Notebook

BIOREMEDIATION TO THE PIGPEN It was a stinky summer at the EnviroPork hog facility near Larimore, N.D., with penalties pending for violating state odor regulations, and neighbors complaining loudly about the foul fragrance. Making matters worse, the manure lagoon associated with the facility threatened groundwater supplies. Happily, researchers from the University of North Dakota Energy and Environmental Research Center (EERC) had a low-tech solution: barley straw. Using a cannon, they shot a foot-thick straw covering over the two-acre manure lagoon. It worked so well in containing and eventually dissipating the odor that they built a barley-straw wall to dampen odor from the hog barns. Why barley? "The straw probably creates surfaces for adsorption. Barley straw works best because of its waxy coating. It is very water resistant, and doesn't sink easily. Other straws become saturated and sink," explains David Rush, a research associate at EERC. Presumably, barley straw harbors bacteria that consume the offending chemicals and break them down to carbon dioxide and water, but the researchers don't yet know the exact scenario. "The compounds broken down were most likely ammonia and hydrogen sulfide, really stinky stuff. Fatty acids were probably involved in producing the odor too, but how the microbes affected it all, we don't yet know," Rush adds. VARIED GUISES Doing science involves communicating science--within the technical community, to academics in other disciplines, to students, and to the public. "Communicating Science," held at Hamilton College in Clinton, N.Y., Oct. 3-5, convened an eclectic group to identify the obstacles that distort dissemination of scientific information. Jinnie Garrett, a professor of biology at the college and a yeast geneticist, organized the meeting because "some of us have become so focused on narrow areas of molecular biology that we never have the time to think about much else." Talks addressed shortcomings of scientific investigations that confuse communication, removing sexism and racism from course content, and the public's discomfort with the uncertainty of science. Dorothy Nelkin, university professor of sociology at New York University, bashed both scientists and the media: "In the 1990s, journalists are playing the hottest discoveries and the latest miracle cures to attract readers and sell magazines. Journalists are manipulated by scientists seeking publicity to keep funding coming." But then journalists had their turn, with an expert panel contrasting scientists to journalists, and pointing out how scientists can improve their communication skills. Richard Harris, science reporter for National Public Radio and president of the National Association of Science Writers, described the role of the journalist differently than Nelkin. "My job is to tell stories, to capture the essence of things. The world is full of facts--but how can we frame them? A journalist's job is to raise the 'what ifs.' Scientists are sometimes too reluctant to speculate." ON THE ORIGIN OF LIFE--AND DEATH Since 1953, researchers have made simple organic molecules of life, such as amino acids, using various inorganic ingredients. By doing so they hoped to understand the origin of life on early Earth. One key missing piece of the puzzle has always been the source of reduced nitrogen, presumably ammonia, since the early atmosphere contained primarily molecular dinitrogen. Experiments from a group led by Robert Hazen at the Carnegie Institute of Washington, D.C, may now fill this void (J. Brandes et al., Nature, 395:365-7, 1998). In line with recent thinking, the researchers mimicked deep sea thermal vents by exposing water, nitrogen gas, nitrite, or nitrate to iron oxide or sulfide minerals, and they raised the temperature and pressure. They hypothesized that the minerals would catalyze ammonia formation just as they promote other origin of life reactions. The researchers were right--big time. Early Earth ammonia not only may have built simple molecules such as amino acids, but by accumulating in the atmosphere, this greenhouse gas could have helped raise Earth's temperature in spite of a weak, young sun. Sadly, this research has a tragic human dimension. Coauthor Benjamin Cooper, a high school intern, was a key player in the project. Two days before he was to present the work at a symposium, Cooper was killed instantly when an out-of-control dump truck overturned on his car. Recalls postdoctoral researcher Jay Brandes, "He was really exceptional. I taught him to do the ... analysis for nitrogen compounds, as well as several other types of experiments. Ben was enthusiastic about everything, from library literature searches to analyzing data from the latest runs. He analyzed most of the data in the report. We at the lab were devastated. I made the decision that I would try to get the article into the best journal that I could." DR. ASTROBIOLOGY Following the University of Washington's unsuccessful application to become one of the first institutions selected for NASA's new Astrobiology Institute (S. Bunk, The Scientist, 12 [13]:1, June 22, 1998), the university recently scored a tidy consolation prize. It was awarded a five-year, $2 million National Science Foundation grant, supplemented by $500,000 in university funds, to set up the world's first doctoral program in astrobiology. "We want Ph.D. students trained in cross-disciplinary environments," explains UW microbiology professor James Staley, principal investigator for astrobiology, which embraces both terrestrial and extraterrestrial life sciences. All the grant money will be dedicated to student research, he adds. Diplomas will contain an endorsement noting an emphasis in astrobiology, and degrees may be awarded in any of 11 participating programs: oceanography, astronomy, aeronautics and astronautics, genetics, chemistry, biochemistry, microbiology, atmospheric sciences, geophysics, geological sciences, and history. Staley offers an example of cross-disciplinary research: students might work with