April 2006

FEATURELSIA 2006 Our fourth annual event celebrates excellence in life science product development and services BY JEFFREY M. PERKEL AND ISHANI GANGULI It has been said that scientists stand on the shoulders of giants. Generally that refers to researchers' intellectual forebears, but it also is true of the life science industry - technology giants that provide the scientific community with the tools, equipment and

FEATUREThe Ecology of Tumors   Courtesy of Nasa Ames Research CenterBy perturbing the microenvironment, wounds and infection may be key to tumor development.BY PARAIC A. KENNY, CELESTE M. NELSON, AND MINA J. BISSELLNo tumor is an island. Chemical and physical forces exerted by the diverse cellular populations that surround a tumor - its so-called microenvironment - shape development and progression. Manipulating these 'ecologi

FEATUREThe Ecology of Tumors Leukemia and Cancer Stem Cells BY IRVING WEISSMAN AND MICHAEL CLARKECancers and normal tissue stem cells have much in common: Both have self-renewal capacity, and both develop into differentiated progeny. But do true cancer stem cells exist? We believe that they do and that this realization will have a major impact on the understanding and treatment of cancers. Putative cancer stem cells can be recognized by three attr

FEATUREThe Ecology of Tumors Stem cells for brain cancer BY PETER B. DIRKSNeural stem cell biology took off in 1992 when Brent Reynolds and Samuel Weiss, working at the University of Calgary, discovered that culturing mammalian brain cells in serum-free conditions (in EGF and bFGF), yielded clonally derived colonies of undifferentiated neural cells (neurospheres). This culture system demonstrated that cells within these colonies showed cardinal pr

FEATURERestoring Natural Capital In putting a price tag on endangered species and degraded ecosystems, ecologists and economists have joined forces to formulate a new rationale for environmental issues: restoring natural capital© Erich Schlegel/Dallas Morning News/CorbisBY PADDY WOODWORTHEcological restoration is expensive. The United States government is slated to spend almost $8 billion restoring parts of the Florida Evergla

FEATURERestoring Natural Capital Courtesy of M. Powell Working for Water in South Africa The sides of the Baviaanskloof ("Baboon Canyon") in South Africa's Eastern Cape Province range from very steep to vertical. Halfway up a 45-degree slope, under the supervision of spirited 19-year-old Abbey-gail Lukas, 10 men and women are planting thick cuttings of a plant locally known as Spekboom (Portulacaria afra) in circles three meters apart.

FEATURESeeing is Believing © ROBIN LYNNE GIBSON/GETTYGraphical presentation strives to make sense of exploding quantities of data BY ANNE HARDING The amount of information life scientists have at their fingertips has mushroomed and continues to grow. In a bid to better access and manipulate this flood of information rather than suffocate on its abundance, researchers are turning to evolving visual techniques. Without them, mor

FEATURESeeing is Believing Delivering Diverse Data to Multiple Audiences: the PharmGKB Model BY RUSS B. ALTMANThe Pharmacogenetics and Pharmacogenomics Knowledgebase (PharmGKB, www.pharmgkb.org) is charged with catalyzing research for understanding how genetic variation relates to the variation in drug response. The PharmGKB has a mission of providing both primary data and derived knowledge to its users. Primary data consists

FEATUREBest Places to Work 2006: Industry   Courtesy of Transform PharmaceuticalsWhat makes a company a great place to work? In our fourth annual survey, industry scientists share their insights.BY KAREN PALLARITOBrian Hopkins, a PhD research scientist and project leader at Infinity Pharmaceuticals, joined the Cambridge, Mass., company in May 2002 partly because he liked its DOS (diversity-oriented synthesis

FEATUREBest Places to Work 2006: Industry Top 40 Companies Rank in 2006 Rank in 2005 Company Name/Location Country Total Number of Employees Worldwide Most Highly Ranked Factors Least Highly Ranked Factors 1 1 Tec Laboratories Albany, OR USA 100 or fewer Management Research Environment Integ

