Category Archives: Genome

16.11.2012 - (idw) Schwedischer Forschungsrat - The Swedish Research Council

In a major international study, the pig genome is now mapped. Researchers from Uppsala University and the Swedish University of Agricultural Sciences (SLU) have contributed to the study by analysing genes that played a key role in the evolution of the domesticated pig and by mapping endogenous retroviruses (ERV), retroviruses whose genes have become part of the host organisms genome. The findings are now being published in the journals Nature and PNAS.

Together with an international team of geneticists and retrovirologists, Uppsala University researchers have charted the pig genome.

The pig is one of our most important domesticated animals, and it was high time for its genome to be mapped, says Professor Leif Andersson, who participated in the project.

The major project to chart the pig genome shows that the wild boar originated in Southeast Asia about 4 million years ago. The findings also reveal that domestication started nearly 10,000 years ago, taking place in several independent locations all over the European and Asian land mass. It was also common that wild boar mixed with domesticated pigs, especially in Europe during early agriculturalisation, with free-ranging animals.

Uppsala researchers Patric Jern, Alexander Hayward, Gran Sperber, and Jonas Blomberg used the computer program RetroTector and detailed sequence comparisons in so-called phylogenetic studies to map the retrovirus part of the pig genome. What all retroviruses, such as HIV in humans, have in common is that they need to become part of the host cells genome in order to produce new viruses. When a germ line-cell is infected there is a chance for the virus to be passed on to the host organisms offspring, and for millions of years retroviruses remotely related to HIV have colonised vertebrates, leaving traces in their genetic make-up as endogenous retroviruses (ERV).

The researchers were able to see that pigs have fewer ERVs than humans, however, unlike human ERVs, some pig ERVs have the capacity to reproduce and infect, which might pose a risk when transplanting pig organs to humans. The article constitutes a baseline for assessing that risk, but it also provides an enhanced understanding of how retroviruses have spread among vertebrates in the course of their evolution.

Carl-Johan Rubin, Leif Andersson, and their associates have been in charge of looking for the genes that have had the greatest importance in the evolution of the domesticated pig. One of the most striking differences between the wild boar and the domesticated pig is that the latter has a considerably longer back, including more vertebrae. The researchers have now identified three gene regions that are critical for understanding this difference. Two of them correspond to genes that explain variation in body length in humans, another instance of genes having a very similar function across different species.

The findings are now being published in Nature and PNAS:

Groenen et al. (2012) Pig genomes provide insight into porcine demography and evolution, Nature, DOI: 10.1038/nature11622

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Finally! The pig genome is mapped

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 team of international researchers sequenced the genome of the domesticated pig, Sus scrofa domesticus, and compared it to the DNA sequences of 10 wild boars hailing from Asia and Europe. They also compared the pig genome to genomes from humans, mice, dogs, horses and cows.

The results were published in the journals Nature and the Proceedings of the National Academy of Sciences on Wednesday.

"This new analysis helps us understand the genetic mechanisms that enable high-quality pork production, feed efficiency and resistance to disease," Sonny Ramaswany, the director of the U.S. Department of Agriculture's National Institute of Food and Agriculture, said in a statement Wednesday. "This knowledge can ultimately help producers breed high-quality swine, lower production costs and improve sustainability."

One interesting tidbit is that pigs have more genes related to smell than humans, mice or dogs -- which is not surprising when you think of truffle-hunting pigs. One would think that with such a perceptive nose, the pig would be a picky eater. But the genetic analysis also found that pigs have significantly fewer taste receptors for bitter flavors, which may be why they can eat things that we would find disgusting.

"Understanding the genes that shape the characteristics of pigs can point to how and why they were domesticated by humans," Archibald said. "Perhaps it was their ability to eat stuff that is unpalatable to us humans."

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Pig Genome Sequenced, Scientists Bring Home Bacon

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.

