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Podcasts, Science, Stanford News

Goggles Optional: Stanford podcast aims to “influence the culture of how science is viewed”

Goggles Optional: Stanford podcast aims to “influence the culture of how science is viewed"

BiggishGogglesCommunicating science to a non-specialist audience is an art. Or is it a science? David Zhang, PhD, a postdoctoral research fellow in immunology and rheumatology, and colleagues bring some of each to Goggles Optional, a lively podcast series produced by Stanford scientists to capture’s the public’s interest in research.

Since November 2013, Zhang and the rest of the Goggles Optional team, made up of postdocs and grad students, have recorded a weekly audio program featuring news, research headlines, expert guest speakers, game-show antics and songs, all exploring the latest, most significant and/or weirdest happenings in the field. (You can check out the full list of free podcasts on their website here or download them from iTunes.)

The 13 episodes so far have covered science news from stem cells to staph infections and explored civilian-interest questions such as why we sleep. With more than 7,000 downloads so far, Goggles Optional will expand to include conversations with industry leaders in science. Zhang notes that when spotlighting research, Goggles Optional interviews the first author of a paper to give listeners the perspective from “inside the trenches” and provide grad students and postdocs an opportunity to talk about their work.

Thirteen members strong, the Goggles Optional team includes writers, hosts, a social media specialist and a webmaster. (For a good read, scroll through their bios.) All those involved volunteer their time.

How can these full-time scientists also be broadcast journalists? I wondered that, too.

Collaboration is key. “I give all the credit to the team,” Zhang says, emphasizing that the high volume of work required to produce the series wouldn’t get done without each member’s contributions. Their process, which begins by digging through Nature, PNAS and the like, is streamlined using a shared Google Doc for gathering content ideas. Then, on Monday night, the group meets for a two-hour writing session followed by two hours of audio recording at Stanford’s KZSU studio. The scientists write in pairs or larger groups to decide for each segment, “Is it true?” and “Is it funny?”

The team wants to make science news a table topic in the average educated household. Zhang notes, “I think we have a responsibility as scientists to not just focus on our work, but really to share science with the broader community.” He said the sequester‘s devastating cuts to NIH funding was a key example of the need for this kind of outreach. “I don’t know if we have a right to complain as scientists if we’re not putting the effort to share with the public why science is so important,” Zhang says. That’s why he’s driven to clock non-lab hours in the recording studio – as part of a long-term goal “to influence the culture of how science is viewed in our country.”

Previously: You are what you read: The academic diet of the 21st-century medical studentHawkeye Pierce (i.e. Alan Alda) teaches scientists how to better communicate about their workHelping the public make sense of scientific research and Alan Alda on communicating science. Yes, M*A*S*H’s Hawkeye Pierce
Photo courtesy of David Zhang

Applied Biotechnology, Genetics, Research, Science, Stanford News

RNA Rosetta stone? Molecules’ second, structural language predicted from their first, linear one

RNA Rosetta stone? Molecules' second, structural language predicted from their first, linear one

Rosetta stoneThe RNA whisperer is at it again.

In a study just published in Nature, Stanford’s Howard Chang, MD, PhD – an expert in all things RNA – and his colleagues detail how they were able to translate from one language spoken by this versatile biomolecule to another, more obscure but important one.

RNA is best known as the intermediate material in classic protein production. A so-called “messenger RNA” molecule serves as a mobile, short-lived copy of its more durable lookalike, DNA, the stuff genes are made of. Gene-reading machines in a cell’s nucleus produce RNA copies of protein-coding genes. Unlike a gene, which is a sequence of chemical letters situated somewhere on a big, bulky chromosome, a messenger RNA molecule can float out of the nucleus to the cell’s watery cytoplasm where proteins get made, and transmit a gene’s instructions to the protein-making machinery.

But RNA does more than simply specify which proteins are going to get made. A messenger RNA molecule’s 3-dimensional shape, for example, conveys bountiful information telling the cell’s protein-producing proletariat where to bring it, what to do with it when it gets there, and when and and how much protein to make from it.

