Category Archives: Genome

Edico Genome Interview with Dr. Eric Topol and Pieter van Rooyen
Dr Eric Topol, Director of the Scripps Translational Science Institute, chats with Pieter van Rooyen, Founder and CEO of Edico Genome.

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Edico Genome Interview with Dr. Eric Topol and Pieter van Rooyen - Video

Energun - Mutation Of The Genome (Original Mix)

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Energun - Mutation Of The Genome (Original Mix) - Video

GC8 Exhaust, STI Genome Muffler
MY00 GC8 WRX with 3inch TBE, UEL Headers, Catless Uppipe and STI Genome Muffler with the restrictor removed.

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GC8 Exhaust, STI Genome Muffler - Video

PUBLIC RELEASE DATE:

8-May-2014

Contact: Jim Dublin jdublin@dublinandassociates.com 210-227-0221 Cold Spring Harbor Laboratory

SAN ANTONIO, May 8, 2014 A new method for isolating and genome sequencing an individual malaria parasite cell has been developed by Texas Biomed researchers and their colleagues. This advance will allow scientists to improve their ability to identify the multiple types of malaria parasites infecting patients and lead to ways to best design drugs and vaccines to tackle this major global killer. Malaria remains the world's deadliest parasitic disease, killing 655,000 people in 2010.

Malaria parasite infections are complex and often contain multiple different parasite genotypes and even different parasite species. So when researchers take a blood sample from a malaria infected patient, and look at the parasite DNA within they end up with a complex mixture that is difficult to interpret.

"This has really limited our understanding of malaria parasite biology" says Ian Cheeseman, Ph.D., who led this project. "It's like trying to understand human genetics by making DNA from everyone in a village at once. The data is all jumbled up what we really want is information from individuals."

To achieve a better understanding of malaria parasites single celled organisms that infect red blood cells Cheeseman and colleague Shalini Nair, developed a novel method for isolating an individual parasite cell and sequencing its genome. These "single cell genomics" approaches have been adopted in cancer research to identify how tumors evolve during the progression of a disease but it has been difficult to adapt them to other organisms.

"One of the real challenges was learning how to cope with the tiny amounts of DNA involved. In a single cell we have a thousand million millionth of a gram of DNA. It took a lot of effort before we developed a method where we simply didn't lose this," said Nair, the first author on the work.

Their method is set to change how researchers think about infections. "One of the major surprises we found when we started looking at individual parasites instead of whole infections was the level of variation in drug resistance genes. The patterns we saw suggested that different parasites within a single malaria infection would react very differently to drug treatment" said Nair. "We're now able to look at malaria infections with incredible detail. This will help us understand how to best design drugs and vaccines to tackle this major global killer," Cheeseman added.

A paper describing this work, funded by the Texas Biomedical Forum, National Institutes of Health, a Cowles Postdoctoral Training Fellowship and the Wellcome Trust, was published online May 8 in the journal Genome Research. The work was led by Texas Biomed's Cheeseman with collaborators at the University of Texas Health Science Center San Antonio, Case Western Reserve University, the Cleveland Clinic Lerner Research Institute, the Shoklo Malaria Research Unit, Thailand, and the Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Malawi. The other Texas Biomed author on is Tim Anderson, Ph.D.

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Single cell genome sequencing of malaria parasites

May 8, 2014

Image Caption: The velvet spiders genome has now been mapped. This image shows a group of social velvet spiders jointly killing their prey. Credit: Peter Gammelby, Aarhus University.

Anne-Mette Siem, Aarhus University

For the first time ever, a group of Danish and Chinese researchers has sequenced the genome of the spider. This knowledge provides a much more qualified basis for studying features of the spider. It also shows that humans share certain genomic similarities with spiders.

The fact that the eight-legged creepy spider in some ways resembles humans is one of the surprising conclusions after researchers at Aarhus University and the Beijing Genomics Institute (BGI) succeeded in sequencing its genome.

