Thursday, March 30, 2000

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Biospace Celera and Human Genome Project Still Talking, Says Collins
"Collins was careful to emphasize that his excitement over nearing the end is "because I'm a physician." He predicted that within five to seven years, thanks both to the genomic sequence and information on genetic variations called SNPs (single nucleotide polymorphisms) "we will uncover all the genetic contributions of every common illness -- cardiovascular disease, asthma, Parkinson's, cancer, and stroke."

""Within 10 years, I believe we will be able to design individualized preventive medicine regimens based on one's susceptibility profile," said Collins. Such a profile will be derived from a chip "read-out" of an individual's own genomic sequence. "This will become a fairly standard part of mainstream medicine," Collins said. Within 15 years, Collins envisions "a full-flowering of gene-based drugs.""

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JAMIA Integration and Beyond: Linking Information from Disparate Sources and into Workflow
"The vision of integrating information—from a variety of sources, into the way people work, to improve decisions and process—is one of the cornerstones of biomedical informatics. Thoughts on how this vision might be realized have evolved as improvements in information and communication technologies, together with discoveries in biomedical informatics, and have changed the art of the possible. This review identified three distinct generations of "integration" projects. First-generation projects create a database and use it for multiple purposes. Second-generation projects integrate by bringing information from various sources together through enterprise information architecture. Third-generation projects inter-relate disparate but accessible information sources to provide the appearance of integration. The review suggests that the ideas developed in the earlier generations have not been supplanted by ideas from subsequent generations. Instead, the ideas represent a continuum of progress along the three dimensions of workflow, structure, and extraction. "

JAMIA Integration and Beyond: Panel Discussion
"I think one of the toughest things we all have to deal with is updating our dictionaries. In the simplest cases, the name of an organism is changed and we just have to do the maintenance. It is tougher, when, as with Citrobacter, they do genetic studies and say, "Oh, it's really six different organisms, not one." We have the human genome project coming very quickly. Even that is just the tip of the iceberg. We're not only going to see all the genes; we're then going to see clinical tests based on gene expression. Essentially, you'll be able to look at something on the order of 180,000 gene products and whether they're up or down regulated. How are we going to integrate such an incredible amount of data at a time when we're going to also be changing how we think about these processes? Classification and simple mapping are not going to work, because the lumpers and splitters are going to be arguing furiously on a daily basis."

Wednesday, March 29, 2000

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UIUC Collaboratory for Structural Biology
"The Theoretical Biophysics Group at the University of Illinois is proud to announce the initial public release of BioCoRE, a collaborative research environment. BioCoRE software is freely available for use at the Theoretical Biophysics Group website. BioCoRE development is supported by the NIH National Center for Research Resources.

Modern computational structural biology requires scientists to employ a wide range of tools and techniques to solve complex problems while keeping accurate and complete records of research activities. Additional complications are introduced by the need to effectively engage in interdisciplinary collaborations with geographically dispersed colleagues. The software BioCoRE, a collaborative research environment for molecular modeling and simulations, addresses these challenges."

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BioMail free literature alert tool
"BioMail regularly (weekly by default) searches for articles, which have recently appeared in the PubMed® Medline® database, using customized search terms. Then it e-mails lists of the found articles to the user. As a result, you can see all the articles in your field of interest without performing the Medline® search manually. An account can have several different searches. Registration and use of BioMail is free and unrestricted by institution or country. "

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LinuxWorld Farming, Linux-Style
"Gone are the days when any pioneer with a bit of hardware, hard code, and hard work could run a small Linux farm and compete with the best plantations. The smart folks at biotech firm Incyte Genomics of Palo Alto, Calif., have just invented agribusiness. You remember everything you ever tried to tell your boss or colleagues about Linux's stability, price performance, and reliability? Well, Incyte has put those ideas to the test and come up grinning like a bandit.

To map the human genome, Incyte runs the world's largest commercial Linux farm, with more than 2,000 Linux processors chomping away on tens of millions of jobs per day. In its datacenter, laid out like a temple in the middle of Incyte's corporate headquarters, space costs a king's ransom -- but the company has come up with clever ways to address that problem..."

Sunday, March 26, 2000

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The New York Times On Road to Human Genome, a Milestone in the Fruit Fly
[requires 'free' registration]
"Opening a new window into the mysteries of animal design and the nature of life, biologists described here today how they had decoded almost the entire genetic rule book for making the Drosophila fruit fly, an organism whose study is deeply interwoven with the progress of modern biology. "

"As fly biologists emphasize with the slightest prompting, the fly's genes and proteins have turned out to be surprisingly similar to those of people. Of the 289 genes known to cause human disease in mutated form, 177 have direct counterparts in the fly, Dr. Rubin and his colleagues have concluded after reviewing all the genes in its genome.

