Category Archives: Genome

Waldorf Rocket Synth being powered by Genome MIDI Sequencer on my iPad
Very easy to access CC #39;s using Genome as always.

By: Ashley Elsdon

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Waldorf Rocket Synth being powered by Genome MIDI Sequencer on my iPad - Video

How to download the human genome - DNA (sketch)
What happens when human DNA falls into the public domain? Writer Gregg Lopez Cast Matthew Harris Gregg Lopez Brent Pope.

By: topstoryweeklyvideos

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How to download the human genome - DNA (sketch) - Video

Years of talk about cutting the price of sequencing a human genome to $1,000 has made one prominent genomics guru more than a little cranky. Mick Watson wrote on his blog Tuesday that such talk is "utter crap."

Watson, a genomicist/bioinformatician who heads a genomics center at the Roslin Institute, isn't at all sheepish about voicing his disdain for popular and scientific media accounts of the impending $1,000 genome. What set him off was a marketing statement in the new journal PeerJ that talked of a $99 genome.

Two even more prominent genomics experts I contacted for comment, J. Craig Venter and Eric Topol, say Watson is both right and wrong. Right that the full cost of a human genome today is much more than $1,000. Wrong because the price of that genome continues to drop, so a $1,000 genome is indeed fast approaching.

But first, some details on Watson's complaint.

Watson says just the cost of chemicals for doing a medical-grade human genome runs to more than $1,000. (Because today's DNA sequencers are fast but far from error-free, genomes must be run many times -- at least 30x is the standard -- to eliminate errors. Venter and colleagues learned that the hard way when they synthesized a bacterial genome, put it in a host cell that had its DNA removed, and nothing happened. An apparently trivial mistake -- one base pair deleted -- made the whole genome fail. They tried again and succeeded, once they had fixed the error. That's the difference between research-grade and medical-grade genomes, Venter says.)

Throw in equipment depreciation, data storage, overhead, staff time and the need for genome sequencing companies to make money, Watson says, and the current cost is more than $2,000.

"Obviously, Illumina dont charge themselves list price for reagents, and nor do LifeTech, so its possible that they themselves can sequence 30x human genomes and just pay whatever it costs to make the reagents and build the machines; but this is not reality and its not really how sequencing is done today," Watson wrote on his blog. "These guys want to sell machines and reagents, they dont want to be sequencing facilities, plus they still have to pay the staff, pay the bills, make a profit and return money to investors."

Apples and oranges, Venter said.

"Sequencing cost is the only thing anyone measures and is approaching $1k in theory, the accuracy of whole genomes is not of diagnostic quality, and the informatics cost more than the sequencing," Venter said by email. "I have been saying this for years."

Venter cited a 2011 article he wrote for Science pointing out the progress and challenges that remain.

Read this article:
$1,000 genome a mirage?

Betsy Read, a professor of molecular cell biology at CSUSM, examines a solution of Emiliania huxleyi. Read led an international team of researchers who sequenced a "pan genome" for the organisms. Photo courtesy of Cal State San Marcos.

A ubiquitous phytoplankton found in oceans around the world could hold the key to fields ranging from climatology to dentistry, since a team of scientists led by Cal State San Marcos researchers unlocked the genomes for 14 different strains of the algae.

Their findings, published last week in the journal Nature, decoded the DNA of related strains of the algae Emiliania huxleyi. Their study is one of only a handful to unravel the genomes of marine algae and the first ever to document a pan genome - a set of core genes shared by diverse algal varieties.

Its still very rare to have a whole genome sequence for any marine phytoplankton, said Sonya Dyhrman, a professor of microbial oceanography at Columbia University and a co-author of the study. Its absolutely unprecedented to have multiple strains of the same species sequenced.

While the different strains share 70 to 80 percent of their DNA, about 20 to 30 percent of their genes are unique to each strain. That diversity allows them to inhabit virtually all the worlds oceans except the polar seas, said lead author Betsy Read, a professor of molecular cell biology at CSUSM.

They have this tremendous ability to adapt, she said. This is why we can pull them from almost every bucket of water in the ocean.

Read released the findings in the journal Nature last week, in collaboration with CSUSM computer science professor Xiaoyu Zhang, Dyhrman and about two dozen co-authors from a far-flung network of institutions in the United States, Germany, England, France.

The findings, Dyhrman said, are as valuable to microbiology as decryption of the human genome has proven to medicine.

Any time you unlock that code, it gives you this Rosetta stone to understand how that organism works and how it interacts with its environment, she said.

The algae are the third most abundant phytoplankton, and are a key component of the ocean food chain, nourishing animals including crustaceans, shellfish and other filter feeders.

