Diatoms are eukaryotes that have a unique cell wall made from silica. They are keys to better understanding the environmental health of the marine ecosystems since they are the major residents in the world’s waters and are responsible for most of the regulation of carbon and production of oxygen in these waters.
Researchers compared the P. pseudonana genome to the previously sequenced diatom, Thalassiosira pseudonana to further understand diatom evolution, function and prevalence. P. tricornutum has 27.4 million base pairs of DNA, and 10,402 genes making it slightly smaller than T. pseudonana.
JCVI researchers, Dr. Andrew Allen, and Dr. Jonathan Badger, developed novel phylogenomic profiling techniques to identify the origins of the diatom genes. They found that more than 300 of these genes were of bacterial origin. This finding has significant implications in understanding diatom evolution and should enable better understanding of how diatoms utilize nutrients found in their environments.
First author Dr. Chris Bowler of the Ecole Normale Supérieure and his colleagues are also trying to understand the role that iron plays in the Phaeodactylum’s development. Iron is even more precious than nitrogen in the ocean and its absence in the southern hemisphere is likely a major cause of oceanic deserts of photosynthesis there. Bowler’s team has demonstrated that when iron deficiency occurs processes such as photosynthesis and nitrogen assimilation are suppressed.
Recently, Allen, Bowler and colleagues published a paper in the journal PNAS describing how diatoms metabolize iron and how they adapt to low iron environments. In this study, the team determined that some of the genes responsible for the diatoms’ abilities to survive in low iron availability are bacterial and that diatoms appear to have a bacterial-like iron binding protein.
JCVI researchers are funded by NSF grants in the Biological Oceanography and Microbial Genome Sequencing programs.
Both organizations will work together to create a unique knowledge resource in genomics called 'Genomics Gateway'. The vision of this partnership is to present applications of genomics in pursuit of improved and affordable healthcare and therapeutics. The Gateway will feature leading scientists, developments and progress in this area through webinars, interactive interviews, and blogs amongst other vehicles.
The Gateway will be featured as new sections on the OBBeC Biotech portal powered by deSciner and Gene Logic's thought leadership forum.
“We are extremely delighted to be working with Gene Logic to incorporate such rich knowledge resource into OBBeC Portal,” says Tim El-Sheikh, Managing Director and CEO of deSciner Business Network. “We always strive to provide our worldwide readers with high quality and informative content from leading scientists and businesses from around the globe, discussing strategic issues and best practices in biotechnology, Bio-IT and healthcare sectors, all through a single online interface.”
Anu Acharya, CEO, Gene Logic says, “We have a very strong corporate social responsibility program through which we reach out to our community. Genomics over the years has been defined and re-defined and we are now seeing exciting applications of genomics in the biotech sector. As a leader in the genomics space, we are pleased to partner with deSciner to present the latest in the genomics and discovery space through various programs we have planned.”
Dr. Ashwin Sivakumar, Director Marketing & Alliances, Gene Logic says, “State-of-the-art technologies like Genotyping, Differential Gene Expression, Genome Wide Association, SNPs et cetera have contributed immensely to global biomarker discovery programs as we all continue our pursuit for improved and affordable therapeutics. This alliance with deSciner is a first of its kind partnership where we have broken traditional barriers to feature pioneering work of the genomics community and present news relating to advancements in this sector.”
According to an announcement from Wellcome Trust Sanger Institute, a team of researchers at the institute have decoded the genome of a malaria parasite that has a host range from monkeys to man. Identified originally in monkeys, the parasite was first reported in a human infection just over 40 years ago.
"This contract sets the stage for the FDA to have IT to acquire, analyze and act on data critical for import protection, food protection and medical product safety plans," said Dr. Andrew C. von Eschenbach, Commissioner of Food and Drugs. "We are creating a high-tech, efficient, data management system designed to meet the needs of those who must accomplish our mission -- protecting and promoting the health of the American public."
