November 2000

News

The State of Bioinformatics
The State of Bioinformatics
Disentangling the good from the bad--gene and protein data, that is--may be the toughest task for today's bioinformatics scientists assembling new models for proteins, says Greg Paris, executive director of biomolecular structure and computing at Novartis Pharma Research in Summit, N.J. "One of the major advances has been the speed with which new genomes can be characterized and at least partially annotated, and there are very good gene-finding tools that help in this endeavor," he explains. "T
Merging IT and Biology
Merging IT and Biology
Much of the promise of bioinformatics likely lies with the big money and novel approaches of the private sector. At a late October symposium titled "Biosilico 2000," several bioinformatics company executives came together at the Trump Plaza in New York City to discuss the state of the immensely expansive and increasingly heterogeneous field of bioinformatics. Not surprisingly, many touted their products and business plans; but they also discussed and compared philosophies for engaging in the dau
New PTO Unit Examines Bioinformatics Applications
New PTO Unit Examines Bioinformatics Applications
Last year, the U.S. Patent and Trademark Office (PTO) routinely assigned patent applications for bioinformatics inventions to examiners in diverse departments. Then the office made a projection, based on input from companies, that it would receive more than 300 such applications in the fiscal year that ended Sept. 30. To ensure consistent treatment for the predicted flood of filings, PTO created Art Unit 1631 (AU1631) last December. This unit now consists of 10 examiners holding degrees, sometim
Big Plans for Kansas City
Big Plans for Kansas City
The Stowers Institute for Medical Research Predictions and plans abound these days concerning Kansas City--that border town straddling Missouri and Kansas known for its jazz, barbecue, and riverboat gambling--as a future leader in biomedical research. But perhaps the most eloquent recent argument that such an ambitious goal might be achieved was a standing ovation given on Nov. 8 by 1,200 of the city's business and scientific community leaders to James E. Stowers Jr. and his wife, Virginia G. St
News Notes
News Notes
Accuracy in Recounts It can take a pathologist, moving a micrometer across a slide under a microscope, days to measure 10 different layers in a skin tissue sample. It can also take days to count regrown or restenosed endothelial cells to gauge the effect of a drug on, say, ruptured coronary artery elastic lamina. And a second pathologist may get different results. But Mark Braughler of TissueInformatics, speaking at the Techvest Tissue Repair, Replacement, and Regeneration conference in New Yor

Letter

The Global Agenda, Revisited
The Global Agenda, Revisited
The letter by Alfred E. Harper1 on the anti-scientific attitudes and superstition that persists among the general public and politicians was juxtaposed on my desk with a fascinating article in my local newspaper. There, in the Newark Star Ledger of Oct. 29, 2000 (Section 1, page 3), was an article from Reuters describing a lawsuit filed by the American Civil Liberties Union on behalf of an Oklahoma City high school student suspended last December for casting a spell that caused a teacher to beco
Biased Reviewers?
Biased Reviewers?
Regarding the Commentary by Edzard Ernst on peer reviewers and alternative treatements,1 how can this study be called a randomized and controlled study when the reviewers are "conditioned beforehand" with the fact that one of the treatments is "unconventional"? Did the study authors identify the nature of the unconventional treatment? Was it scientifically valid with respect to obesity? Was there a rationale reason for using it? Ernst gives no consideration to these factors. The results r

Commentary

Patenting Life: The Harvard Mouse that Has Not Roared
Patenting Life: The Harvard Mouse that Has Not Roared
There has been little notice of the Canadian government's recent action in a 15-year patent dispute with Harvard University, even though it may restoke the fires of controversy about the patenting of life.1 Last month, the government appealed to the Canadian Supreme Court the award to Harvard of a patent on a transgenic mouse.2 The university filed the patent application in June 1985 for the Harvard Oncomouse, so named because it is genetically engineered to be susceptible to cancer.1 The Canadi

Perspective

The Scientific Muse
The Scientific Muse
The worldwide impact of discoveries over recent years in genetics is evident, but also worth considering is the potential effect on the performance of biology. Could these achievements spark an upsurge in creativity elsewhere within the life sciences? The reason this may be likely is that, since the dawn of the 20th century--and even earlier, going back to Gregor Mendel's experiments--the gene has been an abstraction par excellence, a chemical entity described without direct evidence of its exi

Research

Stem Cells Tapped to Replenish Organs
Stem Cells Tapped to Replenish Organs
Credit: Eric LaywellAn astrocyte monolayer that can be coaxed into becoming multipotent neural stemlike cells Editors Note: This is the second of two articles on issues raised by recent stem cell discoveries. The first article appeared in the November 13 issue "All politics is local" was a famous maxim of Thomas "Tip" O'Neill, the late speaker of the House of Representatives, and the same can be said of medically useful stem cells. Progenitor cells may prove to be more or less pluripotent in th
Research Notes
Research Notes
HEADY Role in Hydra Hydra, a multicellular, lower-eukaryotic, freshwater polyp, is known for its developmental idiosyncrasies. Slice off its head or its foot, and within two days either regenerates perfectly at the proper location. Although developmental biologists have some understanding of the molecular machinery involved in this feat, they have yet to isolate and prioritize many of the factors that play a role. In a recent paper, two scientists report the discovery of a signaling peptide ca

