Monthly Archives: November 2012

Public release date: 15-Nov-2012 [ | E-mail | Share ]

Contact: Frank Blecha blecha@k-state.edu 785-532-4537 Kansas State University

MANHATTAN, Kan. -- An international scientific collaboration that includes two Kansas State University researchers is bringing home the bacon when it comes to potential animal and human health advancements, thanks to successfully mapping the genome of the domestic pig.

The sequenced genome gives researchers a genetic blueprint of the pig. It includes a complete list of DNA and genes that give pigs their traits like height and color. Once all of the genetic information is understood, scientists anticipate improvements to the animal's health as well as human health, as pigs and humans share similar physiologies.

"With the sequenced genome we have a better blueprint than we had before about the pig's genetics and how those genetic mechanisms work together to create, such as the unique merits in disease resistance," said Yongming Sang, research assistant professor of anatomy and physiology at Kansas State University.

For three years, Sang worked on the genome sequencing project with Frank Blecha, associate dean for the College of Veterinary Medicine and university distinguished professor of anatomy and physiology.

A report of the international study appears as the cover story for the Nov. 15 issue of the journal Nature.

The sequencing effort was led by the Swine Genome Sequencing Consortium. Researchers with the consortium invited Sang and Blecha to work on the project because of their expertise and published studies on the antimicrobial peptides and interferons that pigs use to genetically defend themselves against disease.

Sang and Blecha focused on these two families of immune genes, looking for gene duplications and gene-family expansions throughout the pig's 21,640 protein-coding genes, in an effort to help scientists with future pig-related research.

Sang also completed much of the genome annotation for Kansas State University's contributions. Genome annotation involves identifying, categorizing and recording the potential functions of thousands of individual genes and gene cluster locations in the pig genome.

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Researchers sequence swine genome , discover associations that may advance animal and human health

A new DNA sequencing technique has enabled researchers to map for the first time the influential chemical modifications known as methylation marks throughout the genome of a pathogenic bacterium. By comparing these patterns between related strains of the bacteria, they stumbled upon a way that viruses that infect bacteria (known as bacteriophages) can dramatically alter their host.

Howard Hughes Medical Institute investigator Matthew K. Waldor of Brigham and Womens Hospital, led the new study in collaboration with Eric Schadt at Mount Sinai School of Medicine. Their findings were published November 8, 2012, in the journal Nature Biotechnology.

This is like having a new microscope that can see things never before visible. Matthew K. Waldor

Waldor had been studying the strain of E. coli blamed for the large 2011 outbreak of illness in Germany. He says it was clear from the early stages of the outbreak that the pathogen causing the illness were not typical, and he was curious about what gave rise to their unusual virulence. In the course of their investigation, he and his colleagues observed that certain genes were methylated differently in the disease-causing E. coli strain (E. coli O104:H4) than they were in less virulent strains.

An organism's essential genetic blueprint lies in the sequence of nucleotides that make up its DNA, but additional information is encoded in chemical modifications to those nucleotides. In animals and plants, methylation -- the addition of methyl groups to specific DNA sites -- is known to turn off genes. In a few model bacterial species, DNA modification is known to influence chromosome replication, gene expression, and virulence. But scientists lack a complete picture of the effects of DNA methylation in bacterial genomes.

When Waldor and his colleagues investigated the altered pattern of methylation they had observed, they noticed that a unique bacteriophage (a virus) had infected the virulent E. coli strain. Furthermore, when that bacteriophage invaded the bacterial cell, it came equipped with a protein that can add methyl groups to their DNA.

We wondered whether the phages methylation system would influence the methylation of the bacteria it infected, says Waldor, and whether it could even influence the virulence of the organism.

To answer this question, Waldors team turned to a relatively new technique called single-molecule real-time (SMRT) DNA sequencing. Most methods for sequencing DNA report only the sequence of adenines, cytosines, guanines, and thymines the four nucleotides, or bases, that make up the genetic code. But SMRT sequencing works differently. With this technique, you monitor DNA synthesis and at the same time you get information about the order of the bases, you also get information about the kinetics of how each base is added, Waldor explains. In 2010, researchers at Pacific Biosciences discovered that chemical modifications of the bases change these kineticsthe addition of a base might be slowed down if the template base has a methyl group attached, for example.

That suggested that the chemical modifications of genes could be mapped out using SMRT sequencing. Waldors group went even further than analyzing a single gene: they used SMRT to map the methylation patterns of the entire E.coli O104:H4 genome. They found more than 50,000 methylated sites. Our paper is the first to show that this technique really can be used on a genome-wide level with single nucleotide resolution, says Waldor.

The scientists went on to show that the E. coli strain they were studying has eleven enzymes for controlling methylation. Seven of these enzymes, called methyltransferases, had never been researched before. Waldors group determined what gene sequences these methyltransferases tended to add methyl groups to. Then they devoted their attention to the methyltransferase donated to the disease-causing E.coli O104:H4 from the bacteriophage that had infected it.

Originally posted here:
Genome -wide Methylation Map of Disease-Causing E. coli Reveals Surprises

Could bacon get any tastier?

Pig scientists and breeders say indeed it could, now that the pig genome has been sequenced and a trove of new genetic information is available.

Tenderness, fat content and meat color are targets for breeders hoping to improve the pork on our plates.

Tenderness, fat content and meat color are targets for breeders hoping to improve the pork on our plates.

The Swine Genome Sequencing Consortium, an international group of researchers, published their analysis of the genome this week in Nature.

The group spelled out the pattern of DNA on all of the chromosomes of a female domesticated pig. That data is now freely available to anyone in swine science and beyond.

For thousands of years, humans have been breeding swine, choosing pigs that had favorable traits such as bigger size or leaner meat to create a new generation of pigs with those characteristics.

With the full genome, breeders will now be able to pinpoint the specific genes behind those traits. They will take "pigs that have at least one copy of the favorable version [of a gene] and use that pig to breed the next generation," says Jack C.M. Dekkers, a professor of animal breeding and genetics at Iowa State University in Ames. Some researchers may even use the information to do genetic modification of pigs.

The animal was a prime candidate for genome sequencing because it is a model for biomedical research and a critically important food source, notes Lawrence Schook, vice president for research at the University of Illinois and a co-author on the study.

Tastier pork could certainly be an outcome of this research, too, Schook and Dekkers say. What makes a pig tasty, however, is subject to debate and cultural preference. In some parts of Asia, Schook notes, breeders value fat content more than American breeders do.

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Pig Genome Project May Pave The Way For Better Bacon