Category Archives: Transhuman News

The detailed annotation of the pig genome will speed along efforts to help breed healthier and meatier pigs and to create more faithful models of human disease

By Alison Abbott and Nature magazine

Duroc pigs, stars of the show. Image: Flickr/Max Westby

T. J. Tabasco is something of a porcine goddess at the University of Illinois, Urbana-Champaign, where her ruddy, taxidermied head looks down from the office wall of geneticist Lawrence Schook. Now she has been immortalized in this weeks Nature not by name, but by the letters of her DNA.

Scientists are salivating. For the past couple of decades they have been slowly teasing information from the pig genome, applying it to breed healthier and meatier pigs, and to try to create more faithful models of human disease. This weeks draft sequence of T. J.s genome (see page 393), with its detailed annotation a reference genome will speed progress on both fronts, and perhaps even allow pigs to be engineered to provide organs for transplant into human patients. Agriculture in particular will benefit fast, says Alan Archibald of the Roslin Institute in Edinburgh, UK, one of the papers lead authors. The pig industry has an excellent track record for rapid adoption of new technologies and knowledge.

T. J., a domestic Duroc pig (Sus scrofa domesticus), was born in Illinois in 2001. The next year, Schook and his colleagues generated a fibroblast cell line from a small piece of skin from her ear and commissioned clones to be created from it, so that they could work on animals all with the same genome. One set of clones was created at the National Swine Resource and Research Center (NSRRC) in Columbia, Missouri, along with genetically engineered pigs with genes added or deleted to mimic human diseases.Making such pigs has got increasingly easier as knowledge of the genome increases, says physiologist Randall Prather, a co-director of the NSRRC, which is funded by the National Institutes of Health (NIH).

The NIH launched the NSRRC in 2003 to encourage research in pig disease models. Pigs are more expensive to keep than rodents, and they reproduce more slowly. But the similarities between pig and human anatomy and physiology can trump the drawbacks. For example, their eyes are a similar size, with photoreceptors similarly distributed in the retina. So the pig became the first model for retinitis pigmentosa, a cause of blindness. And four years ago, researchers created a pig model of cystic fibrosis that, unlike mouse models, developed symptoms resembling those in humans.

Geneticist and veterinarian Eckhard Wolf at the Ludwig-Maximilian University in Munich, Germany, has exploited the similarity between the human and pig gastrointestinal system and metabolism like us, pigs will eat almost anything and then suffer for it to develop models of diabetes. One pig model carries a mutant transgene that limits the effectiveness of incretin, a hormone required for normal insulin secretion. Mice with the transgene developed unexpectedly severe diabetes, but the pigs have a more subtle pre-diabetic condition that better models the human disease. This shows the importance of using an animal with a relevant physiology, says Wolf.

Pig models are now being developed for other common conditions, including Alzheimers disease, cancer and muscular dystrophy. This work will be enriched by the discovery, reported in the genome paper, of 112 gene variants that might be involved in human diseases. Knowledge of the genome is also allowing scientists to try to engineer pigs that could be the source of organs, including heart and liver, for human patients. Pig organs are roughly the right size, and researchers hope to create transgenic pigs carrying genes that deceive the immune system of recipients into not rejecting the transplants.

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'Draft Sequence' of Pig Genome Could Benefit Agriculture and Medicine

Lawrence LeBlond for redOrbit.com Your Universe Online

Methicillin-resistant Staphylococcus aureus (MRSA), a dangerous staph infection often associated with medical procedures in hospitals and doctors offices, has had its genome sequenced by UK researchers.

The successful mapping of the bacteria has given researchers an upper hand in controlling an infection in a local hospital that has so far been found in 12 babies in the maternity ward there. Using fast genome sequencing technology, the researchers suggest they could also find a way to control other hospital superbugs like salmonella and E. coli, and diseases such as tuberculosis.

The sequencing was completed by researchers at Wellcome Trust Sanger Institute, the University of Cambridge and Cambridge University Hospitals. Using the advanced DNA sequencing technology they were able to confirm the presence of an ongoing outbreak of MRSA in real time. Their efforts led to the stoppage of the outbreak, saving countless patients from further harm. While other methods have been used to track down hospital infection outbreaks, this new method is by far the fastest and most accurate.

