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Category Archives: Genome

Dr. Magliocco on the Genome of Melanoma Tumors – Video

Posted: November 2, 2013 at 12:42 pm


Dr. Magliocco on the Genome of Melanoma Tumors
Anthony M. Magliocco, MD, chair of pathology, executive director of esoteric labs at Moffitt Cancer Center, discusses the difficulties of analyzing the genom...

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'Genome Hacker' Builds Family Trees With Millions of Branches

Posted: November 1, 2013 at 6:42 pm

Megan Garber for The Atlantic 2013-11-01 16:02:00 UTC

There may be a new record for the largest family tree ever assembled. It dates back to the 15th century. It is comprised of 13 million individuals. And it is only one part of an even larger collection of genomic information: a collection compiled by the computational biologist Yaniv Erlich and stored not in albums or on walls, but in machines.

Presented at the annual meeting American Society of Human Genetics in Boston, and discussed in the journal Nature, the mega-repository could offer a new way for researchers to analyze the relationships between human genotypes and phenotypes between, essentially, nature and nurture.

In the past, such expansively branched informational trees would have been painstaking to cultivate. We have documentation, sure, of family relationships and the traits associated with them church records, hospital logs, that kind of thing but gathering those documents for analysis took time. Assembling genealogical data for even just a few thousand individuals, Erlich noted during his ASHG presentation, could take years.

So here's where the hacking comes in: Erlich and his team, rather than gathering those data themselves, went to a more streamlined source: geni.com, which is a genealogy website with 43 million public profiles. Those profiles offered a wealth of information, typically including not just individuals' birth and death dates, but also the locations of their births and deaths. Occasionally, they'd even contain photos uploaded by the site's users.

What resulted, in turn, was an extensive collection of trait-and-gene information, ripe for analysis. And it was from that collection that Erlich and his colleagues were able to compile what Nature calls "a single uber-pedigree" involving some 13 million individuals. "We Are Family," as performed by a huge swath of humanity. (But performed anonymously: In making that and similar pedigrees available to other researchers, Erlich and his team stripped names from the data to protect individuals' privacy.)

So what does a database like that the family tree, digitized get us? For one thing, it allows for a kind of longitudinal analysis of given traits, helping researchers to gain insights into the nature-versus-nurture aspects of those traits as they played out over time.

It can also offer insights into how traits are, ultimately, controlled. Given a trait like fertility, say, are there a few genes that exert broad influence ... or is fertility influenced by many genes that have smaller effects? It might also help us understand inherited diseases. (See, for example, the Iceland-based genetics firm deCODE, which is taking advantage of the country's famously rich genealogical data to help determine genetic signatures that can influence diseases and their treatment.)

For all that, Nature notes, it's unclear how, exactly, researchers will use the database for their own purposes. ("Some scientists at the meeting expressed enthusiasm for the project," Heidi Ledford puts it, "but were hard-pressed to come up with a specific experiment using the data.")

Put another way, though, the biggest uses for the results of Erlich's genome-hacking may simply be to come. And those uses would rely on developments that are cultural as much as scientific; on medical records being stored and analyzed in digital, and potentially public, forms. Imagine Erlich's database being linked to individual medical information. Imagine it being linked to DNA sequence data. As Nancy Cox, a human geneticist at the University of Chicago, tells Ledford: "Weve really only begun to scratch the surface of what these kinds of pedigrees can tell us."

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Prof. David Finnegan – The Human Genome: Everybody Has One – Video

Posted: at 6:42 pm


Prof. David Finnegan - The Human Genome: Everybody Has One
Professor David Finnegan, Head of the Institute of Cell Biology, presents "The Human Genome: Everybody Has One". Despite the complexity of the human genome, ...

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Nissan’s Passion Genome Maps Shared Likes

Posted: at 6:42 pm

Ten years after scientists mapped the human genome, auto manufacturer Nissan has created the Passion Genome, an interactive social campaign that maps likes and connections.