This means the genes could be manipulated in the fly as a step toward devising remedies for the human diseases."

Science The Drosophila Genome Sequence: Implications for Biology and Medicine
[summary - can be viewed for free once registered]
"The 120-megabase euchromatic portion of the Drosophila melanogaster genome has been sequenced. Because the genome is compact and many genetic tools are available, and because fly cell biology and development have much in common with mammals, this sequence may be the Rosetta stone for deciphering the human genome.”

Science Genomics: The End of the Beginning
[summary - can be viewed for free once registered]
"The sequencing of the complete genome of the fruit fly Drosophila (Adams et al., Myers et al., Rubin et al.) is a remarkable feat that tells us much about the organization of the genomes of complex creatures. In a Perspective, Brenner looks to the future, to the next big step forward, which will be deciphering what the protein product of each gene does and how each gene is switched on and off. ”

ABC News Gene Mapping Company Says Intentions Misunderstood
"Celera Genomics feels mightily misunderstood these days.

The company, which just announced it has mapped virtually all the genes in the scientifically important fruit fly, first came under fire for its proposals to use a quick-and-dirty method known as "shotgun sequencing" to make a diagram of all the genes in the human body.

Then it was accused of planning to keep all this information to itself, patenting the genes to prevent anyone else from benefiting from the knowledge."

""After we are done with it anyone can have it -- free," Paul Gilman, in charge of policy planning for Celera, said in an interview at the company's headquarters in Rockville.

"Unless you're a database company and you want to repackage it and say 'hey, we've got the genome'."

"Showing off the two rooms of computers that the company uses to piece together information about fragments of DNA and to support its pharmaceutical and biotech subscribers, Gilman said information alone is not a product.

He gave as an example database giant Lexis-Nexis, which sells its online service as a way of searching publicly available information. Its power lies not in the actual newspaper articles and legal documents, which anyone could find with a little bit of effort, but in the shortcuts it provides to finding that information.

"We want to be the next Lexis-Nexis of biology," Gilman said. "We want to become synonymous with modern-day research.""

Saturday, March 25, 2000

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HMS Beagle Celera previews genome data access terms
[requires 'free' registration]
"Celera Genomics says that within a few days it will make public the terms for getting access to its human genome data. The company says there will be no constraints on the way academic researchers can use it, except that the data may not be passed along to others. Celera will charge between $5,000 and $20,000 annually for the data, software, annotation, and use of its supercomputer. A consensus sequence will be available to nonsubscribers on Celera's Web site or DVD. Celera expects its strength to lie in its computing tools, not its raw data. The company's comments are a responseto last week's joint statement by Bill Clinton and Tony Blair urging the public release of all human genome data - and to the subsequent sharp decline in its stock price.

Reference: Butler, D. 2000. U.S./U.K. statement on genome data prompts debate on "free access". Nature 404(6776):324-325."

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Wired Shopping for Single Genes
"A genetic information company Thursday began offering a program that will allow researchers to access individual genes that were previously part of a prohibitively expensive database.

Using Incyte Genomics' LifeSeq Gene-by-Gene program, researchers outside large pharmaceutical companies can tap into the company's huge database and buy one gene at a time -- saving them the six months it typically takes to isolate genes in the lab."

"Researchers using the new program can purchase gene-sequence data, or have physical copies of gene clones shipped overnight, for between $5,000 and $20,000, depending on how much information Incyte has on the gene."

""This is just the first step in an even broader plan. [Incyte's] animal sequences, proteins, SNPs by the end of the year will all be online..."

Wednesday, March 22, 2000

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spotfire.net SPOTFIRE LAUNCHES SPOTFIRE.NET, THE FIRST WEB PORTAL FOR TECHNICAL DECISION-MAKING COMMUNITIES
"Spotfire®, Inc., today launched Spotfire.netTM, the first Web-based decision-analytics portal for scientific and industrial decision-making communities."

"Spotfire.net empowers technical decision makers to work effectively within the data-intensive, fast-paced environments of product discovery, development, manufacturing, and marketing by: accessing required data wherever it resides; interactively exploring and analyzing large amounts of data; and, collaborating across teams, across departments, and across geographies."