DNA is famously double-stranded. That’s because, of its four component chemical “letters,” two in particular share a strong mutual attraction, biophysically speaking. Happily, the other two letters have a chemical crush on one another as well. So, when the letters composing one DNA strand are complementary to those on a closely opposed strand (and they virtually always are), the two strands lock in a lasting embrace to form a stable double helix.

RNA molecules are strings of four different chemical letters almost identical to those constituting DNA. But unlike DNA, an RNA molecule typically travels solo, as a single-stranded chain of those four chemical letters. It is thus a rather playful, floppy molecule. Nonetheless, the same alphabetical affinities that produce DNA’s double helix are at work in an RNA molecule, albeit in a more fleeting form: Small sequences of chemical letters along an RNA molecule find themselves attracted to complementary sequences elsewhere on the same molecule, causing it to fold into so-called secondary structures featuring pinched double-stranded sections alternating with bulges and loops, hairpins and hinges.

Chang’s gang has figured out how to predict, based on an RNA molecule’s linear chemical sequence, the way it will fold up into its secondary structure. They were able to do this for  thousands of differently shaped RNA molecules found in one type of human cell – about a thousandfold increase over the number of such structures that had been laboriously determined to date, Chang told me. That has consequences for understanding disease mechanisms and, potentially, for drug discovery as well.

Looks like RNA research is shaping up.

Previously: Night of the living dead gene: Pseudogene wakes up, puts chill on inflammation, New job description for RNA, oldest professional biomolecule and iPhone app shows 2D structures of thousands of RNA molecules
Photo by OliBac

Events, Science, Stanford News

Hawkeye Pierce (i.e. Alan Alda) teaches scientists how to better communicate about their work

Hawkeye Pierce (i.e. Alan Alda) teaches scientists how to better communicate about their work

Alan_Alda_MASH_1972 - smallAs a teenager, I wanted to grow up to be Alan Alda. Actually, I wanted to be Hawkeye Pierce, the wise-cracking Army surgeon Alda played on the iconic television series M *A *S * H. I loved M*A*S*H, and Hawkeye was The Man. He was the funniest character, the best surgeon, and the biggest partier and, whenever the show got serious, he displayed the most passion for people and justice. (And since I was a gangly kid with red hair and acne, it probably didn’t hurt that Hawkeye got all the women, too.)

This came back to me when I attended Alda’s recent lecture on the importance of science communication held at Stanford’s Li Ka Shing Center for Learning and Knowledge. The talk was part of a two-day workshop conducted by the staff of the Alan Alda Center for Communicating Science at Stony Brook University to teach Stanford scientists how to more effectively speak and write about their work.

I couldn’t help but smile when he ambled out to greet the capacity crowd. It’s Hawkeye! He was a few decades older (aren’t we all) and had swapped olive drab fatigues for a natty gray suit, but his voice and smile were the same, as was his distinctive, infectious laugh.

For more than an hour Alda used personal anecdotes, video clips, audience participation and a lot of humor to argue that too many scientists are holding themselves back – as well as science itself – due to their inability to explain their work in clear, understandable language. Whether speaking to policy makers, the public through the media, potential funders, or even scientists from other disciplines, the meaningful exchange of ideas and information is too often lost in incomprehensible detail and specialized jargon. (Alda got a big laugh with a story of a multidisciplinary collaboration that dissolved due to an argument over the correct meaning of a “probe.”)

The consequences are serious, though, with government research budgets under constant pressure and large portions of the population blithely disregarding scientific consensus on issues like climate change and evolution. Alda challenged the scientific community to do a better job educating policy makers and the public, and his center provides some unique tools to do so.

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Clinical Trials, In the News, Research, Science, Stanford News

The Lancet documents waste in research, proposes solutions

The Lancet documents waste in research, proposes solutions

Science is hard work. So hard, in fact, that it’s pretty disheartening to hear that much of that effort is wasted. A major series of research papers was published yesterday in The Lancet documenting five major causes of waste in research (if you’re interested, the culprits include inefficiencies in setting research priorities, inappropriate study design and analysis, problems in research regulation and management, a lack of accessibility of research results and incomplete or unusable reporting of data).