FEATUREBest Places to Work 2006: Industry Most Important Factors Rank in Large in 2006 Rank in Large in 2005 Factor Category Rank in Small in 2006 Rank in Small in 2005 1 1 My work gives me personal satisfaction. Job Satisfaction 1 1 2 9 My company provides the equipment and services I ne

FEATUREBest Places to Work 2006: Industry   Top Companies on Most Important Factor Categories   Management Research Environment Job Satisfaction 1 Tec Laboratories Tec Laboratories Tec Laboratories 2 Asterand Asterand Amgen 3 Raven Biotechnologies Genentech Promega 4 Infinity Pharmaceuticals Amgen Transf

FEATUREBest Places to Work 2006: Industry   Top Large Companies (more than 5,000 employees) Rank in 2006 Rank in 2005 Name/Location Type No. of R&D employees Total No. of New Jobs in 2005 2005 Net Income Significant developments in the past year (among large companies)            

FEATUREBest Places to Work 2006: Industry   Top Small Companies (5,000 employees or less) Rank in 2006 Rank in 2005 Name/Location Type No. of R&D employees Total No. of New Jobs in 2005 2005 Net Income Significant developments in the past year (among large companies)             1

More on peer reviewYour recent article on peer review1 omitted the fact that far too many journals do not report back to their reviewers. Only if a reviewer gets the decision letter plus the other reviews will he be able to learn and improve. Learning about the decision only when the paper makes it - or doesn't - to Medline is not sufficient.Manfred Gessler Theodor Boveri Institute for Life SciencesWuerzburg, Germanygessler@biozentrum.uni-wuerzburg.deYour

Mina Bissell is Distinguished Scientist at the Lawrence Berkeley National Laboratory, which she joined in 1972. Bissell writes about the ecology of tumors on page 30 with Berkeley colleagues Paraic Kenny and Celeste Nelson. Bissell was first intrigued by how cells - particularly cancer cells - preserve their identities in vivo, since "you put them in a dish... and they forget where they came from." "The tumors are not an island," she says. "We need to be treating cancer as the prob

What do natural disasters and cancer have in common? Ecology.

VITAMIN D FIGHT? >> On April 8th, at the 13th Workshop on Vitamin D in Victoria, British Columbia, Barbara Gilchrest, who gained notoriety for asking a colleague at Boston University to resign after he wrote a book that championed sunlight for the prevention of cancer, will be paired up with Edward Giovannucci, who champions sun exposure for adequate vitamin D. Gilchrest's talk will be entitled "Sun Protection and Vitamin D: Three Dimensions of Obfuscation."ECOLOGICA

Credit: COURTESY OF JOHN HURLEY FOR THE PROGERIA RESEARCH FOUNDATION" /> Credit: COURTESY OF JOHN HURLEY FOR THE PROGERIA RESEARCH FOUNDATIONLeslie Gordon's son Sam was 22 months old when he was diagnosed with Hutchinson-Gilford Progeria syndrome, a devastating disease in which children age rapidly and usually die between their 7th and 20th birthdays. Gordon, an MD/PhD, and her MD husband, Scott Berns, discovered an astonishing void of information on the disease, which is so rare that it

The list of fired medical journal editors became longer in February when the two top editors at the Canadian Medical Association Journal were fired after a dispute with the publisher over an article about emergency contraception. The deposed editors have joined a distinguished club whose members include: George Lundberg, whom the American Medical Association deposed as editor of the Journal of the American Medical Association after he published a sex survey in 1999 at the height of the

Credit: COURTESY OF ROBERTA FARRELL, ZYGEM" /> Credit: COURTESY OF ROBERTA FARRELL, ZYGEM Twenty-five years ago, New Zealand researchers Roy Daniel and Hugh Morgan made an arduous six-week expedition across sea, ice, and snow in search of thermophilic bacteria on the volcanic slopes of Mount Erebus, the world's most southerly active volcano. Erebus rises some 3,660 meters from Ross Island, in the icy oceans near Antarctica. As the two men made their way to within 90 meters of the summit,

