Department News
Gene Mutations Cause Massive Brain Asymmetry
June 25, 2012Hemimegalencephaly is a rare but dramatic condition in which the brain grows asymmetrically, with one hemisphere becoming massively enlarged. Though frequently diagnosed in children with severe epilepsy, the cause of hemimegalencephaly is unknown and current treatment is radical: surgical removal of some or all of the diseased half of the brain.
In a paper published in the June 24, 2012 online issue of Nature Genetics, a team of doctors and scientists, led by researchers at the University of California, San Diego School of Medicine and the Howard Hughes Medical Institute, say de novo somatic mutations in a trio of genes that help regulate cell size and proliferation are likely culprits for causing hemimegalencephaly, though perhaps not the only ones.
Coauthors include two Bioinformatics and Systems Biology program members: Joseph G. Gleeson, M.D., and Vineet Bafna, Ph.D.
Varying Drug Levels in the Body Could Speed the Emergence of Drug-Resistant Bacteria
June 19, 2012Strains of bacteria able to resist multiple antibiotics pose a growing threat to public health, yet the means by which resistance quickly emerges aren’t well understood. Scientists led by physics professor Terence Hwa at the University of California, San Diego, thought that the variety of environments in which bacteria encounter antibiotic drugs could play an important role. They have developed a mathematical model, published in the June 18 early online edition of the Proceedings of the National Academy of Sciences, that demonstrates how that would work.
Sequencing Protein-making Part of Genome Can Change Diagnosis and Patient Care
June 13, 2012In the June 13 issue of Science Translational Medicine, an international team led by researchers from the University of California, San Diego School of Medicine reports that the new technology of exome sequencing is not only a promising method for identifying disease-causing genes, but may also improve diagnoses and guide individual patient care.
In exome sequencing, researchers selectively and simultaneously target and map all of the portions of the genome where exons reside. Exons are short, critical sequences of DNA in genes that are translated into proteins – the biological workhorses involved in virtually every cellular function, plus various structural or mechanical duties.
The researchers, headed by principal investigator Joseph G. Gleeson, MD, professor of neurosciences and pediatrics at UC San Diego and Rady Children’s Hospital-San Diego, sequenced the exomes of 118 patients who had been diagnosed with specific neurodevelopmental diseases. In each of the cases, all known genetic causes of their disease had been previously excluded.
UC San Diego Researchers Receive New CIRM Funding
May 25, 2012Five scientists from the University of California, San Diego and its School of Medicine have been awarded almost $12 million in new grants from the California Institute for Regenerative Medicine (CIRM) to conduct stem cell-based research into regenerating spinal cord injuries, repairing gene mutations that cause amyotrophic lateral sclerosis and finding new drugs to treat heart failure and Alzheimer’s disease. Awardees include two faculty members in the Bioinformatics and Systems Biology Program: Lawrence Goldstein, who is studying Alzheimer's Disease, and Gene Yeo, who is studying Lou Gehrig's disease.
New Drug Target Improves Memory in Mouse Model of Alzheimer’s Disease
May 7, 2012Researchers at the University of California, San Diego, the Medical University of South Carolina, the University of Cincinnati, and American Life Science Pharmaceuticals of San Diego have validated the protease cathepsin B (CatB) as a target for improving memory deficits and reducing the pathology of Alzheimer’s disease (AD) in an animal model representative of most AD patients. The study has been published in the online edition of the Journal of Alzheimer’s Disease.
According to investigator Vivian Y. H. Hook, PhD, professor of the UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences and professor of neurosciences, pharmacology and medicine at the UCSD School of Medicine, and professor in the Bioinformatics and Systems Biology Graduate Program, the study is important because it could lead to new therapeutics that improve the memory deficits of AD.