The researchers discovered the outbreak had extended into the wider community, which also could not have been reached using previous methods. The new technologies also led the team to link the outbreak to an unsuspecting carrier, who was treated to eradicate the infection.

We are always seeking ways to improve our patient care and wanted to explore the role that the latest sequencing technologies could play in the control of infections in hospitals, Dr. Nick Brown, consultant microbiologist at the Health Protection Agency and infection control doctor at Addenbrookes Hospital Cambridge, said in a statement.

What we have glimpsed through this pioneering study is a future in which new sequencing methods will help us to identify, manage and stop hospital outbreaks and deliver even better patient care, added Brown.

Doctors were concerned when they started detecting MRSA in babies at Rosie Hospital in Cambridge. In all, doctors found infections in 12 babies at the facilitys maternity ward during routine screening. But their testing could not give them a clear picture if the infection was from a single outbreak or if separate cases were being brought into the hospital.

With no other alternatives, doctors turned to science for an answer.

In their study, the researchers analyzed MRSA isolates in the 12 babies with DNA sequencing technology and demonstrated clearly that all the MRSA bacteria were closely related, indicating there was an official outbreak. Their study also showed the outbreak was more extensive than previously realized, discovering that more than twice as many people were carrying or were infected with the same strain. Many of these additional cases were people who had recent links to the hospital but were otherwise healthy and living in the community when they developed a MRSA infection.

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Researchers Put An End To MRSA Superbug After Successful Genome Sequencing

T. J. Tabasco, star of the show.

Lawrence Schook

T. J. Tabasco is something of a porcine goddess at the University of Illinois, Urbana-Champaign, where her ruddy, taxidermied head looks down from the office wall of geneticist Lawrence Schook. Now she has been immortalized in this weeks Nature1 not by name, but by the letters of her DNA.

Scientists are salivating. For the past couple of decades they have been slowly teasing information from the pig genome, applying it to breed healthier and meatier pigs, and to try to create more faithful models of human disease. This weeks draft sequence of T. J.s genome (see page 393), with its detailed annotation a reference genome will speed progress on both fronts, and perhaps even allow pigs to be engineered to provide organs for transplant into human patients. Agriculture in particular will benefit fast, says Alan Archibald of the Roslin Institute in Edinburgh, UK, one of the papers lead authors. The pig industry has an excellent track record for rapid adoption of new technologies and knowledge.

T. J., a domestic Duroc pig (Sus scrofa domesticus), was born in Illinois in 2001. The next year, Schook and his colleagues generated a fibroblast cell line from a small piece of skin from her ear and commissioned clones to be created from it, so that they could work on animals all with the same genome. One set of clones was created at the National Swine Resource and Research Center (NSRRC) in Columbia, Missouri, along with genetically engineered pigs with genes added or deleted to mimic human diseases.Making such pigs has got increasingly easier as knowledge of the genome increases, says physiologist Randall Prather, a co-director of the NSRRC, which is funded by the National Institutes of Health (NIH).

Geneticist Martien Groenen, part of the team that sequenced the pig genome, chews the fat with Thea Cunningham.

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The NIH launched the NSRRC in 2003 to encourage research in pig disease models. Pigs are more expensive to keep than rodents, and they reproduce more slowly. But the similarities between pig and human anatomy and physiology can trump the drawbacks. For example, their eyes are a similar size, with photoreceptors similarly distributed in the retina. So the pig became the first model for retinitis pigmentosa, a cause of blindness. And four years ago, researchers created a pig model of cystic fibrosis2 that, unlike mouse models, developed symptoms resembling those in humans.

Geneticist and veterinarian Eckhard Wolf at the Ludwig-Maximilian University in Munich, Germany, has exploited the similarity between the human and pig gastrointestinal system and metabolism like us, pigs will eat almost anything and then suffer for it to develop models of diabetes. One pig model carries a mutant transgene that limits the effectiveness of incretin, a hormone required for normal insulin secretion3. Mice with the transgene developed unexpectedly severe diabetes, but the pigs have a more subtle pre-diabetic condition that better models the human disease. This shows the importance of using an animal with a relevant physiology, says Wolf.

