April 2008

Kenneth Buetow is the director of the National Cancer Institute Center for Biomedical Informatics and Information Technology. He is also an intramural researcher at NCI, working on genomics. In 2004, Buetow and colleagues launched the cancer Biomedical Informatics Grid (caBIG) to help researchers manage and integrate the ever-growing dataset of clinical, genomic, imaging, pathological, and proteomic

Related Articles English-Only Science in a Multilingual World: Costs, Benefits, and Options How Could International Scientific Communication Be Made Fairer and More Efficient? Ammon Presentation (PPT) Ammon Presentation (PDF) Vergara Presentation (PPT) Vergara Presentation (PDF) Over the past centuries, first Latin and then French, German, and Russian, have receded in perceived importance as languages of science. Other powerful languages, with extensive

Many, perhaps most, scientists are grateful that English has become the international language, but an informative protest comes from Prof. Tsuda Yukio of Japan, who has taught in the U.S. Related Articles How Could International Scientific Communication Be Made Fairer and More Efficient? Language and the Ingenuity Gap Ammon Presentation (PPT) Ammon Presentation (PDF) Vergara Presentation (PPT) Verga

Related Articles English-Only Science in a Multilingual World: Costs, Benefits, and Options Language and the Ingenuity Gap Ammon Presentation (PPT) Ammon Presentation (PDF) Vergara Presentation (PPT) Vergara Presentation (PDF) 1. Characterization of the present situation I) One aspect of globalization is the emergence of one single global lingua franca of science, English. It has advantages for all scientists as well as for mankind as a whole in that it enhances interna

The War on Animal Research What it's like to be hounded by activists who will stop at nothing to stop your research. By P. Michael Conn Photographs by Bill Cramer Related Articles 1,2 I believe in the value of animal research in basic science. I have spoken and written about the importance of humane animal research and how it benefits both humans and animals.Because of my position at the OHSU primate center, an animal rights activist had urged subscribers

Who's who in activism A sample of groups opposed to animal research, and how to tell them apart Related Articles The War on Animal Research Activists in the News UCLA sues animal rights groups Combating Malevolence Animal activists sentenced Oxford resumes building animal lab Name: People for the Ethical Treatment of Animals (PETA) Website: https://www.peta.org/ Key Features: Says it's the largest animal rights group worldwide

Stopping the Cane Toad When Australian scientists failed to find a virus to control one of the most insidious invasive species, they decided to build one. Is it worth the risk? By Brendan Borrell All photos by Brendan Borrell Related Articles: 1 "Everyone was very excited about that," he says, because it meant that there might be a pathogen that would kill the cane toad and only the cane toad. In 1993, CSIRO received another $2 million AUD ($1.4

Slideshow: The Cane Toad When Australian scientists failed to find a virus to control one of the most insidious invasive species, they decided to build one. Is it worth the risk? All photos by Brendan Borrell In our April issue, Brendan Borrell traveled to Australia to chronicle scientists' efforts to design a virus that stops the cane toad. View this slideshow for a first-hand look at what it's like to try to stop one of the world's most insidious invasive spec

Toadbusting By Brendan Borrell Related Articles: Stopping the Cane Toad Slideshow: The cane toad Going batty Lyall Grieve was among the first to see the carnage return to Mark's Dam last December. It was another sunbaked afternoon on the Kimberley plateau in northwestern Australia when the khaki-clad herpetologist stepped out of his Toyota Hi-Lux and onto the red soil. He hiked up a dry, grassy hill to the top of the dam when he spotted the skelet

Heading for the BIG Time The NCI's bioinformatics network,caBIG, integrates cancer data fromacross the United states.Its goal: to speed the transition from research to therapy By Kenneth Buetow Artwork by Brendan Monroe Related Articles A sampling of how you can use caBIG caBIG in Action I was at the National Cancer Institute's (NCI) Intramural Program Scientific Retreat this past January listening to a plenary presentation by Cambridge Un

A sampling of how you can use caBIGRelated Articles Heading for the BIG Time caBIG in Action Biobanking management with caTissue Access a library of well characterized, clinically annotated biospecimens. Use the tool to keep an inventory of a user’s own samples. Track the storage, distribution, and quality assurance of specimens. Molecular discovery The caIntegrator – Combines proteomics, gene expression, and othe

caBIG in Action Here is a hypothetical case study that uses caBIG tools and databases: Here is a hypothetical case study that uses caBIG tools and databases:--> In the cancer glioblastoma multiforma (GBM), does expression of key genes predict disease outcome? How might these genes interact in biological networks that would influence therapeutic targeting? var FO = { movie:"https://www.the-scientist.com/supplementary/flash/54511/64.swf", width:"550", height:"500", majorver

Christine Jacobs-Wagner's studies of a bacterial species have changed how scientists think about cell shape and polarity.

