Category Archives: Genome

DNA Sequencing
Rashmi Okay so we are teaching DNA sequencing (DS) , so obviously the first question that comes into mind is what is DS? Does any one know? **Wait for audience to reply** Simran (Yes/No) DS is any process used to map out the sequence of Nucleotides that make up the DNA Strand, and we use it to completely analyze a particular gene #39;s structure and how it is related to its expression and specific polypeptide production Enghuot The Sanger dideoxy method was developed in 1977 by Frederick Sanger and his colleagues using the principles of DNA replication -- a process that requires a single stranded DNA template, a primer, DNA polymerase, and free nucleoside triphosphates. Rashmi Sanger and his colleagues managed to determined the sequence of the an entire genome of a bacteriophage containing 5386 base pairs. Simran Okay, now we are going to explain the Sanger Dideoxy Method. If you turn to page 301 you #39;ll see what we are talking about. Enghuot The first thing that happens is that the DNA template is heated until the two strands are separated. Rashmi We take one of the strands and add a short, single-stranded radioactively-labeled primer to the end of it. In Sanger #39;s method, 4 reaction mixtures are set up. Each one including a primed single stranded DNA to be sequenced, DNA Polymerase, a supply of nucleotides ACGT, and a small amount of labelled chain terminating variant of one of the nucleotides. Simran The last is known as a dideoxy analogue, this is a dideoxynucleotide ...From:Rashmi PrakashViews:0 0ratingsTime:06:41More inEducation

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DNA Sequencing - Video

SAN FRANCISCO, Nov. 28, 2012 (GLOBE NEWSWIRE) -- The Agency for Science, Technology and Research's (A*STAR) Genome Institute of Singapore (GIS) today announced the launch of a research collaboration with Appistry, a leading US-based provider of high-performance computing and analytics for managing and storing "big data."

"We are excited about this collaboration as it leverages on our computational genomics platform," said Professor Huck Hui NG, GIS executive director. "Through this collaboration, we will develop a pipeline which enables us to analyze next generation sequencing data more effectively."

"Appistry's technology will enable GIS to take a huge amount of data and rapidly advance their analytics and efficiently use their science to improve public health," said Sultan Meghji, Appistry's vice president of product strategy, who is speaking today on life science's "big data" challenge at the World Genome Data Analysis Summit in San Francisco.

GIS strategically focuses on scientific discovery through a fusion of genomic and computational approaches with cell and medical biology. The collaboration is dedicated to accelerating the development of research methods and discoveries in human genome analytics and genomics. GIS aims to act as an Asian hub for collaboration among clinical genomics researchers in many pioneering fields, including clinical diagnostics and cancer biology.

"We expect this collaboration to inspire, enable, and accelerate efforts in the emerging field of complex pedigree and traits analytics and to catalyze discoveries and advance the understanding of this important area of biology," said Prof. Michael Rossbach, head of the Office of Business Development at GIS.

GIS's regional research collaboration with Appistry builds upon Appistry's recent selection as the distributor for The Broad Institute's next generation Genome Analysis Tool Kit (GATK), the world's most widely used software for data processing and variant calling of next-generation sequencing data.

"The push toward translational and personalized medicine requires organizations to wrap their science within systems and applications that can provide actionable results from big data," said Meghji. "Our global partnership with Broad and our regional partnership with GIS better enable our customers to capture the scientific best practices and capabilities they need in an environment that scales to modern throughput demands."

Meghji's presentation at the World Genome Data Analysis Summit can be viewed online at http://www.appistry.com/wgdas.

Deborah Ausman

Appistry

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Leading Big Data Company Appistry Joins Genome Institute of Singapore to Accelerate Genomics in Asia

A consortium of scientists said Wednesday they had made major progress in deciphering the genome of bread wheat, a vital crop whose DNA is notoriously complex.

Publishing in the journal Nature, they said they had analysed between 94,000 and 96,000 genes in bread wheat (Triticum aestivum).

The plant's genome is nearly five times as big as humans', they said.

The genes exist in what is in fact a triple genome, reflecting bread wheat's legacy as the 8,000-year-old offspring of three species of grasses.

Gene sequencing will help plant breeders in their search for strains that offer higher yields and are better able to tolerate floods, droughts and salty soils, the researchers said.

Wheat today accounts for a fifth of the world's calorific intake, and this importance can only grow, given the world's rising population and the impact of climate change on food production, say experts.

