First Base: All RiseIn a
tour de force of genomic technology and computational biology, researchers at the Whitehead/MIT Center for Genome Research have produced a comparative study of four strains of yeast, with dramatic implications for our understanding of gene inventory and regulatory DNA sequence motifs that direct gene expression.
Manolis Kellis, Eric Lander, and colleagues sequenced the approximately 12-million basepair genomes of three yeast species – Saccharomyces paradoxus, S. Bayanus, and S. mikatae – and compared them with the sequence of S. cerevisiae, the first eukaryotic genome sequenced in 1996. Back then, sequencing a yeast genome required hundreds of researchers and more than a year; today, a single high-throughput center blasts through the sequence in about a week.
Two major results emerge from this comparative genomics study. First, Kellis and colleagues show that more than 500 putative genes predicted by algorithm approaches are spurious, dropping the total number of yeast genes below 6,000. Second, they newly identify 42 conserved regulatory sequence motifs. The lessons from this study in yeast are directly relevant to the future study and understanding of the human genome.
M. Kellis et al. “ Sequencing and comparison of yeast species to identify genes and regulatory elements.”Nature 423, 241-254 (2003).
Second Base: Decades of the BrainThe Massachusetts Institute of Technology (MIT) has broken ground on the McGovern Institute for Brain Research. The 85,000-square foot research facility is named after MIT alumnus Patrick J. McGovern and his wife, Lore Harp McGovern. Patrick McGovern is the founder of Bio-IT World’s parent company, IDG.
McGovern said he had a long-standing interest in communications and learning. “In the mid-1990s, we realized that the tools to advance brain studies had really taken a quantum leap forward,” citing the emergence of high-performance computing and biomedical imaging. MIT beat out seven universities that were competing for the $350 million gift, which will be spread out over 20 years.
The institute is growing steadily under the directorship of Phillip Sharp, Nobel laureate for his discovery of alternative RNA splicing. The best-known faculty member is MIT’s Robert Horvitz, who shared the Nobel Prize for Physiology or Medicine last year.
See executive editor John Russell’s news story on bio-itworld.com:
Third Base: Duke Fast BreakFascinating developments in American academia, as universities and medical centers seek to build the right multidisciplinary facilities to pioneer research for decades to come. One of the most interesting recent initiatives is at Duke University, where Canadian geneticist Hunt Willard has been recruited to direct its $270-million Institute for Genome Sciences and Policy (IGSP tagline: Creating a Humane Genetic Future). The institute consists of a network of five centers, including one for bioinformatics and computational biology, and another for ethics and law, directed by Robert Cook-Deegan (author of Gene Wars).
In a recent editorial in Science, Willard and two Duke colleagues sketched some of the future challenges for information-based medicine fueled by the genome project: “Information systems can now draw meaningful statistical inferences pertinent to each individual from massive data sets that include genomic data, imaging results, and biomarker analyses along with traditional clinical variables. Such evidence, made available to clinicians working at the point of care, can direct the most appropriate preventive and therapeutic actions.”
Sliding Home: Kids Say the Darndest ThingsDuring a recent presentation on genetics and DNA before a quizzical group of fourth graders in Providence, Rhode Island, I asked the class if they happened to know the name of the first animal to be cloned.
Clearly they needed a clue. “She’s named after a famous country music singer…” I said helpfully. Still no response. “Beginning with the letter ‘D’… anybody?”
Suddenly, one boy raised his arm, his beaming smile indicating that he was confident he knew the answer.
“The Dixie Chicks!” he said.
The highlight of this presentation, aside from educating the class on the finer points of country music, is the live preparation of some DNA, using nothing more than some dish-washing liquid, meat tenderizer, salt, rubbing alcohol, and a couple of onions. Should you try this at your local school, be advised: The kids will undoubtedly ask you what DNA tastes like, and inquire if they would have similar luck from other potential sources, such as a severed finger.
A full recipe for blending your own DNA, along with many other slides for children, is available from the American Museum of Natural History:
Email me at kevin_davies@bio-itworld.com.