05-09-2012 13:49 Scientists have completely reanalysed the human genome, and found that the code of life is far more complex than they every imagined. .

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Scientists go deeper into DNA - Video

The 46 human chromosomes is where DNA resides. On Wednesday, scientists from around the world reported their findings on a nine-year project to study the 97 percent of the genome that's not, strictly speaking, made up of genes. (National Cancer Institute)

A colossal international effort has yielded the first comprehensive look at how our DNA works, an encyclopedia of information that will rewrite the textbooks and offer new insights into the biology of disease.

For one thing, the effort might help explain why complex diseases such as diabetes, high blood pressure and psychiatric disorders are so difficult to predict and, often, to treat.

The findings, reported Wednesday, reveal that the human genome is packed with at least 4 million on-off switches that tell our genes what to do and when. The switches reside in bits of DNA that once were dismissed as "junk" but turn out to play critical roles in controlling how cells, organs and other tissues behave.

The discovery, considered a major medical and scientific breakthrough, has enormous implications for human health because many complex diseases appear to be caused by tiny changes in hundreds of gene switches.

The findings are the fruit of an immense federal project, involving 440 scientists from 32 labs around the world. As they delved into the "junk" parts of the DNA that are not actual genes containing instructions for proteins they discovered it is not junk. At least 80 percent of it is active and needed.

The result is an annotated road map of much of this DNA, noting what it is doing and how. It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.

The findings have applications for understanding how alterations in the non-gene parts of DNA contribute to disease, which might lead to new drugs.

They can also help explain how the environment can affect disease risk. In the case of identical twins, small changes in environmental exposure can slightly alter gene switches, with the result that one twin gets a disease and the other does not.

"It's Google maps," said Eric Lander, president and founding director of the Broad Institute of Harvard and the Massachusetts Institute of Technology.

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Scientists decode "junk" DNA to show complex inner workings of genes

A massive DNA database has generated a map of the genetic switches which impact everything from hair loss to cancer and opened the door to revolutionary treatments for a host of deadly diseases, researchers say.

'This is a major step toward understanding the wiring diagram of a human being,' said lead researcher Michael Snyder of Stanford University.

The Encyclopedia of DNA Elements - or ENCODE - has enabled scientists to assign specific biological functions for 80 per cent of the human genome and has helped explain how genetic variants affect a person's susceptibility to disease.

It also exposed previously hidden connections between seemingly unrelated diseases such as asthma, lupus and multiple sclerosis which were found to be linked to specific genetic regulatory codes for proteins that regulate the immune system.

A key insight revealed in a host of papers published in the journals Nature, Science and Cell is that many diseases result from changes in when, where and how a gene switches on or off rather than a change to the gene itself.

'Genes occupy only a tiny fraction of the genome, and most efforts to map the genetic causes of disease were frustrated by signals that pointed away from genes,' said co-author John Stamatoyannoupoulos, a researcher at the University of Washington.

'Now we know that these efforts were not in vain, and that the signals were in fact pointing to the genome's 'operating system.''

Another significant finding is that this blueprint of genetic switches can be used to pinpoint cell types that play a role in specific diseases without needing to understand how the disease actually works.

For instance, it took researchers decades to link a set of immune cells with the inflammatory bowel disease Crohn's. The ENCODE data was able to swiftly identify that the genetic variants associated with Crohn's were concentrated in that subset of cells.

This in-depth map of the human genetic code has also altered scientific understanding of how DNA works.

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DNA data unlocks map to genetic disease

When the human genome was sequenced a decade ago, scientists hailed the feat as a technical tour de force but they also knew it was just a start. The "HHA000078">DNA blueprint was finally laid bare, but no one knew what it all meant.

Now an international team has taken the crucial next step by delivering the first in-depth report on what the endless loops and lengths of DNA inside our cells are up to.

The findings, detailed Wednesday in more than two dozen reports in the journals Nature and Science and other publications, do much more than provide a straightforward list of genes. By creating a complicated catalog of all the places along our DNA strands that are biochemically active, they offer new insight into how genes work and influence common diseases. They also upend the conventional wisdom that most of our DNA serves no useful purpose.

Defining this hive of activity is essential, scientists said, because it transforms our picture of the human blueprint from a static list of 3 billion DNA building blocks into the dynamic master-regulator that it is. The revelations will be key to understanding how genes are controlled so that they leap into action at precisely the right time and place in our bodies, allowing a whole human being to develop from a single fertilized egg. In addition, they will help explain how the carefully choreographed process can go awry, triggering birth defects, diseases and aging.