Hot Paper

HD Cell Death Mechanisms
HD Cell Death Mechanisms
For this article, Eugene Russo interviewed Michael E. Greenberg, a professor of neurobiology and neurology at the Children's Hospital, Harvard Medical School. Data from the Web of Science (ISI, Philadelphia) show that Hot Papers are cited 50 to 100 times more often than the average paper of the same type and age.   F. Saudou, S. Finkbeiner, D. Devys, and M.E. Greenberg, "Huntingtin acts in the nucleus to induce apoptosis but death does not correlate with the formation of intranuclear incl
SNARE Crystal Structure
SNARE Crystal Structure
For this article, Eugene Russo interviewed Axel T. Brunger, a Howard Hughes Medical Institute investigator and professor of molecular and cellular physiology at Stanford University. Data from the Web of Science (ISI, Philadelphia) show that Hot Papers are cited 50 to 100 times more often than the average paper of the same type and age. R.B. Sutton, D. Fasshauer, R. Jahn, A.T. Brunger, "Crystal structure of a SNARE complex involved in synaptic exocytosis at 2.4 angstrom resolution," Nature, 395:

Technology

A Perfect Ten
A Perfect Ten
Gentra Systems' AUTOPURE LS™ Nucleic Acid Purification System Automated nucleic acid purification systems capable of handling small samples (up to 1 ml) have become a time- and money-saving asset in recent years. However, clinical laboratories and clinical research groups requiring larger sample volumes have had to rely on time-consuming manual methods to purify nucleic acids--until now. Gentra Systems of Minneapolis has introduced the AUTOPURE LS system, the first instrument capable of is
Faster Diagnoses OnCyte
Faster Diagnoses OnCyte
When properly understood, knowledge of the interaction and communication of cells with each other and their environment can be applied to the diagnosis and treatment of disease. For example, a recent study1 has shown that expression of CD11b on the surface of neutrophils increases during infection. This observation is the basis for a rapid screening test for dangerous early-onset neonatal infections that can provide confirmation of an infection in a few hours, as opposed to one or two days. Beca
Revealing Images
Revealing Images
There seems to be no end to the stream of optical technologies hitting the market. Cambridge Research & Instrumentation (CRI) Inc., of Woburn, Mass., has developed CellView and SpindleView imaging systems to apply the company's LC-PolScope™ technology1,2 to the subcellular organization of living cells without stains or fluorescent labels. Many subcellular structures are oriented polymers that are spatially organized, or anisotropic. This anisotropy causes the speed of light to v

Technology Profile

Bioinformatics, Genomics, and Proteomics
Bioinformatics, Genomics, and Proteomics
Data Mining Software for Genomics, Proteomics and Expression Data (Part 1) Data Mining Software for Genomics, Proteomics and Expression Data (Part 2) High-throughput (HT) sequencing, microarray screening and protein expression profiling technologies drive discovery efforts in today's genomics and proteomics laboratories. These tools allow researchers to generate massive amounts of data, at a rate orders of magnitude greater than scientists ever anticipated. Initiatives to sequence entire genom
Up to Speed on PCR
Up to Speed on PCR
Real-time PCR Systems Cepheid's Smart Cycler System PCR--a technique so common in today's laboratories that it is easy to forget its revolutionary impact--enables the specific amplification and detection of as little as a single copy of a particular nucleotide sequence. However, PCR has the potential to be used not just for the detection of specific sequences, but also for their quantification, because of the quantitative relationship between the amount of starting target sequence and the amoun

Profession

Retooling for Bioinformatics
Retooling for Bioinformatics
Nurturing a career in bioinformatics takes a certain kind of aptitude, despite its popularity. First off, you have to like being intimately involved with computers, agree those who already work in this burgeoning field. "For some, staring at a glowing, blue screen all day is like a ring of Dante's inferno," says Larry Hunter, past president of the International Society of Computational Biology (ISCB) and director of the Center for Computational Pharmacology at the University of Colorado School o
Funding Opportunities in the Life Sciences
Funding Opportunities in the Life Sciences
Organizations are welcome to submit information for consideration for future listings by contacting kdevine@the-scientist.com Click to view the PDF file: Funding Opportunities in the Life Sciences
Profession Notes
Profession Notes
Boosting Network Performance Information technology is playing an increasingly significant role in all facets of today's world, including scientific research. The National Science Foundation recently announced a new research collaboration to develop software that automatically tunes network protocols in computer operating systems to fully exploit available network bandwidth. NSF has given a three-year, $2.9 million award to the Pittsburgh Supercomputing Center, the National Center for Atmospher

Opinion

Cellular Phones: Are They Safe to Use?
Cellular Phones: Are They Safe to Use?
© 2000 Anthony Canamucio Resolving the question of whether cellular phones are safe has been complicated by conflicting information about electromagnetic fields (emfs): no danger; yes there is danger; well, we don't know. This has been unsettling for the public and has put pressure on health policy decision makers to act. But can they take action based on the biological data now available? I think not. In fact, I believe it would be unethical to use much of it to make public health decision