January 2006

Welcome to the inaugural monthly issue of The Scientist.

Ira Mellman is chair of the Yale School of Medicine's department of Cellular Biology and an affiliate investigator at the Ludwig Institute for Cancer Research. He says that while "the idea that one can manipulate a patient's immune system to help combat cancer" is promising - the subject of his piece on page 47 - "it's simply that we don't know enough," he says. As a "lab guy," Mellman lobbies in Washington, DC, to bring

Write: The Scientist, 400 Market Street, Suite 1250, Philadelphia, PA 19106 Email: letters@the-scientist.com Fax: (215)351-1143 Hereditary sterility for species eradication Re: "Precision Extinction."1 Traps, poison, epizooties, and other measures seem too crude in the face of so many genetic advances. What could be more specific than species-reproduction controls? This could be an i

Credit: Yeast: Francis Leroy, BioCosmos" /> Credit: Yeast: Francis Leroy, BioCosmos ID IN THE SCHOOLS » On January 3, the new Dover, Pennsylvania school board ? sans intelligent design advocates who waged a court battle over whether the school district curriculum should include the teaching of ID in science ? is set to meet to discuss the issue. Board members expect to have the decision of the judge who presided over the case by then.

FEATUREIs This Life? BY JACK LUCENTINI Hordes of green, sub-microscopic balloons float in a watery mixture in Jack Szostak's laboratory at Harvard Medical School. They come in a variety of shapes: spheres, blimps, worms. And as Szostak examines magnified images of them, he can't help but notice a striking resemblance to bacterial ecosystems, puls

FEATUREIs This Life?Just What Is Synthetic Biology? The term "synthetic biology" appears in the title of a 1913Nature article but then disappears until the 1980s, at which pointits use seems interchangeable with recombinant DNA technology.today, the term is used to describe the wholesale engineering of geneticcircuits, entire genomes, and even organisms and has appea

By Drew Endy FEATUREIs This Life?Useful Construction How to design a chassis for synthetic biological systems Drew Endy is an assistantprofessor in the biologicalengineering division andcofounder of MassachusettsInstitute of Technology's syntheticbiology working group.Creation implies an act that is based on some combinationof perfect

By Clyde A. Hutchison III, Hamilton O. Smith, and J. Craig Venter FEATUREIs This Life?The New Biological Synthesis It's time to rewrite life's operating system Anything beyond the minimal gene set can be viewed as add on functions to improve adaptability and metabolic versatility.From top to bottom: Clyde A. Hutchinson is a distinguished investigator, Hamilton Smith is scientific director, and J. Craig Venter is

FEATUREThe Banned Pesticide in Our Soil © JIM REED/GETTY IMAGES BY ALISON MCCOOK For years, commercial growers have been using methyl bromide to strip their soil of pathogens that impede plant growth. Colorless, odorless, cheap to make (often formed as a byproduct of other bromide manufacturing processes) and relatively easy to use, methyl

FEATUREWhere Next for Cancer Immunotherapy? JIM DOWDALLS/PHOTO RESEARCHERS INC.The promise will only be realizedwith more supportBy Ira MellmanDespite its obvious scientific appeal, immunotherapy as anapproach to cancer has yet tolive up to expectations. Initial attemptsat using cytokines to stimulate anticancerT cells, or deploying toxin-conjugatedmonoclonal antibodies a

FEATURESave in the Lab By Melissa Lee PhillipsAs a graduate student and postdoc, Doug Juers never hadto worry about money; he worked in Howard HughesMedical Institute-funded labs that were flush with cash.Since recently joining the departments of physics andbiophysics, biochemistry, and molecular biology at Whitman Collegein Walla Walla, Wash., however, Juers has had to learn

In a 2005 paper in Trends in Biotechnology, David Deamer presented 12 requirements to creating a protocell capitulates life. Then have ben accomplished in different labs and in different ways. Because researchers have used RNA as both a macromolecular catalyst and as an information store, some of the boundaries between objectives become blurred. That's one of the reasons that Deamer says once the 11th requirement is met and macrom

