Category Archives: Genome

Fast Turn-Around Genotyping without a Reference Genome #PAGXXIII
Dr. James Schnable from the University of Nebraska-Lincoln has developed a technology called #39;tunable Genotyping by Sequencing #39; (tGBS) http://www.data2bio.co...

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Fast Turn-Around Genotyping without a Reference Genome #PAGXXIII - Video

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NVIDIA GPUshave been used to uncover the inner workings of the human genome, finding that it works in folds in the same way as origami.

Researchers from Baylor College of Medicine, Rice University, MIT and Harvard University said they used the graphics processors to map in unprecedented detail how the human genome folds.

This new information might provide new clues for cell function as well as new approaches to combat cancer and other complex diseases, Nvidia said.

Led by Erez Aiden, assistant professor of genetics at Baylor and assistant professor of computer science and computational and applied mathematics at Rice, the project found that the human genome is folded into around 10,000 loops.

These loops form when two widely separated bits of DNA come into contact in the folded version of the genome in a cell's nucleus.

The researchers learned that these loops and other genome folding patterns are an essential part of genetic regulation.

Genes can be switched on or off just by folding the genome into different shapes, allowing cells to take on a wide range of functions.

The research team relied on high-performance computer clusters and custom algorithms via the Nvidia GPUs to analyse large quantities of genome data.

"We faced a real challenge because we were asking how each of the millions of pieces of DNA in the database interact with each of the other millions of pieces," said Miriam Huntley, a doctoral student at Harvard's School of Engineering and Applied Sciences.

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Nvidia GPUs could help combat cancer in human genome research

Consumer doggie DNA testing is old hat at this point, having been around since 2007. But cat-lovers who wish to decipher their pets breed are out of luck no such tests exist for felines.

That fact reflects the state of the underlying science. Since the first full dog genome was sequenced ten years ago, geneticists have identified hundreds of genes behind canine diseases and physical traits. By comparison, just a handful of such genes have been identified in cats.

But a group of geneticists is working to close this gap by sequencing 99 domestic cats. This week the researchers unveiled the first results from their 99 Lives initiative.

In 2007, the first cat genome sequenced was that of an Abyssinian named Cinnamon. However, errors and gaps in the data stalled efforts to map genes, and the complete, high-resolution genome wasnt published until 2014. Cinnamons genome taught us that domestic cats arent vastly different than their wild counterparts, despite 9,000 years of domestication.

Dogs have been the clear favorite of geneticists because they suffer from many of the same ailments as humans and their intensive inbreeding makes it easy to spot gene variations. Further, according to Nature, dogs also benefit from a bloc of enthusiastic breeders, veterinarians and owners who make recruiting easy for dog geneticists.

To balance the scales, geneticist Leslie Lyons of the University of Missouri launched the 99 Lives initiative. Its goals are simple: to expand coverage of the cat genome, improve the quality of data and identify genetic variations behind specific feline diseases.

But humans could also be beneficiaries of the research. According to Nature, Cat versions of type 2 diabetes, asthma, retinal atrophy and numerous other conditions have close similarities to human disease. Cats can also become infected with a virus that is closely related to HIV and experience symptoms similar to those of people with AIDS.

To date, Lyons team has sequenced the genomes of 56 cats at a cost of roughly $7,500 apiece. Funding for the research has been raised through donations from breeders and private owners alike. Currently, her team is studying the genetic basis of feline dwarfism and the genes that give cats silver or gold coats, to name a few.

You can help further cat genome researcher through donations, or collecting DNA samples from your own feline friends. You can learn how to participate by visiting Lyons website.