The contracts, with a minimum value of $25,000 in orders per contractor, were awarded to: Buccaneer, of Warrenton, Va.; Computer Sciences Corporation, Rockville, Md.; Dynanet, of Elkridge, Md.; Electronic Data Systems, Herndon, Va.; General Dynamics, Fairfax, Va.; Human Touch, McLean, Va.; IDL-Pragmatics, Vienna, Va.; Interactive Technology Solutions, Silver Spring, Md.; Telesis, Rockville, Md.; and Unisys, Reston, Va.
According to the announcement, the ten contractors will compete for data information technology task orders through this contract. The FDA has awarded three task orders under the ICT 21 contract for the design and migration of all systems applications to two new data centres, which will be the cornerstone of the FDA IT infrastructure and bioinformatics modernization for the next decade. The three task orders were awarded to:
IT Solutions (Task Order 1 - funded initially at $3,000,000) provides the design and implementation as well as migration of existing FDA applications to the newly configured White Oak Data Centre, which will support all FDA test and development applications.
Buccaneer (Task Order 2 - funded initially at $3,000,000) provides the operations and maintenance of the White Oak Data Centre.
EDS (Task Order 3 - funded initially at $12,000,000) provides the design, implementation, migration and operations and maintenance of existing FDA applications to a Contractor Owned Contractor Operated hosted data centre for FDA production operations.
All FDA software applications and hosting operations will transition to the new data centres over a two-year period. The resulting enhanced computing power and greater responsiveness will provide the FDA with the tools it needs to ensure that all products reaching the American public are safer and more effective.
The company is building, what it claims to be, the world's largest commercial human genome sequencing centre.
Starting next spring the company will be offering a complete human genome sequencing services to pharmaceutical and biotechnology companies as well as other medical researchers that were previously priced out of the market. By offering a sequencing service instead of following the traditional instrument sales model, Complete Genomics is relieving its customers of operational, computational and capital purchase burdens, allowing them to focus their resources on scientific discovery.
"We will be the first company to sequence complete human genomes for less than $1,000 in material costs," said Dr. Clifford Reid, chairman, president and chief executive officer of Complete Genomics. "This breakthrough materials cost, combined with our low per-genome instrument, labour and overhead costs, will allow us to offer complete human genomes for just $5,000 in Q2 2009."
"This $5,000 price point, combined with the scale of our sequencing centre, will dramatically increase the availability and affordability of human genome sequencing. For the first time, our customers can conduct systematic studies of the genetic basis of disease and drug response. Our sequencing services will be one of the core enablers of the impending revolution in personalized medicine," Reid added.
"Many chronic and life-threatening human diseases have a genetic basis, and Complete Genomics' sequencing service will allow medical researchers to study disease pathways comprehensively and cost-effectively in a large number of individuals. The ability to compare a significant number of genomes of people with a disease against those without the disease is central to enabling drug discovery and the development of new diagnostics," added Dr. George M. Church, professor of genetics at Harvard Medical School, director of the Center for Computational Genetics and member of Complete Genomics' Scientific Advisory Board.
According to the announcement, after the company launches its third-generation human DNA sequencing service in Q2 2009, it plans to sequence 1,000 genomes in the same year. The company will then sequence 20,000 genomes in 2010.
The company also, in conjunction with partners, intends to open additional genome sequencing centres across the U.S. and abroad. Over the next five years, the company projects that 10 such centres will be able to sequence 1 million complete human genomes.
"One million genomes represent 1,000 people each in 1,000 disease studies," Reid said. "Our customers will conduct these studies to reveal the genetic basis of all major human diseases including cancer, psychiatric and neurological diseases, metabolic and cardiovascular diseases, autoimmune diseases, and many other poorly understood multifactorial diseases."
A key component of Complete Genomics' sequencing centre is its data centre, purpose-built to manage and analyze the staggering amount of genetic data that will be generated by sequencing thousands of human genomes. Because the data generated by a single human genome would fill 1,000 laptop computers, each with 100 GB of disk storage, data management for Complete Genomics' genome centre will be a massive undertaking. The company plans to have 10,000 processors with five petabytes (5 million gigabytes) of disk storage in 2009 and will further increase its capacity to 60,000 processors with 30 petabytes of disk storage in 2010. Complete Genomics expects to sequence 200 genomes per day by the end of 2010, making it the world's highest-throughput human genome sequencing centre. To put this in context, fewer than 20 complete human genomes have been sequenced in the world to date.