"The human genome was a bit like getting 'War and Peace' in Russian: It's a great book containing all of human experience, but [if] I don't know any Russian it's very hard to read," said Ewan Birney, a computational biologist at the European Bioinformatics Institute in England who coordinated the analysis for the project. Now scientists are on their way to having the translation, he said.

More than 400 scientists have conducted upward of 1,600 experiments over five years to produce the Encyclopedia of DNA Elements, which goes by the nickname ENCODE. If graphically presented, the data it has generated so far would cover a poster 30 kilometers long and 16 meters high, Birney estimated.

Already, it is revealing surprises.

The results overturn old ideas that the bulk of DNA in our cells is useless albeit inoffensive junk just carried along for the evolutionary ride. Back in 2003, when the human genome was finished, scientists estimated that less than 2% carries instructions for making proteins, which become physical structures in our bodies and do the myriad jobs inside cells. The conventional wisdom was that the rest of the genetic code didn't do very much.

But the new analysis shows that more than 80% of the human genome is active in at least one biological process that the ENCODE team measured. Nearly all of it could turn out to be active when the data are more complete.

A huge chunk of that activity is wrapped up with gene regulation dictating whether the instructions each gene carries for making a unique protein will be executed or not. Such regulation is key, because pretty much every cell in the human body carries the entire set of 21,000 protein-making genes. To adopt its unique identity, each cell be it one in the pancreas that makes insulin or one in the skin making pigment or hair must activate only a subset of them.

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ENCODE project sheds light on human DNA and disease

STONY BROOK, NY--(Marketwire -09/05/12)- Applied DNA Sciences, Inc. (APDN), (Twitter: @APDN), a provider of DNA-based anti-counterfeiting technology and product authentication solutions, announced today an agreement with SMT Corporation of Sandy Hook, Connecticut (SMT). SMT, the well known electronics parts distributor, will begin SigNature DNA marking components that leave its facility. The botanical SigNature DNA mark is designed to provide customers with the assurance that its parts were sourced at a known and respected distributor.

The agreement between APDN and SMT follows closely on the heels of the mandate by the Defense Logistics Agency that microcircuits supplied to DLA be SigNature DNA-marked. The mandate appeared at an announcement on the DLA Internet Bulletin Board System on August 7.

Tom Sharpe, Vice President of SMT, is a recognized thought-leader of the anti-counterfeiting efforts launched by government and industry. He testified this past November before the Senate Armed Services Committee regarding counterfeit electronic parts in the U.S. military supply chain. He has focused on mitigating the counterfeit threat in high reliability electronics, and established a leading inspection resource to restrict entry of counterfeit obsolete chips.

Mr. Sharpe pointed out that the agreement includes, but goes beyond, the parts supplied by SMT to the military. "Our defense and aerospace customers can now engage with assured provenance back to SMT at any points further downstream in the supply chain. The SigNature DNA mark will also assure customers and users downstream that the chips have undergone the rigorous testing and inspection applied by SMT on components before they leave our facility."

The agreement comes just as the new federal electronics anti-counterfeiting laws are due to come into effect. In Section 818 of the National Defense Authorization Act for Fiscal Year 2012, the Department of Defense must require suppliers of electronics parts to "monitor and eliminate" counterfeits from the military supply chain. A key milestone is due at the end of this month, when the DoD is instructed to write the new anti-counterfeiting wording into the DFARS (Defense Federal Acquisition Regulations Supplement, the main military procurement document). The APDN-SMT agreement is an effort toward early compliance with that law by an important player in the industry.

Sharpe stated: "We take great pride in stepping forward at the beginning of what promises to be a milestone in reducing counterfeit risk to the military and to private industry. We are determined to protect our warfighters by providing the highest reliability in materiel."

"I commend the unwavering diligence of the SMT Corporation in their systematic testing, and their first-to-market application of the SigNature DNA Provenance Mark," stated Janice Meraglia, Vice President, Government and Military Programs at APDN. "Tom Sharpe's willingness to take a proactive stand is in line with the integrity he and his team demonstrate on a daily basis."

President and CEO of Applied DNA Sciences, Dr. James A Hayward, called the agreement with SMT "a landmark step, and a model for the industry." Dr. Hayward pointed out that "Provenance Marking," as the company calls its program for SMT, combines with "Authentication Marking," as applied at electronic manufacturers to provide 360 degree, all-around coverage for the industry. Dr. Hayward added: "Together, they form an umbrella protection, which can provide assurance of originality from manufacturers when available, and assurance of provenance in other cases."