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Cats Are Finally Getting Geneticists' Attention

Juicebox VR creates a virtual reality representation of data generated by the Hi-C method for three-dimensional genome sequencing. Every 2D position in the landscape corresponds to a pair of 1D positions, or loci, in the three-billion-letter-long human genome. The height at the 2D position represents how often the two loci are in contact in the nucleus of a cell.Since nearby loci frequently bump into one another, a massive 'wall' of short-range contacts bisects the landscape. Square plateaus coming off the diagonal correspond to condensed genomic domains, called contact domains. Peaks in the landscape correspond to loops in the genome. Contact domains are often demarcated by loops, which is why the square domains frequently have peaks in their corner.The controller will fly in whichever direction you look. Look straight up for a super jump.Juicebox VR was created by Muhammad Shamim, Ido Machol, and Erez Lieberman Aiden.The data is drawn from:Suhas Rao*, Miriam Huntley*, Neva C. Durand, Elena Stamenova, Ivan Bochkov, Jim Robinson, Adrian Sanborn, Ido Machol, Arina Omer, Eric Lander and Erez Lieberman Aiden. A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping, Cell (2014).* contributed equallyNote that the data used to generate the landscape is an extremely tiny region from a full, genome-wide map. The full contact map for the human genome is a trillion times larger than this map.Learn more about our work at http://www.aidenlab.org.Music: Ascent by StellardroneIMPORTANT: To properly view the app, a Virtual Reality headset, such as Google Cardboard, Durovis Dive, or Samsung Gear VR should be used.Content rating: Everyone

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Juicebox VR

Finding the Telltale Genome
Whenever a cell divides, its genetic code is copied into the new cell. But sometimes an imperfect copy is made, and the result is called a mutation. Most of the time, this does nothing; sometimes...

By: World Science Festival

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Finding the Telltale Genome - Video

14.01.2015 - (idw) Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH

Genome of the Escherichia coli type strain finally sequenced DNA includes potentially pathogenic segments The colon bacillus Escherichia coli is one of the best studied model organisms in the life sciences. However, the reference organism for this species, its so-called type strain, has been overlooked in microbial genomics until now. In the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, the DNA of type strain DSM 30083T has now been sequenced and compared to that of close relatives of the strain. This study not only allows an entirely new view of the numerous E. coli strains that play relevant roles in medicine and biotechnology, including the EHEC pathogen and Shigella, but they also yielded a generally applicable method for determining the subspecies of any bacterial species. The research was conducted at the Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures GmbH, Braunschweig, Germany, and at the Joint Genome Institute, Walnut Creek, CA, USA.

The colon bacterium Escherichia (E.) coli to microbiologists and biotechnologists is like a pet bacterium and looks back on an exciting history. Initially described as "Bacterium coli commune" by bacteriologist Theodor Escherich in 1886, its original isolate was lost at the beginning of the 1920s. It was not until 1941 that it was isolated again, this time by Fritz Kaufmann at the State Serum Institute in Copenhagen, Denmark, who also deposited it in in several collections of microbial strains and provided a scientific description. Today, E. coli is likely the best understood microorganism in the world and serves as an important indicator for the quality of drinking and recreational waters.

"It seems strange that the number one, the type strain of a bacterium that has entire scientific conferences dedicated to it as a model organism, had not been fully sequenced until now", said Christine Rohde, Head of the E. coli strain collection at DSMZ, Braunschweig, Germany. "Initially, scientists primarily sequenced the genomes of pathogenic strains of E. coli, or of genetically modified strains of biotechnological relevance. In addition, physicians and hygienists in their daily practice use serotypes that are quickly determined by antibody tests in order to differentiate between different strains of E. coli. As Markus Gker, a bioinformatics scientist at DSMZ added: Complete bacterial genomes are of fundamental importance for diagnostics in humans, for biotechnology, and for the search for antimicrobial agents. Today, this is truer than ever, as some strains of E. coli have developed into dangerous pathogens such as EHEC or EAHEC. The E. coli type strain was sequenced as part of the GEBA project that focuses on type strains exhibiting an unusual physiology or occupying a key place in the phylogenetic tree. This is the only microorganism in the project that was included based on its importance as a model organism.

