August 2007

Systems biology is... Two scientists founded BioSeek to do their version of systems work. Is it a stretch? Brendan Borrell ARTICLE EXTRAS 1 "I really didn't like the early descriptions of systems biology from Hiroaki Kitano and Lee Hood, where their definition of systems biology was, 'We have to measure all of the components over time and then we're going to build a model of the system,'" says Berg, who (with Butcher) founded BioSeek in Burlingame, Calif. To her, the defi

Slideshow: Solving the Easter Island mysteries var FO = { movie:"http://images.the-scientist.com/supplementary/flash/53425/easter.swf", width:"600", height:"580", majorversion:"8", build:"0"}; UFO.create(FO, "ufoDemo"); Please download the Adobe Flash Player to view this content:

Systems biology at biotechnology and pharmaceutical companies In an effort to restock the dwindling pipeline of new treatments, systems biology is increasingly becoming a part of drug discovery efforts. Company Approach Location Bioseek Screen novel compounds with combinations of human primary cells to measure activity and understand their mechanism of action Burlingame, California Gene Network Sciences Use models to improv

Do Chimps Have Culture? photo: © DLILLC / Corbis What can we learn from the fact that chimps can teach each other? By Bob Grant Related Articles Primate customs Non-chimp animal culture An entourage of subordinate chimps is gathered eagerly around Steward, the big alpha-male chimpanzee, at the Yerkes National Primate Research Center outside of Atlanta. They're watching Steward brandish a Plexiglas stick at an oblong polycarbonate box sitting behi

Non-chimp Animal Culture By Bob Grant ARTICLE EXTRAS 1 that sponging is a socially learned behavior and likely not the result of genetic inheritance. "We were the first to consider extensive genetic data to actually exclude genetic explanations for the behavior," says Krützen. He and his team took tissue samples from 185 dolphins in Shark Bay, thirteen of which were known adult spongers. Only one of these spongers was male. The researchers genotyped each individual for 12 bi-par

Selling Systems Biology Can this still-unproven (and much-hyped) field revolutionize drug discovery? By Brendan Borrell ARTICLE EXTRAS 1,2 suggested that the drug works primarily in patients with mutations in the ErbB1 epidermal growth factor receptor. The inner workings of the ErbB receptor family, with its sprawling pathways and multiple phosphatases, had long been a headache for drug makers. That complexity showed itself in this instance, too - sometimes the drug wa

The Bytes Behind Biology BigBen's 21 cabinets hold 4,136 processors Performing 21 trillion calculations per second, a supercomputer in Pittsburgh provided the first atomic-level look at the inner workings of the nuclear pore complex. That's just one of its accomplishments. By Andrea Gawrylewski ARTICLE EXTRAS 1 Preexisting models, based on electron microscopy and experimental work, had suggested four calcium binding sites to facilitate neurotransmission. Stiles

Primate Customs var FO = { movie:"http://images.the-scientist.com/supplementary/flash/53438/infographic.swf", width:"580", height:"600", majorversion:"8", build:"0"}; UFO.create(FO, "ufoDemo"); Please download the Adobe Flash Player to view this content:

Video: Frog Neuromuscular Junction var FO = { movie:"http://images.the-scientist.com/supplementary/flash/53439/bio.swf", width:"400", height:"320", majorversion:"8", build:"0"}; UFO.create(FO, "ufoDemo"); Please download the Adobe Flash Player to view this content: Frog neuromuscular junction fly-through. Shown in red is a large muscle fiber (diameter 50 micrometers) that is innervated by a myelinated axon colored in white. The interface between muscle and a

Adding 'super' to 'computer' By Andrea Gawrylewski ARTICLE EXTRAS The bytes behind biology The visible human Video: Frog neuromuscular junction The International Headquarters of the Westinghouse Electric Company in Monroeville, Pa., is a black glass-paneled fortress dedicated to nuclear energy research. All except the basement, that is, where underneath the formidable security check-in desk, and the two towers of labs and offices and sunlit hallways, more than 4,000 Pit