Stanford’s John Ioannidis, MD, DSci, who has studied the subject extensively, co-authored the accompanying commentary and the article “How to Increase Value When Research Priorities are Set.” He is also the first author of “Increasing Value and Reducing Waste in Research Design, Conduct and Analysis.” (Stanford health research and policy experts  Rob Tibshirani, PhD, and Mark Hlatky, MD, are senior and co-author, respectively, of the article.)

It’s not all doom and gloom, however. The series does suggest ways to overcome these seemingly pervasive obstacles. From the opening article:

How might things be different? One protection from these distorting drivers would be the creation of a set of balancing counter-influences. So, instead of being judged on the basis of the impact factors of the journals in which their work is published, academics might be judged on the methodological rigour and full dissemination of their research, the quality of their reports, and the reproducibility of their findings. If these factors were to contribute substantially to promotion, funding, and publication decisions, institutions might even go so far as to audit the performance of their staff and, when substandard, pay more attention to continuation of professional development and appraisal of the research workforce.

Previously “U.S. effect” leads to publication of biased research, says Stanford’s John Ioannidis, Shaky evidence moves animal studies to humans, according to Stanford-led study and Neuroscience studies often underpowered, say researchers at Stanford, Bristol

Aging, Fertility, Genetics, Research, Science, Stanford News

Male roundworms shorten females’ lifespan with soluble compounds, say Stanford researchers

Male roundworms shorten females' lifespan with soluble compounds, say Stanford researchers

2927367197_d663f8af63_zIt’s almost too good to be true. A Thanksgiving story about sex, death, gender conflict and… roundworms. A Stanford study published today in Science Express suggests that, in some species of worms and flies, males secrete compounds specifically to shorten the lifespan of nearby females. As a result, their mere presence initiates an inexorable early death sequence that the researchers call “male-induced demise.”

(Let’s all pause here for a deeply satisfying comparison to certain relationships in our own lives…)

The researchers, including Stanford geneticist and longevity expert Anne Brunet, PhD, and postdoctoral scholar Travis Maures, PhD, studied the laboratory roundworm, C. elegans, which has hermaphrodites rather than true females. Their research indicates that male roundworms secrete as-yet-unidentified molecules that act on hermaphrodites sequestered on the other side of a laboratory dish, or those added to a laboratory dish from which a batch of males had recently been evicted. Those hermaphrodites have a lifespan more than 20 percent shorter than controls not exposed to males.

The finding appears to counteract previous theories suggesting that the act of mating (which in worms can be – shall we say – quite rowdy) is responsible for the hermaphrodites’ early demise. As I wrote in our press release:

For several years, it’s been known that the presence of some male worms and flies can shorten the lifespan of their female or hermaphroditic counterparts. But it’s not been clear why. Some researchers have speculated that the physical stress of mating may lead to their early death.

The Stanford research, however, suggests something more than sex is to blame — specifically, that the males are carrying out a calculated plan at the molecular level to off the baby-makers after they’ve done their jobs.

The motive? Brunet and Maures speculate the murderous spree could be triggered by a need to conserve resources for newly produced young, or to prevent other males from mating with the same female. From the release:

“In worms, once the male has mated and eggs are produced, the hermaphrodite mother can be discarded,” Brunet said. “The C. elegans mother is not needed to care for the baby worms. Why should it be allowed to stay around and eat? Also, if she dies, no other male can get to her and thus introduce his genes into the gene pool.”

The researchers found that the continuous presence of young males shortened the average lifespan of C. elegans hermaphrodites by more than 20 percent. This effect persisted even when the genders were prevented from co-mingling, or when the hermaphrodites were sterile — indicating that neither the physical stress of copulation nor the energy demands of producing offspring were entirely responsible for early death. Affected hermaphrodites also displayed symptoms of aging, including slower movement, an increased incidence of paralysis, general decrepitude and structural decline.

It’s almost unbearably tempting to extend these findings to mammals or even humans.The presence of males leads to general decrepitude and structural decline in nearby females? I’ll go with it. And they exert this lifespan shortening effect over both space and time? Check. (In my house this is accomplished by my husband’s refusal to put his dishes in the dishwasher before leaving the house, but your trigger may vary.)