A genome with pathogenic potential

There are major physiological and genomic differences between the E. coli type strain and the harmless laboratory strain K-12. Due to its serotype, the type strain had been grouped into the biological containment level 2, and its genome sequence now confirmed its pathogenic potential, said Jrn Petersen, an expert of plasmid biology at the DSMZ. Unlike laboratory strain K-12, the E. coli type strain harbors an additional circular plasmid of 131,289 base pairs in its genome of 5,038,133 base pairs; this plasmid exhibits a sequence identity of 99% with plasmids from pathogenic E. coli isolates. These strains cause, e.g., colibacillosis in poultry and meningitis in newborns, with the horizontally transferable plasmid being responsible for their virulence, explained Petersen.

Sophisticated computer-aided phylogenetic analysis

Thanks to the complete genome sequence of the E. coli type strain, the Braunschweig scientists were able to examine whether the huge number of previously sequenced isolates of E. coli actually belong to the same species, using modern taxonomic techniques in the process. To this end, we analyzed more than 250 strains of E. coli and also verified their published taxonomic classification in subgroups, the 'phylotypes'. This bioinformatics-based analysis was performed with the state-of-the-art GGDC method. This technique is analogous to classical DNA-DNA hybridization in the laboratory, but yields significantly more exact results," as Markus Gker explained.

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Meier-Kolthoff JP et al. (2014). Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy. Stand Genomic Sci 9: 2 http://www.standardsingenomics.com/content/pdf/1944-3277-9-2.pdf

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The Number One of Enterobacteria Deciphered

The genetic sequencing of cats has now officially taken off

The first cat genome sequence from an Abyssinian named Cinnamon was reported in 2007. Credit:Valerius Geng via Wikimedia Commons

Cats may have beaten dogs on the Internet but felines have been a rare breed in genetics labs compared with their canine counterparts. Now, at last, cats are clawing their way into genomics.

At a meeting this week in San Diego, California, a close-knit group of geneticists unveiled the first results from an effort to sequence the genomes of 99 domestic cats. The work will benefit both humans and felines, the researchers say, by mapping the mutations underlying conditions that afflict the two species, such as kidney disease.

Its a great time to be in cat genomics, says William Murphy, a geneticist at Texas A&M University in College Station who is involved in the effort. Plummeting costs for DNA sequencing now make it possible to do genomics cheaply and cat genomics, long under-funded compared with similar efforts in dogs, is benefiting, he says. Were finally at the point where we can do all sorts of things we wanted to do 5 or 10years ago.

The first cat genome sequence from an Abyssinian named Cinnamon was reported in 2007. But the sequence contained significant gaps and errors, which slowed efforts to map genes. A high-quality version of Cinnamons genome was not publisheduntil late 2014. Domestic dogs, meanwhile, have become a darling of geneticists: their full genomewas reported in 2005, and the sequence has been continually improved. Hundreds of genes underlying canine diseases and traits are estimated to have been discovered, compared with as few as a dozen for cats.

The discrepancy can be traced back to the early 2000s. After the completion of the human, mouse and rat genomes, the US National Institutes of Health organized a commission to decide on their next target; the dog genome was selected for high-quality sequencing, whereas cats were put on hold.

That got some cat geneticists backs up. The truth is there were more powerful people interested in dogs, says Stephen OBrien, director of the Theodosius Dobzhansky Center for Genome Bioinformatics in StPetersburg, Russia, who led the initial cat-sequencing efforts.

But canine researchers were able to make a compelling case. Pet dogs suffer from many of the same conditions as humans, from narcolepsy to arthritis. And the intensely inbred nature of dog breeds made it relatively easy to identify disease-causing genes: because there is little genetic variation within any particular breed, the genes that cause disease in affected individuals stand out.

Dogs had other advantages, too. The existence of kennel clubs, which maintain breed standards and are full of enthusiastic pet owners and veterinary surgeons, helped dog geneticists to recruit subjects for study. Given the resources they had, they were discovering new genetic diseases in breeds almost daily, says Niels Pedersen, a veterinary scientist at the University of California, Davis.

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Cats Claw Their Way into Genomics

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