April 2001

News

Is a Human Proteome Project Next?
Is a Human Proteome Project Next?
Three dozen scientists, officials, and executives from academia, government, and business are speaking this week at a conference in McLean, Va., titled "Human Proteome Project: Genes Were Easy." This event, which is expected to draw at least 400 other participants, is the first sizable public meeting devoted to the possibility and advisability of a proteome project, according to organizer Chris Spivey, a conference director at Cambridge Healthtech Institute in Newton Upper Falls, Mass. The Vir
On the Fast Track in Functional Proteomics
On the Fast Track in Functional Proteomics
Graphic: Leza Berardone Researchers in Canada and Denmark are employing mass spectrometry, three-dimensional tissue biology, and supercomputing to blaze a trail in functional proteomics research. In the process, they're putting their company, MDS Proteomics Inc., on the fast track in the latest race to develop new drug targets and eventually better treatments for all kinds of diseases. By using this combination of technologies, MDS Proteomics is accelerating the process of identifying, analyzin
New Technology Spurs on Proteomics
New Technology Spurs on Proteomics
Graphic: Leza BerardoneOne recent morning at the Applied Biosystems proteomics research center in Framingham, Mass., scientist Jason Marchese patiently used a pipettor to place tiny samples onto a 2-inch-by-2-inch plate. He was surrounded by technology as simple as 2-D gel electrophoresis apparatus and as cutting-edge as a high-throughput system that uses automated robotics for multidimensional liquid chromatography separation of proteins and an automated workstation that uses the latest in mass
Aptamers Identify Protein Signatures
Aptamers Identify Protein Signatures
Graphic: Leza BerardoneA technique not deemed "sexy" enough for commercialization a decade ago may finally find its niche in proteomics. SomaLogic Inc. of Boulder, Colo. is pioneering aptamers, which are modified DNA molecules that bind specific proteins in body fluid samples. Aptamers are initially selected for specific binding activities from a huge starting pool, then variants are obtained during subsequent rounds of amplification. The technology builds on the ability of aptamers to bind tena
Debating Shelby
Debating Shelby
Sentiments expressed at a March 12 National Academy of Sciences workshop suggest that scientists and policy-makers remain very concerned about data access issues related to the now infamous Shelby Amendment. The amendment, a two-line provision added by Sen. Richard Shelby (R-Ala.) to an omnibus appropriations law for fiscal year 1999, subjects federally funded scientific research to requests for data made under the Freedom of Information Act (FOIA).1 Its inclusion sparked a debate between indust
Bowl of Hope, Bucket of Hype?
Bowl of Hope, Bucket of Hype?
When a research team led by Ingo Potrykus of the Swiss Federal Institute of Technology in Zurich and Peter Beyer of the University of Freiburg in Germany announced last year that they had produced beta carotene, or provitamin A, in rice grains,1 the news created quite a stir.2 For one thing, getting "golden rice," as it was quickly dubbed (for its color, not its monetary value) required a biotech tour de force. Potrykus and Beyer inserted two genes from daffodil and one from a bacterium into ri
News Notes
News Notes
The Federal government's Interagency Task Force on Microbial Resistance has issued an 84-item plan to combat the growing public health problem presented by microbes' increasing ability to shrug off antibiotics. This recently released first part of the plan is aimed at domestic concerns, including the use of antibiotics and other drugs in agriculture (H. Black, "Agricultural antibiotics scrutinized," The Scientist, 14[12]:1, June 12, 2000). The Food and Drug Administration is proposing to withdra

Commentary

'Ome Sweet 'Omics-- A Genealogical Treasury of Words
'Ome Sweet 'Omics-- A Genealogical Treasury of Words
"So intricate and inscrutable a mystery is the origin of language that in 1866 the French Society of Linguistics formally banned further research on the subject." --J. H. Dirckx, 1977. (Dx + Rx: A Physician's Guide to Medical Writing) Genomics and Proteomics are the buzzwords of the dawning millennium. There is no counting of www.-ics.com and www.-ix.com sites to be found on the Web. That most of these terms, old and new, have been contrived as slogans to attract attention, does not diminish t

Letter

Teaching Creationism
Teaching Creationism
Regarding "Fighting Darwin's Battles,"1 I spent a day discussing creationism in my science classroom last year. It was right after the controversy in Kansas, and the Channel One news program was highlighting it for a time. I made the point to my kids that I thought that creationism should be taught in the social studies classroom, and should include creation stories from all cultures and religious traditions. I went so far as to read to them, creation stories from Hindu, Native American, and J

Research

Designing a More Accurate Protein Census
Designing a More Accurate Protein Census
Graphic: Leza BerardoneApplied Biosystems will soon begin testing new mass spectrometry machines designed to identify proteins in as many as 1,000 samples per hour. For the machines to work as planned, however, each sample must be prefractionated down to just a handful of proteins, according to Stephen A. Martin, director of the company's proteomics research center in Framingham, Mass. This example suggests how the slower protocols leading to mass spec are as important to the progress of proteom
Research Notes
Research Notes
There may be more significance to the color of one's eyes than cues to wardrobe selections. One study links dark eyes to lower incidence of noise-associated hearing loss (M.-L. Barrenas, F. Lindgren. "The influence of inner ear melanin on susceptibility to TTS in humans," Scandinavian Audiology, 19:97-102, 1990), and another indicates that having brown eyes raises the risk of hearing loss following cisplatin chemotherapy (T.N. Wendell et al., "Cisplatin in children: hearing loss correlates with
Better Mouse Memory Comes at a Price
Better Mouse Memory Comes at a Price
Researchers have discovered that transgenic mice previously shown to outperform their normal counterparts on learning and memory tests1 are also more sensitive to chronic pain.2 This finding suggests that memory formation and pain sensation might share components of a common physiological pathway in mice, and therefore, possibly in other vertebrates such as humans. These "Doogie" mice (scientifically manipulated mice that make more than the usual amount of the NR2B subunit of the NMDA [N-methy