Credit: © TED SOQUI/CORBIS" /> Credit: © TED SOQUI/CORBIS With its tropical climate and persistent moisture, New Orleans has long been a hotbed of fungal disease and research. But when hurricane Katrina blew through, the town quite literally became one giant mycology laboratory. "We're the mold capital of America now," says Seth Pincus, director of the Research Institute for Children at Children's Hospital, New Orleans. Mold is everywhere, on everything. Pincus, an immunologist,

Wildlife biologist Rick Hopkins Credit: COURTESY OF RICK HOPKINS" />Wildlife biologist Rick Hopkins Credit: COURTESY OF RICK HOPKINS When Vicki Long visited California's Western Riverside County Regional Conservation Authority to find out what it was doing to protect the mountain lion, her favorite cat, from land development, she decided the answer was "not enough." And while she had read every study she could get her hands on as part of her life-long fascination with the mountain lion, al

Here's how to prevent critical biological data repositories from disappearing into the ether

Will India rise up against the oppression of foreign clinical trials?

Here's what a search engine for your cerebral cortex might look like

Tony Hunter discovered tyrosine kinases because he was lazy - then the fun began

The fall and rise (and fall) of a pharmacogenetics poster child

Credit: © DAN BRANDENBURG" /> Credit: © DAN BRANDENBURG Models don't always have to be correct to be helpful. In 2004, Paul Talalay and his team at Johns Hopkins University published evidence that the sensory protein Keap1 dissociates from the transcription factor Nrf2, allowing Nrf2 to induce detoxifying enzymes that protect the cell from carcinogens and oxidants.The team demonstrated that external chemical cues, such as sulforaphane found in broccoli, directly modified two

Credit: © 2004 NATURE PUBLISHING GROUP" /> Credit: © 2004 NATURE PUBLISHING GROUP With all the hubbub surrounding microRNAs in plants and invertebrates after their discovery, it was only a matter of time before a functional role was found in mammals. In 2004, graduate student Soraya Yekta, and Whitehead Institute for Biomedical Research member David Bartel found a role for microRNA miR-196 in HOXB8 regulation in mice.1 Naturally, it was assumed such a mechanism would exist in mammals. But

Credit: CUSTOM MEDICAL STOCK PHOTO /SCIENCE PHOTO LIBRARY" /> Credit: CUSTOM MEDICAL STOCK PHOTO /SCIENCE PHOTO LIBRARY While much research focuses on T and B cells entering lymphoid organs, Jason Cyster says he's more curious about how they get out. He and colleagues at the University of California San Francisco found a clue to lymphocyte escape, both from the thymus and secondary lymphoid organs, in an immunosuppressant drug, FTY720. The drug sequesters T and B cells in lymphoid organs

M.N. Alder et al., "Diversity and function of adaptive immune receptors in a jawless vertebrate," Science, 310:1970-3, Dec. 23, 2005.A computational analysis indicates that agnathans [jawless fishes] have the potential to generate from 1014 to 1017 different variable lymphocyte receptor (VLR) genes through a process of somatic rearrangement, a level of diversity comparable to that of mammalian antibodies.John JaenikeUniversity of Rochester, NYN.M. Alto et al., "Identification

Credit: M.J. STEVENS ET AL., PHYS REV LETT, 91:118102, 2003, ©2003 AMERICAN PHYSICAL SOCIETY" /> Credit: M.J. STEVENS ET AL., PHYS REV LETT, 91:118102, 2003, ©2003 AMERICAN PHYSICAL SOCIETY According to a popular model, membrane fusion occurs when soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) proteins on one membrane form a complex with SNARE proteins on another.Barry Lentz of the University of North Carolina, Chapel Hill, Axel Brunger of Stanford Uni

Stat5a and b have given immunologists mixed messages. Nearly a decade of work pointed to a central role for these transcription factors in T- and B-cell development as well as development of some leukemias, but an N-terminal deletion knockout made in the late 1990s produced relatively mild effects. Recent work on a full-length knockout in mice falls much more in line with what the community had expected.1,2 One group doing the work contains members who had previously contended with the puzz

