Applied Biosystems and the ISB have embarked on a collaboration to develop new technologies and applications in proteomics. ISB intends to use the Applied Biosystems 4700 Proteomics Analyzer with TOF/TOF Optics and the ICAT reagent technology as major platforms in its efforts to study the dynamics of complex biological systems to better understand human immunity and identify strategies for preventing disease.
This partnership is focusing on the development of more effective ways to analyze proteins in the pathways that comprise complex biological systems by using mass spectrometry, chemical tagging strategies and bioinformatics, including improved LC MALDI workflows for high throughput quantitative proteomics studies. The effort combines Applied Biosystems expertise in the development and application of mass spectrometry, chemistry and software to advanced proteomics workflows with ISB’s expertise in systems biology.
Scientists from ABI’s Proteomics Research (PRC) Center will leverage Applied Biosystems existing proteomics expertise and internal research capabilities while facilitating collaboration with complementary technology partners. The goal is to achieve advances in the production of high quality information by means of significant improvements in throughput automation, sensitivity and cost efficiency.
In May 2005, the Institute for Systems Biology (ISB) established a strategic partnership with GenoLogics Life Sciences Software, Inc. (GenoLogics) to collaborate on increasing the widespread utility of the ISB's open source software tools within the life sciences community.
The ISB has played a pioneering role in developing new open source tools for data collection and analysis, as well as new scientific instruments and approaches supporting genomics, proteomics, and high-speed cell sorting. GenoLogics will collaborate to enhance the functionality and usability of the ISB's open source tools and integrate these tools into its industry-leading lab management and informatics platform — ProteusLIMSTM. In addition, the GenoLogics value-added support network will facilitate installation and broaden the reach of the tools for a wider group of researchers.
Dr. Ruedi Aebersold, notes, "The partnership with GenoLogics is aligned with our mission as an integrating force in biology and medicine, and our goal of rapidly developing and disseminating new technologies and computational tools to individual scientists and labs all over the world. As a leader in providing lab information management systems for proteomics research, GenoLogics' ability to enhance and integrate our tools into their platform will only serve to accelerate the dissemination and help transform today's technologies. We plan to extend this relationship as the ISB develops additional new bioinformatics tools and GenoLogics extends its lab management and informatics platform into systems biology."
Michael Ball, chief executive officer of GenoLogics commented, "We are extremely pleased to partner with Dr. Ruedi Aebersold and the ISB. The Institute is at the cutting edge of developing tools around data analysis for new types of biological data. By integrating these tools into our ProteusLIMS platform, it will expand the use of lab information management systems to enable researchers to put their information in context and facilitate advancement of scientific discovery in disease prediction and prevention."
About GenoLogics
GenoLogics develops bioinformatics solutions that help life science and pharmaceutical laboratories specializing in the emerging field of proteomics research, to manage, integrate and analyze enormous volumes of scientific and lab data to advance health science research. As proteomics and systems biology technologies progress from the research lab into commercial drug and clinical diagnostics applications, GenoLogics continues to develop additional functionality in its software to meet these unique needs. More than a workflow solution, ProteusLIMS is a comprehensive and integrated lab, instrument, and scientific data management system that transforms the data management process into a sophisticated analytical system that aids research and scientific discovery. The company is headquartered in Victoria, B.C., Canada. For more information, please visit www.genologics.com.
ISB uses computer technology to model not just the functions of individual genes and proteins, but their complex interactions within a cell, tissue, organ or whole organism. This information is complex and requires tremendous computational power. ISB has established a partnership with IBM to explore research collaborations that will leverage the technology framework from IBM and provide ISB with the capability it needs to quickly analyze and integrate data, and accelerate its research efforts.
The first major project was launched in November, 2004 utilizing IBM’s newly acquired grid-computing platforms to fold proteins in three dimensions in order to develop a better understanding of how they function. IBM has employed its three million computers of IBM’s grid-computing platform, a resource that ISB could never build by itself. By giving ISB access to this tremendous computational capacity, IBM is facilitating the completion in approximately six months of a project that would take ISB’s own supercomputers at their current speed approximately 100,000 years. ISB researchers hope that understanding the functions of these proteins from the human genome will help them better understand how they relate to the networks of life and hence may provide insights into the causes and potential cures for diseases like cancer, malaria, and tuberculosis.
Additionally, the ISB selected IBM to provide its infrastructure technology and is using IBM servers, storage and data integration products to support its research on protein-protein interactions to better understand and predict diseases, and identify potential preventions and treatments. Deployment of ISB’s information technology infrastructure was completed in late 2002.
IBM systems installed include a 64-node IBM eServer xSeries 1300 Cluster, with two micropressors per node. This highly scalable, prepackaged cluster is being used to process data from a network of mass spectrometers, which identify and analyze proteins -- critical steps in the process of determining protein-protein interactions. ISB researchers are now also using IBM’s DiscoveryLink software to integrate proteomics data in disparate formats and file types and from a variety of public and private data sources.
In September 2005, Institute of Systems Biology (ISB) adopts Kreatech Biotechnology's (ULS) nucleic acid labeling technology in a collaboration on new assays
The continuing scientific collaboration between the Institute of Systems Biology and Kreatech's product development team has resulted in an arrangement between Kreatech and the ISB for the use of Kreatech's commercial products. Kreatech's platinum based "Universal Linkage System" (ULS), a non-enzymatic way of labeling nucleic acids with detectable molecules such as fluorophores, has been adopted by Dr. Nitin Baliga's research group and is now the preferred labeling method for both bacterial gene expression profiling and Chip on Chip assays that have been developed at the ISB.
