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Biomed Bites, Research, Technology, Videos

Decoding proteins using your very own super computer

Decoding proteins using your very own super computer


Welcome to the latest edition of Biomed Bites, a weekly feature that introduces readers to some of Stanford’s most innovative researchers. 

A quick review: DNA codes for RNA, which directs the formation of proteins, the body’s teensy building blocks and messengers. But like individual widgets, proteins still aren’t ready for prime time as soon as they pop off the assembly line.

First they must be folded, partnered with other proteins and crafted into a three-dimensional shapes. Then, they can go about the work of life.

Stanford biochemist Vijay Pande, PhD, has been studying proteins for quite some time, and early on he realized that experimentally, proteins aren’t that easy to examine. They’re small and they rely on precise environmental cues. Once stripped from the cell, proteins behave and assemble differently, perhaps even not at all.

“So we take a very different approach,” Pande says in the video above:

We’ve been pioneering new simulation methods to not just be able to look at the problem experimentally, but to use large-scale computer simulations to understand why proteins would fold correctly, or why they would not fold correctly such as in the case with disease.

By using a very unusual approach where we get people around the world to donate computer time to us, we assembled the most powerful supercomputer in the world to tackle problems like protein folding and protein misfolding.

More than 183,000 computers now contribute to Pande’s project, Folding@home. Perhaps yours will be 183,001.

Learn more about Stanford Medicine’s Biomedical Innovation Initiative and about other faculty leaders who are driving biomedical innovation here.

Previously: Using a smartphone and the Folding@home app to advance disease research, What computation tells us about how our bodies work and Nobel winner Michael Levitt’s work animates biological processes

Autoimmune Disease, Chronic Disease, Immunology, Stanford News, Videos

Chronic fatigue syndrome gets more respect (and a new name)

Chronic fatigue syndrome gets more respect (and a new name)

As has been widely reported, an Institute of Medicine (IOM) report released yesterday acknowledged that chronic fatigue syndrome is a real and serious disease and renamed the disorder “systemic exertion intolerance disease” to better reflect its key symptoms.

Stanford professor José Montoya, MD, who served as a reviewer on the IOM report, is featured in the video above, which accompanied Washington Post coverage of the development. The Post article goes on to say:

“We just needed to put to rest, once and for all, the idea that this is just psychosomatic or that people were making this up, or that they were just lazy,” said Ellen Wright Clayton, a professor of pediatrics and law at Vanderbilt University, who chaired the committee of the Institute of Medicine, the health arm of the National Academy of Sciences.

Although the cause of the disorder is still unknown, the panel established three critical symptoms for the condition (also known as myalgic encephalomyelitis):

  • A sharp reduction in the ability to engage in pre-illness activity levels that lasts for more than six months and is accompanied by deep fatigue that only recently developed.
  • Worsening of symptoms after any type of exertion, including “physical, cognitive or emotional stress.”
  • Sleep that doesn’t refresh the sufferer.

The panel also requires that a patient have one of two other disease manifestations, either cognitive impairment or orthostatic intolerance. Orthostatic intolerance is an autonomic nervous system disorder that is caused by an abnormal increase in heart rate and low blood pressure, believed to be triggered by the disease.

Susan Kruetzer, an SEID patient interviewed by Erin Allday in this San Francisico Chronicle article, expressed guarded optimism about the report’s ability to generate more research funding and patient support, saying “What I want to see is someone in Congress get pretty riled up by this report — have them see how many people are affected, how these people are really ill, how they’ve been mistreated,” Kreutzer said. “I’d just like to light a fire. I don’t know if this report will do that, but I suppose it gives us some ammunition.”

Previously: Some headway on chronic fatigue syndrome: Brain abnormalities pinpointed, Unbroken: A chronic fatigue syndrome patient’s long road to recovery and Deciphering the puzzle of chronic fatigue syndrome

Cardiovascular Medicine, Stanford News, Videos

C’mon, be heart healthy

C'mon, be heart healthy

Is your heart healthy? Are you at risk for heart disease? In recognition of American Heart Month, Stanford Health Care has launched a campaign to help people find the answers to those questions. The interactive video above, and this Q&A on preventing heart disease, are good places to start.

Previously: Lack of exercise shown to have largest impact on heart disease risk for women over 30, Mysteries of the heart: Stanford Medicine magazine answers cardiovascular questions, Ask Stanford Med: Answers to your questions about heart health and cardiovascular research, Either you’re a woman or you know one: Help spread the message of women’s heart health and Why some healthy-looking young adults may still be at risk for heart disease

Addiction, Obesity, Science, Videos

Discussing how obesity and addiction share common neurochemistry

Discussing how obesity and addiction share common neurochemistry

In a TEDMED talk published last week, renowned neuroscientist Nora Volkow, MD, discusses using insights from her research on drug addiction and brain chemistry to better understand the obesity epidemic.

Volkow, who directs the National Institute on Drug Abuse at the NIH, thought compulsive drug-taking behavior seemed remarkably similar to not being able to control what one eats. And indeed, with the help of PET scans that image living human brains, she found that the brain chemistry behind these two stigmatized problems is very similar.