"This work moves us one step closer to a comprehensive and highly detailed genome sequence for bread wheat, which along with rice and maize is one of the three pillars on which the global food supply rests," said co-author Jan Dvorak, a professor of plant sciences at the University of California at Davis.

"The world's population is projected to grow from seven to nine billion by 2050," said Dvorak.

"It is clear that, with no new farmable land available to bring into cultivation, we must develop higher-yielding varieties of these three cereals to meet the growing global demand for food."

A complete, "polished" version of the genome may still lie several years away, cautioned Neil Hall of the University of Liverpool, northwestern England, which led the research.

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Cracked wheat: Scientists make inroads into wheat genome

Europe-based scientists have mapped the genome of the probiotic BLIS K12 strain, finding no negative traits and supporting the safety of the strain.

The high-quality draft genome sequence of this probiotic S. salivariusstrain will contribute to our understanding of the role of this species in the oropharyngeal ecology of human health, wrote scientists from Nestec Ltd., Nestl Research Center in Switzerland, and Institut National de la Recherche Agronomique in France in the Journal of Bacteriology .

BLIS

One of the best known probiotics for oral health was developed by scientists at the University of Otago in New Zealand: BLIS K12 is a specific strain of Streptococcus salivarius (S. salivarius), which secretes powerful antimicrobial molecules called BLIS: Bacteriocin-Like-Inhibitory Substances.

BLIS K12 is an oral probiotic that is said to support healthy bacteria in the mouth for long-term fresh breath and immune support.

The ingredient was recently added to Stratum Nutritions portfolio of specialty bioactive ingredients.

Dr. Barry Richardson, CEO of BLIS Technologies, welcomed the genome sequencing as a significant milestone in the commercial development of the BLIS K12 probiotic and once again confirms the excellent safety of the organism.

According to Stratum, the sequencing of the BLIS K12 genome is significant because it allows the company and other independent researchers to rapidly identify the presence (or absence) of nucleotide sequences that are associated with undesirable traits such as virulence factors or antibiotic resistance genes.

The BLIS K12 genome does not contain phenotypically active gene sequences associated with these negative traits, added the company.

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Scientists map genome for BLIS K12 probiotic

Common wheat (Triticum aestivum) might seem as boring as the sliced bread it is baked into. But genetically, it is vexingly complex. Its genome is about six times as big as our own, and its genes are distributed among six sets of chromosomes (we humans have just two). In fact, the T. aestivum genome contains chunks of genomes from three different "parent," ancestral grasses that were bred to create wheat. This convolution and wheat's high level of repeating sequences (some 80 percent of the plant's DNA appears in duplicate or triplicate) have foiled early attempts to sequence its full genome, which has long been seen as a key to improving its cultivation to feed a swelling human population. (About one fifth of all the calories the human population eats come from wheat.) Now a new research effort has reaped an important swath of the sequence. The findings were published online November 28 in Nature (Scientific American is part of Nature Publishing Group). The genetic complexity of wheat stems in large part from humanity's long history of domesticating the crop. This species as we now know it emerged some 8,000 years ago as a cross of goat grass (Aegilops tauschii) and emmer wheat (Triticum dicocoides), which was itself a hybrid that contained two parent genomes on four sets of chromosomes. To harvest the common wheat's genome, researchers needed a quick and efficient sequencing technology that could plow through the 17 gigabases of genetic code. The team selected shotgun sequencing, in which random segments of a genome are broken into chunks, copied and then reassembled where overlapping patterns are detected. To help parse the morass of genetic code, researchers compared the wheat genetic data to that of other grains, such as corn and rice. They also mapped the new sequences to those from the closest-known relatives for the three different parent genomes: A. tauschii, Aegilops speltoides and Triticum urartu, as well as Triticum durum (drum wheat), which contains both T. urartu and A. speltoides genomes. Being able to assign more than two thirds of genes to the three respective ancestral genomes "is particularly valuable to wheat researchers because it allows them to differentiate genes and DNA markers," Peter Langridge of the Australian Center for Plant Functional Genomicsat the University of Adelaide wrote in an essay appearing in the same issue of Nature. This matching can be "a difficult and time-consuming process," he noted. With these methods, the researchers estimate that the common wheat genome contains some 94,000 to 96,000 individual genes. Many of the gene groups that have expanded with time and breeding are related to growth and energy use. Better understanding the location of these genes might help crop scientists make further improvements on different traits to improve yield, drought and disease tolerance, or nutritional profiles. Scientists have yet to completely crack the wheat genome. "This is just one step in the global effort to produce a high-quality draft of the bread wheat genome sequence," said Jan Dvorak, a professor of plant sciences at the University of California, Davis and co-author of the new study, in a prepared statement. Still, the analysis represents a a major advance that should yield practical benefits. "The identification of genetic markers in the genome will help breeders accelerate the wheat breeding process and integrate multiple traits in a single breeding program," said study co-author Anthony Hall, also at Liverpool's Institute of Integrative Biology, in a prepared statement. "This research is contributing to ongoing work to tackle the problem of global food shortage."