User: Wei Yan, University of Nevada, Reno Project: Probing temporospatial expression of small RNAs in testis. Problem: Northern blots are cumbersome and lack sensitivity, and RT-PCR isn't geared toward amplifying short nucleotide sequences. Related Articles Amplifying Trouble Tips for tricky PCR Staying clean Dilution Defixation Single cells

Most life scientists are working at an enormous disadvantage, and their resentment is growing.

Mendel upended? I was interested in this story1 when the 2005 paper came out, suggesting that Arabidopsis mutants could revert to wild type, and I started doing some experiments to test Susan Lolle and Robert Pruitt's ideas. My early data seemed to support the notion that reversion was happening (although it was not consistent with RNA-mediated reversion). When Steve Jacobsen's paper came out I decid

Credit: Right: courtesy of Australian Animal Health Laboratory" /> Credit: Right: courtesy of Australian Animal Health Laboratory GRANT ME GRANTS » In "Click To Submit", we present tips for how to submit grants electronically. For some in-person advice, enroll in one of eight two-day grant writing courses offered in April by Grant Writing USA. Courses will take place across the cou

A flying fox Credit: Right: courtesy of Australian Animal Health Laboratory" />A flying fox Credit: Right: courtesy of Australian Animal Health Laboratory Taking a saliva sample from the world's largest bat is not easy under ordinary circumstances, but obtaining that same sample from a SARS-infected flying fox — while using a 4-foot cotton swab and wearing a pressurized biosafety suit with double-layered rub

Hákon Hákonarson and deCODE genetics CEO Kári Stefánsson used to consider each other friends. Hákonarson, the former vice president of business development at the Icelandic biopharmaceutical company, used to ride horses with Stefánsson and spend time with him outside of work. That all ended in May, 2006, when Hákonarson left deCODE to direct and help form the new Center for Applie

A Taconic animal care technician inspects a genetically engineered mouse model in a gnotobiotic isolator at the Germantown, NY facility. Credit: Courtesy of Taconic" />A Taconic animal care technician inspects a genetically engineered mouse model in a gnotobiotic isolator at the Germantown, NY facility. Credit: Courtesy of Taconic In the world of lab-mouse breeders, only a few players are in the big leagues. In re

Max Rothschild (left) in Uganda. Credit: courtesy of Max Rothschild" />Max Rothschild (left) in Uganda. Credit: courtesy of Max Rothschild The Rothschild lineage is often associated with Jewish tradition, banking, and fantastic wines. But Max Rothschild, a researcher at Iowa State University, is associated with some decidedly nonkosher animals: pigs. And, more recently, shrimp. When he was about 7 or 8 years old, Rothschild had a different kind

Log cfu/ml of bacteria recovered from sterile water in which crackers had been dipped 3 or 6 times, discarded after each dip, with or without being bitten before dipping. Credit: Data courtesy of Paul Dawson" />Log cfu/ml of bacteria recovered from sterile water in which crackers had been dipped 3 or 6 times, discarded after each dip, with or without being bitten before dipping. Credit: Data courtesy of Paul Dawson Who hasn't in

Joshua Lederberg (1925—2008) was one of the most influential scientists of the 20th century, and my good friend.

Electing a proscience president is only half the battle.

Why I believe findings that disprove a hypothesis are largely not worth publishing.

Can microRNAs help diagnose, classify, and stage human cancers?

Credit: © Zephyr / Photo Researchers, Inc." /> Credit: © Zephyr / Photo Researchers, Inc. The paper: K. O'Reilly et al., "mTOR inhibition induces upstream receptor tyrosine kinase signaling and activates Akt," Cancer Res, 66:1500—8, 2006. (Cited in 95 papers) The finding: It's known that rapamycin inhibits lymphoma growth but not solid tumor growth. Rapamycin activates Akt — an en

Credit: left: Jim Dowdalls / Photo Researchers, Inc." /> Credit: left: Jim Dowdalls / Photo Researchers, Inc. The paper: N. Houstis et al., "Reactive oxygen species have a causal role in multiple forms of insulin resistance," Nature, 440:944—8, 2006. (Cited in 109 papers) The finding: Evan Rosen, from Beth Israel Deaconess Medical Center in Boston, and other colleagues tested whether a common mechanism

The paper: A. Birmingham et al., "3' UTR seed matches, but not overall identity, are associated with RNAi off-targets," Nat Methods, 3:199—204, 2006. (Cited in 94 papers) The finding: In 2006, Devin Leake and colleagues at Dharmacon Research wanted to determine the accuracy of current algorithms for predicting siRNA mismatch events used in silencing. To do t

A cancer biologist recalls his work on immunosuppression.

