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Archive - May 2012

Date

May 28th

Variations in Single Gene Can Lead to Too Little or Too Much Growth

UCLA geneticists, together with collaborators, have identified the mutation responsible for IMAGe syndrome, a rare disorder that stunts infants' growth. The twist? The mutation occurs on the same gene that causes Beckwith-Wiedemann syndrome, which makes cells grow too fast, leading to very large children. Published online on May 27, 2012 in Nature Genetics, the UCLA findings could lead to new ways of blocking the rapid cell division that allows tumors to grow unchecked. The discovery also offers a new tool for diagnosing children with IMAGe syndrome, which until now has been difficult to accurately identify. The discovery holds special significance for principal investigator Dr. Eric Vilain, a professor of human genetics, pediatrics, and urology at the David Geffen School of Medicine at UCLA. Nearly 20 years ago, as a medical resident in his native France, Dr. Vilain cared for two boys, ages 3 and 6, who were dramatically short for their ages. Though unrelated, both children shared a mysterious malady marked by minimal fetal development, stunted bone growth, sluggish adrenal glands, and undersized organs and genitals. "I never found a reason to explain these patients' unusual set of symptoms," explained Dr. Vilain, who is also director of the UCLA Institute for Society and Genetics. "I've been searching for the cause of their disease since 1993." When Dr. Vilain joined UCLA as a genetics fellow, the two cases continued to intrigue him. His mentor, then UCLA geneticist Dr. Edward McCabe, recalled a similar case from his previous post at Baylor College of Medicine. The two scientists obtained blood samples from the three cases and analyzed the patients' DNA for mutations in suspect genes, but uncovered nothing. Drs.

Giant Cells Protect Potentially Deadly Fungus During Infection

Giant cells called "titan cells" created by the fungus Cryptococcus neoformans protect the fungus during infection, according to two University of Minnesota researchers. Kirsten Nielsen, Ph.D., an assistant professor in the department of microbiology, and recent Ph.D. recipient Laura Okagaki believe their discovery could help develop new ways to fight infections caused by Cryptococcus. The findings will be published in the June 2012 issue of the journal Eukaryotic Cell. Cryptococcus, a fungus frequently found in dust and dirt, is responsible for the deaths of more than 650,000 AIDS patients worldwide each year. It is also a potentially deadly concern among chemotherapy and organ transplant patients. Currently, Cryptococcus causes more annual deaths in sub-Saharan Africa than tuberculosis. "While most healthy individuals are resistant to Cryptococcus infections, the fungus can cause deadly disease for those with already weak immune systems," said Dr. Nielsen. When inhaled, Cryptococcus can cause an infection in the lungs. This infection can spread to the brain and result in meningitis, an often-deadly inflammation of the brain and spine. Drs. Nielsen and Okagaki found that titan cells, or Cryptococcus cells ten to twenty times the size of a normal cell, are too large to be destroyed by the body's immune system. The researchers also found that the presence of titan cells can protect all Cryptococcus cells in the area, even the normal-sized Cryptococcus cells. "This tells us that titan cell formation is an important aspect of the interaction between the human/host and the organism that allows Cryptococcus to cause disease," said Dr. Nielsen.