Follow Scientific American on Twitter @SciAm and @SciamBlogs. Visit ScientificAmerican.com for the latest in science, health and technology news. 2012 ScientificAmerican.com. All rights reserved.

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New Slice of Wheat Genome Could Help Feed Growing Global Population

Genome mapping could prove key in preventing superbugs in hospitals, an Australian researcher said Friday, urging its use to prevent countless deaths from antibiotic-resistant infections.

Mark Walker, director of the Australian Infectious Diseases Research Centre at the University of Queensland, said the technology would allow medical staff to determine whether patients had contracted identical bugs.

Tracing the source of an infection would then become simpler and health workers could concentrate their resources on controlling its spread.

"What we've done is demonstrated that the technology is able to answer questions that could not previously be asked," Walker told AFP after his research was published in the US journal Science.

"That has potential to answer specific questions in the hospital setting that will help in controlling... hospital acquired infections."

Until now, he said, it had been impossible to know whether closely-related bacteria causing infections were transferred from patient to patient, or were being passed on by poor clinical practice, a carrier, a contaminated instrument or something else.

By taking a bacteria sample from an infected patient and sequencing the genome, a researcher ends up with some two or three million base pieces of paired genetic information.

They can then compare the sequence to that of a sample taken from another patient and determine whether or not they have an identical bug.

"If you know that the bacteria is absolutely identical, then that really confirms that what you're seeing in a hospital where people are getting sick is that the bug is transferred," he said.

He said in one instance in Britain this type of approach determined that cases of a bug in a neo-natal ward were identical, prompting the hospital to test all health workers.

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Genome mapping may stop superbug deaths: researcher

Dr Bartha Knoppers on the Power of Genomics
As part of the Genome Canada / Gairdner Foundation Genomics: The Power and the Promise conference being held in Ottawa, we shot some quick videos of various people across Canada talking about the potential power of genomics. The Power and Promise conference and gala dinner brings together some of the top experts in the field of genomics and examines the impact of genomics on Canada #39;s bioeconomy, health, agriculture, and the environment.From:OntarioGenomicsClipsViews:0 0ratingsTime:01:15More inScience Technology

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Dr Bartha Knoppers on the Power of Genomics - Video

R7 representation of uncontrolled Connectrons
A graphic showing where the sources of the uncontrolled Connectrons occur in all the chromosomes of the mouse genome.From:Richard J. FeldmannViews:2 0ratingsTime:02:46More inScience Technology

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R7 representation of uncontrolled Connectrons - Video

R4 representation of Connectrons
A graphic showing how sources on other chromosomes determine Connectrons on chromosome 1 of the mouse genome.From:Richard J. FeldmannViews:0 0ratingsTime:06:01More inScience Technology

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R4 representation of Connectrons - Video

Simplified Access and Mining of The Cancer Genome Atlas (TCGA) Copy Number Data
The Cancer Genome Atlas (TCGA) has generated a wealth of genomic information for a wide range of cancers. Much of the data is available publicly on the internet via the TCGA portal. Although the data portal provides access to download processed data as well as the ability to issue simple queries, the utility of this tool is rather limited for most research applications. BioDiscovery has solved these issues by 1) downloading the publically available (Level 3) data and associated phenotypic data onto a single, secure, cloud-based repository-Nexus DB 2) providing free and easy access to this data to Nexus Copy Number users and 3) providing user-friendly tools (Nexus Copy Number and Nexus DB) to analyze and mine this data. In this presentation we will show how to search and query this data with Nexus Copy Number and Nexus DB to find, for example, projects with a particular aberration signature or projects with specific affected genes. We will also discuss possible issues with the level 3 data and how the raw data can be used to obtain a more accurate representation of the data.From:BioDiscoveryIncViews:0 0ratingsTime:48:13More inScience Technology

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Simplified Access and Mining of The Cancer Genome Atlas (TCGA) Copy Number Data - Video