Read more here:
Algae genome could aid medical, climate research

Newswise The Smithsonians National Museum of Natural History, in partnership with the National Human Genome Research Institute of the National Institutes of Health, recently opened Genome: Unlocking Lifes Codea multimedia exhibition that explores how the genomic revolution is influencing peoples lives and the extraordinary impact it is having on science, medicine and nature.

The exhibition looks at the complexities of the genomethe complete set of genetic or hereditary material of a living organismand chronicles the remarkable breakthroughs that have taken place since the completion of the Human Genome Project 10 years ago. With cutting-edge interactives, 3-D models, custom animation and engaging videos of real-life stories, the exhibition examines both the benefits and the challenges that genomics presents to modern society.

Genome: Unlocking Lifes Code will be on view at the National Museum of Natural History through Sept. 1, 2014, when it will begin a tour of venues throughout North America.

Genomic research is a vital tool for exploring the mysteries of the natural world, and it is an important part of Smithsonian science, said Kirk Johnson, the Sant Director of the National Museum of Natural History. Genome: Unlocking Lifes Code will help our visitors understand how genomics is transforming what we know about ourselves and how we make important life decisions.

Genome: Unlocking Lifes Code celebrates the anniversaries of two landmark scientific discoveries: the 10th anniversary of the Human Genome Projects first completely sequenced human genome and the 60th anniversary of James Watson and Francis Cricks discovery of DNAs double helix structure.

This exhibition reflects a remarkably productive collaboration between two scientific icons of the U.S. governmentthe Smithsonian Institution and the National Institutes of Health, said Dr. Eric D. Green, director of the National Human Genome Research Institute, one of the 27 institutes and centers that make up NIH in Bethesda. Our ability to share the science of genomics with the more than 7 million annual visitors to the National Museum of Natural History is profoundly exciting for the broader genomics research community.

When visitors enter the 4,400-square-foot exhibition they will be immersed in an interactive environment that communicates the pervasiveness of genomic science and provides new ways of looking at themselvesas individuals, as members of a family and a species, and as part of the diversity of all life.

Genome: Unlocking Lifes Code is organized around four themed areas, offering visitors personalized and interactive experiences that examine what a genome is (The Genome Within Us), how it is related to medicine and health (Your Genome, Your Health), how it connects them to all of life (Connections: Natural World and Genomic Journey) and how it is a part of their own personal story (Genome Zone):

-- The Genome Within UsAt the center of the exhibition, museumgoers will explore how the genome is a part of their own bodies. They will discover what a genome is, where it is located in the human body (in the cell nucleus), why it matters and how it influences life, all through an introductory animation. Visitors will see a three-dimensional model of a human genome and watch historic interviews with Human Genome Project researchers. They can also participate in a media interactive that explores the ethical, legal and social implications of advancing DNA sequencing technologies and submit their responses on an interactive station and find out how their views compare with those of other visitors. An electronic news-ticker display will provide an ongoing stream of recent developments in genomics.

-- Your Genome, Your HealthVisitors will explore the many ways in which genome sequencing benefits patients through improved health care. They can learn about genes, genomic solutions to mysterious medical diseases, and through a futuristic DNA interactive, search for the right medicine for a given disease. An interactive puzzle presents how genetic, environmental and random factors influence an individuals risk for a particular disease.

Excerpt from:
Smithsonian Genome Exhibition Unlocks 21st-Century Science of Life

Code For Life The Human Genome
The Human Genome,genome sequencing,human genome sequencing,human genome sequence,human genome,what is genome sequencing,gene sequencing,cost of genome sequen...

By: worldhealthable

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Code For Life The Human Genome - Video

June 16, 2013 Because of their central importance to biology, proteins have been the focus of intense research, particularly the manner in which they are produced from genetically coded templates -- a process commonly known as translation. While the general mechanism of translation has been understood for some time, protein synthesis can initiate by more than one mechanism. One of the least well understood mechanisms is known as cap-independent translation.

Now, John Chaput and his colleagues at Arizona State University's Biodesign Institute have produced the first genome-wide investigation of cap-independent translation, identifying thousands of mRNA sequences that act as Translation Enhancing Elements (TEEs), which are RNA sequences upstream of the coding region that help recruit the ribosome to the translation start site.

The new study outlines a technique for mining whole genomes for sequences that initiate cap-independent translation within the vastness of the genome.

The research has important implications for the fundamental understanding of translation in living systems, as well as intriguing potential in the biomedical arena. (Many viral pathogens are known to use cap-independent translation to hijack and redirect cellular mechanisms to translate viral proteins.)