Currently available kits from Kreatech are optimized for labeling of amplified RNA for gene-expression analysis and for labeling of genomic DNA for microarray based comparative genomic hybridization (arrayCGH). This collaboration with the ISB will help Kreatech to position the ULS technology in new application areas.
"We are pleased and very proud with the fact that a renowned institute like the Institute of Systems Biology has made the switch to our technology", says Alexander Altink, Kreatech's CEO. The labeling kits used by the ISB include the unique purification columns (KREApure), blocking buffer (KREAblock) and ULS bound with Dyomics' DY Dyes. "We have been working with this technology for a while and we like both the reproducible labeling efficiencies as well as the one-step purification of labeled material", says Dr. Nitin Baliga, Assistant Professor at the ISB.
About KREATECH Biotechnology
KREATECH Biotechnology B.V., a private company founded in 1990, focuses on the creation, development, production and marketing of innovative diagnostic and life science products. KREATECH's proprietary Universal Linkage System (ULS) offers a reliable, robust and easy to use non-enzymatic technology that can be applied to a broad range of biomolecules and labeling agents. KREATECH is committed to achieve and maintain the highest standards in production and Quality Control as well as in the relationships with our customers and partners. The company's quality policies are demonstrated by the implementation of ISO 9001 (2000) and ISO 13485 (GMP 2003) guidelines.
More information on KREATECH can be accessed at www.kreatech.com
Plexera Bioscience, a wholly owned subsidiary of Lumera Corporation (NASDAQ:LMRA), announced today that it has extended its collaboration agreement with the Institute for Systems Biology (ISB). The goal of the collaboration is to use instrumentation based on Plexera's Kx ArrayTM technology to identify biomarkers associated with drug toxicity and cancer.
As previously announced, ISB researchers have demonstrated a label-free assay to determine protein expression patterns using a panel of specific antibodies printed on specialized sensor chips and analyzed on the company's the novel kinetic array analyzer.
"We are quite pleased with the progress of the past year" said Dr. Leroy Hood, President of the Institute for Systems Biology. "Plexera's platform provides unique advantages in biomarker discovery and we are committed to moving the science forward."
"Early results from ISB have been proof positive that our technology adds significant value to the biomarker discovery market. We feel that with a continued emphasis on this project, we will arrive at a very important publication and will establish methods by which others will be able to develop their own assays," said Dr. Timothy Londergan, COO of Plexera Bioscience.
As previously discussed by the company, biomarkers are important indicators of disease and their identification can lead to the development of targeted drug solutions to prevent or arrest the disease. Biomarker screening has been an increasing area of research growing from $5.4 billion in 2005 to an estimated $21 billion by 2012 according to Business Insights, a market research firm.
About Plexera Bioscience
Plexera Bioscience is focused on providing the life sciences market with tools, content, and methods that simplify and accelerate proteomic discovery for improved diagnostics and therapeutics. For more information, please visit http://www.plexera.com/.
Showcase Study on Systems Approaches to Prostate Cancer Research
The Institute has partnered with Lynx to study prostate cancer gene expression. The agreement features the application of Lynx’s Massively Parallel Signature Sequencing, or MPSS, technology to uncover differentially expressed genes in prostate cancer. The resulting MPSS analyses will be combined with data from ISB to generate a showcase study for a systems biology approach for studying prostrate cancer.
Systems biology involves the analysis of all parameters of a biological system. This includes an accurate and quantitative analysis of the transcriptome all genes that are expressed in a sample. Since MPSSTM technology is uniquely designed to sample virtually all mRNAs in a sample and to provide precise quantitative data in a digital format, it is believed to be an ideal tool for systems biology applications.
Prostate cancer is the most commonly diagnosed malignancy in men and the second leading cause of cancer related deaths in the United States, accounting for over 35% of all the cancers affecting men. Approximately 20% of those diagnosed will eventually die from the disease. Prostate cancer follows a pattern of progression from localized disease that is androgen dependent to a more advanced, invasive, metastatic disease, which is often associated with the loss of androgen dependence and patient mortality. The molecular mechanisms involved in the switch from androgen dependence to independence is not well understood.
We believe that these initial experiments will clearly demonstrate the unique utility of MPSSTM as a tool to generate the type of gene expression data sets and the standards necessary for systems biology research.
Systems biology requires sophisticated technological tools for success, such as those developed by Lynx. This collaboration provides the Institute with enormous opportunities to develop and apply systems biology tools in gene expression research, facilitating the integration of Lynx’s innovative MPSSTM technology with our own in an interactive environment.
In 2001, the Institute received a $5 million gift from Merck & Co., Inc. to support the Institute’s pioneering work in molecular biotechnology and genetics. This funding has provided the Institute with critical discretionary resources for attacking leading-edge technical, biological and medical projects.
Scientists from the ISB proteomics group and from Merck and its wholly owned subsidiary Rosetta Inpharmatics have been collaborating on three levels. First, they work on the development of advanced tools for the analysis and storage of quantitative data generated with the ICAT reagent technology. Second, they are collaborating to develop new experimental approaches to generate accurate quantitative protein profiles that are complementary to the gene expression profiles generated with the Rosetta/Merck ink jet technology, and third, proteomic researchers from Merck and Co. have visited the ISB for training in proteomics technologies.
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