Welcome to the biweekly electronic newsletter from Stanford Bio-X for members of the Bio-X Corporate Forum. Please contact us if you would like to be added or removed from this distribution list, or if you have any questions about Stanford Bio-X or Stanford University.

Obama's $100 million brain research initiative taps several Stanford scientists

President Barack Obama announced [on April 2nd] a bold research initiative aimed at developing new technologies and methods for understanding the human brain. Several Stanford scientists will play critical roles in the Brain Research through Advancing Innovative Neurotechnologies, or BRAIN, project, which calls for initial funding of $100 million. "As humans we can identify galaxies light-years away," Obama said at a White House ceremony. "We can study particles smaller than an atom, but we still haven't unlocked the mystery of the three pounds of matter that sits between our ears." The challenge of filling this knowledge gap is significant: The BRAIN initiative has the incredibly ambitious task of mapping the brain's roughly 100 billion neurons and the trillions of connections between them and then determining how signals pass between these neural circuits and how that process is controlled. (To read more about this, please click here.)

Bill Newsome to lead new interdisciplinary neuroscience institute

William Newsome, PhD, a professor of neurobiology, has been appointed to direct Stanford's new interdisciplinary neuroscience institute. The campus-wide brain research initiative will catalyze new interdisciplinary collaborations at the boundaries of neuroscience and a broad array of disciplines. "The study of the brain is no longer, if it ever was, just a problem of biology," said Newsome, who recently was appointed the Harman Family Provostial Professor. "Traditionally trained biologists, like myself, are generating massive new data sets made possible by new technologies, but we frequently don't know the best way to analyze them." He continued: "We need theoreticians trained in applied physics, statistics and engineering to help understand what the data mean, and we need molecular biologists and geneticists to contribute even more tools for precise manipulation of neural circuits. Newsome is also the director of the Bio-X NeuroVentures program. On April 2, he was enlisted to co-lead the working group for President Obama's $100 million BRAIN initiative, which also will seek interdisciplinary solutions to unraveling the mysteries of the brain. ... The new institute, which will be incubated in Bio-X's Clark Center, will seek to attract new faculty — the "glue people" Newsome describes as having a foot in neuroscience while coming from another discipline — in order to catalyze novel interactions between current faculty and make new and different science possible. Another major focus will involve raising funds to support young researchers, specifically graduate students and postdoctoral fellows who may already have a degree or PhD in a relevant discipline but want to learn neuroscience. (To read more about this, please click here.)

Seed Grant Program

SEED GRANTS FOR SUCCESS - Stanford Bio-X Interdisciplinary Initiatives Program (IIP)

The Bio-X Interdisciplinary Initiatives Program represents a key Stanford Initiative to address challenges in human health. The IIP awards approximately $3 million every other year in the form of two-year grants averaging about $150,000 each. From its inception in 2000 through the fifth round in 2010, the program has provided critical early-stage funding to 114 different interdisciplinary projects, involving collaborations from over 300 faculty members, and creating over 450 teams from five different Stanford schools. From just the first 4 rounds, the IIP awards have resulted in a 10-fold-plus return on investment, as well as hundreds of publications, dozens of patents filed, and most importantly, the acceleration of scientific discovery and innovation.

In 2012, Stanford Bio-X selected 23 new seed grant projects as the winners of the 6th round. Please go here to view the list of awardees, along with the titles of their projects and the abstracts of the research. Competition was intense as the awardees were chosen from 118 Letters of Intent (LOIs). Selection criteria included innovation, high-reward, and interdisciplinary collaboration. (To view the 114 other IIP projects that have been funded from the first 5 rounds, please click here.) In addition, SANOFI has also funded 4 new Bio-X IIP Seed Grant projects from round 6!

** On February 25, 2013, Stanford Bio-X held its latest annual IIP Seed Grant Symposium at the Clark Center. It was attended by over 150 people, and the symposium included 8 podium presentations and 116 poster presentations. The podium talks represented research from a wide array of fields (such as gene delivery to interactive gaming in biology to tele-robotic systems to stem cells to hedgehog signal transductions and more), with each project exemplifying the Stanford Bio-X mission of crossing boundaries to bring about interdisciplinary research and solutions in the field of life bioscience. The talks will be posted online shortly for viewing. To view previously recorded talks, please go here.

We are cultivating and are highly successful in building meaningful collaborations with numerous corporate colleagues. New collaborations through our seed grant projects are highly encouraged. To learn about how to get involved, please contact Dr. Hanwei Li or Dr. Heideh Fattaey.

Fellowships

BIO-X FELLOWSHIPS

Every year, graduate students and postdoctoral scholars of Bio-X affiliated faculty are highly encouraged to apply for the Bio-X Fellowships, which are awarded to research projects that are interdisciplinary and utilize the technologies of different fields to solve different biological questions. Students are encouraged to work collaboratively with professors of different departments, thus creating cross-disciplinary relationships among the different Stanford schools. Our fellows have conducted exciting research, resulting in publications in high-impact journals and have been offered excellent positions in industry and academia.

