Accuracy in Recounts
It can take a pathologist, moving a micrometer across a slide under a microscope, days to measure 10 different layers in a skin tissue sample. It can also take days to count regrown or restenosed endothelial cells to gauge the effect of a drug on, say, ruptured coronary artery elastic lamina. And a second pathologist may get different results. But Mark Braughler of TissueInformatics, speaking at the Techvest Tissue Repair, Replacement, and Regeneration conference in New York on Nov. 9, said his computer system accomplishes the former task in seconds, the latter in hours. TissueInformatics is a 38-employee Pittsburgh company that uses robotics to capture digital images of tissues from slides at high resolution and fuse them into a complete tissue representation. It uses remote imaging to acquire images worldwide for a syndicated tissue bank. Its software quantifies the structural components of skin, cornea, blood vessels and the sites of positive immunochemical and in situ hybridization staining--that is, any structural or molecular tissue component that can be made visible. Its relational database allows flexibility in the mining and correlation of quantitative structural tissue data with genomic and other functional information. Braughler noted that the potential market for tissue bioinformatics, which includes drug discovery and development, tissue engineering, biotech R&D, and agricultural biotech R&D, is worth $46 billion. As TVs outside the conference room blared news of recounts in the U.S. presidential election, Braughler pointedly added that his system gets the same results, every time.
DOE: Getting the Bugs Out
The Department of Energy Joint Genome Institute in Walnut Creek, Calif., announced in early November the completion of its "microbial marathon"--draft sequences of 15 bacterial genomes. According to Paul Predki, the institute's associate director for production genomics and a member of Berkeley Lab's Genomics Division, "Sequencing the human genome was first proposed by the DOE in 1984 as a means of carrying out its mission of understanding the potential health risks posed by energy use and production. Microbes are generally evaluated on their relevance to DOE goals such as environmental and energy relevance. However, we have sequenced a few microbes because of their high medical, agricultural, or scientific interest." The marathon followed the institute's completion of draft sequences of human chromosomes 5,16, and 19 as well as Enterococcus faecium, an antibiotic-resistant bacterium that is one of the leading causes of hospital-acquired infections. The sequencing efforts included a collaboration with the California Institute of Technology on Magnetospirillum magnetotacticum, which Caltech geobiologist Joseph Kirschvink believes is the best candidate for the ancestor of all mechanisms of biomineralization on Earth, including the ability to form bones and teeth. Kirschvink thinks the similarity of the organism's magnetic structures to magnetic particles found in an ancient Martian meteorite shows that the genes controlling magnetite biomineralization may be of Martian origin. (Others are hypothesizing about the ability of bacteria to survive on Mars following the discovery of a Bacillus in a salt crystal millions of years old [R.H. Vreeland et al., "Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal," Nature, 407:897--900, October 19]). As for DOE's future work, Predki explains, "We are one of the largest high-throughput sequencing centers in the world, and we dedicate approximately 25 percent of our sequencing capacity to microbial sequencing." Predki says that microbial genomes all take approximately two weeks to prepare. "After that, it varies from one-half to one-third days on our 84 sequencing machines. We plan on having microbial marathons next March and August. We're gathering candidates now. The challenge will be deciding what NOT to sequence!"
The Heat is On
In an effort to mitigate the growing problem of antibiotic resistance, researchers at the Wistar Institute in Philadelphia are pursuing new strategies based on antimicrobial peptide molecules certain insects have as an infection defense. Laszlo Otvos Jr., an associate professor, reports two related research efforts are under way: evaluation of some peptide analogs for antibiotic potential and the design of new peptides for a strain-specific target protein. Otvos and colleagues discovered that the microbial receptor targeted by the insect peptide is the 70 kDa bacterial heat shock protein (HSP), called DnaK (L. Otvos Jr. et al., "Interaction between heat shock proteins and antimicrobial peptides," Biochemistry, American Chemical Society Web-publication date Oct. 21, 2000, print date Dec. 6, 2000). HSPs are found in all organisms and provide the energy necessary for proteins when subjected to heat, such as in an infection, to fold properly. Thus, when the insect peptide binds to DnaK, it disrupts the bacterium's protein repair system. "When a bacterial HSP sees the insect-derived peptides, it cannot fold proteins anymore," says Otvos. These insect peptides do not bind to the human equivalent of the bacterial receptor, thereby greatly increasing their potential for pharmaceutical-related applications. "In vivo studies have shown that the native peptide efficiently protected the mice but was toxic to compromised animals at a high dose," reports Otvos. "We have been successful in developing an analogous peptide to circumvent the toxicity problem. This is the first-ever idea that we can inhibit chaperone-assisted protein folding. It is a very new idea." Otvos says that although three pharmaceutical companies and one biotechnology company are interested in potential technology transfer with Wistar, "the companies do not want to go into agreements until the peptides' utility is affirmed by decade-old validated in vitro conditions or additional in vivo data are provided. In vivo is more costly than in vitro. Now that we have identified the binding site, we are trying to get investors so that we can proceed with the design and production of strain-specific antimicrobial peptides."
Penn Gene Therapy Lawsuit Settled
The case that sent shockwaves through the field of gene therapy may finally have attained some closure. The family of Jesse Gelsinger, the Arizona teenager who died a year ago during a gene therapy experiment at the University of Pennsylvania, announced early this month that they had settled their wrongful death lawsuit against Penn and others. The lawsuit, filed in September, named Penn, the Children's National Medical Center (CNMC) of Washington, D.C., the Children's Hospital of Philadelphia, Sharon Hill, Pa-based Genovo Inc., CNMC researcher Mark L. Batshaw, and Penn gene therapy researchers James M. Wilson and Steven E. Raper. William Kelley, former dean of Penn's medical school, and Arthur Caplan, director of Penn's Center for Bioethics, were also named but were dismissed from the lawsuit prior to the settlement. By mutual agreement between the parties, the amount of the settlement was not disclosed. The Gelsinger family also received a written apology from Penn, something that Jesse's father, Paul Gelsinger, had specifically requested subsequent to the settlement. In a joint statement, Penn suggested that the agreement reached will "enable Penn to concentrate on moving forward with its aggressive efforts to improve its oversight and monitoring of human subject research." According to Gelsinger, the Gelsinger family plans to use the money to fund a family-run private foundation. They also intend to establish via the National Organization for Rare Disorders a public fund that is dedicated to metabolic disorders research. "I didn't have to settle this," Gelsinger told The Scientist in a telephone interview. "But it may have ruined a few careers and I'm not interested in doing that."