The problem has to do with fewer dopamine D2 receptors; in her words, that’s “the biochemical signature of a brain where the capacity to control strong urges has been compromised.” She goes on to talk about such things as pleasurable stimuli versus conditioned stimuli, deprivation states, and how modern society could engineer environments that encourage health.

Volkow ends on a sociological note, challenging the moralizing idea that addiction and obesity indicate a failure to self-regulate:

Dismissal of addiction and obesity as just problems of self-control ignores the fact that for us to be able to exert self-control would require the proper function of the areas in our brains that regulate our behaviors… It’s like driving a car without brakes. No matter how much you want to stop, you will not be able to do it.

Previously: How eating motivated by pleasure affects the brain’s reward system and my fuel obesity; The brain’s control tower for pleasure; New tools from NIDA help diagnose and treat drug abuse

Global Health, Media, Patient Care, Pediatrics, Research, Technology, Videos

OPENPediatrics offers opportunity to help physicians, and sick children, worldwide

OPENPediatrics offers opportunity to help physicians, and sick children, worldwide

6948764580_97d353e8d4_zAs chief of critical care at Boston Children’s Hospital, Jeffrey Burns, MD, MPH, was asked to consult on the case of a young girl who fell ill while vacationing with her family in Guatemala. He had treated a similar case in the U.S. before, but he encountered unexpected technological hurdles.

That spurred Burns — working with many partners, including IBM — to create OPENPediatrics.org, a platform that allows physicians to share skills and resources to treat sick children. Burns described his hopes for the site in a 2014 article in Medtech Boston:

Our goal was to create something called a community of practice where instead of being broad and thin like a MOOC (Massive Open Online Classes), we would be narrow and much more deep, and the content would actually be peer reviewed by doctors and nurses who care for critically ill children, because those are essentially our primary users,” Burns says.

The site, which launched last year, offers forums for health-care workers worldwide to share experiences and a multimedia library with videos and animations — including some interactive features — on everything from nasopharyngeal suctioning to Faciltating Parent Presence During Invasive Procedures.

Burns and his team have been thinking how to leverage the platform to support research.

(A confession: I learned about OPENPediatrics through an article in Wesleyan magazine. Stanford’s Cardinal brethren on the East Coast, Wes, like Stanford fosters interdisciplinary projects and, I’m proud to say, is the alma mater of two of us in the medical school’s relatively small Office of Communication.)

Previously: Stanford undergrad works to redistribute unused medications and reduce health-care costs, Stanford Medicine X: From an “annual meeting to a global movement”  and Euan Ashley discusses harnessing big data to drive innovation for a healthier world
Photo by Intel Free Press

Big data, NIH, Research, Videos

Fly through the inside of a mouse lung

Fly through the inside of a mouse lung

Take a 50-second ride through the inside of an adult mouse lung in this video created by Rex Moats, PhD, scientific director at Children’s Hospital Los Angeles. A post published today on the NIH Director’s Blog describes the animation and points out that the video is a prime example of how scientists are using big data to make biomedical research more accessible to the public:

We begin at the top in the main pipeline, called the bronchus, just below the trachea and wind through a system of increasingly narrow tubes. As you zoom through the airways, take note of the cilia (seen as goldish streaks); these tiny, hair-like structures move dust, germs, and mucus from smaller air passages to larger ones. Our quick trip concludes with a look into the alveoli — the air sacs where oxygen is delivered to red blood cells and carbon dioxide is removed and exhaled.

… [Moats] created this virtual bronchoscopy from micro-computed tomography scans, which use X-rays to create a 3D image. The work demonstrates the power of converting Big Data (in this case, several billion data points) into an animation that makes the complex anatomy of a mammalian lung accessible to everyone.

Speaking of the power of big data, the Big Data in Biomedicine conference returns to Stanford May 20-22. For more information about the program or to register visit the conference website.

Previously: Big data = big finds: Clinical trial for deadly lung cancer launched by Stanford study and Peering deeply – and quite literally – into the intact brain: A video fly-through

Biomed Bites, Mental Health, Neuroscience, Research, Videos

A visual deluge may provide clues to ADHD treatment

A visual deluge may provide clues to ADHD treatment

It’s time for Biomed Bites, a weekly feature that introduces readers to some of Stanford’s most innovative researchers.

Looking out my window, I see a man dressed in red sweats on a bike. There’s my neighbor’s white truck parked in the street. A tree just starting to bud. A fire hydrant. A woman fertilizing roses. Closer, there’s my grey-and-white cat, Grizzly, bathing in the sun. My glass of ice water. My phone. Scattered papers.

And that’s probably only one-thousandth of the things I see right now. (I didn’t even mention the computer.) How do I make sense of that visual onslaught? How do I navigate, perceive threats, respond to changing conditions?

Well, that’s part of the puzzle Stanford neurobiologist Tirin Moore, PhD, is working to figure out.

“I’m a systems-level neurobiologist, which means I study how networks of neurons combine to either process sensory information or to control complex behaviors,” Moore explains in the video above.