Hot Paper

Survival Factors and Apoptosis
Survival Factors and Apoptosis
For this article, Tom Hollon interviewed Anne Brunet, a postdoctoral fellow in the division of neurosciences, 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. A. Brunet, A. Bonni, M.J. Zigmond, M.Z. Lin, P. Juo, L.S. Hu, M.J. Anderson, K.C. Arden, J. Blenis, M.E. Greenberg, "Akt promotes cell survival by phosphorylating and inhibiting a forkhea
Ordering the Events of Apoptosis
Ordering the Events of Apoptosis
For this article, Tom Hollon interviewed Seamus J. Martin, professor of medical genetics at the Smurfit Institute, Trinity College in Dublin, Ireland. 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. E.A. Slee, M.T. Harte, R.M. Kluck, B.B. Wolf, C.A. Casiano, D.D. Newmeyer, H.G. Wang, J.C. Reed, D.W. Nicholson, E.S. Alnemri, D.R. Green, S.J. Martin, "Ordering the cytochrome c-initiated ca

Technology

Don't Clone Those Genes!
Don't Clone Those Genes!
If the expression products of a large number of different genes need to be rapidly analyzed, for instance during functional genomic research, consider the Transcriptionally Active PCR (TAP) Express™ Rapid Gene Expression kit from Gene Therapy Systems (GTS) Inc. of San Diego. TAP Express is the first commercially available system for the construction of transcriptionally active PCR fragments that can be expressed in mammalian cells. In this approach, researchers use nested PCR to generate t
Automated Staining
Automated Staining
Possibly the most difficult aspect of manual histopathological staining is maintaining consistency. BioGenex of San Ramon, Calif., has overcome this problem with the introduction of the i6000 Automated Tissue and Cell Staining System, the successor to the OptiMax Plus.1 Philipp Novales-Li, director of scientific affairs at BioGenex, states that the i6000 "allows for industrial-scale and high-throughput walkaway automation, while bringing about standardized, accurate, and reliable results." At 30
Tissue Cultural Revolution
Tissue Cultural Revolution
Courtesy of BioCrystalThe OptiCell culture systemDespite the explosion in cell biology research, the practice of cell culture has changed very little since the 1940s. However, with the OptiCell™ system, BioCrystal Ltd. of Westerville, Ohio, takes a bold step to simplify and streamline the cell culture process. OptiCell offers a complete cell culture system built around the OptiDyne™ membrane, a novel gas-permeable, optically clear substrate. Each sterile OptiCell is composed of two m

Technology Profile

2-D Glasses
2-D Glasses
Suppliers of 2-D Electrophoresis Equipment Courtesy of Bio-RadBio-Rad's Mini-PROTEAN 3 system Graphic: Leza BerardoneThe inevitable inventory of genes that will be produced by the Human Genome Project heralds the start of a new era: the Age of Proteomics. Although DNA is the blueprint for life, it is the set of proteins that are actually transcribed and translated that determine the function of a particular cell. Proteomics is the study of the complete protein complement of the cell, tissue, o
Finding a Mate
Finding a Mate
Available Two-hybrid Systems Graphic: Leza BerardoneGenome sequencing has produced a vast supply of proteins in need of a functional identity. One way to identify a protein's function is to identify its interacting partners, because proteins often work in pairs or as part of large complexes. Scientists traditionally have used biophysical or biochemical methods (such as affinity chromatography or co-immunoprecipitation) to study protein-protein interactions. More recently, two-hybrid and phage-d

Profession

Career Paths in Proteomics
Career Paths in Proteomics
Graphic: Leza BerardoneThis is the beginning," pronounced J. Craig Venter, president of Celera Genomics in Rockville, Md., at a press conference at the American Association for the Advancement of Science annual meeting in February. "There [are] 30,000 genes, and up to one-quarter of a million proteins [encoded by them] in 100 trillion different combinations--that's how many cells we have. That's why we don't think this is the blueprint for humanity; it's the starting point of understanding how t
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 bmaher@the-scientist.com Click to view the PDF file: Funding Opportunities in the Life Sciences
Writing a Paper that Will Get Published
Writing a Paper that Will Get Published
The experts agree: "Publish or Perish" is still alive and well in the research community. "The cardinal rule is, 'A scientific experiment is not complete until the results have been published,'" notes Bob Day, professor emeritus, department of English, University of Delaware, and author of a book on scientific paper publishing.1 In addition to "completing an experiment," publication in scientific literature serves as a means to secure knowledge ownership claims and is an efficient vehicle for

Opinion

Violence and the Brain: An Urgent Need for Research
Violence and the Brain: An Urgent Need for Research
While the social sciences have devoted much attention to the origin and prevention of violence, relatively little biomedical study has been conducted. Human behavior is determined by a combination of genetic and environmental influences governing brain structure and function. Violence, therefore, ultimately derives from the operations of the brain, and recognizing the importance of neurobiology will inform and invigorate study of this urgent problem. A working group under the auspices of the A