DNA Replication Protein Also Has a Role in Mitosis and Cancer

The foundation of biological inheritance is DNA replication – a tightly coordinated process in which DNA is simultaneously copied at hundreds of thousands of different sites across the genome. If that copying mechanism doesn't work as it should, the result could be cells with missing or extra genetic material, a hallmark of the genomic instability seen in most birth defects and cancers. University of North Carolina (UNC) School of Medicine scientists have discovered that a protein known as Cdt1, which is required for DNA replication, also plays an important role in a later step of the cell cycle, mitosis. The finding presents a possible explanation for why so many cancers possess not just genomic instability, but also more or less than the usual 46 DNA-containing chromosomes. The new research, which was published online on May 13, 2012 in Nature Cell Biology, is the first to definitively show such a dual role for a DNA replication protein. "It was such a surprise, because we thought we knew what this protein's job was – to load proteins onto the DNA in preparation for replication," said Jean Cook, Ph.D., associate professor of biochemistry and biophysics and pharmacology at the UNC School of Medicine and senior study author. "We had no idea it also had a night job, in a completely separate part of the cell cycle." The cell cycle is the series of events that take place in a cell leading to its growth, replication and division into two daughter cells. It consists of four distinct phases: G1 (Gap 1), S (DNA synthesis), M (mitosis), and G2 (Gap 2). Dr. Cook's research focuses on G1, when Cdt1 places proteins onto the genetic material to get it ready to be copied. In this study, Dr. Cook ran a molecular screen to identify other proteins that Cdt1 might be interacting with inside the cell.

Genome Sequence of Widely Planted Foxtail Millet Completed

BGI, the world's largest genomics organization, in cooperation with Zhangjiakou Academy of Agricultural Science, has completed the genome sequence and analysis of foxtail millet (Setaria italica), the second-most widely planted species of millet. This study provides an invaluable resource for the study and genetic improvement of foxtail millet and millet crops at a genome-wide level. Results of the latest study were published online on May 13, 2012 in Nature Biotechnology. Foxtail millet is an important cereal crop providing food and feed in semi-arid areas. It is the top-one crop in ancient China. It promises to serve as an important model for comparative genomics and functional gene studies, due to its small genome size (~490M), self-pollination, rich genetic diversity (~6000 varieties), complete collection of germplasm, and the availability of efficient transformation platforms. It is also evolutionarily close to several important biofuel grasses, such as switchgrass and napier grass. "The lower yield of traditional cultivars has largely limited cultivation and utilization of foxtail millet," said Dr. Gengyun Zhang, Vice President of BGI. "Hybrid cultivars, recently developed by Professor Zhihai Zhao in Zhangjiakou Agricultural Academy of Science, doubled the yield of foxtail millet. I expect that the results of this study could set an example of applying the genome sequence to better understanding and quicker developing new varieties of a neglected crop with higher yield, better grain quality, and stress tolerance." In this study, researchers from BGI carried out next-generation sequencing and de novo assembly for "Zhang gu," one strain of foxtail millet from Northern China. The final genome assembly was 423 Mb, and 38,801 protein-coding genes have been predicted, of which ~81% were expressed.

May 23rd

Virus “Barcodes” Offer Rapid Detection of Mutated Strains

Dr. Julian Hiscox and Dr. John Barr of the University of Leeds’ Faculty of Biological Sciences are working with the Health Protection Agency (HPA) Porton to build a bank of molecular signatures that will help identify the severity of virus infection from characteristic changes seen in cells. Currently the team is barcoding different strains of influenza virus and human respiratory syncytial virus (HRSV) - a virus associated with the onset of asthma in young children. "Diseases such as flu infect and hijack our cells, turning them into virus-producing factories," says Dr. Hiscox. "The infection causes the balance of proteins in a cell to change - some proteins are overproduced and others suppressed. Which proteins are affected and by how much varies depending on the type of virus, allowing us to identify a unique barcode of disease for each." The research, published May 14, 2012 in Proteomics, investigates changes in lung cells infected with swine flu from the 2009 outbreak compared with seasonal flu. The team used a labeling technique called SILAC to measure and compare thousands of different proteins in a sample. This technique was used alongside mass spectrometry to identify the proteins most affected by viral infection and used these as molecular signatures to provide the “barcode” of disease. The paper reports how several processes in the cell were affected by the virus, with most changes seen in proteins involved in cell replication. "Swine flu affects the lungs in a similar way to seasonal flu and this was reflected in the barcodes we found for each," explains Dr. Barr. "Using this test might have been a way to identify how lethal the 2009 swine flu pandemic was going to be, lessening worldwide panic.