The experience allows participants to see the passions, or Facebook likes, they share with their friends in a so-called Passion Portrait, or a "personalized, interactive visualization of themselves," the brand says.

The Passion Portrait includes "DNA-type imagery" and is a "cool, shareable piece of technology," says Erich Marx, director of interactive and social media marketing at Nissan.

"After exploring their top six passion categories, users can explore the entire Passion Genome to see where they fit within an expanded virtual universe of people and passions from across the world," the brand says.

In order to create a Passion Portrait, users connect with Facebook and select a profile photo. The site then analyzes the user's passions.

Unfortunately, at the time of publication, ClickZ was not able to get beyond the "Analyzing Passions" segment of the experience, despite multiple attempts.

However, according to Marx, users ultimately see which of their friends have the same likes in categories such as activities, colleges, bands, TV shows and food.

In addition, it allows users to see if they share likes with everyone who has participated in the Passion Genome.

A Nissan rep would not disclose how many Passion Portraits have been created to date, but says the target is "pre-nesting couples in their early 30s that know who they are and what makes them happy."

What's more, users who share a Passion Portrait via Facebook or Twitter using the hashtag #MyPassionPortrait will be entered for a chance to win one of eight $1,000 gift cards from Amazon.com and have their portraits featured on the Passion Genome website. That's because the Versa Note has a limited time partnership in which it could be ordered through Amazon, although buyers have to go to a dealership to finalize the deal, Marx says. The Amazon deal is not ongoing, but rather a way to "[have] some fun and build awareness," he adds.

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Precision BioSciences and DuPont Pioneer Announce Publication of Plant Genome Engineering Success

Posted: October 31, 2013 at 5:42 am

RESEARCH TRIANGLE PARK, N.C. & DES MOINES, Iowa--(BUSINESS WIRE)--

Precision BioSciences, Inc., and DuPont Pioneer today announced that The Plant Journal has published an article detailing collaborative cutting-edge research to generate male-sterile corn plants. Researchers at Pioneer used Precisions advanced genome engineering technology, called DNE, to knockout or disable the function of the ms26 gene in corn. Knocking out this gene has enabled Pioneer to produce corn plants that are male-sterile, a powerful tool for hybrid seed production.

The article further details how the Precision and Pioneer research teams were able to optimize a DNE gene-editing tool to maximize its efficiency in corn. This optimization process, which involves modulating the DNA-cutting activity of a gene-editing enzyme, can only be performed with Precisions proprietary DNE technology. The optimization step was found to be critical for high-efficiency gene-editing activity in corn.

We are thrilled with the results published by The Plant Journal, said Jeff Smith, Precision BioSciences Chief Science Officer and one of the studys authors.This is a clear demonstration of why DNEs unique combination of high-targeting flexibility, site-specificity, and activity modulation is so critical for the production of high-value products.

The collaboration to develop DNE technology for agricultural applications began in 2008 and has already delivered actionable results. The work described in this publication enables the creation of genetic male sterile plants similar to those used in the Pioneer proprietary Seed Production Technology (SPT) process. This work paves the way to extend SPT process to additional crops and genes. The SPT process is an innovative technology developed to increase the quality, productivity and efficiency of hybrid seed production. Pioneer has implemented the process in its hybrid seed corn production fields, and is working toward its deployment in other crops, such as rice.

Our collaboration with Precision Biosciences is a great example of two leading technology experts coming together to deliver new value to the agricultural industry, said Michael Lassner, DuPont Pioneer Vice President of Trait Discovery and Technology. This is the first of many applications we are exploring for the optimized DNE technology.

About Precision BioSciences

Precision BioSciences mission is to continually provide, improve, and enable the worlds most powerful genome engineering technology. Precisions proprietary Directed Nuclease EditorTM (DNE) technology enables the production of genome editing enzymes that can insert, remove, modify, and regulate essentially any gene in mammalian or plant cells.