Pig models are now being developed for other common conditions, including Alzheimers disease, cancer and muscular dystrophy. This work will be enriched by the discovery, reported in the genome paper, of 112 gene variants that might be involved in human diseases. Knowledge of the genome is also allowing scientists to try to engineer pigs that could be the source of organs, including heart and liver, for human patients. Pig organs are roughly the right size, and researchers hope to create transgenic pigs carrying genes that deceive the immune system of recipients into not rejecting the transplants.

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Pig geneticists go the whole hog

Various genomic tricks help Bactrian camels to live in harsh conditions, and give them an ability to regulate insulin signalling pathways and withstand massive blood glucose and salt levels

By Nidhi Subbaraman and Nature magazine

Bactrian camels have evolved to live in very cold and dry climates. Image: He Meng

Sky-high blood glucose levels, a diet loaded with salt and a tendency to pack away fat sounds like a recipe for a health disaster in a human. But in a Bactrian camel, these are adaptations that may help it survive in some of the driest, coldest and highest regions of the world.

Researchers in Mongolia and China have begun to unravel the genomic peculiarities behind the physiological tricks that camels use to survive in the harshest of conditions. In a paper published today in Nature Communications, the scientists describe the draft genomes of wild and domesticated Bactrian camels.

When they first explore a new genome, geneticists are most interested in the rapidly evolving sections. These hot zones of activity typically contain genes that define the species, coding for the characteristics that set it apart from its closest relatives.

We found that many genes related to metabolism are under accelerated evolution in the camel, compared with other even-toed ungulates such as cattle, says Yixue Li, director of the Shanghai Center for Bioinformation Technology in China and a co-author of the paper.

All in the blood Camels, as ruminants like cattle and sheep, digest food by chewing the cud. But many of the Bactrian genome's rapidly evolving genes regulate the metabolic pathway, suggesting that what camels do with the nutrients after digestion is a whole different ball game. It was surprising to me that they had significant difference in the metabolism, says Kim Worley, a molecular geneticist at Baylor College of Medicine in Houston, Texas. The differences could point to how Bactrians produce and store energy in the desert.

The work shows that camels can withstand massive blood glucose levels owing in part to changes in genes that are linked to type II diabetes in humans. The Bactrians' rapidly evolving genes include some that regulate insulin signaling pathways, the authors explain. A closer study of how camels respond to insulin may help to unravel how insulin regulation and diabetes work in humans. Im very interested in the glucose story, says Brian Dalrymple, a computational biologist at the Queensland Bioscience Precinct in Brisbane, Australia.

The researchers also identified sections of the genome that could begin to explain why Bactrian camels are much better than humans at tolerating high levels of salt in their bloodstreams. In humans, the gene CYP2J controls hypertension: suppressing it leads to high blood pressure. However, camels have multiple copies of the gene, which could keep their blood pressure low even when they consume a lot of salt, suggest the authors of the latest work.

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Camel Genome Holds Desert Survival Secrets

By Kate Kelland ReutersResearchers have used DNA sequencing for the first time to identify, analyze and put a halt to an infectious disease outbreak in a hospital.

The success of the technique, which used fast genome sequencing technology to control an outbreak of the MRSA superbug on a baby ward, suggests it could be used to control hospital bugs, salmonella and E.coli infections and diseases like tuberculosis, scientists said.

"What we have glimpsed through this pioneering study is a future in which new sequencing methods will help us to identify, manage and stop hospital outbreaks," said Nick Brown, an infection control doctor at Addenbrooke's Hospital Cambridge, who co-led the study and presented the findings at a briefing.

MRSA, or methicillin-resistant staphylococcus aureus, is a drug-resistant bacterial infection, or superbug, and a serious public health problem. When outbreaks occur in hospitals it can lead to the closure of whole wards with many people infected.

The bug kills an estimated 19,000 people in the United States per year. Although rates of MRSA infection have come down significantly in Britain in recent years, it still presents a major threat with several hundred deaths a year and high hospital costs involved in managing infected patients.