Ruth Williams Elected to National Academy of Sciences
May 1, 2012The National Academy of Sciences today elected three professors at the University of California, San Diego to membership in the prestigious National Academy of Sciences, one of the highest honors bestowed on U.S. scientists and engineers. Roberto Malinow, Ruth Williams and William Young were among the 84 new members and 21 foreign associates elected to the academy today “in recognition of their distinguished and continuing achievements in original research.” Ruth Williams, a professor in the Department of Mathematics, is a member of the Graduate Program in Bioinformatics and Systems Biology.
Express Yourself: How Zygotes Sort Out
February 16, 2012Writing in the February 17, 2012 issue of the journal Cell, researchers at the Ludwig Institute for Cancer Research, the University of California, San Diego School of Medicine and the Toronto Western Research Institute peel away some of the enduring mystery of how zygotes or fertilized eggs determine which copies of parental genes will be used or ignored.
In the Cell paper, a team of scientists, led by Bing Ren, PhD, head of the Laboratory of Gene Regulation at the Ludwig Institute for Cancer Research at UC San Diego, describe in greater detail how differential DNA methylation in the two parental genomes set the stage for selective expression of imprinted genes in the mouse. Differential DNA methylation is essential to normal development in humans and other higher organisms. It involves the addition of hydrocarbon compounds called methyls to cytosine, one of the four bases or building blocks of DNA. Such addition alters the expression of different genes, boosting or suppressing them to help direct embryonic growth and development.
Researchers Induce Alzheimer’s Neurons From Pluripotent Stem Cells
January 25, 2012Led by researchers at the University of California, San Diego School of Medicine, scientists have, for the first time, created stem cell-derived, in vitro models of sporadic and hereditary Alzheimer’s disease (AD), using induced pluripotent stem cells from patients with the much-dreaded neurodegenerative disorder.
“Creating highly purified and functional human Alzheimer’s neurons in a dish – this has never been done before,” said senior study author Lawrence Goldstein, PhD, professor in the Department of Cellular and Molecular Medicine, Howard Hughes Medical Institute Investigator and director of the UC San Diego Stem Cell Program. “It’s a first step. These aren’t perfect models. They’re proof of concept. But now we know how to make them. It requires extraordinary care and diligence, really rigorous quality controls to induce consistent behavior, but we can do it.”
The feat, published in the January 25 online edition of the journal Nature, represents a new and much-needed method for studying the causes of AD, a progressive dementia that afflicts approximately 5.4 million Americans. More importantly, the living cells provide an unprecedented tool for developing and testing drugs to treat the disorder. Coauthors include Bioinformatics faculty members Lawrence Goldstein and Kun Zhang.
DNA Mismatch Repair Happens Only During A Brief Window of Opportunity
December 22, 2011In eukaryotes – the group of organisms that include humans – a key to survival is the ability of certain proteins to quickly and accurately repair genetic errors that occur when DNA is replicated to make new cells.
In a paper published in the December 23, 2011 issue of the journal Science, researchers at the Ludwig Institute for Cancer Research and the University of California, San Diego School of Medicine have solved part of the mystery of how these proteins do their job, a process called DNA mismatch repair (MMR).
Using Saccharomyces cerevisiae, or baker’s yeast, as their model organism, the researchers, led by Richard D. Kolodner, PhD, Ludwig Institute investigator and UCSD professor of medicine and cellular and molecular medicine, discovered that newly replicated DNA produces a temporary signal for 10 to 15 minutes after replication which helps identify it as new – and thus a potential subject for MMR.
Researchers Create Living ‘Neon Signs’ Composed of Millions of Glowing Bacteria
December 18, 2011In an example of life imitating art, biologists and bioengineers at UC San Diego have created a living neon sign composed of millions of bacterial cells that periodically fluoresce in unison like blinking light bulbs.
Their achievement, detailed in this week’s advance online issue of the journal Nature, involved attaching a fluorescent protein to the biological clocks of the bacteria, synchronizing the clocks of the thousands of bacteria within a colony, then synchronizing thousands of the blinking bacterial colonies to glow on and off in unison.
Coauthors include two members of the Bioionformatics and Systems Biology program: Ph.D. candidate Phillip Samayoa and Prof. Jeff Hasty.