storm erupts over publishing of Henrietta Lacks genome