To date, Stanford Bio-X has a total of 126 Bio-X Fellows, including the 18 newest Fellowship awardees announced at last year's BIO-X FELLOWS SYMPOSIUM. Currently, Bio-X is in the process of reviewing its 10th year of applications and we look forward to continuing the support of our students' graduate training in interdisciplinary biosciences.

To view the numerous projects that have been awarded over the years, please click here.

BIO-X UNDERGRADUATE SUMMER RESEARCH PROGRAM

The Bio-X Undergraduate Summer Research Program supports undergraduate research training through an award designed to support interdisciplinary undergraduate summer research projects. The program is an invaluable opportunity for students to conduct hands-on research, learn how to carry out experiments in the laboratory, and develop the skills to read and analyze scientific literature.

To date, 176 students have been awarded the opportunity to participate in the Bio-X Undergraduate Summer Research Program. Currently, Stanford Bio-X is in its 8th call for applications. This is eligible to Stanford students who wants to work in the labs of Bio-X affiliate faculty.

Participating undergraduates are also required to present poster presentations on the research that they've conducted during the program. Please click here for title lists of past posters that our undergraduates have presented.

Many fruitful collaborations and relationships have been established with industry through fellowships. Please contact Dr. Hanwei Li or Dr. Heideh Fattaey if you'd like to learn more about how to get involved with these fellowship programs.

News

How an interdisciplinary chef cooked up imaging technique
Bio-X Affiliated Faculty Adam de la Zerda, also former Bio-X Fellow

When Adam de la Zerda commuted home from his postdoctoral chemistry work at UC-Berkeley, he often stopped at a French restaurant in San Mateo. But he didn't join the other diners. Instead, he headed for the kitchen where he swapped his lab books for cookbooks and stood in as a sous chef. "There's a lot of chemistry in cooking," said de la Zerda. His favorite culinary creation was quail eggs and caviar, with the eggs cooked "sous vide" style, a technique that vacuum-seals food in bags and then slow cooks the meal in water. In consultation with the chef, de la Zerda perfected the dish by calculating tissue deterioration rates to find the ideal incubation time. Managing a spot as a sometime-sous chef isn't anyone's typical pastime, but it's characteristic of de la Zerda. The 28-year-old faculty member, recently appointed an assistant professor in the Department of Structural Biology, has a passion for interdisciplinary pursuits. Originally from Israel, de la Zerda was "dead set" on getting his degree in theoretical quantum physics when he applied for graduate school in electrical engineering at Stanford. That was the logical next step after an undergraduate focus on computer engineering and physics. But, when he saw an engineering friend choose an adviser from the Music Department, de la Zerda suddenly appreciated he was at a university that didn't dwell on departmental divisions. "When I realized that, I thought: 'What else can I do?'" Spurred by the loss of a good friend to cancer, de la Zerda wanted to improve treatment strategies. ... To explore new solutions, de la Zerda joined the lab of Sam Gambhir, MD, PhD, professor and chair of radiology and director of the Molecular Imaging Program at Stanford. There, he developed and patented a technology named photoacoustic molecular imaging under the guidance of Gambhir and in collaboration with Pierre Khuri-Yakub, PhD, professor of electrical engineering. ... "Stanford is a very unique place as people do not classify you only for your accomplishments, but also for where your passion is," he said. "It's almost a mission" to tell other students to reach beyond what they think they know, he added. "I want them to know the sky's the limit here." Although he's only been on the Stanford faculty since August, de la Zerda's wide-ranging efforts have garnered numerous awards. Most recently, he was listed in Forbes magazine "30 under 30" in science and health care and received the Dale F. Frey Award from the Damon Runyon Cancer Research Foundation, as well as the Director's Early Independence Award from the National Institutes of Health.

Getting CLARITY: Hydrogel process developed at Stanford creates transparent brain
Bio-X Affiliated Faculty Karl Deisseroth

Combining neuroscience and chemical engineering, researchers at Stanford University have developed a process that renders a mouse brain transparent. The postmortem brain remains whole — not sliced or sectioned in any way — with its three-dimensional complexity of fine wiring and molecular structures completely intact and able to be measured and probed at will with visible light and chemicals. The process, called CLARITY, ushers in an entirely new era of whole-organ imaging that stands to fundamentally change our scientific understanding of the most-important-but-least-understood of organs, the brain, and potentially other organs, as well. The process is described in a paper published online April 10 in Nature by bioengineer and psychiatrist Karl Deisseroth, MD, PhD, leading a multidisciplinary team, including postdoctoral scholar Kwanghun Chung, PhD. "Studying intact systems with this sort of molecular resolution and global scope — to be able to see the fine detail and the big picture at the same time — has been a major unmet goal in biology, and a goal that CLARITY begins to address," Deisseroth said. "This feat of chemical engineering promises to transform the way we study the brain's anatomy and how disease changes it," said Thomas Insel, MD, director of the National Institute of Mental Health. "No longer will the in-depth study of our most important three-dimensional organ be constrained by two-dimensional methods."

