This is the twice-per-month electronic newsletter for basic, preclinical and translational research news related to the Johns Hopkins School of Medicine. Please forward freely. Direct comments or questions to Joanna Downer, PhD, in the Office of Corporate Communications (4-5105, jdowner1@jhmi.edu).
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IN THIS ISSUE:
***Nobel Prize Reception, 4 p.m., Nov. 5, Turner Concourse***
+ Thorough, Searchable Database of Human Proteins Unveiled
+ Rods and Cones Treat Light-Detecting Molecules Identically
NEWS BRIEFS:
Desiderio to Head Institute for Basic Biomedical Sciences
University-Wide Conflict of Interest Training Deadline Oct. 31
Routine Animal Research Inspections Nov. 3-14
Pevsner Textbook: Bioinformatics and Functional Genomics
Hopkins Offers Part-Time Bioinformatics Master's
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10/2/03
Thorough, Searchable Database of Human Proteins Unveiled
In the October issue of Genome Research, an international team of scientists has unveiled a human protein database they say will change the way biology is done.
The Human Protein Reference Database (HPRD), which currently contains scientist-compiled entries on the 3,000 most-studied human proteins, including their known roles in health and disease, is expected to hold comprehensive information on 10,000 human proteins by year's end. Importantly, this database includes known interactions between proteins, creating a web that ties separate discoveries together.
"This is the real beginning of systems biology in the human," says principal investigator Akhilesh Pandey, PhD, assistant professor in Hopkins' McKusick-Nathans Institute of Genetic Medicine. "We believe that manual curation -- lots of scientists poring through the literature -- is the key to building a more accurate and more complete database."
To create the database entries, dozens of trained biologists, most at the Institute of Bioinformatics in India, started with the database Online Mendelian Inheritance in Man, aka OMIM. Focusing on these genes' proteins, the scientists critically reviewed hundreds of thousands of scientific papers, making connections between papers and resolving inconsistencies. They also pulled information from smaller existing databases to complete each protein's entry.
The HPRD currently contains everything that's known about proteins involved in diseases, such as so-called breast cancer genes BRCA1 and BRCA2, and proteins in key pathways, such as families of enzymes that modify other proteins. It includes only experimentally proven or widely accepted facts about the proteins, without mixing in computer-generated predictions the way some other databases do, says Pandey, who serves as chief scientific adviser to the Institute of Bioinformatics.
More Info
Genome Research 2003;13(10):2363-2371
10/2/03
Rods and Cones Treat Light-Detecting Molecules Identically
Johns Hopkins scientists have discovered that the eye's vision-producing rods and cones cannot tell the difference between their respective light-detecting molecules. The findings appeared in the Oct. 2 issue of Nature.
At the heart of the researchers' side-by-side comparison is the quest to solve a fundamental mystery of vision: how rods and cones have such different sensitivities to light despite using very similar processes to detect it.
Rods function in near darkness, while rarer cones function in bright light, providing vibrant color vision. In each cell type, the process of forming vision begins when light activates a cell-specific molecule, called a visual pigment, and ends when the cell emits an electrical signal.
For their experiments, the Hopkins researchers created frogs whose rods contained, in addition to their usual pigment, a pigment found only in cones. The researchers expected the rods to treat the two pigments differently -- picking up signals only from its native pigment and spurning the other -- or to behave a little like cones.
"Surprisingly, the cell's response to light was identical regardless of which pigment was activated," says King Wai Yau, PhD, professor of neuroscience in Hopkins' Institute for Basic Biomedical Sciences. "It's as though the label of 'rod' pigment and 'cone' pigment is gone. The pigments alone do not explain the cells' functional differences."
Only the cone pigment's inherent instability seemed to contribute to rods' and cones' sensitivity differences. Unlike rod pigment, cone pigment becomes "activated" even without exposure to light, causing cones to generate false signals that reduce their sensitivity. Through a number of calculations, postdoctoral fellow Vladimir Kefalov, PhD, determined that, in primates, this cone pigment "noise" could account for roughly half of the normal sensitivity difference between cones and rods.
More Info
Desiderio to Head Institute for Basic Biomedical Sciences -- Stephen Desiderio, MD, PhD, professor of molecular biology and genetics at The Johns Hopkins University School of Medicine, has been named director of the school's Institute for Basic Biomedical Sciences. The Institute was formed in December 2000 to unite the school's eight basic science departments and several hundred scientists. Also a Howard Hughes Medical Institute investigator, Desiderio replaces Jeremy Berg, PhD, who is leaving Hopkins to head the National Institute of General Medical Sciences at the National Institutes of Health.
More Info
University-Wide Conflict of Interest Training Deadline Oct. 31 -- Individuals who submit private agreements to the Office of Policy Coordination for review and approval, and all individuals proposing arrangements that are subject to review by the Committee on Conflict of Interest must complete the "Conflict of Interest and Commitment" online training module by Oct. 31, 2003. All other University faculty, staff, researchers, students, trainees and administrators (including administrative assistants) must complete the course by Dec. 31. The training module is at https://secure.lwservers.net .
http://www.hopkinsmedicine.org/research/coi_training_module.html
Routine Animal Research Inspections Nov. 3-14 -- The Institutional Animal Care and Use Committee (IACUC) will be conducting its semi annual inspections of all facilities and laboratory space where animals are housed or used in research from Nov. 3 through 14. This includes all animal use areas on the Homewood campus, the East Baltimore campus (the School of Medicine, School of Public Health and School of Nursing), Bayview Campus and the Farm. The IACUC conducts inspections and reviews the animal care program every six months to ensure compliance with applicable federal policies and regulations. During the inspection periods, laboratories using animals in research should have a knowledgeable individual available to answer questions and records should be readily available. Any questions about the inspections or regulations regarding the use of animals in research can be directed to the IACUC at 443-287-3738.
http://www.jhu.edu/animalcare
Pevsner Textbook: Bioinformatics and Functional Genomics -- Jonathan Pevsner, PhD, associate professor of neurology at the Kennedy Krieger Institute and Johns Hopkins, has written a new textbook, Bioinformatics and Functional Genomics. The 750-page book covers bioinformatics -- the interface of biology and computers -- and ending with chapters on the human genome and human disease. Chapters on protein structure, viruses, bacteria and other topics also have a slant toward human disease relevance, Pevsner notes.
http://www.bioinfbook.org
Hopkins Offers Part-Time Bioinformatics Master's -- Johns Hopkins University's part-time programs will begin offering a master's degree sequence in bioinformatics starting next spring at the university's Montgomery County Campus in Rockville. The new program, aimed at working adults, will be presented through a collaboration between the university's Whiting School of Engineering's Part-Time Programs in Engineering and Applied Science and the Zanvyl Krieger School of Arts and Sciences' Advanced Academic Programs. Courses will be aimed at preparing students for work in one of the biotech industry's fastest growing business sectors.
http://www.bioinformatics.jhu.edu
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