However, it is more a discovery on an awesome scale. The sequencing has far greater significance for our future understanding of the spiders special properties

In brief, weve acquired a tool for everyone interested in spiders, say Kristian W. Sanggaard and Jesper S. Bechsgaard, Aarhus University. Together with Xiaodong Fang, BGI, they are the first authors of the study, which has been published in Nature Communications. By describing the spider genome, the researchers have roughly speaking drawn up its genetic map. This map can be used in future to navigate to and delve into different areas of the spiders functions which will now be easier to describe.

What is a spider?

The researchers worked with two types of spiders, representing two of the three main groups in the spider family. One of these is a small velvet spider and the other is a tarantula.

The researchers succeeded in sequencing the velvet spiders genome, while there are still some unsolved gaps in the genetic map of the tarantula.

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Spider Genome Sequenced For The First Time

PUBLIC RELEASE DATE:

9-May-2014

Contact: David Gilbert degilbert@lbl.gov 925-927-2541 DOE/Joint Genome Institute

Despite its name, the Dead Sea does support life, and not just in the sense of helping visitors float in its waters. Algae, bacteria, and fungi make up the limited number of species that can tolerate the extremely salty environment at the lowest point on Earth.

Some organisms thrive in salty environments by lying dormant when salt concentrations are very high. Other organisms need salt to grow. To learn which survival strategy the filamentous fungus Eurotium rubrum uses, a team of researchers led by Eviatar Nevo from the University of Haifa in Israel, Igor Grigoriev of the U.S. Department of Energy Joint Genome Institute (DOE JGI), and Gerhard Rambold, University of Bayreuth, Germany and their colleagues studied its genome. They described their findings in the May 9, 2014 issue of Nature Communications.

"Understanding the long-term adaptation of cells and organisms to high salinity is of great importance in a world with increasing desertification and salinity," the team wrote. "The observed functional and structural adaptations provide new insight into the mechanisms that help organisms to survive under such extreme environmental conditions, but also point to new targets like the biotechnological improvement of salt tolerance in crops." In principle this discovery could revolutionize saline agriculture worldwide by laying the groundwork of understanding necessary to appropriately using salt resistance genes and gene networks in crops to enable them to grow in desert and saline environments.

The DOE JGI team first sequenced, assembled and annotated the 26.2-million base genome of E. rubrum. The team found that the genome contained just over 10,000 predicted genes. They also found that the E. rubrum proteins had higher aspartic and glutamic acid amino acid levels than expected. When the team compared E. rubrum's gene families against those in two other halophilic species (Wallemia ichthyophaga and Hortaea werneckii), they found that high acidic residues were common in all three species, a general trait all salt-tolerant microbes share.

To learn more about the fungus' tolerance for salt, Tami Kis Papo at the University of Haifa grew samples in liquid and solid media at salinities from zero up to 90 percent of Dead Sea water. The researchers found that it had viable spores when grown in 70 percent diluted Dead Sea water, conditions equivalent to an algal bloom in the Dead Sea 20 years ago. A study conducted by Alfons R. Weig at the University of Bayreuth of E. rubrum's transcriptome, that small fraction of the genome that encodes the RNA molecules in order to carry out instructions to build and maintain cells, showed that in high salinity conditions, the fungal cells need to keep cell membrane transport under tight control. "This clearly indicates that the fungus tries to cope 'actively' with its extreme environment and does not simply fall into dormancy," the team noted, "as might be expected by the greatly reduced growth rates."

In addition to contributing to a better understanding of salt tolerance mechanisms for agriculture, this work may also have applicability to the DOE's interests in developing new strategies to improve biofuels production. For instance, the DOE JGI and its partners are sourcing microbial and fungal enzymes for more effective biomass pretreatment with ionic liquids, environmentally benign organic salts often used as green chemistry substitutes for volatile organic solvents.

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Salt needed: Tolerance lessons from a dead sea fungus

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Newswise A new method for isolating and genome sequencing an individual malaria parasite cell has been developed by Texas Biomed researchers in San Antonio and their colleagues. This advance will allow scientists to improve their ability to identify the multiple types of malaria parasites infecting patients and lead to ways to best design drugs and vaccines to tackle this major global killer. Malaria remains the worlds deadliest parasitic disease, killing 655,000 people in 2010.

Malaria parasite infections are complex and often contain multiple different parasite genotypes and even different parasite species. So when researchers take a blood sample from a malaria infected patient, and look at the parasite DNA within they end up with a complex mixture that is difficult to interpret.