However, such nefarious tactics are likely to seriously backfire when a mother (or a set of parents) is needed to care for helpless offspring. In that case, males would appear to have little incentive to kill off their partners. Even so, the results indicate that this tactic has been going on for millions of years:

Although the researchers first studied a domesticated strain of C. elegans, they were also able to observe male-induced demise in a wild strain of C. elegans, as well as in two other, distantly related species of worm — confirming that the phenomenon has been conserved over about 20 to 30 million years of evolution. The male-induced demise even occurred in species of roundworm that have true males and true females in an equal mix (similar to mammals), suggesting that this phenomenon is not just due to idiosyncrasies of C. elegans such as hermaphroditism or a low proportion of males.

“The observation that this male-induced demise is present in several species of worms and has also been shown in flies suggests that it could have some adaptive benefits,” Brunet said. “It will be interesting, of course, to determine whether males also affect the lifespan of females in other species, particularly mammals.”

Previously Longevity gene tied to nerve stem cell regulation, say Stanford researchers and NIH awards nine Stanford faculty funding for innovative research
Photo by Ryan Somma

Research, Science

A call for self-reflection in the biomedical research community

In an opinion piece for The Scientist, co-authors David Rubenson, associate director for administration and strategic planning at the Stanford Cancer Institute, and Paul Salvaterra, PhD, a professor of neuroscience at the Beckman Research Institute of the City of Hope, argue for reform in biomedical research processes. Rubenson and Salvaterra propose that the research community commit to studying aspects of their field such as research funding, peer review, academic promotions and regulatory burdens.

From the piece:

The nation’s business schools concern themselves with financial, organizational, and cultural incentives in corporate and non-profit organizations. Government agencies employ numerous think tanks to evaluate long-term policies. There is, however, virtually no scholarly tradition for analyzing the biomedical research process. “One off” studies by the Institute of Medicine or the occasional ad hoc committees cannot substitute for a sustained program of research and analysis.

“The stakes are enormous,” the authors write. “The [biomedical research] enterprise is too important, large, and complex to be governed casually and with little awareness of the factors shaping it.”

Previously: NIH funding mechanism “totally broken,” says Stanford researcher, NIH re-thinking its rules on grant application submissions and Starting a new career in academic medicine? Here’s a bible for the bedside: The Academic Medicine Handbook

Chronic Disease, Mental Health, Neuroscience, Research, Science, Stanford News

Star-shaped cells nab new starring role in sculpting brain circuits

Star-shaped cells nab new starring role in sculpting brain circuits

starfishA healthy person’s brain has thousands, or maybe millions, of times as many synapses – contact points that relay signals from one nerve cell, or neuron, to the next – as there are stars in the Milky Way. In a blog entry not so long ago, I wrote:

In a sense, “you” are your synapses. They’re the defining features of the brain circuits that fire up or chill out to generate every thought that passes through your mind and every flicker of emotion or glimmer of recollection you experience. You wouldn’t want to leave home without them. Some of us get no choice. Massive synapse loss accompanies neurodegenerative diseases from Alzheimer’s to Parkinson’s to multiple sclerosis.

In a paradigm-shifting discovery just published in Nature, Stanford researchers found that a common but mysterious class of non-neuronal brain cells, called astrocytes because of their star-like shape, actively refine nerve-cell circuits throughout life by selectively eliminating synapses. much as a sculptor chisels away excess bits of rock to create an artwork.

Astrocytes, which account for between one-third and half of all the cells in our brains, belong to a general category of brain cells collectively called “glia,” from the Greek term for glue. That’s because until not long ago, neuroscientists (note the bias in that term) figured that these seemingly passive cells weren’t much more than packing peanuts for the “really cool” cells, neurons, that hog the lion’s share of attention.

Neurons, which compose merely 10 percent of all the cells in a healthy human brain, are so celebrated they’ve lent their name to brain science: neurology. But a team led by pioneering Stanford gliologist (I made that term up) Ben Barres, MD, PhD, has shown in the new study that astrocytes play a starring role in sculpting the very synaptic connections that are central to consciousness, cognition, motion and emotion.