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Individual.com Oscar Gruss Issues Bioinformatics Report
"Oscar Gruss & Son Incorporated has issued an in-depth biotechtechnology review entitled "Trends in Commercial Bioinformatics."

Author Jason Reed, Ph.D., equity research analyst at Oscar Gruss, provides a detailed examination of the emerging commercial market for "bioinformatics technology" -- the computational tools, databases and information technology services that support genomic and related research."

Tuesday, March 21, 2000

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Bioresearch Online TIGR Reports Complete Genome of Two Chlamydia Strains
"In the first publication of two complete genomes, scientists at The Institute for Genomic Research (TIGR; Rockville, MD) report the DNA sequence of the Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39 genomes in the current issue of Nucleic Acid Research. These findings complement recently published Chlamydia genomes completed at Stanford University, and could provide new insight into the genes responsible for causing a range of serious human infections."

"The C. trachomatis strain sequenced by TIGR is infectious in mice, while the Stanford strain causes human sexually transmitted diseases (STDs). Nonetheless, there were very few differences in the genomes of the two bacteria. Comparison of the two strains might reveal those genes that contribute to the human Chlamydial infection, which could be applied to developing vaccines and therapeutics. One strain similar to a toxin found in E. coli O157:H7—the food-poisoning bug. The significance of this is not presently known. The toxin was not found in the human STD strain.

The genomes of C. pneumoniae sequenced by TIGR and Stanford were extremely similar—providing evidence that one extremely successful clone of the bacterium has infected a large proportion of the human population. However, small differences between the genomes may help explain individual variation in the severity of disease in patients infected with C. pneumoniae."

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Yahoo! News Celera to Do Breast Cancer Gene Study
"Celera Genomics, one of the companies racing to use information from gene-mapping to make profits, said on Monday it had hooked up with a cancer center to find genes associated with breast cancer.

Celera, based in Rockville, said it signed an agreement with the Duarte, California-based City of Hope Cancer Center to get clinical information from breast cancer patients and sequence their DNA.

``We hope that this collaboration will enable clinical investigators to develop better ways to prevent, diagnose, and treat breast cancer,'' Dr. Sam Broder, chief medical officer of Celera and a former director of the National Cancer Institute, said in a statement."

"They will look for single nucleotide polymorphisms (SNPs), which are single-letter alterations in the nucleotides, the four different molecules known as A, T, G and C that combine in long strings to make up the genetic code."

redux [02.18.00]
Science SNP Mappers Confront Reality and Find It Daunting
[summary - can be viewed for free once registered]
"The genetic markers called SNPs have been widely touted as the key to personalized medicine, with drugs tailored to an individual's genotype and simple tests to determine one's risk of specific diseases. But a closed meeting held last week, sponsored by the SNP Consortium and the U.S. National Human Genome Research Institute, concluded that those promises may be harder to achieve than expected, and that more SNPs may be required to track down a particular disease gene than previously estimated.”

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ER2000 International Workshop on Conceptual Modelling for Knowledge Discovery and Management Systems - KDMS2000
Knowledge discovery systems (and knowledge discovery components of larger systems) are constructed to automate the analysis of large volumes of structured or semi-structured data. They contain data mining algorithms that apply heuristics to generate rules that can then be passed to either a user for further investigation or directly to a system to modify the system's behaviour. However, the results from data mining routines, whilst constrained, are dependent on the knowledge found within the data and thus the nature of the rules and the behaviour of the system cannot be entirely predicted a priori. Moreover, the semantics of the rules discovered are critically dependent on the model of the data being mined. Nevertheless, the development of reliable, robust and responsive systems that employ data mining components is important as the potential benefits of employing knowledge discovery are large. It is important, therefore, that there be a solid conceptual foundation in terms of data, rule and process modelling. "

"In this workshop, we aim to create a forum for both researchers and practitioners in the areas of knowledge discovery and knowledge management systems for the discussion of various open issues, research topics, techniques, practices and lessons learned from industry for reducing this gap. In this respect we are less interested in data mining algorithms themselves, than in their application to real-world projects and their integration within existing systems."

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BBC News Tests spark fears of genetic underclass
"The UK Government is considering allowing insurance companies to use genetic testing to assess a person's risk of inheriting a serious illness."