About Applied DNA Sciences

APDN is a provider of botanical-DNA based security and authentication solutions that can help protect products, brands and intellectual property of companies, governments and consumers from theft, counterfeiting, fraud and diversion. SigNature DNA and smartDNA, our principal anti-counterfeiting and product authentication solutions that essentially cannot be copied, provide a forensic chain of evidence and can be used to prosecute perpetrators.

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Applied DNA Sciences Contracts With SMT for SigNature(R) DNA on Electronics

Public release date: 5-Sep-2012 [ | E-mail | Share ]

Contact: Dr. Henrik Nilsson henrik.nilsson@bioenv.gu.se 46-317-862-623 Pensoft Publishers

Like all sources of information, DNA sequences come in various degrees of quality and reliability. To identify, proof, and discard compromised molecular data has thus become a critical component of the scientific endeavor - one that everyone generating sequence data is assumed to carry out before using the sequences for research purposes.

"Many researchers find sequence quality control difficult, though", says Dr. Henrik Nilsson of the University of Gothenburg and the lead author of a new article on sequence reliability, published in the Open Access journal MycoKeys. "There just isn't any straightforward document to put in their hands to give them a flying start. As a result, scientists differ in the degree to which they are aware of the need to exercise sequence quality control and in what measures they take." Previous studies have highlighted several shortcomings of publicly available DNA sequences - more than ten percent of the fungal DNA sequences may be misidentified at the species level, for example.

"A second complication", adds co-author Prof. Urmas Koljalg of the University of Tartu, "is that the software available for sequence quality management tend to be very complex and resource intensive. It borders on the unfair to expect everyone to have access to, and to master, such computer environments. Fortunately, a whole lot can be done towards quality control of DNA sequences using just manual means and a web browser. The current MycoKeys paper describes these means to help those biologists who do not have a strong background in computer science."

The article - "Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences" - compiles principles and observations to assist the reader in the quality management of sequence data. Although focusing on fungi, the guidelines are general and apply to most groups of organisms and genes. The guidelines target traditional DNA sequencing and are broadly applicable to datasets used in systematics, taxonomy, and ecology.

Co-author Dr. Martin Hartmann of the Swiss Federal Research Institute WSL concludes, "We hope that our guidelines will assist the readers in sharpening their datasets so that, eventually, the trend of increasing noise in the public sequence databases can be arrested. Molecular data offer so much promise that we simply cannot afford to lose accuracy to bias and artifacts."

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Nilsson RH, Tedersoo L, Abarenkov K, Ryberg M, Kristiansson E, Hartmann M, Schoch CL, Nylander JAA, Bergsten J, Porter TM, Jumpponen A, Vaishampayan P, Ovaskainen O, Hallenberg N, Bengtsson-Palme J, Eriksson KM, Larsson K-H, Larsson E, Kljalg U (2012) Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences. MycoKeys 4: 37-62. doi: 10.3897/mycokeys.4.3606

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DNA sequences need quality time too - guidelines for quality control published

CAMBRIDGE, Mass.--(BUSINESS WIRE)--

GnuBIO, Inc. (www.gnubio.com) is expanding its operations and relocating to a newly constructed facility dedicated to the research and development, as well as the near term commercial activities of the growing company. The new 11,000 sq. ft. facility, located at One Kendall Square in Cambridge, Massachusetts, will have enhanced office and laboratory space to provide additional infrastructure that will enable the companys continued growth and transition from R&D to commercialization of its desktop DNA sequencing technology. The building will be equipped with manufacturing and fabrication facilities in addition to general laboratory and office space to house the growing team. Additional hires in product development, software, development,sales and marketing staff will be housed in the new space as GnuBIO prepares for the launch of its first commercial product.

This move to a larger and more sophisticated facility marks an important milestone for GnuBIO, as it will afford us the space to transition into the commercial phase of the company, said John Boyce, President and CEO of GnuBIO, http://www.gnubio.com. The additional space will allow us to bring all initial manufacturing capabilities, from the consumables to the instrumentation, in house. The new facility will also provide the necessary space for the first critical hires for our commercial team.

GnuBIOs platform technology is a fully integrated next-generation desktop DNA sequencing platform, based on established microfluidics and emulsion technology licensed from the laboratory of Professor David Weitz at Harvard University. The emulsion and microfluidic technology, combined with novel molecular biology assays, has led to the development of a scalable, accurate DNA sequencing platform that encompasses all of the steps required for DNA sequencing into a single platform. It is designed to run complete and customized sequencing workflow more efficiently and at a lower cost than currently available systems, with a list price of only $50,000 per system with no extra equipment or servers needed. The company is currently working with leading institutions and molecular diagnostic companies, both in the US and abroad, to develop customized and standard panels that will be run on the GnuBIO system http://www.gnubio.com.