microbiologists and geologists in analyzing microbial fossils from deep sea hydrothermal vents that are no longer colonized, then could compare these data to living microbes found in newer vents. Such techniques could be useful in studying microbial fossils that originate from beyond Earth, if any are discovered. "We have contacts with NASA and we will continue to develop them," he declares. Pacific Northwest National Laboratory in Richland, Wash., and ZymoGenetics of Seattle (which studies enzymes from unusual bacteria), also will participate in the program. Beginning in 1999, the goal is to produce a dozen Ph.D.s after five years. GUILTY PLEA The Augusta, Ga., trial of Richard Borison ended on Oct. 8 when Borison, the ex-head of the Department of Psychiatry and Health Behavior at Medical College of Georgia (MCG), pleaded guilty to 36 of 113 counts of theft, making false statements and violations of the state racketeering law. In what may have been the largest criminal prosecution in Georgia history, Borison was accused of diverting more than $10 million in research funds from pharmaceutical companies to his own corporations. Borison was testing drugs for mental disorders including schizophrenia, depression, and Alzheimer's disease at MCG and the Augusta Veterans Affairs hospital. Bruce Diamond, an accomplice and member of the same department, reached a plea agreement in December and was to testify against Borison. Diamond is serving a five-year sentence in a Georgia state prison; Borison was sentenced to 15 years. As part of their pleas, Borison and Diamond will pay stiff fines and return more than $5 million. Assets, including art and antiques allegedly bought with the funds were seized. Borison and Diamond forfeited their medical licenses. MCG became aware of the wrongdoing in June 1996 when a VA researcher concerned about the way patients were being handled came forward. After confronting Borison, officials impounded his research records and notified the attorney general. Though the trial is over, the case isn't closed--others may have been involved, and harm done to patients is still under investigation (the Food and Drug Administration concluded that several prescription drugs tested by the defendants are safe, based on other studies). According to Malcolm Kling, interim vice president for research, MCG has been "looking internally, [to determine] what our weaknesses are, and what we should do about them." As a result, it "instituted a new process for monitoring industry-supported clinical trials". Kling also sounded a cautionary note: this is "something all academic centers need to be aware of--likely, we're not alone." DISEASE (gene symbol)GENEMAP'96GENEMAP'98 Asyndrome (JAG1) Yes Yes Angelman Syndrom (AS) Yes Yes Multiple Endocrine Neoplasia (MEN1) Yes Yes Niemann-Pick Disease (NPC1) Yes Yes Nonsyndromic Deafness (DFNA1) YesYes Opitz G/BBB Syrndrome (OS) Yes Yes Torsion Dystonia Yes Yes Familial Mediterranean Fever (MEFV) No Yes Juvenile Glaucoma No Yes Stargardt's Disease (STGD1) No Yes Tuberous Sclerosis (TSC1) No Yes X-linked Situs inversus (ZIC3) NoNo Autoimmune dystrophy (APECED) No No Holt-Oram Syndrome (HOS1) No No Pendred Syndrome (PDS) No No Spinocerebellar Ataxia Type 7 (SCA7) No No The Web version of GeneMap98 provides maps for each chromosome, including chromosome X (above). The site also has additional information, such as the comparison of disease genes mapped in 1996 vs those mapped in 1998 (left). According to the site, following the publication of the 1996 gene map, scientists reported the isolation of 16 genes by positional approaches. Later analysis revealed that at the time of their cloning, seven out of 16 of these genes had already been isolated as expressed sequence tags (ESTs) and then mapped. Dta from the current map bring the number of known disease genes to 11. MAPPING GENES Gene mappers have reached the halfway point. As part of the Human Genome Project, a team of 64 academic, government, and industry scientists recently unveiled GeneMap98, a complete mapping of the chromosomal positions of the 30,181 genes located thus far--nearly twice the number reported in an October 1996 gene-map version. Two to three times more accurate than before, the complete 1998 map will appear in the Oct. 23 issue of Science and is currently available on the Internet at www.ncbi.nlm.nih.gov/genemap98. According to Greg Schuler, one of the map creators, the site, which has received an average of 3,400 hits per day since its inception, is intended as both a research tool for scientists and an educational tool for students of science. Disease researchers may, for example, use the map to zero in on sought-after disease-causing genes by establishing links between those diseases and genome landmarks called sequence-tagged sites (STSs). "Many of these [mapped] genes are just expressed sequences of unknown function that might turn out to be the candidate they're looking for," says Schuler who's a staff scientist at the National Center for Biotechnology Information, a branch of the National Library of Medicine, and the leader of the project along with the Sanger Centre of Cambridge, England. Several disease genes isolated in the last two years had, as it turns out, already been on the 1996 map. A third updated gene map is likely, says Schuler, but it will not boast as impressive an improvement over its predecessor as the 1998 version. Mappers are running out of bits of sequence, an essential ingredient for designing the gene markers to be mapped. Schuler estimates that there are 10,000 to 12,000 novel bits of sequence left. "Maybe some new ones will be coming in, but we can't expect a huge number," he says. Also, as DNA sequencing continues, the primary task of the Human Genome Project, a lot of genes will essentially end up getting mapped by default. Once scientists have the DNA sequence of a clone that contains a mapped gene, they can easily locate any other gene on that same clone.

Notebook

The Scientist Staff

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