Department News
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.
Non-Coding RNA Relocates Genes When It’s Time To Go To Work
November 10, 2011Cells develop and thrive by turning genes on and off as needed in a precise pattern, a process known as regulated gene transcription. In a paper published in the November 9 issue of the journal Cell, researchers at the University of California, San Diego School of Medicine say this process is even more complex than previously thought, with regulated genes actually relocated to other, more conducive places in the cell nucleus.
Coauthors include Bioinformatics and Systems Biology faculty members Michael G. Rosenfeld, M.D. and Pieter C. Dorrestein, Ph.D.
Dr. Lawrence Goldstein Keynote Speaker at World Stem Cell Summit
October 4, 2011Dr. Lawrence Goldstein - Director of UC San Diego's stem cell program in Pasadena for World Stem Cell Summit
Researchers Sequence Dark Matter of Life
September 19, 2011Researchers have developed a new method to sequence and analyze the dark matter of life—the genomes of thousands of bacteria species previously beyond scientists’ reach, from microorganisms that produce antibiotics and biofuels to microbes living in the human body.
Scientists from UC San Diego, the J. Craig Venter Institute and Illumina Inc., published their findings in the Sept. 18 online issue of the journal Nature Biotechnology. The breakthrough will enable researchers to assemble virtually complete genomes from DNA extracted from a single bacterial cell. By contrast, traditional sequencing methods require at least a billion identical cells, grown in cultures in the lab. The study opens the door to the sequencing of bacteria that cannot be cultured—the lion’s share of bacterial species living on the planet.
The UC San Diego coauthors are computer science postdoctoral researcher Hamidreza Chitsaz; mathematics professor Glenn Tesler; and computer science professor Pavel Pevzner.
Roger Chang and Colleagues Construct Metabolic Network of Algae
August 15, 2011Ph.D. candidate Roger Chang and colleagues including Prof. Bernhard Palsson and alumnus Jason Papin, have reconstructed the metabolic network for the algae strain Chalydomonas einhardtii, a potential source of biofuel.
Article at Molecular Systems Biology.
Additional coverage in Science, New Energy and Fuel, and Biomass Magazine.
Andrew McCammon Among Three UCSD Professors elected to the National Academy of Sciences
May 13, 2011The National Academy of Sciences today elected three professors at the University of California, San Diego to membership in the National Academy of Sciences, one of the highest honors bestowed on U.S. scientists and engineers.
Andrew McCammon, the Joseph E. Mayer Chair of Theoretical Chemistry, Howard Hughes Medical Institute investigator and distinguished professor of chemistry and biochemistry, and pharmacology, and faculty in the Bioinformatics and Systems Biology Graduate Program, has invented theoretical methods for accurately predicting and interpreting how molecules interact with one another, methods that play a growing role in the design of new drugs and other materials.
Tiny Talk on a Barnacle's Back
May 10, 2011Even the merest of microbes must be able to talk, to be able to interact with its environment and with others to not just survive, but to thrive. This cellular chatter comes in the form of signaling molecules and exchanged metabolites (molecules involved in the process of metabolism or living) that can have effects far larger than the organism itself. Humans, for example, rely upon thousands of products derived from microbially produced molecules, everything from antibiotics and food supplements to ingredients used in toothpaste and paint.
Remarkably, most of what’s known about how microbes communicate with each other is the result of indirect observation and measurements. There has been no general or informative technique for observing the manifold metabolic exchange and signaling interactions between microbes, their hosts and environments. Until now. In a paper published in the May 5 online issue of the journal Angewandte Chemie, researchers at UC San Diego and Scripps Institution of Oceanography report using a new form of imaging mass spectrometry to dramatically visualize multiplex microbial interactions.
Two coauthors are from the Bioinformatics & Sytems Biology Program: Prof. Pieter C. Dorrestein and Prof. Nuno Bandeira.
Nearly 30 Percent of New CIRM Awards go to UC San Diego Stem Cell Researchers
May 4, 2011UC San Diego scientists garnered 8 of the total 27 of Basic Biology III awards announced today by the Independent Citizens' Oversight Committee (ICOC) of the California Institute for Regenerative Medicine, the state agency created by California voters to pursue the promise of stem cells in science and medicine. “Basic science has been our strength at UC San Diego because we have dedicated time and energy to developing our expertise in stem cells,” said Larry Goldstein, PhD, director of the UC San Diego Stem Cell Program. “Through our excellence in scientific research fundamentals, UCSD stem cell researchers are creating the basis for future advances in this exciting field.”