Julian Parkhill from Britain's Sanger Institute, who also worked on the study, said there is a "real health and cost burden from hospital outbreaks" which could be significantly reduced or eliminated if they were contained swiftly.

In the study, staff at Addenbrooke's hospital using routine screening over a six month period found 12 patients carrying MRSA. Because they were only using standard tests, which provide limited information, the infection control team was not able to tell if the 12 were part of an outbreak, or were unconnected cases that did not present a threat.

MRSA is a bug present in around one percent of the population at any time, and does not always cause infection.

Parkhill and Brown's team analyzed MRSA samples from the 12 patients with DNA sequencing technology and found that all the MRSA bacteria were closely related, confirming an outbreak.

By tracing relatives and other people who had recent links to the hospital, they also found the outbreak was more extensive than previously thought, with twice as many people carrying or infected with the MRSA strain.

Excerpt from:
Genome sequencing halts superbug outbreak

LONDON (Reuters) - Researchers have used DNA sequencing for the first time to identify, analyze and put a halt to an infectious disease outbreak in a hospital.

The success of the technique, which used fast genome sequencing technology to control an outbreak of the MRSA superbug on a baby ward, suggests it could be used to control hospital bugs, salmonella and E.coli infections and diseases like tuberculosis, scientists said.

"What we have glimpsed through this pioneering study is a future in which new sequencing methods will help us to identify, manage and stop hospital outbreaks," said Nick Brown, an infection control doctor at Addenbrooke's Hospital Cambridge, who co-led the study and presented the findings at a briefing.

MRSA, or methicillin-resistant staphylococcus aureus, is a drug-resistant bacterial infection, or superbug, and a serious public health problem. When outbreaks occur in hospitals it can lead to the closure of whole wards with many people infected.

The bug kills an estimated 19,000 people in the United States per year. Although rates of MRSA infection have come down significantly in Britain in recent years, it still presents a major threat with several hundred deaths a year and high hospital costs involved in managing infected patients.

Julian Parkhill from Britain's Sanger Institute, who also worked on the study, said there is a "real health and cost burden from hospital outbreaks" which could be significantly reduced or eliminated if they were contained swiftly.

In the study, staff at Addenbrooke's hospital using routine screening over a six month period found 12 patients carrying MRSA. Because they were only using standard tests, which provide limited information, the infection control team was not able to tell if the 12 were part of an outbreak, or were unconnected cases that did not present a threat.

MRSA is a bug present in around one percent of the population at any time, and does not always cause infection.

Parkhill and Brown's team analyzed MRSA samples from the 12 patients with DNA sequencing technology and found that all the MRSA bacteria were closely related, confirming an outbreak.

By tracing relatives and other people who had recent links to the hospital, they also found the outbreak was more extensive than previously thought, with twice as many people carrying or infected with the MRSA strain.

The rest is here:
Scientists use genome sequencing to halt superbug outbreak

November 14, 2012

Brett Smith for redOrbit.com Your Universe Online

A massive team of international researchers has announced the successful sequencing of the first female domestic pigs genome.

There have already been may similarities established between pigs and humans and the new genomic analysis reveals some new twists and a few distinctions to that relationship, according to reports on the work published in the journals Nature and Proceedings of the National Academy of Sciences (PNAS).

It is exciting that the genomic sequence of the domestic pig now is in the public domain and available to enable more powerful approaches to domestic swine and pork improvement, said Ronnie Green, from University of Nebraska and an early supporter of the pig genome sequencing project at the U.S. Department of Agriculture (USDA). It will also aid efforts to use the pig as a model for biomedical research and the improvement of human health.

Besides having utilitarian implications, the project also told the story of the pig by comparing it to the known genetic code of wild boars that originated in Southeast Asia about 4 million years ago. The genetic analysis showed that domestication of these animals started nearly 10,000 years ago, across various parts of Europe and Asia.