The lead author of the study is Brian P. Wellensiek, a senior scientist in Biodesign's Center for Evolutionary Medicine and Informatics. The group's results appear in the current issue of the journal Nature Methods.

During most protein synthesis in eukaryotic cells, cap-dependent translation dominates. The process begins after DNA is first transcribed into mRNA, with the aid of an enzyme polymerase. mRNA now forms the coded template from which the translated proteins will be generated. The mRNA code consists of sequences made from 4 nucleic acids, A, C, G & U, with each 3-letter grouping (known as a codon), corresponding to one amino acid in the protein being synthesized.

A key component in the translation process is the ribosome, which migrates along the single stranded mRNA, reading the codons as it goes. Before it can do this however, it must locate a special structure at the 5' end of the mRNA strand known as the cap. In normal cap-dependent translation, the ribosome is recruited to the 5' end of mRNA via a specialized cap-binding complex.

Cap-independent translation allows the ribosome to begin reading the mRNA message without having to first locate the 5' cap structure. Cap-independent translation occurs in eukaryotic cells during normal processes including mitosis and apoptosis (or programmed cell death). It is also a feature in many forms of viral translation, where the viral transcript is able to recruit the ribosome and co-opt its function to preferentially translate viral RNA.

In the current study, Chaput designed an in vitro selection strategy to identify human genome sequences that initiate cap-independent translation. The technique is able to select candidates from a pool of trillions of genomic fragments. Once a set of sequences was identified as translation enhancing elements, they were shown to function effectively in both cell-free and cellular translation systems.

As Chaput explains, most research on cap-independent translation has been conducted using RNA fragments derived from viruses. "These RNA molecules will fold into shapes that appear to mimic some of the initiation factors that that you would find in eukaryotic translation," he says. More recently, similar RNA molecules have been identified in cellular systems, though the sequences tend to be much shorter and function in a different manner.

Originally posted here:
Mapping translation sites in the human genome

WASHINGTON, DC.- The Smithsonians National Museum of Natural History, in partnership with the National Human Genome Research Institute of the National Institutes of Health, opened Genome: Unlocking Lifes Code June 14a multimedia exhibition that explores how the genomic revolution is influencing peoples lives and the extraordinary impact it is having on science, medicine and nature.

The exhibition looks at the complexities of the genomethe complete set of genetic or hereditary material of a living organismand chronicles the remarkable breakthroughs that have taken place since the completion of the Human Genome Project 10 years ago. With cutting-edge interactives, 3-D models, custom animation and engaging videos of real-life stories, the exhibition examines both the benefits and the challenges that genomics presents to modern society.

Genome: Unlocking Lifes Code is on view at the National Museum of Natural History through Sept. 1, 2014, when it will begin a tour of venues throughout North America.

Genomic research is a vital tool for exploring the mysteries of the natural world, and it is an important part of Smithsonian science, said Kirk Johnson, the Sant Director of the National Museum of Natural History.

Genome: Unlocking Lifes Code will help our visitors understand how genomics is transforming what we know about ourselves and how we make important life decisions.

Genome: Unlocking Lifes Code celebrates the anniversaries of two landmark scientific discoveries: the 10th anniversary of the Human Genome Projects first completely sequenced human genome and the 60th anniversary of James Watson and Francis Cricks discovery of DNAs double helix structure.

This exhibition reflects a remarkably productive collaboration between two scientific icons of the U.S. governmentthe Smithsonian Institution and the National Institutes of Health, said Dr. Eric D. Green, director of the National Human Genome Research Institute, one of the 27 institutes and centers that make up NIH in Bethesda. Our ability to share the science of genomics with the more than 7 million annual visitors to the National Museum of Natural History is profoundly exciting for the broader genomics research community.

When visitors enter the 4,400-square-foot exhibition they will be immersed in an interactive environment that communicates the pervasiveness of genomic science and provides new ways of looking at themselvesas individuals, as members of a family and a species, and as part of the diversity of all life.

Genome: Unlocking Lifes Code is organized around four themed areas, offering visitors personalized and interactive experiences that examine what a genome is (The Genome Within Us), how it is related to medicine and health (Your Genome, Your Health), how it connects them to all of life (Connections: Natural World and Genomic Journey) and how it is a part of their own personal story (Genome Zone):

The Genome Within UsAt the center of the exhibition, museumgoers will explore how the genome is a part of their own bodies. They will discover what a genome is, where it is located in the human body (in the cell nucleus), why it matters and how it influences life, all through introductory videos produced by the History channel. Visitors will see three-dimensional models of a human genome and watch historic interviews with Human Genome Project researchers. They can also participate in a media interactive that explores the ethical, legal and social implications of advancing DNA sequencing technologies and submit their responses on an interactive station and find out how their views compare with those of other visitors. An electronic news-ticker display will provide an ongoing stream of recent developments in genomics.