"One opponent of the wider use of genetic testing said it was part of a "terrifying trend" that would lead to a culture of "cherry picking"."

redux [02.25.00]
Science U.K. Plans Major Medical DNA Database
[summary - can be viewed for free once registered]
"Following the examples of Iceland, Sweden, and Estonia, the United Kingdom is drawing up plans to create a national database linking the DNA of 500,000 of its citizens to their medical records and lifestyle details. Its main goal is to tease apart the genetic and environmental components of conditions such as cardiovascular disease and cancer and, eventually, to come up with new drugs to treat--or even prevent--these conditions. An expert panel is currently hammering out a strategy for setting up the database and is due to report its recommendations next month.”

redux [02.13.00]
The Daily Davos Beyond the Genome
"By the spring of this year, the first draft of the human genome -- the sequence of all the genetic instructions needed to make up a human being -- will be published on the Web. But that is only the end of the beginning. Scientists still have very little idea of what most of the 100,000 or so human genes actually do, and finding out will take them into a very different area of research.

The raw material of the genome program has been anonymous samples of DNA, manipulated by complex laboratory machines that turn out information like a production line turns out widgets. But the new era of post-genome research involves analysing real people and their confidential medical records. The records are needed to match the genes that people carry with the diseases they may develop. Only then will gigabytes of genetic data into new treatments for cancer or heart disease. And that is why socialised healthcare is a vital part of post-genome research.

Countries such as the U.S., which provide healthcare through private enterprise, are useless for this sort of genetic inquiry. Only those countries which have organized the delivery of healthcare to their population in a way that is independent of the marketplace have built up the universal medical records necessary to make sense of the patterns of disease."

Monday, March 20, 2000

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The Gene Letter Wherefore art thou disease genes?
"One of the big surprises arising from the sequencing of the human genome is how common genetic variations (mutations) are. Earlier guesses may have underestimated the actual frequency by 200 or 300 percent. And though "hot spots" exist, the high rate - about one in every 300 sites in the genome - appears to be spread evenly across all DNA regions.

But among all the DNA variations in our genomes, a true "disease gene" will never be found. That's because the concept of a gene which has altered function resulting in disease is primarily a social construction, not a biological one. It arises in part from our persistent need to gain more scientific insight in to disease and illness."

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Wired News Chilly Genetic Reaction
"The Icelandic public is accusing its government of taking huge payments from the company licensed to create a nationwide genetic database of the country's entire population.

A public outcry escalated last week following newspaper editorials and a forum sponsored by Mannvernd, an organization strongly opposed to deCODE Genetic's plans to create the Icelandic Health Sector Database."

redux [02.06.00]
BBC News Iceland sells its genetic history
"It has never been done before and no-one really knows how successful it will be, but it has already divided the country and now the whole world is watching and waiting."

"The Icelandic Government has given a licence to a US-funded corporation to study the medical records, family trees and genetic information of each and everyone of the country's 270,000 citizens."

Icelandic Healthcare Database Overview
"A centralised database is an idea that requires this form of temporary protection in order to flourish, just as the author of a book requires copyright and, for a fixed period, exclusive right to sell the work. Without a special or exclusive licence of some form, it is impossible to establish a privately-run database."

Sunday, March 19, 2000

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CCP11 The Bioinformatics Industrialization Workshop - Bioinformatics Comes of Age.
"Pilot Workshop Cosponsored by IBM, The Task Force on Bioinformatics of the International Union of Pure and Applied Biophysics, and The Whitehead Institute for Biomedical Research A limited number of spaces are available for a pilot workshop addressing the transformation of bioinformatics into a robust discipline, supporting high-throughput exploration and exploitation of genomic data in industry, government, research institutions and academia. The workshop will emphasize the coupling of genomics and related processes, such as proteomics and protein modeling, and the support tools of integration, data mining, and deep computing. Participants will also explore bioinformatics for health care, including pharmaceutical prediction and modeling."

Saturday, March 18, 2000

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HMS Beagle Patenting Genes Is It Necessary and Is It Evil?
[requires 'free' registration]
"Last October, biologists' neck hair rose when J. Craig Venter announced his company, Celera, had filed 6,500 provisional patent applications for human genes. Henry Ford mass-produced automobiles - it seems evident we are now entering an era in which intellectual property is rolling off the assembly lines. Is this really the ultimate legacy of Watson and Crick's elegant double helix? And what does it portend for the future of biology?"

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HMS Beagle Blossoming Bioinformatics: The Princeton Bioinformatics Symposium
[requires 'free' registration]
"At Princeton University on January 19, 2000, the Department of Molecular Biology and the brand-new Institute of Genomic Analysis sponsored a one-day Bioinformatics Symposium. The meeting attracted graduate students and postdoctoral fellows - the bulk of the audience - plus scientists from the central New Jersey pharmaceutical belt."