Precision BioSciences vision is to be the conduit through which the worlds greatest genome engineering challenges are solved. Precision has successfully utilized its DNE technology to create innovative products in partnerships with many of the worlds largest biopharmaceutical and agbiotech firms. Internally, Precision is developing DNE-based products for biologics manufacturing and human therapeutics. For additional information, please visit http://www.precisionbiosciences.com.

About DuPont Pioneer

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This 'Genome Hacker' Is Building Family Trees With Millions of Branches

Posted: October 29, 2013 at 10:41 pm

Shutterstock/Martin M303

There may be a new record for the largest family tree ever assembled. The thing dates back to the 15th century. It is comprised of 13 million individuals. And it is only one part of an even larger collection of genomic information: a collection compiled by thecomputational biologist Yaniv Erlichand stored not in albums or on walls, but in machines. Presented at the annual meetingAmerican Society of Human Genetics in Boston, and discussed in the journal Nature, the mega-repositorycould offer a new way for researchers to analyze the relationships between human genotypes and phenotypesbetween, essentially, nature and nurture.

In the past, such expansively branched informational trees would have been painstaking to cultivate. We have documentation, sure, of family relationships and the traits associated with themchurch records, hospital logs, that kind of thingbut gathering those documents for analysis took time. Assembling genealogical data for even just a few thousand individuals, Erlich noted during his ASHG presentation, couldtake years.

So here's where the hacking comes in.Erlich and his team, rather than gathering those data themselves, went to a more streamlined source: geni.com. Which is a genealogy website with43 million public profiles. Those profiles offered a wealth of information, typically including not just individuals' birth and death dates, but also the locations of their births and deaths. Occasionally, they'd even contain photos uploaded by the site's users.

What resulted, in turn, was an extensive collection of trait-and-gene information, ripe for analysis. And it was from that collection that Erlich and his colleagues were able to compile what Nature calls "asingle uber-pedigree" involving some 13 million individuals. "We Are Family," as performed by a huge swath of humanity.(But performed anonymously: In making that and similar pedigreesavailable to other researchers, Erlich and his team stripped names from the data to protect individuals' privacy.)

So what does a database like thatthe family tree, digitizedget us? For one thing, it allows for a kind of longitudinal analysis of given traits, helping researchers to gain insights into the nature-vs.-nurture aspects of those traits as they played out over time.It can also offer insights into how traits are, ultimately, controlled. Given a trait like fertility, say, are there a few genes that exert broad influence ... or is fertility influenced by many genes that have smaller effects? It might also help us to understand inherited diseases. (See, for example, theIceland-based genetics firm deCODE, which is taking advantage of the country's famously rich genealogical data to help determine genetic signatures that can influence diseasesand their treatment.)

For all that, Nature notes, it's unclear how, exactly, researchers will use the database for their own purposes. ("Some scientists at the meeting expressed enthusiasm for the project," Heidi Ledford puts it, "but were hard-pressed to come up with a specific experiment using the data.")Put another way, though, the biggest uses for the results of Erlich's genome-hacking may simply be to come. And those uses would rely on developments that are cultural as much as scientific: on medical records being stored and analyzed in digital, and potentially public, forms. Imagine Erlich's database being linked to individual medical information. Imagine it being linked to DNA sequence data. AsNancy Cox, a human geneticist at the University of Chicago,tells Ledford: "Weve really only begun to scratch the surface of what these kinds of pedigrees can tell us."

Via Nature

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This 'Genome Hacker' Is Building Family Trees With Millions of Branches

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Surprises discovered in decoded kiwifruit genome – Video

Posted: at 10:41 pm


Surprises discovered in decoded kiwifruit genome
Surprises discovered in decoded kiwifruit genome.