Credit: JASON VARNEY/http://www.varneyphoto.comVARNEYPHOTO.COM" /> Credit: JASON VARNEY/http://www.varneyphoto.comVARNEYPHOTO.COM As a medical student at Catholic University in Rome, Enza Maria Valente remembers helping her genetics professor, a priest in his sixties, as he struggled to calculate probabilities for passing on a genetic disorder. "I would just pick up the answer even before he finished the calculations," she says.Despite her pedigree predilection, Va

An industry/academia/government coalition puts microarray reproducibility to the test

There are many ways to observe programmed cell death; here are six of the most common ones

Credit: COURTESY OF MARISA DOLLED-FILHAST, HISTO Rx" /> Credit: COURTESY OF MARISA DOLLED-FILHAST, HISTO Rx Traditional histopathology analysis has two basic problems. First, it isn't granular enough: Pathologists typically grade overall marker-staining intensity using a four-point scale. The other problem is that these measurements don't account for the sometimes-subtle changes in subcellular localization that can indicate disease. Beta-catenin, for instance, is a biomarker for colon can

Are ethical objections to patents headed for the US?

Is diagnostics the best bet for companies such as Celera that once put its money on drug development?

The National Academy of Sciences is organizing a new committee to periodically update voluntary guidelines it issued last year (http://nap.edu/catalog/11278.html?onpi_newsdoc02162006) on human embryonic stem cell research. A call by several scientific organizations and individual scientists prompted the decision, according to Bill Kearney, spokesperson for the Academy. The committee, under the auspices of the organization's National Research Council and Institute of Medicine, will be suppor

Credit: © PHOTODISC" /> Credit: © PHOTODISC A new collaborative between the US Food and Drug Administration, National Cancer Institute (NCI), and Centers for Medicare and Medicaid Services will bring scientific rigor and validation to biomarker research, say the agencies. The Oncology Biomarker Qualification Initiative (OBQI; www.fda.gov/oc/mous/domestic/FDA-NCI-CMS.html) will be "a partnership between these three agencies to really for the first time collectively think about how we creat

New York State researchers would like to jump on the bandwagon for state- supported embyonic stem cell research. The heads of 17 New York universities and institutions with substantial biomedical research programs released a white paper (www.rochester.edu/news/pdfs/stemcellwhitepaper.pdf) in February that makes a scientific and economic case for the state to fund such research. The document, urges Albany legislators to pass two stem cell funding bills that would allocate $300 million and $125

Use references to learn about candidates and not just to confirm their claims

The field of biocuration expands as the data grow

Credit: COURTESY OF YALE UNIVERSITY PRESS" /> Credit: COURTESY OF YALE UNIVERSITY PRESS On every other Thursday evening, Ellen Daniell and six San Francisco Bay Area scientists come together to talk about managing their careers. In addition to all being successful, they are all women. In 1977, researchers from the University of California, San Francisco, formed the original gathering, simply referred to as "Group." Its members have been giving each other practical and emotional suppor

Mentoring skills aren't as readily taught as cell culture or microarray analysis, but on the receiving end, such skills can make or break a career. Scientists at the University of Wisconsin-Madison have devised a way to address what they call a critical gap in faculty training, and they have reported their outcomes in a recent issue of Science (311:473-4, Jan. 27, 2006).Based on a survey of more than 150 mentors and undergraduate researchers, trained mentors were significantly more li

Credit: COURTESY OF GREG HAMM" /> Credit: COURTESY OF GREG HAMM In the middle of 1981, Greg Hamm was a 30-year-old software programmer newly hired by the European Molecular Biology Laboratory to head up its DNA data library-a database that did not yet exist. So he set about making one. "We had journals publishing sequence data in increasingly small point size type, which was useless," he says. "It was clear that one thing that was needed was a transmission format, a way to send the data f