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Nature Science Update Too Darn Hot
"...two US physicists claim to have figured out how it is that complex systems, from computer networks to rainforests, can be robust in the face of anticipated disturbances, yet too fragile to cope with unexpected events. They call this state 'highly optimized tolerance' (HOT). A HOT system, they say, can cope with all the 'slings and arrows' that it is designed to withstand, but can fail catastrophically if presented with some unforeseen challenge."

"The key consideration, they say, is 'design'; it is this that allows a HOT state to operate under conditions that, were it to be generated at random, would be highly unstable to small perturbations. In nature, 'design' equates with natural selection, which effectively allows the evolutionary process to 'make choices' amongst random mutations.”

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Science SNP Mappers Confront Reality and Find It Daunting
[summary - can be viewed for free once registered]
"The genetic markers called SNPs have been widely touted as the key to personalized medicine, with drugs tailored to an individual's genotype and simple tests to determine one's risk of specific diseases. But a closed meeting held last week, sponsored by the SNP Consortium and the U.S. National Human Genome Research Institute, concluded that those promises may be harder to achieve than expected, and that more SNPs may be required to track down a particular disease gene than previously estimated. ”

Thursday, March 16, 2000

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BBC News Balancing interests in the genome race
"It is clear from the reaction of some publicly-funded scientists to the Clinton-Blair statement that they resent the idea that big business is involved in decoding the human genome, the basic instructions for life. They would rather the corporations stay out of it.

Despite the impression given in some quarters, it is a gross oversimplification to suggest that all publicly-funded scientists are good and working for the betterment of humanity and private companies are secrecy for the sake of profit alone."

"In order to reap the rewards of the genomic revolution, both public and private companies must be involved. Both will make public their raw data. From then on, it will be up to the market.

And I predict that in a decade some of these companies will be the medical equivalent of Microsoft - but even bigger. "

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Yahoo! News PE Biosystems Forms Proteomics Research Center Announces Two Major Research Collaborations
"The Proteomics Research Center's mission is to define novel tools for proteomics, focus on the advancement of the science of proteomics, and develop practical application-based systems for the fields of research, drug discovery and development, and health care.

Complete genome sequences form the basis for understanding the biology of life. Proteomics, the study of the array of proteins produced by a genome, is an emerging field that is expected to utilize the rapidly expanding wealth of newly available genomic information for a better understanding of complete biological systems. This insight into biology could lead to the identification and development of new therapeutics and diagnostics and significant advances in personalized health care."

Tuesday, March 14, 2000

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CNN U.S. and Britain to make Human Genome Project results public
"President Clinton and British Prime Minister Tony Blair have agreed that all discoveries from the Human Genome Project will be made available to the global scientific community in order to assist health research.

The two countries have agreed to a joint statement to be released Tuesday in both the United States and Britain, applauding researchers who have already made their human genome data available and calling on all researchers to follow their lead."

Celera CELERA STATEMENT ON THE POLICY STATEMENT OF PRESIDENT CLINTON AND PRIME MINISTER BLAIR ON THE AVAILABILITY OF GENOMIC INFORMATION
"Celera Genomics welcomes the statement. Its own mission is completely consistent with the goals of assuring that the world’s researchers have access to this important information to enable advances and discoveries that will improve the human condition. Since the announcement of Celera’s formation we have made a clear commitment that upon our completion of the consensus human genome we would publish it in a peer-reviewed scientific journal and make it available to researchers for free."

USA Today Feds may have tried to bend law for gene map Health agency denies any 'conspiracy' to recruit biotech company in race to finish project
"Federal officials and a British charity secretly attempted to enlist biotechnology firm Incyte Pharmaceuticals in a race to complete the Human Genome Project and win a bitter two-year battle against another company, Celera Genomics of Rockville, Md."

"At stake in the contentious battle is scientific glory and potential control over access to information about virtually all human diseases and possible cures. Scientists predict that the first group to complete the human genetic blueprint will win a Nobel Prize and a pedestal in the halls of history."

Monday, March 13, 2000

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Yahoo! Finance TIGR Researchers Report Complete Genome Sequence Of Neisseria Meningitidis B and its Use for Development Of Novel Men B Vaccine By Chiron
"Investigators at The Institute for Genomic Research (TIGR) today announced that they have determined the complete genetic blueprint for Neisseria meningitidis, the primary causative agent of bacterial meningitis. Herve Tettelin led the team at TIGR that determined the order of all of the 2.27 million individual chemical base units making up N. meningitidis' DNA."

