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Archive - Feb 2014

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February 2nd

Same Protein Found Critical to Both Hematopoietic Stem Cell Function and Cancer Stem Cell Function

Researchers at the University of California, San Diego School of Medicine, and collaborating institutions have identified a protein critical to hematopoietic stem cell function and blood formation. The finding has potential as a new target for treating leukemia because cancer stem cells rely upon the same protein to regulate and sustain their growth. Hematopoietic stem cells give rise to all other blood cells. Writing in the February 2, 2014 advance online issue of Nature Genetics, principal investigator Tannishtha Reya, Ph.D., professor in the Department of Pharmacology, and colleagues found that a protein called Lis1 fundamentally regulates asymmetric division of hematopoietic stem cells, assuring that the stem cells correctly differentiate to provide an adequate, sustained supply of new blood cells. Asymmetric division occurs when a stem cell divides into two daughter cells of unequal inheritance: One daughter differentiates into a permanently specialized cell type while the other remains undifferentiated and capable of further divisions. "This process is very important for the proper generation of all the cells needed for the development and function of many normal tissues," said Dr. Reya. When cells divide, Lis1 controls orientation of the mitotic spindle, an apparatus of subcellular fibers that segregates chromosomes during cell division. "During division, the spindle is attached to a particular point on the cell membrane, which also determines the axis along which the cell will divide," Dr. Reya said. "Because proteins are not evenly distributed throughout the cell, the axis of division, in turn, determines the types and amounts of proteins that get distributed to each daughter cell. By analogy, imagine the difference between cutting the Earth along the equator versus halving it longitudinally.

A Cheaper, Faster, and Reliable Way to Detect Staph Infections in Under an Hour

Chances are you won't know you've have a staph infection until the test results come in, days after the symptoms first appear. But what if your physician could identify the infection much more quickly and without having to take a biopsy and ship it off for analysis? Researchers at the University of Iowa (UI) may have found a way to do this. The team has created a noninvasive chemical probe that detects a common species of staph bacteria in the body. The probe ingeniously takes advantage of staph's propensity to slash and tear at DNA, activating a beacon of sorts that lets doctors know where the bacteria are wreaking havoc. "We've come up with a new way to detect staph bacteria that takes less time than current diagnostic approaches," says Dr. James McNamara, assistant professor in internal medicine at the UI and the corresponding author of the paper published online on February 2, 2014 in Nature Medicine. "It builds on technology that's been around a long time, but with an important twist that allows our probe to be more specific and to last longer." The UI-developed probe targets Staphylococcus aureus, a species of staph bacteria common in hospitals and found in the general public as well. The bacteria causes skin infections, can spread to the joints and bones and can be fatal, particularly to those with weakened immune systems. "Every year in the U.S., half a million people become infected by S. aureusbacteria, and 20,000 of those who become infected die," adds Dr. Frank Hernandez, a post-doctoral researcher at the UI and first author on the paper.

Brain-Driven Prostheses Research Identifies Process by Which Brain Regions Can Cooperate When Necessary

Stanford researchers may have solved a riddle about the inner workings of the brain, which consists of billions of neurons, organized into many different regions, with each region primarily responsible for different tasks. The various regions of the brain often work independently, relying on the neurons inside that region to do their work. At other times, however, two regions must cooperate to accomplish the task at hand. The riddle is this: what mechanism allows two brain regions to communicate when they need to cooperate yet avoid interfering with one another when they must work alone? In a paper published online on February 2, 2014 in Nature Neuroscience, a team led by Stanford electrical engineering professor Dr. Krishna Shenoy reveals a previously unknown process that helps two brain regions cooperate when joint action is required to perform a task. "This is among the first mechanisms reported in the literature for letting brain areas process information continuously but only communicate what they need to," said Dr. Matthew T. Kaufman, who was a postdoctoral scholar in the Shenoy lab when he co-authored the paper. Dr. Kaufman initially designed his experiments to study how preparation helps the brain make fast and accurate movements – something that is central to the Shenoy lab's efforts to build prosthetic devices controlled by the brain. But the Stanford researchers used a new approach to examine their data that yielded some findings that were broader than arm movements. The Shenoy lab has been done pioneering work in analyzing how large numbers of neurons function as a unit. As they applied these new techniques to study arm movements, the researchers discovered a way that different regions of the brain keep results localized or broadcast signals to recruit other regions as needed.

Japanese Company Releases Data Indicating Fundamental Advance in Single-Molecule DNA and RNA Sequencing

On January 27, 2014, Quantum Biosystems, Inc., headquartered in Osaka, Japan, announced the release of raw data access to the first reads from its novel platform for electrical single-molecule DNA and RNA sequencing. The company released reads showing an accuracy of more than 99% in non-homopolymer regions and homopolymer indels at a rate of ~10%. This release allows researchers to evaluate the platform and engage in its validation and development. According to the company, this marks a major milestone in the single-molecule electrical sequencing of DNA. The work reported by Quantum Biosystems was completed using its breakthrough novel Quantum Sequencing platform (image). The platform allows the direct sequencing of single-stranded DNA and RNA without labeling or modification, on silicon devices that can be produced on the same production lines as consumer-grade integrated circuits. As the system uses no proteins or other reagents, it is potentially ultra-low cost, enabling consumer-level genome sequencing, according to the company. Based on research conducted at the University of Osaka, the Quantum Biosystems platform uses sub-nanometer gaps and picoamp-level currents to directly detect the conductance of single DNA and RNA molecules. This breakthrough in molecular sensing promises to bring about a fundamentally new class of sensors. Quantum Biosystems was formed in January of 2013 and is developing 4th-generation DNA and RNA sequencing systems for the low-cost and high-throughput analysis of whole genomes. While present systems require complicated sample preparation, and costly instruments, the Quantum Biosystems platform has no such barriers to entry and is well-positioned to bring about what some have called “the democratization of DNA sequencing,” Quantum Biosystems asserts.

January 31st

TCGA Study Identifies Potential Therapeutic Targets for Bladder Cancer

Investigators with The Cancer Genome Atlas (TCGA) Research Network have identified new potential therapeutic targets for a major form of bladder cancer, including important genes and pathways that are disrupted in the disease. They also discovered that, at the molecular level, some subtypes of bladder cancer – also known as urothelial carcinoma – resemble subtypes of breast, head and neck, and lung cancers, suggesting similar routes of development. The researchers' findings provide important insights into the mechanisms underlying bladder cancer, which is estimated will cause more than 15,000 deaths in the United States in 2014. TCGA is a collaboration jointly supported and managed by the National Cancer Institute (NCI) and the National Human Genome Research Institute (NHGRI), both parts of the National Institutes of Health. "TCGA Research Network scientists continue to unravel the genomic intricacies of many common and often intractable cancers, and these findings are defining new research directions and accelerating the development of new cancer therapies," said NIH Director Francis Collins, M.D., Ph.D. In this study, published online on January 29, 2014 in an open-access article in Nature, investigators examined bladder cancer that invades the muscle of the bladder, the deadliest form of the disease. The current standard treatments for muscle-invasive bladder cancer include surgery and radiation combined with chemotherapy. There are no recognized second-line therapies – second choices for treatments when the initial therapy does not work – and no approved targeted agents for this type of bladder cancer. Approximately 72,000 new cases of bladder cancer will be diagnosed in the United States in 2014.