February 2003

Frontlines | Out of Agonists Comes an Antagonist Reprinted with permission from Nature Pseudomonas aeruginosa can devastate the lungs of a person with cystic fibrosis or a suppressed immune system, for these bacteria are more than the sum of their parts. When their numbers reach a critical mass, signaling from accumulated microbial "autoinducers" triggers production of virulence factors and formation of a biofilm, a polysaccharide shield that protects the bacterial colony from an immune re

Frontlines | The Worm that Turned Reproduced with permission from The Institute of Biology from Arme The unisex contraceptive is a slippery fish for Big Pharma. Chris Arme of Keele University, UK, reckons the parasite Ligula intestinalis could provide some clues, however. Apparently, tapeworm secretions switch off egg and sperm production in freshwater carp. As reproduction can kill female carp, some suggest that host sterilization increases the worm's chances of being passed on to fish-ea

Frontlines | Look Out Broadway (or Maybe Not) New York City has historically been fertile ground for innovative dramatic and musical performances. So, after Helen Davies brings her adaptations of classic songs to Greenwich Village, can a Broadway musical be far behind? Or are there enough angels out there to fund the "Yesterdays" of leprosy, or other tunes of herpes? What started off as mnemonic aids for Davies, professor of microbiology at the University of Pennsylvania, to get her studen

Foundations | Lewis and Clark Expedition, Fritillaria affinis 1804-1806 Courtesy of The Academy of Natural Sciences of Philadelphia, Ewall Sale Stewart Library Courtesy of The Academy of Natural Sciences of Philadelphia, Ewall Sale Stewart Library In 1803, President Thomas Jefferson asked his private secretary, army Captain Meriwether Lewis, to lead a first-time expedition to the Pacific Coast. One goal: collect indigenous flora. Two centuries later, botanist Richard McCourt of the Academ

Off The Cuff | What is your favorite or least favorite aspect of your work environment? "My colleague has a brewery for research and teaching in our building. He produces some fine-tasting research." --Dennis T. Gordon, Fargo, ND "This working environment here is a metaphor for the TV show Survivor." --Dan Chavez, Carbondale, Ill. "The worst is to have to show up and say something every week for the lab meeting." --Khadir Raddassi, Boston, Mass. "The dingy cinder block walls of

5-Prime | The Null Hypothesis: More than Zero What? Perhaps primary among the challenges and conditions that face life scientists is the infinite variability between individuals. An important tool for measuring those disparities is the Null Hypothesis Significance Test (NHST). It begins by proposing no difference between samples or populations being tested. Of course, "no difference" is an exact point among infinite alternatives, the probability of which is virtually zero. That's why resea

Datapoints | Academic Largesse: Top-Ranked Institutions with Government Funding USNIH Awards (in millions $US) 1. Johns Hopkins University457.4 2. University of Pennsylvania376.0 3. University of Washington356.2 4. University of California, San Francisco350.4 5. Washington University303.6 6. University of Michigan302.2 7. University of California, Los Angeles273.5 8. Harvard University270.2 9. University of Pittsburgh264.6 10. Yale University256.7 Source: NIH, FY2001   USSF Biology

Erica P. Johnson 1. In 1600, Giordano Bruno (1548-1600) repeatedly refused to recant his endorsement of Copernicus' sun-centered map of the galaxy. He was burned at the stake. 2. Antoine-Laurent Lavoisier (1743-1794), who explained combustion and created a system for naming chemicals, pleaded for his life during the French Revolution, citing his unfinished scientific research. "The Republic has no need of scientists," his executioners told him. The next sound was the thump of the guillotine

I have two Iraqi friends, both scientists, both wonderfully witty people. One of them is perhaps the kindest, gentlest, best-humored man I've ever known; I was honored to serve as his best man when he married a Cumbernauld girl of Polish descent. Such Iraqi/Scots-Polish liaisons might often occur in the melting-pot of the US, but in late-1980s Dublin this was quite an exotic event. Unfortunately, no one from the Iraqi side of the family was permitted to be present. A couple of years earlier,

Patricia Cornwell's nonfiction attempt1 to name serial killer Jack the Ripper reads more like fiction than fact. Cornwell has identified Walter Sickert, a well-known Victorian painter, as Jack the Ripper based almost solely on two observations: 1) that Sickert was a nighttime wanderer of London streets during the Ripper's spree, and 2) that Sickert painted spooky scenes reminiscent of Ripper locales and victims. Diehard fact-collecting Ripperologists will gasp at the editorialized renderings

Over the years several letters and articles in The Scientist have expressed concern about the use of antibiotics in domestic animal production and the potential for selection of antibiotic-resistant bacteria. Recently, an American Academy of Microbiology report called for efforts to develop new agricultural methods that reduce dependence on antibiotics, such as the use of competitive exclusion bacteria in poultry to combat the Salmonella problem.1 While the competitive exclusion approach in