May 18th

San Francisco Personalized Medicine Conference 5.0 Will Focus on Epigenetics

The fifth annual Personalized Medicine Conference (5.0) hosted by San Francisco State University, this year with a focus on epigenetics, will be held on Thursday, May 24, 2012 from 8:00 am to 7:30 pm at the South San Francisco Conference Center. To view the conference website and to register for the conference, please go to http://personalizedmedicine.sfsu.edu/. Scheduled speakers include Michael Snyder, M.D., Ph.D., Chair/Director, Department of Genetics & Stanford Center for Genomics and Personalized Medicine, Stanford University; Brian Kennedy, Ph.D., CEO, Buck Institute for Age Research; Cristina Gentilini, Ph.D., Commercial Research Scientist, Swedish Biomimetics 3000; Jorge A. Leon, President/CEO, Leomics Associates, Inc.; and Stephen M. Anderson, Ph.D., CSO of Oncology and Genetics, LabCorp. The organizers note that epigenetics, or genetic changes above and beyond the DNA sequence level, have profound implications for personalized medicine, pharmacogenomics, aging, and oncology. While personalized medicine is poised to transform healthcare over the next several decades, it has become abundantly clear that the DNA sequence itself is only part of the story. The regulation of gene expression, and how it changes in health and disease, and in response to therapy, are crucial. The organizers invite you to attend this conference and learn the latest information on how epigenetics is and will be impacting personalized medicine. The conference will also be an excellent networking opportunity for health and industry professionals, educators, and scientists. Seating is limited, so register soon. Sponsors of the conference include Genentech, Celgene, LabCorp, and BioMarin, among many others. To obtain additional information concerning the conference, you may email the organizers at dnamed@sfsu.edu or telephone Arlene Essex at 415-405-4107.

May 18th

Rabies Evolution Rate in Bats Varies with Location

The rate at which the rabies virus evolves in bats may depend heavily upon the ecological traits of its hosts, according to researchers at the University of Georgia (UGA), the U.S. Centers for Disease Control and Prevention and Katholieke Universiteit (KU) Leuven in Belgium. Their study, published May 17, 2012 in PLoS Pathogens, found that the host's geographical location was the most accurate predictor of the viral rate of evolution. Rabies viruses in tropical and sub-tropical bat species evolved nearly four times faster than viral variants in bats in temperate regions. "Species that are widely distributed can have different behaviors in different geographical areas," said Dr. Daniel Streicker, a postdoctoral associate in the UGA Odum School of Ecology and the study's leader. "Bats in the tropics are active year-round, so more rabies virus transmission events occur per year. Viruses in hibernating bats, on the other hand, might lose up to six months' worth of opportunities for transmission." Understanding the relationship between host ecology and viral evolution rates could shed light on the transmission dynamics of other viruses, such as influenza, that occur across regions, infect multiple host species, or whose transmission dynamics are impacted by anthropogenic change. The team's findings could eventually help public health officials better predict when rabies virus transmission could happen in different environments and as environments change, but Dr. Streicker cautions that more research into the rabies virus genome and bats' overwintering ecology is needed. "If viral evolution is faster, it could potentially lead to greater genetic diversity in crucial parts of the viral genome that allow it to shift hosts," he said. "For rabies, we don't yet know what those are, so identifying them will be key.