The visible human By Andrea Gawrylewski ARTICLE EXTRAS The bytes behind biology Adding 'super' to 'computer' Video: Frog neuromuscular junction In 1991, Vic Spitzer and David Whitlock at the University of Colorado at Boulder went hunting for cadavers - one male, one female. It took two years to find bodies that were considered normal - meaning of feasible proportions (no more than six feet tall, 20 inches wide, and 14 inches deep), and no history of cancer, operatio

The Brain on Stress A young scientist at Rockefeller tries to figure out what's going on in the brains of adolescent rats. By Jenny Marder 4 years ago, Russell Romeo committed a small act of subterfuge. Without telling his boss, he ordered 60 white lab rats from an animal research facility in Harlan, NY, and had them shipped to his laboratory at Rockefeller University. They arrived, 10 to a box, on a crisp, cloudless Tuesday in March. He gave them a week to recover from

"On non-scientific forums, it's best to keep your qualifications to yourself." Altitude or attitude? In "Kids climb Everest,"1 Janet Stocks reports that kids and adults had vivid dreams and difficulty sleeping, and seems to imply that this is a result of high altitude. Take any kid or adult transport them to an exotic place like Nepal, with its fantastic scenery, peoples, cultural and gastronomic experiences (both positive and negative) and I bet exc

Can systems biology save the drug industry?

A recent graduate of the Columbia University Graduate School of Journalism, Jenny Marder is freelance journalist from Los Angeles whose writing has earned awards from the Los Angeles Press Club, the Association of Health Care Journalists, and the California Newspaper Publisher's Association. From 2004 to 2006, Marder covered local politics and started a health beat at the Long Beach Press-Telegram in California. Here, she writes about Russell Romeo, a researcher who

The mass manufacture of penicillin during World War II stimulated urgent interest in other medicinally important soil microorganisms.

Related Articles A Space for Children Maternity leave and childcare go hand in hand as factors that women carefully consider when making plans about their career and family. Governments around the world have taken different approaches to mandating maternity leave that works for the family and the economy. See how US policy on maternity leave compares to a few other countries. Longer Leaves: In Europe, mandatory leave is 14 weeks, though nearly

Industry knows that onsite childcare is good for retention. Is academia starting to catch on?

Norbert Riedel's focus on science has helped pull Baxter out of a slump.

Image analysis software offers more screening possibilities than ever, so how should you power your next screen?

Credit: © Cody Pickens" /> Credit: © Cody Pickens In May, two years after Chris Voigt moved into his new lab at the University of California, San Francisco, his light-colored wood desks and cabinets still smell like sawdust - just as you'd imagine a traditional toy maker's shop to smell. Voigt doesn't build toys out of wood, however; he builds them out of biological parts. Having trained in chemical engineering, Voigt never intended to become a biologist. As a

HIV-1 strains in humans arose from three independent ape-to-human transmissions in the early 20th century, but the viral adaptation in humans remained unknown until now. Paul Sharp and colleagues from the University of Nottingham Queens Medical Centre in England compared full-length genome sequences of chimpanzee HIV strains with inferred ancestral sequences for three different phylogenetic HIV-1 groups in humans: M, N and O. They found that cross-species transmission in all three gr

Credit: David M. Phillips / Photo Researchers, Inc" /> Credit: David M. Phillips / Photo Researchers, Inc To uncover the inflammatory pathways involved in cell injury and death, Kenneth Rock at the University of Massachusetts and colleagues injected necrotic cells into mice deficient in various toll-like receptors and found that neutrophilic inflammatory response was not significantly reduced.1 Using the same strategy in interleukin-1 (IL-1) receptor-deficient mice, along with mice

T.Y. James et al., "Reconstructing the early evolution of Fungi using a six-gene phylogeny," Nature 443:818-22, Oct. 19, 2007. This paper presents a broad molecular phylogeny of the fungi and highlights the basal nature of the chytrids. This six-gene phylogeny is a major advance for understanding the evolution of fungal traits. Joe Heitman Duke University Medical Center, USA

To characterize transcriptional regulation in human embryonic stem cells Richard Young at the Whitehead Institute and colleagues used a genome-wide analysis with chromatin immunoprecipitation and DNA microarrays, finding that transcription factors OCT4, SOX2, and NANOG target 353 genes, roughly half of which are not expressed. They also found that the three transcription factors co-occupy genes' promoter regions to regulate each others' activity.