Bedside Manner a Placebo Effect? It is interesting to read about the possible activation of endogenous opiate release in the brain as a result patient-physician interaction as a special "placebo effect."1 This reminds me of earlier confidence placed by patients in their family doctor's bedside manner. Frequently, doctors became very popular because of their marvelous bedside manner. Was the placebo intensity proportional to the art of the doctor? Also, how about the osteopathic principle of

Front Page | New Pill Box Possibilities; Super Monkey Moms; Science Seen PhotoDisc GENE THERAPY | New Pill Box Possibilities "Take two genes and call me in the morning"--not exactly what one would expect a family doctor to say, but it could become a common prescription if a new "gene pill" pans out. James Hagstrom, vice president of Mirus, Madison, Wis., says "This technology would be extremely useful for wide ranging therapeutic applications." Hagstrom moderated a talk at the recent Kno

Courtesy of Cold Spring Harbor Laboratory  IDENTIFYING NEW CANCER GENES: (1) Clinicians biopsy cancerous (left) and normal (right) tissues from patient. (2) DNA microarrays containing thousands of individual human genes are exposed to a mixture of labeled dna samples. (3) Red spots indicate genes amplified in cancer cells, green spots show genes deleted. (4) Both classes of genes become potential targets for new diagnostic or therapeutic anti-cancer strategies. In 1994, discovery of the

Images Courtesy of Donald E. Ingber  Cell shape and function, such as directional motility, can be controlled by culturing individual cells on µm-sized extracellular matrix islands of defined geometry created using microfabrication techniques. New motile processes, stained for F-actin (green), extend preferentially from the corners when the cell is stimulated to grow by soluble mitogens. The nucleus is stained blue. A theory has only the alternatives of being wrong or right. A mode

Courtesy of SR Eng  BABY STAINS: The head of a transgenic murine embryo in which a marker enzyme has been specifically expressed in the sensory neurons of the trigeminal and dorsal root ganglia. The marker allows staining of the projections of these neurons into, among other areas, the hindbrain and spinal cord. (S.R. Eng et al., "Defects in sensory axon growth precede neuronal death in Brn3a-deficient mice," J Neurosci, 21:541-9, 2001.) Somewhere in the 200 million bases of the human ge

Image © Nature  MUTATION AND TRUNCATION: These DNA sequence electropherograms show a patient from "family 7" who is homozygous for a cytosine c insertion, as indicated by the arrow. The mutation encodes a truncated NOD2 protein. (Reprinted with permission from Nature, 411:603-6, 2001.) After years of failed promises that researchers would find genes linked to cancers, heart disease, and other complex human ailments, two independent research teams, using different approaches, localiz

Front Page | Better Brewing Through Chemistry; A Peel-ing Cell Culture; Worm Researchers Reach for the Stars PATENT WATCH | Better Brewing Through Chemistry The next time you have a particularly satisfying pint, you may want to thank the biochemists at Japan's Sapporo Breweries, which has patented a way to select better barley biochemically.1 Beer's qualities depend largely on two barley enzymes: b-amylase (BA), which hydrolyzes the starch molecule's penultimate linkage to produce maltos

Graphic: Bob Crimi, Reprinted with permission from Nature Genetics, 32:465-66, Dec. 2002 By all accounts the genomics research community has embraced nucleic acid microarrays. San Jose, Calif.-based growth consulting firm Frost & Sullivan estimates that the market will grow at an annual compounded growth rate of 63% between 1999 and 2004--from $232 million (US) to $2.6 billion.1 Revenue for related equipment such as arrayers and scanners topped the $500 million mark in 2002, says Frost &am

Courtesy of CombiMatrix The research community's rapid acceptance of microarrays notwithstanding, technical challenges remain. Biochip developers continue to grapple with these issues while upgrading their offerings and adding new product lines in response to research trends. Perhaps the biggest challenge to microarray technology is standardization--ensuring that data collected from different microarray platforms can be accurately compared. Compounding this problem is the absence of a unified

Courtesy of CombiMatrix Despite a relatively mature marketplace for array instrumentation, new contenders continue to squeeze between the cracks to vie for market share. Currently, there are both new offerings from old standbys and new faces in the scanner and arrayer world. A number of companies introduced new array platforms last year. Two of these, QIAGEN's SensiChip system and Amersham Biosciences' CodeLink platform, are discussed elsewhere in this issue. Gaithersburg, Md.-based MetriGen

Courtesy of CombiMatrix A number of companies are using the lessons and technologies of traditional genomics--the microarray chief among them--to delve into the more challenging world of functional genomics and proteomics. Most of these new arrays are low-density and, therefore, lack the high-throughput capacity of their DNA and oligo counterparts. Their use is also limited by a variety of technical challenges that are difficult to overcome. Antibody arrays, for example, can be expensive and

The State of the Microarray | Selected Suppliers of Microarray Chips, Spotters, and Readers Courtesy of Amersham Biosciences Note: a = arrays; r = reader; s = spotter Affymetrix www.affymetrix.com - a, r Agilent Technologies www.agilent.com - a,r Akceli www.akceli.com - a Alpha Innotech www.alphainnotech.com - r Amersham Biosciences www.amershambiosciences.com - a, s Applied Precision www.appliedprecision.com - r Apogent Discoveries www.apogentdiscoveries.com - s Axon Instruments www.ax