Scientists Generate Electricity from Viruses

Imagine charging your phone as you walk, thanks to a paper-thin generator embedded in the sole of your shoe. This futuristic scenario is now a little closer to reality. Scientists from the U.S. Department of Energy's Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a way to generate power using harmless viruses that convert mechanical energy into electricity. The scientists tested their approach by creating a generator that produces enough current to operate a small liquid-crystal display. It works by tapping a finger on a postage stamp-sized electrode coated with specially engineered viruses. The viruses convert the force of the tap into an electric charge. This generator is the first to produce electricity by harnessing the piezoelectric properties of a biological material. Piezoelectricity is the accumulation of a charge in a solid in response to mechanical stress. The milestone could lead to tiny devices that harvest electrical energy from the vibrations of everyday tasks such as shutting a door or climbing stairs. It also points to a simpler way to make microelectronic devices. That's because the viruses arrange themselves into an orderly film that enables the generator to work. Self-assembly is a much-sought-after goal in the finicky world of nanotechnology. The scientists describe their work in an article published on May 13, 2012 in Nature Nanotechnology. "More research is needed, but our work is a promising first step toward the development of personal power generators, actuators for use in nano-devices, and other devices based on viral electronics," says Dr. Seung-Wuk Lee, a faculty scientist in Berkeley Lab's Physical Biosciences Division and a UC Berkeley associate professor of bioengineering. He conducted the research with a team that includes Dr.

Researchers Identify Key Genes and Prototype Predictive Test for Schizophrenia

An Indiana University (IU)-led research team, along with a group of national and international collaborators, has identified and prioritized a comprehensive group of genes most associated with schizophrenia that together can generate a score indicating whether an individual is at higher or lower risk of developing the disease. Using a convergent functional genomics approach that incorporates a variety of experimental techniques, the scientists were also able to apply a panel of their top genes to data from other studies of schizophrenia and successfully identify which patients had been diagnosed with schizophrenia and which had not, according to a report published online on May 15, 2012 by the journal Molecular Psychiatry. Evaluating the biological pathways in which the genes are active, the researchers also proposed a model of schizophrenia as a disease emerging from a mix of genetic variations affecting brain development and neuronal connections along with environmental factors, particularly stress. "At its core, schizophrenia is a disease of decreased cellular connectivity in the brain, precipitated by environmental stress during brain development, among those with genetic vulnerability," said principal investigator Alexander B. Niculescu III, M.D., Ph.D., associate professor of psychiatry and medical neuroscience at the IU School of Medicine and director of the Laboratory of Neurophenomics at the Institute of Psychiatric Research at the IU School of Medicine. "For first time we have a comprehensive list of the genes that have the best evidence for involvement in schizophrenia," said Dr. Niculescu, who is also staff psychiatrist and investigator at the Richard L. Roudebush Veterans Affairs Medical Center.

May 12th

San Francisco Personalized Medicine Conference 5.0 Will Focus on Epigenetics

The fifth annual Personalized Medicine Conference (5.0) hosted by San Francisco State University, this year with a focus on epigenetics, will be held on Thursday, May 24, 2012 from 8:00 am to 7:30 pm at the South San Francisco Conference Center. To view the conference website and to register for the conference, please go to http://personalizedmedicine.sfsu.edu/. Scheduled speakers include Michael Snyder, M.D., Ph.D., Chair/Director, Department of Genetics & Stanford Center for Genomics and Personalized Medicine, Stanford University; Brian Kennedy, Ph.D., CEO, Buck Institute for Age Research; Cristina Gentilini, Ph.D., Commercial Research Scientist, Swedish Biomimetics 3000; Jorge A. Leon, President/CEO, Leomics Associates, Inc.; and Stephen M. Anderson, Ph.D., CSO of Oncology and Genetics, LabCorp. The organizers note that epigenetics, or genetic changes above and beyond the DNA sequence level, have profound implications for personalized medicine, pharmacogenomics, aging, and oncology. While personalized medicine is poised to transform healthcare over the next several decades, it has become abundantly clear that the DNA sequence itself is only part of the story. The regulation of gene expression, and how it changes in health and disease, and in response to therapy, are crucial. The organizers invite you to attend this conference and learn the latest information on how epigenetics is and will be impacting personalized medicine. The conference will also be an excellent networking opportunity for health and industry professionals, educators, and scientists. Seating is limited, so register soon. Sponsors of the conference include Genentech, Celgene, LabCorp, and BioMarin, among many others. To obtain additional information concerning the conference, you may email the organizers at dnamed@sfsu.edu or telephone Arlene Essex at 415-405-4107.