Credit: © Jason varney | Varneyphoto.com" /> Credit: © Jason varney | Varneyphoto.com Ken-ichi Noma, a geneticist at The Wistar Institute in Philadelphia, stands at a bench in his lab and squirts a sample of Saccharomyces pombe onto a microscope slide. He adjusts the microscope focus knobs, and an image of green, globular cells wavers on the monitor attached to his microscope. "How are you doing?" he asks the cells.

How to get robust results from your dodgiest PCR

Credit: Left: José-Manuel Benito / wikimedia.org " /> Credit: Left: José-Manuel Benito / wikimedia.org  User: Noreen Tuross, Harvard University, Cambridge, Mass. Project: Using genetic techniques to establish relationships among ancient hominids. Problem: Almost all the DNA in archeological samples is rife with contamination —

Credit: Right: wikimedia.org" /> Credit: Right: wikimedia.org User: Staci Bennett, Minnesota Bureau of Criminal Apprehension, St. Paul Project: Determining "whodunit," based on DNA evidence. Problem: It's sometimes difficult to isolate DNA amenable to PCR from stains in dark denim. Related Articles Amplifying Trouble Tips for tricky PC

Credit: © CNRI / Photo Researchers, Inc." /> Credit: © CNRI / Photo Researchers, Inc. User: Kay Pogue-Geile, National Surgical Adjuvant Breast and Bowel Project, Pittsburgh, Pa. Project: Developing prognostic profiles for breast cancer using tumor samples obtained from clinical trials. Problem: Nucleic acids are degraded and modified by the

Credit: © Pascal Goetgheluck / Photo Researchers, Inc." /> Credit: © Pascal Goetgheluck / Photo Researchers, Inc. User: Norma Nowak, Roswell Park Cancer Institute, Buffalo, NY Project: Conducting pre-implantation genetic diagnoses (PGD) on blastomere-derived cells. Problem: Cells harvested for PGD are traditionally put into a generic buffer and frozen. Th

Use mitochondrial DNA to identify ancient samples.When a creature has spent years in the back of a cave, "it basically is nutrients for all the microbes and worms in the environment," says Edward Rubin, director of the US Department of Energy's Joint Genome Institute in Walnut Creek, Calif. With few intact cells remaining, the chances of finding nuclear DNA extraction are slim. However, there are a few thousand copies of the same m

Coming up with an entirely new approach to cancer therapy can be a headache, as Micromet's Christian Itin has learned.

Want a better way to submit grants electronically? Find out the pros and cons of the most widely-used programs.

A Web-based program, ranging from $495 for an individual yearly subscription up to $500,000 per institution, Cayuse allows users to work online without downloading or needing to integrate any additional programs. /2008/4/1/93/1/ Click to Submit no /2008/4/1/94/2/ ProposalCENTRAL no /2008/4/1/95/1/ Customizable Product Suites no

This Web-based program was developed in conjunction with 43 private granting foundations. The cost for these granting agencies to design an application through ProposalCENTRAL can range from about $15,000 to $150,000 per granting agency. It's free to users, however, who submitted 9,300 applications through ProposalCENTRAL in 2007. /2008/4/1/93/1/ Click to Submit no

Companies such as Click Commerce, InfoEd, and COEUS have developed customized systems for each institution that can include IRB approval applications for clinical trials and approval for testing and research with animals. /2008/4/1/93/1/ Click to Submit no /2008/4/1/94/1/ Cayuse no /2008/4/1/94/2/ ProposalCENTRAL no

Credit: Courtesy of Biotek Instruments Inc." /> Credit: Courtesy of Biotek Instruments Inc. In the late 1970s, researchers who wanted to quantify the results of new immunoprecipitation assays, such as ELISA, had three choices: risk human error and a headache by using a manual reader, break out the cuvets and the spectrophotometer, or pay as much as $15,000 for a bulky automated reader. In 1981, Winooski, Vt.-base