The custom array PhyloChip was developed to simultaneously identify and quantify up to 8,900 distinctive environmental and pathogenic microbial species in a single experiment, in less than nine hours. The PhyloChip is unprecedented in its ability to accurately test any clinical or environmental sample without the need for culturing. The chip has been used by the Department of Homeland Security for bioterror detection, the Japanese Defence Force, the U.S. Department of Energy in bioremediation of contaminated soils to detoxify the earth and the State of California Water Quality Board for monitoring contaminated beaches.
"The speed with which we can now carry out our research far outpaces serial cloning. We offer the potential for numerous applications, including human health assessment, water quality and environmental cleanup, enabling complete evaluation of numerous samples on a daily basis," said Dr Gary Andersen, project leader at Berkeley Lab. "Affymetrix has allowed us to replace expensive and time-consuming cloning and sequencing with a method that will offer a competitive advantage to anyone wanting to detect bacteria in soil, air, water or clinical samples."
In July the PhyloChip won an R&D Magazine award for technology advancement. It was recognized for its ability to quickly, comprehensively and accurately identify species within microbial samples from any environmental source, without any culturing required. The PhyloChip is not yet commercially available. For more information please contact Dr. Andersen at the Lawrence Berkeley National Laboratory.
Based on Affymetrix microarray technology, MPI aims to market its own proprietary products targeted at individual cancer prognosis and prediction of anti-cancer treatment response.
"Our partnership with Affymetrix enables us to translate our discoveries into robust tools with broad clinical utility to greatly improve the prognosis and treatment of millions of people living with cancer. It also boosts the probability of successful anti-cancer drug development in partnership with drug companies," said Jesper Drejet, president and CEO of Medical Prognosis Institute.
"MPI's cancer prognosis tools have the potential to customize treatment schemes, revolutionize the control of this disease and the chances of recovery," said Kevin King, president of Affymetrix. "Agreements such as this continue to validate the need for microarrays for complex signatures for reproducibility and accuracy. We are proud to help MPI advance its ambitions to improve drug therapy choices and provide hope for those struggling with this destructive disease."
As outlined by the companies, this new partnership has been formed to facilitate regulatory submissions in the pharmaceutical industry and will see the integration of Good Products’ electronic document management system (eDMS) g-docs with Adlib Software’s Express Server centralized PDF rendering tool.
The collaboration between the two scientific software providers addresses the need from the pharmaceutical industry for streamlined and compliant regulatory document management. Using the new integrated system, pharmaceutical organizations will be able to store, manage and track regulatory documents and create high quality regulatory submission-ready PDFs with bookmarks and hyperlinks.
g-docs from Good Products offers life sciences organizations an effective, easy-to-use way of managing their documents including tracking document version history, managing approvals, monitoring and recording changes in an audit log. Additionally, g-docs incorporates CoSign, a digital signature solution that allows an individual to digitally sign a document as if they were using ink. CoSign digital signatures have now been upheld in the US court, and are deemed to pass the ‘non- repudiation’ test as well as being compliant with the FDA’s 21 CFR part 11 Guidance.
g-docs uses Adlib Express Server to automatically convert different document formats including Microsoft Office, scanned images, engineering drawings and web and image formats to PDF while meeting the requirements of international regulatory bodies, including the FDA. Moreover, g-docs uses Adlib to automatically maintain audit, version, reference and distribution tables within the rendered documents, saving time and at the push of a button.
Peter Duff, president and CEO, Adlib Software, comments: “Our partnership with Good Products complements the ability to provide compliant document conversion systems to the pharmaceutical industry. The integration of g-docs™ and Express Server accelerates regulatory submissions and enables organizations to manage documents in a compliant way across the whole lifecycle, from creation to regulatory submission.”
“With the increasing standardization of regulatory submissions in an electronic format, and the need to simplify the User experience, both Adlib Software and Good Products recognize the importance of maintaining the consistency and accuracy of electronic documentation from creation to submission,” adds Keith Williams, CEO, Good Products. “We are now looking to work together to develop further enhancements and functionality, enabling deeper integration of Good Products and Adlib Software solutions.”