"This has really limited our understanding of malaria parasite biology" says Ian Cheeseman, Ph.D., who led this project. Its like trying to understand human genetics by making DNA from everyone in a village at once. The data is all jumbled up what we really want is information from individuals.

To achieve a better understanding of malaria parasites single celled organisms that infect red blood cells Cheeseman and colleague Shalini Nair, developed a novel method for isolating an individual parasite cell and sequencing its genome. These single cell genomics approaches have been adopted in cancer research to identify how tumors evolve during the progression of a disease but it has been difficult to adapt them to other organisms.

One of the real challenges was learning how to cope with the tiny amounts of DNA involved. In a single cell we have a thousand million millionth of a gram of DNA. It took a lot of effort before we developed a method where we simply didnt lose this, said Nair, the first author on the work.

Their method is set to change how researchers think about infections. One of the major surprises we found when we started looking at individual parasites instead of whole infections was the level of variation in drug resistance genes. The patterns we saw suggested that different parasites within a single malaria infection would react very differently to drug treatment said Nair. Were now able to look at malaria infections with incredible detail. This will help us understand how to best design drugs and vaccines to tackle this major global killer, Cheeseman added.

A paper describing this work, funded by the Texas Biomedical Forum, National Institutes of Health, a Cowles Postdoctoral Training Fellowship and the Wellcome Trust, was published online May 8 in the journal Genome Research. The work was led by Texas Biomeds Cheeseman with collaborators at the University of Texas Health Science Center San Antonio, Case Western Reserve University, the Cleveland Clinic Lerner Research Institute, the Shoklo Malaria Research Unit, Thailand, and the Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Malawi. The other Texas Biomed author on is Tim Anderson, Ph.D.

This work was supported by a US National Institutes of Health grant No. R37AI048071. Cheeseman can be reached through Jim Dublin at jdublin@dublinandassociates.com or 210-227-0221.

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A New Method for Isolating and Genome Sequencing Malaria Parasites Will Aid in the Understanding of These Infections

The fact that the eight-legged creepy spider in some ways resembles humans is one of the surprising conclusions after researchers at Aarhus University and the Beijing Genomics Institute (BGI) succeeded in sequencing its genome.

However, it is more a discovery on an awesome scale. The sequencing has far greater significance for our future understanding of the spider's special properties.

"In brief, we've acquired a tool for everyone interested in spiders," say Kristian W. Sanggaard and Jesper S. Bechsgaard, Aarhus University. Together with Xiaodong Fang, BGI, they are the first authors of the study, which has been published in Nature Communications. By describing the spider genome, the researchers have roughly speaking drawn up its genetic map. This map can be used in future to navigate to and delve into different areas of the spider's functions -- which will now be easier to describe.

What is a spider?

The researchers worked with two types of spiders, representing two of the three main groups in the spider family. One of these is a small velvet spider and the other is a tarantula.

The researchers succeeded in sequencing the velvet spider's genome, while there are still some unsolved gaps in the genetic map of the tarantula.

"The idea was that, by comparing their genetic makeup, we'd try to see whether we could say anything in general terms about what makes a spider a spider," says Kristian W. Sanggaard. However, it is almost 300 million years since the two types of spiders had a common ancestor, so the researchers could only find a limited number of similarities. "But we found a number of genes -- about two to three hundred -- that have only been found in these two types of spiders and not in other organisms. They could be candidates for genes specific to spiders," says Jesper S. Bechsgaard.

From overview to insight

The researchers were not content with simply mapping the spider genome. They also looked at the protein composition of two of the most interesting areas of the 'crawly cousins' -- silk and venom production. By including the proteins, they did not restrict themselves to providing a map, but they also filled in details on two specific points. James Watson, who was awarded a Nobel Prize for describing the structure of the DNA strand, called genes the 'script' and proteins the 'actors'. By describing the proteins, the researchers thus demonstrated so to speak that their script works. Or -- to keep to the map analogy -- that the genetic map actually leads in the right direction. This is one of the only studies in which the proteins are described along with the genome. This was possible because the Aarhus researchers have some of the most advanced mass spectrometry equipment in the world for sequencing large numbers of proteins.