RNAi: Five Tips to Better Silencing - Table 1: siRNA Construction KitsCompanyKitsiRNAs per kit (or yield in mg RNA/ml)Price (USD)Ambionwww.ambion.comMEGAscript RNAi Kit20$285Silencer siRNAConstruction Kit15$535Epicentrewww.epicentre.comMessageMuterShRNAi Production Kit10$225Genlantiswww.genlantis.comDicer siRNA Generation

RNAi: Five Tips to Better Silencing - Table 2: RNAi-Specific Viral KitsCompanyKitSize (reactions)Price (USD)Ambionwww.ambion.compSilencer Adeno 1.0-CMV System5$520pSilencer 5.1 Retro System20$250Invitrogenwww.ambion.comBLOCK-iT AdenoviralRNAi Expression System20$941BLOCK-iT InducibleLentviral RNAi System20$1594

RNAi: Five Tips to Better Silencing - Table 3: siRNA Transfection ReagentsCompany Maximum transfections/mlPrice/ml (USD)Ambionwww.ambion.comsiPORT neoFXtransfection reagent1,250$185siPORT aminetransfection reagent660$345siPORT lipidtransfection reagent1,250$210B-Bridge Internationalwww.b-bridge.comQuick Step transfection reagent

RNAi: Five Tips to Better Silencing - Table 4: Selected Online siRNA-Design ToolsDeveloperNameURLRef.AmbionsiRNA Target Finderwww.ambion.com/techlib/misc/siRNA_finder.html1DharmaconsiDESIGNwww.dharmacon.com/sidesign/2GenScriptSiRNA Construct Builderhttps://www.genscript.com/ssl-bin/app/rnai?op=known siR

What happened when a small company thinks it can abolish a multibillion dollar industry?

US Office 400 Market Street, Suite 1250 Philadelphia, PA 19106-2501 Phone: (215) 351-1660 Fax: (215) 351-1143 E-mail: info@the-scientist.com Europe Office Middlesex House, 34-42 Cleveland St. London W1T 4LB, United Kingdom Phone: +44 (0) 20 7631 9983 Fax: +44 (0) 20 7631 9926 EDITORIAL EDITOR Richard Gallagher DEPUTY EDITOR Ivan Oransky MANAGING

The retiring president of the UK Royal Society had some choice words.

For birds, getting hauled out of a nest by a scientist and poked with a needle ? an increasingly common occurrence in this season of bird flu ? is pretty stressful. Some German ornithologists who study terns worried that such unpleasant encounters were biasing their research results. So taking a cue from nature, they put a tropical blood-sucking bug, Dipetalogaster maximus, on the job to do their dirty work for them.

"Ok, hands up. I hate nutritionists and phony diet marketers. I hate them because they confuse evidence and theory. I hate them because they make sweeping assertions that something will work in the real world on the basis of tenuous laboratory data. And they either do not understand that, or they do and they are being dishonest. In either case, I hate them." Thus the young physician Ben Goldacre began one of the Bad Scie

Merck owes its victory in a recently concluded Vioxx trial in New Jersey largely to the testimony of J. Michael Gaziano, a Harvard cardiologist who expressed his doubts that Vioxx, and not stress, triggered the 2001 heart attack in Frederick "Mike" Humeston, who argued otherwise. It turns out that Gaziano's brother, Todd, a prominent constitutional law scholar at the conservative Heritage Foundation think tank in Washington, DC, h

The red squirrel (Sciurus vulgaris) has been a cultural icon in Britain at least since the beginning of the 20th century, when Beatrix Potter penned a children's tale about Squirrel Nutkin, an impertinent little chap who lived with his large extended family "in a wood at the edge of a lake." In Potter's day, red squirrels were a familiar sight in parks and gardens across Britain, but no longer. In recent decades, their population

The research environment has evolved; it's time for the postdoctoral experience to do the same

The peace dividend pays off in the challenges of teaching English to former bioterrorism researchers

Synthetic biology requires intelligent design, but not the kind they teach in Kansas

Worried about avian flu? Never mind. What about yellow fever?