"In an accompanying paper, Chiron Corporation, which funded this work, also reported that it has used this detailed information on the microorganism's genetic structure to identify novel vaccine candidates against meningococcal disease. This is the first demonstration of the important role that genomics can play in the development of commercial products."

Science Complete Genome Sequence of Neisseria meningitidis Serogroup B Strain MC58
[summary - can be viewed for free once registered]
"The 2,272,351-base pair genome of Neisseria meningitidis strain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior of N. meningitidis can be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally, N. meningitidis contains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.”

Sunday, March 12, 2000

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The Boston Globe a genome greenmailer?
"In the end, the difference between J. Craig Venter's model and that of Michael Bloomberg is that Bloomberg's head start in business was legitimate. It began with something he really did own, through licensing fees: the data on a huge set of privately owned but publicly traded government bonds.

Venter, on the other hand, wants the Genome Project to grant him a few years' corner on the genome data simply because he muscled in and now threatens to make trouble for all concerned - a business model more like corporate greenmail than legitimate entrepreneurship."

"But one Bill Gates is enough. Let the biotech Bloombergs make their millions downstream from the data itself. The human genome data set is a classic example of the fruits of basic research - its preservation as public knowledge is the greatest test case of the new era. We should ensure its availability to all those who wish to work with it, even if it takes an act of Congress - which, in the end, it probably will."

Financial Post How the market found the map of the human genome
"A complicated war is clearly under way, a war over science, business and ideological strategies. The U.S. government may ultimately determine the victor. But the overall message should be clear. Celera's drive to make profit, as a private competitive company, has already produced major benefits. These include a flood of investment capital drawn from stock market investors (Celera shares, once at $7, are now above $200). A great scientific leap will be achieved years ahead of plan. More companies are entering the field. And Celera, with its new capital, intends to begin packaging its genome science into programs that will be accessible to scientists, researchers, biotech and pharmaceutical companies -- proving, once again, that the private system works better than the public."

Friday, March 10, 2000

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JAMA Clinical Aspects of Genetic Variability in Helicobacter pylori
"Helicobacter Pylori organisms have been infecting human stomachs for centuries. Antigens of these microaerophilic, gram-negative bacteria have been found in stool samples of ancient mummies. Today, it appears that more than half of the world's population is infected with H pylori. These organisms are adapted for survival in the stomach in which infection causes a chronic gastritis that persists for decades.

H pylori infection is strongly associated with peptic ulcer disease, and is widely accepted as a risk factor for gastric adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma.

Recently, some researchers have proposed that H pylori strains that express cytotoxin-associated gene A (cagA) may be especially virulent, and that laboratory tests for cagA status might be useful for directing the management of infected patients. Others have disputed these claims. This report reviews the available epidemiological and clinical data to determine if tests for cagA status should be recommended for clinical application."

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HMS Beagle GenBank: New and improved
[requires 'free' registration]
"An easier-to-use GenBank is scheduled to open for business in April. Annotation of the premier human genome database will be beefed up. It will include more on genetic markers and functions of both genes and their proteins, including the capability to predict the likely function of partial sequences. The new and improved GenBank will also include more links to databases on single nucleotide polymorphisms.

Reference: Smaglik, P. 2000. Revamped GenBank offers extra data links. Nature 404(6774):111."

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HMS Beagle Human genome: Loss of interest?
[requires 'free' registration]
"The U.S. National Advisory Council for Human Genome Research is worried that the approaching completion of the draft genome, now forecast for early summer, is reducing researchers' enthusiasm for finishing the detailed sequence, scheduled for 2003. Their worries are fueled by a spate of new proposals for making use of the draft. Among them are projects to speed up investigations of gene function, such as sequencing the mouse genome, a cDNA library of mammalian genes, and additional bioinformatics methods and databases.

Reference: Smaglik, P. 2000. Genome leaders told to keep their eyes on the main prize. Nature 404(6774):111."

Wednesday, March 08, 2000

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Yahoo! News UK Firm Applies for Patent on Gene Profile System
"A British company has applied for a patent for a gene-profiling system that can quickly reveal a person's genetic make-up and susceptibility to disease.

Genostic Pharma, based in Cambridge and Edinburgh, claims the system could help doctors predict the course of an illness, the best drugs to treat it with the fewest side effects, and how a patient will respond.