We can learn from spiders

Originally posted here:
Mapping the spider genome: Surprising similarities to humans

When someone has leukaemia, differences in how their genome is folded up into the nucleus of their cells can reveal what form of the cancer they have. The finding the first time that the 3D structure of a cell's genome has accurately identified human disease could lead to a better way to predict the course of the disease.

A human genome, with its DNA stretched out, is over a metre long. To fit into the nucleus of a cell, it is crumpled into a little ball held together by proteins. That complex is called chromatin.

The 3D structure of the DNA in each cell affects which genes it uses, or expresses. In some cases, the precise shape of the DNA can have specific effects. For example, if a bit of DNA code that normally controls how strongly nearby genes are expressed is folded over and touches another gene, it can switch that gene on or off even if it's on a completely different chromosome.

Since one of the hallmarks of leukaemia is gene over-expression, Jose Dostie at McGill University in Montral, Canada, and her colleagues wondered whether that was associated with changes in the chromatin shape.

To investigate, the team examined data from 30 DNA samples of cells grown in a lab. These cells originally came from people with three different subtypes of the cancer acute myeloid leukaemia, acute lymphoblastic leukaemia and embryonic carcinoma.

They focused on a particular region of the genome where a set of genes called HOXA are found. These are associated with many cancers, including leukaemia. The team identified the points of contact between the parts of the genome in this region of the chromatin complex and fed these data into a computer model. The model then predicted the chromatin shapes that the three different types of leukaemia would form.

With their model duly trained using known leukaemia samples, the team then tested their system's predictive power. They did this by providing it with data on an unknown set of leukaemia cells, all of which had one of the three leukaemia subtypes. They found that the model could identify the subtype with 93 per cent accuracy.

Finding the leukaemia subtype is the most important factor in defining treatment course, says Dostie. The standard way of diagnosing subtype involves several different clinical and histological tests. The overall level of accuracy is on a par with Dostie's results, but it requires the expertise of several different laboratories, which is not always available.

John Rasko from the University of Sydney in Australia says the method is a long way from being something that could be used to treat patients, but he says it's an exciting research tool. "It has the possibility of shedding light on mechanisms that cause or sustain cancer, and therefore may provide us with new opportunities to develop therapeutics aimed at the 3D structure of DNA," he says.

Musa Mhlanga from the Council for Scientific and Industrial Research in Pretoria, South Africa, says that if the method is verified, the practical challenge to using the technique to help patients will be doing the analysis with small samples. "The big caveat here is that to do these chromatin-confirmation studies at high resolution you need millions of cells. You can't get this from a tumour biopsy."

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3D shape of genome could diagnose leukaemia type

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Newswise The power of genome-wide association studies (GWAS) to detect genetic influences on human disease can be substantially increased using a statistical testing framework reported in the May issue of the journal GENETICS.

Despite the proliferation of GWAS, the associations found so far have largely failed to account for the known effects of genes on complex disease the problem of missing heritability. Standard approaches also struggle to find combinations of multiple genes that affect disease risk in complex ways (known as genetic interactions).

The new framework enhances the ability to detect genetic associations and interactions by taking advantage of data from other genomic studies of the same population. Such information is increasingly abundant for many human populations.

The authors demonstrated that their method improves performance over standard approaches. They also re-examined real GWAS data to find promising new candidates for genetic interactions that affect bipolar disorder, coronary artery disease, Crohns disease, and rheumatoid arthritis.

We think practically everyone whos ever done a case-control GWAS could benefit from reanalyzing their data in this way, said author Saharon Rosset, associate professor of statistics at Tel Aviv University.

This paper offers a significant advance in mapping genes involved in disease. The approach makes use of available data to substantially improve the ability to identify genetic components of disease, said Mark Johnston, Editor-in-Chief of the journal GENETICS.

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CITATION: S. Kaufman and S. Rosset. Exploiting Population Samples to Enhance Genome-Wide Association Studies of Disease. Genetics May 2014 197:337-349 doi: 10.1534/genetics.114.162511 Available online at: http://www.genetics.org/content/197/1/337

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Statistical Test Increases Power of Genetic Studies of Complex Disease