Accused of complicity in Alzheimer’s, amyloid proteins may be getting a bad rap, study finds
Bio-X Affiliated Faculty Lawrence Steinman

Amyloids — clumps of misfolded proteins found in the brains of people with Alzheimer’s disease and other neurodegenerative disorders — are the quintessential bad boys of neurobiology. They’re thought to muck up the seamless workings of the neurons responsible for memory and movement, and researchers around the world have devoted themselves to devising ways of blocking their production or accumulation in humans. But now a pair of recent research studies from the Stanford University School of Medicine sets a solid course toward rehabilitating the reputation of the proteins that form these amyloid tangles, or plaques. In the process, they appear poised to turn the field of neurobiology on its head. The first study, published in August, showed that an amyloid-forming protein called beta amyloid, which is strongly implicated in Alzheimer’s disease, could reverse the symptoms of a multiple-sclerosis-like neurodegenerative disease in laboratory mice. The second study, published April 3 in Science Translational Medicine, extends the finding to show that small portions of several notorious amyloid-forming proteins (including well-known culprits like tau and prion proteins) can also quickly alleviate symptoms in mice with the condition — despite the fact that the fragments can and do form the long tendrils, or fibrils, previously thought harmful to nerve health.

Mining information contained in clinical notes could yield early signs of harmful drug reactions, study shows
Bio-X Affiliated Faculty Nigam Shah

Mining the records of routine interactions between patients and their care providers can detect drug side effects a couple of years before an official alert from the U.S. Food and Drug Administration, a Stanford University School of Medicine study has found. The study, led by Nigam Shah, MBBS, PhD, assistant professor of medicine, was published online April 10 in Nature Clinical Pharmacology and Therapeutics. This approach is a step forward in mining patient-based information, as opposed to coded insurance reports or drug-specific databases, to improve health-care strategies, said engineering research associate Paea LePendu, PhD, the lead author of the paper. The technique is intended to complement the FDA’s Adverse Event Reporting System, which has compiled reports of medication side effects from patients, physicians and pharmaceutical manufacturers since 1968. Clinical notes include the information a caregiver dictates into a patient’s record, such as the patient’s symptoms or medical issues. It would also include what a doctor advises or prescribes for the patient. “If you ask any audience related to health care how much of the clinical knowledge is bundled up in text, you won’t get an answer below 70 percent,” said Shah. “If 70 to 80 percent of the data is locked up in text notes, we asked ourselves, ‘What would be a good way to unlock it?’” Their approach builds on recently published work that developed a gold standard for assessing the performance of data-mining methods.

Researchers turn skin cells directly into the cells that insulate neurons
Bio-X Affiliated Faculty Marius Wernig

Researchers at the Stanford University School of Medicine have succeeded in transforming skin cells directly into oligodendrocyte precursor cells, the cells that wrap nerve cells in the insulating myelin sheaths that help nerve signals propagate. The current research was done in mice and rats. If the approach also works with human cells, it could eventually lead to cell therapies for diseases like inherited leukodystrophies — disorders of the brain’s white matter — and multiple sclerosis, as well as spinal cord injuries. The study was published online April 14 in Nature Biotechnology. Without myelin to insulate neurons, signals sent down nerve cell axons quickly lose power. Diseases that attack myelin, such as multiple sclerosis, result in nerve signals that are not as efficient and cannot travel as far as they should. Myelin disorders can affect nerve signal transmission in the brain and spinal cord, leading to cognitive, motor and sensory problems. Previous research in rodent disease models has shown that transplanted oligodendrocyte precursor cells derived from embryonic stem cells and from human fetal brain tissue can successfully create myelin sheaths around nerve cells, sometimes leading to dramatic improvements in symptoms. “Unfortunately, the availability of human fetal tissue is extremely limited, and the creation of OPCs from embryonic stem cells is slow and tedious,” said the study’s senior author, Marius Wernig, MD, assistant professor of pathology and a member of Stanford’s Institute for Stem Cell Biology and Regenerative Medicine. “It appeared we wouldn’t be able to create enough human OPCs for widespread therapeutic use, so we began to wonder if we could create them directly from skin cells.”

Events

Resources

To learn more about Stanford Bio-X or Stanford University, please contact Dr. Hanwei Li, the Bio-X Corporate Forum Liaison, at 650-725-1523 or lhanwei1@stanford.edu, or Dr. Heideh Fattaey, the Executive Director of Bio-X Operations and Programs, at 650-799-1608 or hfattaey@stanford.edu.