"This, in effect for the first time, defines what will be really useful to know to hopefully enable a doctor to improve his management of the patient,'' Dr Gareth Roberts, the company's director, said in a telephone interview."

"It's a way of delivering individualized patient care.''"

New Scientist A gene profiling system threatens to reveal your innermost secrets
""Where Genostic comes up with thousands of gene variants to put on their chip is a mystery to me," says Francis Collins, director of the US National Human Genome Research Institute near Washington DC. Daniel Cohen, chief genomics officer at Genset of Paris, agrees. "There haven't been enough population studies, as far as I know, to assess with enough precision the risk or predisposition for any of the diseases mentioned in the patent," he says.

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The Washington Post Celera Leaves Door Open To Genetic Research Deal
"A Rockville biotechnology company involved in a rollicking fight over efforts to unravel the human genetic code said yesterday that it remains open to the possibility of collaboration with federally funded researchers pursuing the same goal."

On a central bone of contention--how long commercial restrictions should apply to the combined database--the sides do not appear that far apart. Negotiators from the public genome project have offered Celera up to a year of protection, while Celera executives have told The Washington Post they would accept three years. "

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Salon Who owns your DNA?
""Doesn't it bother you," [Francis] Collins asked [The PTO's John] Doll during a conference in Washington on Thursday, "that your standard would allow patent protection for roughly 40 percent of human genes, and yet if you ask any working scientist what percent of human genes they know the function of, you'd get, maybe 2 percent?" "

Tuesday, March 07, 2000

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Wired News Celera Refutes Accusations
"Celera Genomics president and CEO Craig Venter said Tuesday that his company is willing to continue "good faith discussions toward collaboration" with the public Human Genome Project.

Venter, responding to an ultimatum in a letter from the HGP made public Monday, said he was disappointed by the "dramatically distorted" assertions in the note. He denied accusations that he had blown off making a decision on further talks and scolded the consortium for going public with its claims against Celera."

Monday, March 06, 2000

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The Scientist Biotech Faces Evolving Patent System
[requires 'free' registration]
"How do efforts to improve the system affect the success of biotechnology? Three recent developments could provide clues. First, the U.S. Patent and Trademark Office (PTO), burdened by thousands of applications for gene patents, is proposing new guidelines under which it could reject many pending and future applications. Second, Congress recently enacted the most extensive revision of the patent statute since 1984, and though the law could extend the lives of many biotech patents, it's not entirely benign. Finally, as holders of biotech patents begin to enforce their ownership rights, some scientists want to change a system that they contend denies them affordable, or indeed any, access to disease-linked genes."

"Just to say 'I have a piece of DNA, and it is useful as a gene probe' isn't good enough to pass the [new] utility test," says John Doll, director of biotechnology patent examination at PTO. "What you're going to have to say is, 'My particular piece of DNA probes for this particular gene, disease state, or location on a chromosome.' If you're going to be patenting a chromosome marker, you'll have to tell us what you're marking."

In applying the "substantial" utility requirement, he continues, "we're no longer going to accept 'throw-away utilities.' If you've developed a new transgenic mouse, it will no longer be acceptable as 'snake food.' You have to tell us what the real-world utility is for that mouse. And if you have proteins, you cannot say this protein is a source of an amino acid or is an animal feed supplement.""

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BBC News Gene firm labelled a 'con job'
"Dr John Sulston, director of the Sanger Centre, Britain's leading gene-sequencing lab, has attacked the American company Celera Genomics and its director Dr Craig Venter over their intention to make money selling a combination of public and private DNA data."

"Dr Sulston said that Celera "hoover up all the public data, add a bit of their own and sell it as a packaged product. It is fair enough if people want to buy it. That's up to them."

But he added that the Celera data is something of a "con job," saying that they are "pretending to do something they are not." "

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Financial Times Talks breakdown sparks fresh genome race
"The race to produce the first complete map of mankind's genetic code is back on after the breakdown of co-operation talks between rival public and privately fundedscientific teams.

"In a letter to Celera Genomics, members of the Human Genome Project, state: "While establishing a monopoly on commercial uses of the human genome sequence may be in Celera's business interests, it is not in the best interests of science or the general public.""

Thursday, March 02, 2000

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CCP11 Newsletter Issue 10
InterPro – An integrated documentation resource for protein families, domains and functional sites
"InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects."

PIX - Protein Identification Application
"PIX a World Wide Web based tool to view the results of running many protein analysis programs on your peptide sequence."