How do we filter out what’s important – seeing the dog darting across the street in front of our car, but not focusing on the bird in the tree?

This process is most obvious when it breaks down, such as in patients with Attention Deficit Hyperactivity Disorder, or other attention disorders that affect from 3 to 8 percent of the population, Moore said:

At present, disorders such as ADHD are treatable, but their underlying neural basis is still very much a mystery… Our hope is that by understanding disorders of attention at the level of the neurocircuitry we will be able to arrive at more effective treatments…

Stay tuned to see what he, and his team, figures out.

Learn more about Stanford Medicine’s Biomedical Innovation Initiative and about other faculty leaders who are driving biomedical innovation here.

Aging, Neuroscience, Stanford News, Stroke, Videos

Bio-X undergraduate student finds direction through research

Bio-X undergraduate student finds direction through research

Richie Sapp arrived to Stanford as an undergraduate already interested in studying neuroscience. After talking with several faculty members, he ended up working in the lab of Carla Shatz, PhD, director of Stanford Bio-X.

I interviewed Sapp recently for a series of stories I was working on about undergraduate research opportunities at Stanford. He had participated in a terrific summer program run by Bio-X. I was struck by a few things when we talked, one of which was Sapp’s sincere interest in helping people. He had grown up with a twin brother who had been born with hydrocephaly and as a result had learning delays and is on the autism spectrum. That experience shaped his interest in helping people with similar challenges.

Sapp said that through his experience in the lab he got more out of his undergraduate classes and learned a lot about where he wants to go with his life. He loves the research and discovery, but also wants to go the medical school before pursuing research. Without the experience provided by the Bio-X summer program he might not have known which direction to go.

“The experience of designing experiments and seeing a project through to the end is going to be important for me in whatever I do next,” he said.

Here is the full profile about Sapp, with more about his research experiences.

Previously: Drug helps old brains learn new tricks, and heal

Behavioral Science, Complementary Medicine, Neuroscience, Videos

This is your brain on meditation

This is your brain on meditation

For years, friends have been telling me I should try meditation. I’m embarrassed to admit it’s mostly because of (how can I put this delicately?) a temper that flares when I’m anxious or stressed out. But, as it is for many people, it’s one of those things I haven’t gotten around to. This video by AsapSCIENCE, though, describing the things scientists have discovered about meditators has me thinking about it again.

Meditation is linked to a decreased anxiety and depression, and increased pain tolerance. Your brain tunes out the outer world during meditation, and on brain scans of meditators, scientists can see increased activity in default mode network – which is associated with better memory, goal setting, and self-awareness. The part of the brain that controls empathy has also been shown to be more pronounced in monks who are long-time meditators. From the video:

“[Meditation] also literally changes your brain waves, and we can measure these frequencies. Medidators have higher levels of alpha waves, which have been shown to reduce feelings of negative mood, tension, sadness and anger.”

Much like hitting the gym can grow your muscles and increase your overall health, it seems that meditation may be a way of working out your brain—with extra health benefits.”

Other demonstrated benefits include better heart rate variability and immune system function. I’m glossing over a lot of the information that’s packed into this entertaining little video, but if you’re curious, check out this less-than-three-minute video yourself.

Previously: Study shows benefits of breathing meditation among veterans with PTSDResearch brings meditation’s health benefits into focusUsing meditation to train the brainCan exercise and meditation prevent cold and flu? and How meditation can influence gene activity
Video by AsapSCIENCE

Applied Biotechnology, Biomed Bites, Genetics, History, Research, Videos

Basic research underlies effort to thwart “greatest threat to face humanity”

Basic research underlies effort to thwart "greatest threat to face humanity"

Welcome to this week’s Biomed Bites, a weekly feature that introduces readers to Stanford’s most innovative researchers. 

Stanley Cohen, MD, isn’t a household name. But it probably should be. The Stanford geneticist was instrumental in the discovery of DNA cloning – the technology that underlies innumerable advances in biotechnology and medicine, and led to the founding of biotech giant Genentech.

It wasn’t always thought possible to snip out a gene, stitch it into a new stretch of DNA – often in a different organism – and have it produce a desired protein.

In the video above, Cohen emphasizes that striving to achieve a concrete – and profitable – goal didn’t enable the discovery of gene cloning. First, researchers had to work to understand the basic biological processes. “In order to apply knowledge, it’s necessary to get that knowledge somehow.”

These days, Cohen isn’t resting on his laurels. Instead, he’s striving to thwart what he considers perhaps the “greatest threat to humanity,” drug-resistent microbes.

“My lab is still interested in understanding microbial drug resistance and the way in which microbes exploit host genes to carry out microbial functions such as entering cells, reproducing in cells and exiting from cells,” he said. Scientists need that basic knowledge to develop strategies to thwart the process, he added.

Learn more about Stanford Medicine’s Biomedical Innovation Initiative and about other faculty leaders who are driving biomedical innovation here.

Previously: The history of biotech in seven bite-sized chunks, The dawn of DNA cloning: Reflections on the 40th anniversary and Why basic research is the venture capital of the biomedical world

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