Wild boars bred with pigs throughout their domestication, but the two groups of pigs have maintained many distinct features. Domesticated pigs have a considerably longer back, and therefore more vertebrae. Researchers from Uppsala University and the Swedish University of Agricultural Sciences (SLU) that were involved in the project identified three gene regions that form the genetic basis for this difference. They also found that two of the regions correspond to genes that influence variation in body length in humans.

The researchers also compared the genome to the genetic codes of other mammals and found that the immune response genes are rapidly evolving. They also found several places where pig genes resembled human genes that are associated with disease, such as diabetes or Alzheimers. These discoveries extend the potential of pigs to shed light on both viral and genetic diseases.

One pig genome that was sequenced, the Wuzhishan pig, could provide additional advantages for medical science. Due to its small size and long history of inbreeding, these pigs are easy to handle and have a population composed of mostly genetically identical individuals.

Because the Wuzhishan pig shares several diseases with humans, its genome will provide a wealth of genetic information that will allow a detailed analysis on how the animal reacts to human drug target genes.

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Pig Genome Sequenced: Offers Significant Implications Abroad

LONDON (Reuters) - Scientists have mapped the genome of the domestic pig in a project that could enhance the animal's use in the testing of drugs for human disease.

A study, published in science journal Nature, identified genes that could be linked with illnesses suffered by farmed pigs, providing a reference tool for selective breeding to increase their resistance to disease.

"This new analysis helps us understand the genetic mechanisms that enable high-quality pork production, feed efficiency and resistance to disease," said Sonny Ramaswany, director of the U.S. Department of Agriculture's National Institute of Food and Agriculture.

"This knowledge can ultimately help producers breed high-quality swine, lower production costs and improve sustainability."

Alan Archibald at the University of Edinburgh's Roslin Institute in Scotland, who worked on the project with collaborators in the Netherlands and the United States, said the new genome sequence was the first good draft.

Archibald said while making sense of the analysis would take time, the benefits of genome sequencing flow through more quickly in agriculture than, for instance, human medicine, "because we can use selective breeding".

Identifying genes responsible for diseases that are also seen in people could see pigs used more extensively for drug testing.

For instance, the inherited illness known as porcine stress syndrome, which can cause sudden death in pigs, has similarities to the human condition malignant hyperthermia which causes a fast and dangerous rise in body temperature in some people under general anaesthetic.

Some of the genetic faults that pigs share with humans can be linked with conditions as varied as Alzheimer's disease, diabetes, dyslexia, obesity and Parkinson's disease, the researchers said.

"In total, we found 112 positions where the porcine protein has the same amino acid that is implicated in a disease in humans," they said. (Editing by Dan Lalor)

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Scientists map domestic pig's genome

LONDON (Reuters) - Scientists have mapped the genome of the domestic pig in a project that could enhance the animal's use for meat production and the testing of drugs for human disease.

A study published in science journal Nature identified genes that could be linked with illnesses suffered by farmed pigs, providing a reference tool for selective breeding to increase their resistance to disease.

"This new analysis helps us understand the genetic mechanisms that enable high-quality pork production, feed efficiency and resistance to disease," said Sonny Ramaswany, director of the U.S. Department of Agriculture's National Institute of Food and Agriculture.

"This knowledge can ultimately help producers breed high-quality swine, lower production costs and improve sustainability."

Alan Archibald at the University of Edinburgh's Roslin Institute in Scotland, who worked on the project with collaborators in the Netherlands and the United States, said the new genome sequence was the first good draft.

Archibald said while making sense of the analysis would take time, the benefits of genome sequencing flow through more quickly in agriculture than, for instance, human medicine, "because we can use selective breeding".

Identifying genes responsible for diseases that are also seen in people could see pigs used more extensively for drug testing.

For instance, the inherited illness known as porcine stress syndrome, which can cause sudden death in pigs, has similarities to the human condition malignant hyperthermia which causes a fast and dangerous rise in body temperature in some people under general anesthetic.

Some of the genetic faults that pigs share with humans can be linked with conditions as varied as Alzheimer's disease, diabetes, dyslexia, obesity and Parkinson's disease, the researchers said.

"In total, we found 112 positions where the porcine protein has the same amino acid that is implicated in a disease in humans," they said.

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Scientists go the whole hog in genome mapping