The TIGR Gene Indices: A Resource to Estimate the Transcript Content of Genomes
"The TIGR Gene Indices (TGI) represent a best guess of transcript content in the genomes of ten plant and animal species through the meticulous cataloguing of Expressed Sequence Tags (ESTs) and coding sequences, which are downloaded from Genbank on a continual basis. The TGI species include human, rat, mouse, Drosophila, zebrafish, Arabidopsis, Maize, Rice, Soybean, and Tomato. An eleventh index for potato is planned for introduction in 2000."

ChiMap (Change in Intensity of Multiple Associated Proteomes) program to enable easy identification of significant expression changes in a series of 2D gels.
"Analysis of the cellular proteome involves the characterization, analysis and subsequent identification of thousands of proteins. As two-dimensional gel electrophoresis technology improves it will be possible to characterize better and therefore visualize a larger percentage of the total protein complement. The total cellular protein complement has been estimated as 20,000 separate proteins, many of which will have several post translational modifications. With the steady increase in information on a 2D gel it becomes imperative to develop a set of user-friendly tools to identify features that are interesting for identification by mass spectrometry in addition to enable the tracking of changes in protein expression over a set of defined parameters such as substrate-activation or simply time."

The Power of Patent Information
"Since its launch in 1990, Derwent’s GENESEQ database has rapidly become the world’s largest database exclusively devoted to nucleic acid and amino acid sequences from patents. In 1998, GENESEQ was launched in flat file (ASCII text) EMBL format which enables integration of the database into in-house bioinformatics systems. It is a unique information resource, which allows professional searchers to identify patents containing a given sequence, or a sequence substantially homologous with it, in a single operation.

All patents containing nucleic acid or amino acid sequence information are analysed and any new nucleotide sequences of 10 or more bases, protein sequences of 4 or more amino acids and new primers and probes are added to the database. To date, the database contains over 600,000 records from 40 patent-issuing authorities, including US and PCT. Of the records, some 20% are from foreign language patents from countries including Japan, Germany, France, Latin America, Russia, Korea, China and Hungary, among others.

GENESEQ is updated every two weeks, with about 2,000-3,000 new records added at each update."

Wednesday, March 01, 2000

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HMS Beagle When in doubt, model
[requires 'free' registration]
"Some cellular systems can't be studied biologically, as they are inseparable from the cell. Thus, manipulating one alters the entire system. The authors describe an experiment in which computer modeling helped identify glycosome function in parasites called trypanosomes, which cause African sleeping sickness. In the parasites, these membrane compartments perform the first step in glycolysis. The researchers used models to compare the outcome of glycolysis with and without glycosomes. Analysis showed that cells without glycosomes should metabolize glucose at the same rate as cells with glycosomes, challenging the theory that glycosomes increase the rate of metabolism by concentrating glucose-metabolizing enzymes. However, cells without glycosomes built up chemical intermediates of glucose metabolism and did not recover well from glucose deprivation. This study demonstrates the power of computer modeling for investigations in cell biology that cannot yet be addressed through direct experimentation.

Reference: Bakker, B.M., Mensonides, F.I.C., Teusink, B. et al. 2000. Compartmentation protects trypanosomes from the dangerous design of glycolysis. Proc. Nat. Acad. Sci. U.S.A. 97(5):2087-2092."

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Individual.com DoubleTwist and EraGen Announce Partnership to Provide Master Catalog on DoubleTwist.com
"DoubleTwist(TM), Inc. and EraGen Biosciences Inc. today announced a partnership that will provide proprietary data from EraGen's Master Catalog to users of the life sciences research portal, DoubleTwist.com(TM).

"Master Catalog is a functional genomics database that provides an annotated version of GenBank organized by evolutionary modules."

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Individual.com Gene Logic Completes Atlas of Normal Human Gene Expression
"Over the past 6 months we have characterized the normal gene expression profiles of more than 40 distinct human tissue types, representing over 30 million individual measurements in normal tissues alone," said Dr. Lennon. "This massive set of reference information is a core part of our GeneExpress(TM) database suite which also contains gene expression profiles of many important human diseases. Subscribers to our databases can compare normal with diseased tissues to identify the pathways involved in the onset and progression of diseases. The information can be used for all aspects of drug discovery and development, from target discovery to molecular profiling of drugs to design of clinical trials and, ultimately, disease management for individual patients."

"By the end of 2003, the databases are expected to contain complete profiles on 30,000 tissue samples representing approximately 3 billion gene expression data points."