About GnuBIO: GnuBIO, http://www.gnubio.com, is a privately-held company developing next-generation desktop DNA sequencing technology that will compartmentalize the entire DNA sequencing process, combining all of the steps required for sequencing in a single system, and providing the only fully integrated next-generation sequencing workflow.The GnuBIO sequencingtechnology is based on an emulsion based microfluidic technology which also provides a scalable sequencing solution that allows for interrogation of single genes, gene panels or whole genomes. The user of his GnuBIO system simply injects the patient sample into the GnuBIO cartridge, the appropriate panel is run inclusive of gene capture, PCR, sequencing, and informatics analysis and the results are ready within hours. Unlike any other DNA sequencing system, the entire process is all on the chip the user simply injects genomic DNA, simplifying the complex sample preparation process and breaking the barrier of a an obstacle that has prevented the widespread adoption of DNA sequencing.

New address: One Kendall Square, Building 1400, 2nd Floor, Cambridge, Massachusetts 02139

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Moving Towards Commercialization, Desktop DNA Sequencing Company GnuBIO Announces Relocation To Expanded Facilities

DNA enters pilot for Conax Xtend Multiscreen(TM) pre-integrated partner solution

IBC Expo, Amsterdam, September 5th:Conax,a leading provider of solutions for protecting multi-device content distribution, announced today that Finnish Cable and Terrestrial operator,DNA, has entered a multiscreen pilot with partners Conax,Cubiware,MPS BroadbandandEnvivio. The pilot will include end-user testing with various multiscreen services and devices. It will also address the operational processes and procedures required for DNA to support advanced multiscreen services, and to prepare DNA on the path to the emerging over-the-top market. Together with DNA, the partners will explore the features and functionality of the Conax Xtend Multiscreen(TM) solution.

-"Conax is very excited to be chosen by long-time customer DNA to participate in this very exciting multiscreen pilot project, says Tom Jahr, EVP Products and Partners, Conax. Conax is already providing DNA with best-in-class security and is looking forward to working closely with DNA, and partners Cubiware, MPS Broadband and Envivio to assess feasibility, functionality and price/performance for positioning DNA in the evolving market within OTT content distribution."

Multiscreen background The Conax partnering strategy includes combining complementary technologies in a pre-integrated solution to remove operator risk of untested product combinations for reduced cost, time-to-market and smooth transition to new advanced services for connected devices. Conax Xtend Multiscreen(TM) combinesCubiware's flexible middleware for advanced user interface technologies,MPS Broadband'sMPS Publishing Platform(TM) for publishing and managing video content and Peer2View for distribution acceleration,Envivio's encoder technology and Conax' proven record within security.

- Mikko Saarentaus, Business Director (TV&VAS), DNA, "DNA sees the future of TV to be about multiscreen service. This pilot gives us a great opportunity to learn about the end users' impression on multiscreen services and to better understand the customers' needs and how they like to use the services. The DNA team will work closely with the pilot partners to address the operational processes and procedures required for DNA to offer integrated support for delivering advanced services to connected devices such as hybrid client devices, tablets and smart phones and position our operations for growth within over-the-top content distribution."

Conax' benchmark pre-integrated Conax Xtend Multiscreen(TM) partner solution has the potential to set a new standard in terms of price/performance for multiscreen solutions in the industry - dramatically reducing operational complexity and cost and time-to-market for the delivery of content through advanced services to connected devices, compared to costly competitor solutions with lengthy conformity testing and implementation times.

About DNA (www.dna.fi) DNA Ltd is a Finnish telecommunications company offering high-quality voice, data and digital television services using the latest technology. DNA's customers include private customers, corporations and other organizations. In 2011, DNA recorded a turnover of EUR 728 million and an operating profit of EUR 51 million. DNA has more than 3 million mobile and fixed-line network customers.

About Conax (www.conax.com)

Conax provides future-oriented security solutions that empower multi-screen digital TV content providers around the globe to deliver premium content over the combined Over-The-Top scenario of broadcast, broadband and connected devices, securely and eliminating potential revenue threats. Conax technology secures content for operators representing 125 million pay TV consumers in over 80 countries around the globe.

ISO 9001 & 27001 certified, Conax is headquartered in Oslo, Norway, and represented in Russia, Germany, Brazil, USA, Canada, Mexico, Indonesia, Philippines, Thailand, China, Singapore, with 24/7 Global Support operations in India. Follow Conax onTwitter

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DNA in Finland embarks on the journey to multiscreen with Conax and partners