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National Museum of Natural History genome exhibition unlocks 21st-century science of life

The $14.5 billion U.S. investment in the Human Genome Project, completed a decade ago, has paid off more than 60-fold in new jobs, drugs and a rapidly expanding genetics industry, an analysis has found.

The endeavor to map human DNA in its entirety created $966 billion in economic impact and $59 billion in federal tax revenue, according to the study released last week by United for Medical Research and Battelle, two research advocacy groups.

Dozens of companies have started with the knowledge gained from the project, leading to new diagnostic tests and development of medicines that can be matched with gene variants linked to disease. The project triggered a new era in the life sciences, with new oncology drugs and screenings among the early developments in the field, said Greg Lucier, chief executive officer of Life Technologies.

Up until that time, the pharmaceutical industry was able to have major impact on human health through blockbuster drugs that in retrospect were relatively simple, he said in a telephone interview. The ushering in of the genomic era was the beginning of truly reducing science to engineering, in terms of the understanding of life.

Life Technologies also provided funding for the study. The Carlsbad, Calif.-based maker of gene-sequencing machines agreed to be bought by Thermo Fisher Scientific for $13.6 billion last April. Other companies that provide sequencing services or equipment include Illumina and Oxford Nanopore Technologies. The Human Genome Project also spurred consumer-focused genetics companies such as 23andMe that let people find out what diseases they might be at risk for or where their ancestry lies.

Although it took almost $15 billion and more than a decade for the government-funded DNA effort to fully sequence a human genome for the first time, companies can now sequence a whole genome for about $1,000 and do it in a day.

The Human Genome Project was the starting point of that magnificent, incredible effort, Lucier said.

The market for gene tests may expand to $25 billion from $5 billion within a decade as more doctors use a patients genetic makeup to tailor treatments, according to a report last year from UnitedHealth Group Inc., the largest U.S. health insurer.

This report illustrates the vital role that key federal research funding plays in growing the U.S. economy, creating new industries and innovative technologies and producing the diagnostics and treatments that can save lives, Carrie Wolinetz, president of United for Medical Research, said in a statement.

Some of biggest innovations have been in the field of oncology. The actress Angelina Jolie recently became the new face of breast cancer, after announcing that shed had a double-mastectomy upon discovering that she carried a gene that predicts about a 60 percent chance of developing the disease.

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Genome project spurs boom for life science

When movie star Angelina Jolie went public about her double mastectomy in May and said she chose that course after genetic testing indicated an 87 percent risk of breast cancer, costs of the gene testing were upwards of $3,000, which may or may not be covered by insurance. However, under Obamacare, genetic counseling and testing must be provided without patient cost-sharing for women whose family history indicates high risk.

Myriad Genetics' stock enjoyed a boost after Jolie disclosed having used the company's cancer-screening services. Thursday's Supreme Court decision was in response to a challenge to Myriad patents.

The mixed ruling, which allowed legal protections for synthetically produced genetic material while disallowing those for naturally occurring genes, sent shares surging more than 10 percent before crashing at the end the day and continuing to fall Friday to close at $27.59, 27 percent off Thursday's high. Investors apparently saw the ruling as opening Myriad's core hereditary testing business to competition.

(Read More: Bristol and Merck Shares Surge on Cancer Drug News)

Matthew Foy, with GlaxoSmithKline's independent venture capital fund SR One, offered one example of a breakthrough technology that could be available soon. He said a biotech SR One backs, PsiOxus Therapeutics, produces a cancer drug that self-amplifies as it attacks cancer cells.

"It has a genetically engineered virus. ... When it finds a cancer cell, it makes hundreds of thousands of copies of itself. It bursts the cell, kills the cell, and the environment is now flooded with these copies of the (cancer-cell-fighting) virus," he said. "The idea is it can spread throughout a tumor extremely quickly."

The drug is in Phase I clinical trials, where it is tested on a small group of people.

Silvester said a key aspect of genome technology is that it allows for the different ways people react to treatments.

"Drugs that work for some people can unfortunately not work for others, or even kill people, and that's why they're not brought to the market," he said. "So having the ability to target drugs more effectively is critical."

GlaxoSmithKline shares are up more than 20 percent year-to-date. The British drugmaker this week fired one head researcher and disciplined others over "misrepresented" data.

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Genome Research Benefits More in Reach