2001-2002 VizX Labs As a graduate student, Eric Olson learned something about DNA microarrays: Biochip data management can be vexing. His graduate adviser abandoned a number of microarray experiments because it was too difficult to manage the data using the software supplied with the arrays. Now Olson is director of science for a company that is trying to change that. Seattle-based VizX Labs offers a Web-based, platform-independent microarray data analysis package called GeneSifter. Net͐

Courtesy of ChemoMetec For those charged with the mundane, yet critical, task of counting mammalian cells, ChemoMetec of Allerod, Denmark, offers a simple alternative to hemacytometers. Unlike some other cell counters that measure particle size, ChemoMetec's NucleoCounter™ system counts cells based on DNA fluorescence. After harvesting cells as usual, the researcher--using supplied reagents--lyses and dissolves the cells, adjusts the pH, and aspirates the stabilized nuclei into a dispo

In autoimmune diseases, CD4+ T cells targeted to self- antigens multiply and attack the body's own tissues. The resulting inflammation and cell damage leads to disease such as diabetes, rheumatoid arthritis, lupus, and multiple sclerosis. Now Beckman Coulter Immunomics Operations of San Diego offers a new tool: class II iTAg™ major histocompatibility complex (MHC) tetramers, which allow researchers to quantify CD4+ T cells directed against specific antigens. Complementing the company's

Front Page | Make Your Lab the Best Place to Work; Blending Biology and Computational Skills; Chancellor Clinton?... at Oxford? Courtesy of Beverly Kaye TIP TROVE | Make Your Lab the Best Place to Work Talent-focused, senior leaders create an environment that is fun to work in.... That is critical. It's all about asking yourself, "Do I get on the never ending bandwagon--its perks, its dollars, its perks, its dollars...? Or do I look to other benefits? Am I doing flex-time, do I provide a

Image: Artville US Justice Department investigators want to know how academic scientists spend their time and the government's money. The department is making quiet inquiries at research institutions to determine how they've used their federal funding. Research executives would not say which schools the Department of Justice (DOJ) has approached, and department officials refuse to comment, as is their policy with matters under investigation. The inquiries could go nowhere, or they could heral

Getty Images When Stefanie Dimmeler became professor of molecular cardiology in Frankfurt last year, researchers hailed her as one of Germany's youngest tenured scientists. Obtaining a tenured professorship at age 33 may not seem like something out of the ordinary to some US researchers, but Dimmeler beat most of her German colleagues by 10 years. To help make that country more attractive to bright scientists like Dimmeler, Federal Education Minister Edelgard Bulmahn introduced a law in Janu

File Photo When giving talks on alternative careers for scientists, I often emphasize skills that nontraditional science career employers look for, such as acumen in negotiating, communicating, teamwork, good judgment, business expertise, and adaptability. This skill list--derived from materials prepared by the Stanford University Career Planning and Placement Center--has also been put to good use by postdocs and graduate students to make their laboratories better places to work. Over the pas

Courtesy of Anthony Watts  Anthony WattsProfessor of biochemistry aand Fellow of St Hugh's College, Oxford;Director, National Biological Solid State NMR Facility at Rutherford Appleton Laboratory;Managing editor, European Biophysics Journal Early indications: I've always been interested in science. As a boy, I asked for chemistry sets for presents, was interested in physics and reveled in math. I worked in my spare time fixing electrical goods, giving me a superb start in life with ... p

Obtaining the "ideal" postdoctoral position is an important but tough job. I put ideal in quotes, because applicants have their own criteria for positions that will prepare them for their first professional jobs. This search cannot begin too early, since it mainly involves information gathering. The best advice I've received was: "Do your homework." The first step is to narrow potential fields. Don't take this decision lightly. If you decide to pursue an academic career, you will work in your

Whining and righteousness get you no place in politics. Nevertheless, those are the pop-gun responses of mainstream science to the Bush administration's persistent moves to stack federal science-advisory committees with appointees friendly to its conservative agenda. Here and there, a protesting letter to the editor, a bit of irate testimony on Capitol Hill, preachments to the faithful via an editorial in Science. But when it comes to real politics--raising money and running ads for friendly

We surveyed 751 readers to find out what their ideal occupation would be other than science. The most popular choices were writer (18.3%), doctor (13.0%), and musician (10.7%). More than three times as many readers would prefer to be teachers than lawyers. Of the 32.4% of readers who opted for the ubiquitous "Other," the most popular careers among 143 alternatives listed were artist, photographer, and cabinetmaker/carpenter. And, yes, we do have readers who would like to be professional surfer

First Person | Susan Lindquist Courtesy of Susan Lindquist She holds seminars on how to balance family and career, loves to tango Argentine style, and admits willingly that she would consider working as a journalist. But Susan Lindquist, 52, the first female director of the Whitehead Institute for Biomedical Research, chose her first path--love of science--as her career, and that has landed her in an enviable spot. A highly cited author who is interested in stress response and protein fold