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Genome Hacker Uncovers 13-Million-Member Family Tree

Posted: at 10:41 pm

52462425 story Posted by Soulskill on Tuesday October 29, 2013 @08:00PM from the turns-out-several-million-people-married-their-cousins dept. ananyo writes "Using data pulled from online genealogy sites, a renowned 'genome hacker' has constructed what is likely the biggest family tree ever assembled. The researcher and his team now plan to use the data including a single uber-pedigree comprising 13 million individuals, which stretches back to the 15th century to analyze the inheritance of complex genetic traits, such as longevity and facial features. In addition to providing the invitation list to what would be the world's largest family reunion, the work presented by computational biologist Yaniv Erlich at the American Society of Human Genetics annual meeting in Boston could provide a new tool for understanding the extent to which genes contribute to certain traits. The pedigrees have been made available to other researchers, but Erlich and his team at the Whitehead Institute in Cambridge, Massachusetts, have stripped the names from the data to protect privacy." You may like to read: Post

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Genome Hacker Uncovers 13-Million-Member Family Tree

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Genome hacker uncovers largest-ever family tree

Posted: at 10:41 pm

Andrew Bret Wallis/Getty Images

Using data pulled from online genealogy sites, a renowned genome hacker has constructed what is likely the biggest family trees ever assembled. The researcher and his team now plan to use the data including a single uber-pedigree comprising 13 million individuals, which stretches back to the 15th century to analyse the inheritance of complex genetic traits, such as longevity and facial features.

In addition to providing the invitation list to what would be the worlds largest family reunion, the work presented by computational biologist Yaniv Erlich at the American Society of Human Genetics annual meeting in Boston could provide a new tool for understanding the extent to which genes contribute to certain traits. The pedigrees have been made available to other researchers, but Erlich and his team at the Whitehead Institute in Cambridge, Massachusetts, have stripped the names from the data to protect privacy.

The structures of the trees themselves could provide interesting information about human demographics and population expansions, says Nancy Cox, a human geneticist at the University of Chicago, Illinois, who was not involved in the study. But more interesting, she says, is the possibility that such data may one day be linked to medical information or to DNA sequence data as more people have their genomes sequenced and deposit that information in public databases.

Weve really only begun to scratch the surface of what these kinds of pedigrees can tell us, she says.

Pedigrees provide clues about genetic inheritance. For instance, by comparing an individual to their more distant relatives on the family tree, the change in frequency of a given trait, such as fertility, can indicate to what extent the trait has its roots in genetics. It can also provide clues as to whether the trait is controlled by a few genes that have large effects, or by many genes that each make smaller contributions.

But it takes years to assemble genealogical data for even just a few thousand individuals, said Erlich during a presentation at the meeting on 24 October. In the past, researchers have painstakingly gathered such data from church records and individual volunteers. Erlich and his team decided to streamline the process by collecting data from more than 43 million public profiles on the genealogy website geni.com. The profiles typically included birth and death dates, as well as locations and, occasionally, photos uploaded by the users.

The team assembled the data into family trees that ranged from a few thousand individuals up to 13 million people in size. Erlich says that pedigrees previously available for genetic studies contained hundreds of thousands of family members at best.

Lisa Cannon-Albright, a geneticist at the University of Utah in Salt Lake City, urges caution when using self-reported genealogical data. She has worked extensively with a large Utah genealogy database that is linked to some medical information. Everyone wants to trace their family back to royalty, she says. For these giant pedigrees, we just dont believe them beyond a certain date. Cannon-Albright says that she cuts off her data at the year 1500.

Ultimately, the value of a pedigree is in the information you can link it to, she adds. At the same meeting in Boston, Cannon-Albright presented data from the Utah database suggesting that the Y chromosome, which only passes from father to son, can carry risk factors for prostate cancer. She has also recently launched a new programme to link genealogical data to medical records from the federal Veterans Health Administration.

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Energun – Mutation Of The Genome (Affin 142) – Video

Posted: October 28, 2013 at 10:44 am


Energun - Mutation Of The Genome (Affin 142)
Welcome Energun, a Minsk-based Producer Liveact working on his music since the late 90 #39;s, also running his own label Energun Records and releasing on Decoy...

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Energun - Mutation Of The Genome (Affin 142) - Video

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