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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

Chromatin - Wiki Article
Chromatin is the combination of DNA and proteins that make up the contents of the nucleus of a cell. The primary functions of chromatin are: to package DNA into a smaller volume to fit in the cell, t... Chromatin - Wiki Article - wikiplays.org Original @ http All Information Derived from Wikipedia using Creative Commons License: en.wikipedia.org Author: Richard Wheeler Image URL: en.wikipedia.org ( Creative Commons ASA 3.0 ) Author: Zephyris Image URL: en.wikipedia.org ( Creative Commons ASA 3.0 ) Author: By Richard Wheeler (Zephyris) 2005. Image URL: en.wikipedia.org ( Creative Commons ASA 3.0 ) Author: Zephyris Image URL: en.wikipedia.org ( Creative Commons ASA 3.0 ) Author: Julien Mozziconacci Image URL: en.wikipedia.org ( This work is in the Public Domain. ) Author: Courtesy: National Human Genome Research Institute Image URL: en.wikipedia.org ( This work is in the Public Domain. )From:WikiPlaysViews:0 0ratingsTime:14:15More inEducation

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Chromatin - Wiki Article - Video

Controlling MRSA by DNA sequencing
New, faster sequencing technologies have revolutionised our understanding of genomes, exemplified, for example, in the work of the ENCODE Consortium that described new exploration of the human genome. But it is in tackling infectious agents that widespread application of new sequencing technologies is likely to be used most quickly and comprehensively for healthcare improvement. This study used these new technologies to examine an outbreak of MRSA in a hospital, to uncover new cases and, as the study developed, to intervene in the outbreak to end it more quickly. Sequencing illuminated each person infected and described the transmission of MRSA between people coming to the hospital and within the hospital. This is believed to be the first time that sequencing has been used to close an infectious outbreak and will be published in Lancet Infectious Diseases.From:sangerinstituteViews:20 0ratingsTime:03:39More inScience Technology

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RNA.mp4
For more information, log on to- shomusbiology.weebly.com Download the study materials here- shomusbiology.weebly.com This video tutorial demonstrates the complex secondary and tertiary structures of RNA (ribonucleic acid) Ribonucleic acid (RNA) is a ubiquitous family of large biological molecules that performs multiple vital roles in the coding, decoding, regulation, and expression of genes. Together with DNA, RNA comprises the nucleic acids, which, along with proteins, constitute the three major macromolecules essential for all known forms of life. Like DNA, RNA is assembled as a chain of nucleotides, but is usually single-stranded. Cellular organisms use messenger RNA (mRNA) to convey genetic information (recorded using the letters G, A, U, and C for the nucleotides guanine, adenine, uracil and cytosine) that directs synthesis of specific proteins, while many viruses encode their genetic information using an RNA genome. Some RNA molecules play an active role within cells by catalyzing biological reactions, controlling gene expression, or sensing and communicating responses to cellular signals. One of these active processes is protein synthesis, a universal function whereby mRNA molecules direct the assembly of proteins on ribosomes. This process uses transfer RNA (tRNA) molecules to deliver amino acids to the ribosome, where ribosomal RNA (rRNA) links amino acids together to form proteins. The chemical structure of RNA is very similar to that of DNA, with two ...From:Suman BhattacharjeeViews:0 0ratingsTime:49:32More inEducation

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RNA.mp4 - Video

[Mokona] Daidai Genome ~Cover~
( #65417; #9685; #12526; #9685;) #65417;*: #65381; #65439; #10023; Kimi ga suki desu~ This song is super cute~ *forever squealing* I love the beginning so much it sounds so pretty~ :3 I listened to this song for about.... 3 hours straight~ nonstop xD kekekeke Hope you like it~ :3 OoO Song Title: Daidai/Orange Genome Original Singer: Hatsune Miku Music: #12388; #12394; #12414; #12427; (tsunamaru/mezamep) Lyrics: #12388; #12394; #12414; #12427; (tsunamaru/mezamep) Illustration: f*cla Movie:Not-116 Mastering: #12431; #12371; #12388; #65328; English Translation: LaXnyd (www.youtube.com English Subtitles: Coleena Wu (www.youtube.com *~*~*~*~*~* Facebook: http://www.facebook.com Twitter: twitter.com Tumblr: kuromokonachan.tumblr.com Instagram: Kuromokonachan --- Copyright Disclaimer Under Section 107 of the Copyright Act 1976, allowance is made for "fair use" for purposes such as criticism, comment, news reporting, teaching, scholarship, and research. Fair use is a use permitted by copyright statute that might otherwise be infringing. Non-profit, educational or personal use tips the balance in favor of fair use.From:KuroMokonaChanViews:0 2ratingsTime:03:41More inMusic

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[Mokona] Daidai Genome ~Cover~ - Video

GENOME: METABOLIC REACTIONS: GLYCOLYSIS
METABOLIC REACTIONS: GLYCOLYSISFrom:drjahn41Views:0 0ratingsTime:01:07More inScience Technology

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GENOME: METABOLIC REACTIONS: GLYCOLYSIS - Video