Credit: Adapted from Nature Genetics" /> Credit: Adapted from Nature Genetics The paper: I. Bentwich et al., "Identification of hundreds of conserved and nonconserved human microRNAs," Nat Gen , 37:766-70, 2005. (Cited in 148 papers) [PUBMED] The finding: Isaac Bentwich and colleagues at Rosetta Genomics upped the number of sequenced human microRNAs using a new technique integrating bioinform

The paper: J.V. Zhang et al., "Obestatin, a peptide encoded by the ghrelin gene, opposes ghrelin's effect on food intake." Science , 310:996-99, 2005. (Cited in 99 papers) [PUBMED] The finding: Aaron Hsueh's group from Stanford University isolated a new peptide hormone, dubbed "obestatin." Using in vitro binding studies, the group found that obestatin served as a natural ligand for

Four groups simultaneously identify the same adaptor in the viral RNA immune-response pathway.

A virus has the orange industry in trouble, and growers are partly to blame.

Merck could cut the price of its new vaccine by 90% and still do very well.

Elizabeth Jonas was supposed to be a physician. A summer with Rodolfo Llinás changed all that.

How the industrialization of academic science has ruined research, and what we can do about it.

Giving out smaller grants, but for larger periods of time, will fix a system in distress.

The stone statues of Easter Island Credit: Courtesy of Terry Hunt" />The stone statues of Easter Island Credit: Courtesy of Terry Hunt Related: Slideshow: Solving the Easter Island mysteries On one side of a quarry roughly two-thirds the size of a football field is "El Gigante," a half-finished stone statue seven stories tall, and weighing almost 300 tons. Prehistoric tools lie scattered nearby. Whoever made these head-and-torso statues, kno

Monkeys react to a throw Credit: Courtesy of David Glynn" />Monkeys react to a throw Credit: Courtesy of David Glynn For a couple of months last summer, neuroscientist Justin Wood filmed himself aiming rocks at monkeys. Technically, he was only pretending to hit the monkeys. He just wanted to see how they'd react, in a bid to pin down the neurologic underpinnings of a uniquely human trait: throwing. Early every morning, under a sky streaked with the colors of dawn, the H

Sitting around a table piled with seafood and wine, a group of scientists came up with an idea. It was the Fall of 2005, and the diners were from the DNA sequencing company 454 Life Sciences, celebrating the launch of the company's sequencing technology, the Genome Sequencer 20. 454 was established with the goal of making human genome sequencing an everyday technology, and that night the ambition seemed within reach. At the Stone House restaurant on the marina at Guildford,

You don't have to be smart to be rich, study finds," reads a press release from Ohio State University released on April 24th, 2007. This study determined that people with below-average intelligence are just as wealthy as those with higher IQs, and being smart doesn't prevent you from having financial troubles.Starving PhD students might not be all that shocked. Want to know the elusive secret about how to quiet a screaming baby? Throw away that subscription to

Mohammad Sajid Credit: Courtesy of UCSF" />Mohammad Sajid Credit: Courtesy of UCSF Last July, a British biologist strolled into the US embassy in London to get his temporary (J-1) visa stamped so he could return to his California lab. He wasn't worried, even after he learned he needed to undergo a background check. The last time he left London for the United States, a mere 15 months earlier, a background check delayed him for six months. He was told any later checks would be mu

Credit: Greg Kessler" /> Credit: Greg Kessler STRESS IN HUNGARY >> On page 52 of this issue, Jenny Marder profiles the work of Rockefeller's Russell Romeo, who studies stress hormones in rats. Learn more about cellular responses to stress at the World Conference of Stress in Budapest, August 23-26. For more, see http://www.stress07.com. SUPERCOMPUTING >> Andrea Gawrylewski went to Pittsburgh to see the BigBen Supercom