Throughout his career, Inder Verma has turned unexpected results into important advances

Interrogating bacteria for their essential gene sets

Credit: Courtesy of Margus Pooga" /> Credit: Courtesy of Margus Pooga Controversy still surrounds how certain cationic peptides enter the cell, spurred in part by this paper.1 The so-called cell-penetrating peptides (CPPs), which include short fragments of Tat from HIV-1, appeared to cross plasma membranes directly. This was surprising because the heavily arginated Tat is not the kind of molecule one often sees getting past

Credit: Christian Darkin/Photo Researchers Inc." /> Credit: Christian Darkin/Photo Researchers Inc. Breeders have long known that assisted reproductive technologies lead to a higher incidence of so-called large-offspring syndrome in cattle and sheep. In 2003, Andrew Feinberg of Johns Hopkins and Michael DeBaun of Washington University, St. Louis provided the first evidence that the same phenomenon can occur in humans.1 Using an epidemiol

Credit: Copyright Pasieka/Photo Researchers, Inc." /> Credit: Copyright Pasieka/Photo Researchers, Inc. Alternative splicing promises to help resolve the question of how 25,000 genes could possibly be enough to encode instructions for a huge range of specialized human cells from osteoplast to neuron. Robert Darnell and colleagues at The Rockefeller University, New York, combined microarray analysis with sophisticated bioinformatics too

Hundreds of papers have been published on Nod1 and Nod2, two intracellular proteins that recognize bacterial cell-wall components and play key roles in innate immunity and possibly Crohn disease. Stephen Girardin and colleagues at the Institut Pasteur in Paris recently identified the residues in human Nod1 responsible for recognizing the muropeptide TriDAP.1 Faculty of 1000 reviewer Richard Stevens at Harvard Medical School and Br

Credit: Getty Images" /> Credit: Getty Images M.T. Croft et al., "Algae acquire vitamin B12 through a symbiotic relationship with bacteria," Nature, 438:90?3, Nov. 3, 2005. Besides presenting key data on why [B12] is needed in some algae and not in others, this paper brings to light a ? type of interaction between algae and bacteria that could be of considerable ecological importance. Daniel Vaulot National

Soo-Kyung Lee rushes into her cramped lab at Baylor College of Medicine, apologizing for her lateness?all of two minutes. She opens the door of a spartan office, large enough for a wrap- around desk and a small conference table. The room had been carved out of her lab space she explains later: "I wanted to have my office inside of the lab to have more interaction." The decision is typical, according to colleagues. "She is

These three tech developments could make an appearance on your benchtop this year.

Anxious to get going with RNAi? These tips will make your next knockdown a knockout

Invented a half-century ago by Nobel laureate Wolfgang Paul, the quadrupole mass filter has become an integral part of some of the most sophisticated mass spectrometers. Consisting of four parallel metal rods on which a fixed direct-current voltage and alternating radio-frequency voltage are applied, quadrupole mass filters allow users to selectively filter all ions except for those of a specified mass to charge ratio (m/z), depen

Compelling science doesn't always make a good commercial case. Here's how to tell the difference.

Are intellectual property protections slowing progress?

Throughout your career in the life sciences, you've been socking away money, whether it's into a 401(k), a 403(b), some other IRA, a college fund, or a house. That's good. Inflation, however, can be a wolf at the door. What can you do to protect yourself? Like hindsight, judging the impact of inflation on investments is 20/20, but by that point it's often too late. The only effective way to protect your investments is to defend yo

Credit: Mark Evans" /> Credit: Mark Evans NIH To Student Loaners: Let's make a deal Struggling to make your student loan payments? The National Institutes of Health has a deal for you. In exchange for a two or three-year commitment to conduct specific research at your university or nonprofit institute, the NIH will repay up to $35,000 per year of your undergraduate and graduate school debts as well as any resulting increased tax

The micropipette was invented in 1957 at University of Marburg, Germany by postdoc Heinrich Schnitger. Frustrated by repetitive pipetting of small volumes using glass micropipettes, Schnitger developed a prototype with a spring-loaded piston and a removable plastic tip for containing liquid. All the major features of the present-day micropipettes were incorporated into the prototype, shown above, which was patented in 195