As I once noted:

[Barres] – who trained as a practicing neurologist before circling back for his PhD – couldn’t help noticing, in autopsies, that the brains of people with “neurological” disorders invariably showed obvious signs of glial disarray. So he resolved to devote his career to the study of glial cells…

Thus began a decades-long efforts to unveil the manifold functions of astrocytes and their glial comrades-in-arms (described in detail in this Stanford Medicine article).  Barres and his colleagues have already shown that astrocytes in particular (there are two other glial cell types) play a critical role in determining exactly where and when new synapses are generated. With the finding that astrocytes also single out outmoded or downright counterproductive synapses and gobble them up, it’s increasingly certain that substantial remodeling of brain circuits takes place in the adult brain and that astrocytes are master sculptors of its constantly evolving synaptic architecture. This holds huge implications, according to my press release on the new study:

The findings also raise the question of whether deficits and excesses in this astrocytic function could underlie, respectively, the loss of this remodeling capacity in old age or the wholesale destruction of synapses that erupts in neurodegenerative disorders, such as Alzheimer’s and Parkinson’s disease.

Previously: Protein known for initiating immune response may set our brains up for neurodegenerative disorders, Unsung brain-cell population implicated in variety of autism and Brain imaging, and the ‘image management’ cells that make it possible
Photo by Ed Bierman

Events, Genetics, Science, Stanford News, Videos

Stanford geneticist discusses genomics and medicine in TEDMED talk

Stanford geneticist discusses genomics and medicine in TEDMED talk

In a new video of a TEDMED Great Challenges event titled “Genomics and Medicine: Where promise meets clinical practice,” Stanford geneticist Carlos Bustamante, PhD,  joins colleagues “to explore what is already possible and what is just over the horizon in the world of genomic medicine,” as Eric Green, the Google Hangout event’s host, describes. Green, MD, PhD, the director of the National Human Genome Research Institute of the National Institutes of Health, was joined by Amy McGuire, JD, PhD, of Baylor College of Medicine; James Evans, MD, PhD, of University of North Carolina School of Medicine; and Sharon Terry, president and CEO of the Genetic Alliance patient advocacy organization; and Bustamante.

Previously: Caribbean genetic diversity explored by Stanford/ University of Miami researchersAsk Stanford Med: Genetics chair answers your questions on genomics and personalized medicine and How genome testing can help guide preventative medicine

CDC, Infectious Disease, Medical Education, Patient Care, Public Health, Science, Stanford News

Free online course aims to educate about “pressing public health threat” of antibiotic resistance

Free online course aims to educate about "pressing public health threat" of antibiotic resistance

antibioticsAre you smart about antibiotics? That’s the question the CDC is asking as part of its week-long effort to educate people about antibiotic resistance – something the organization calls “one of today’s most pressing public health threats.” Its Get Smart About Antibiotics website offers valuable tips and information on antibiotic use, and CDC Director Thomas Frieden, MD, MPH, will be answering questions on the topic during a live Twitter chat Friday morning. (Follow the hashtag #CDCchat at 10 AM Pacific time tomorrow to join the conversation.)

Stanford, meanwhile, is aiming to educate medical professionals by launching a free online course called “Antimicrobial Stewardship: Optimization of Antibiotic Practice.” The course, directed by Stan Deresinski, MD, head of Stanford’s Antimicrobial Stewardship Program, will “offer a practical approach to prescribing antibiotic therapy and development of antimicrobial stewardship across all specialties and settings.” As for the need for such a course, the website explains:

Antibiotics are among the most frequently prescribed classes of drugs and it is estimated that approximately 50% of antibiotic use, in both the outpatient and inpatient settings, is inappropriate.  At the same time, in contrast to any other class of drugs, every antibiotic use has a potential public health consequence – inappropriate use may not harm only the individual patient, but contributes to societal harm by exerting an unnecessary selective pressure that may lead to antibiotic resistance among bacteria.

The course is sponsored by the Division of Infectious Diseases and Geographic Medicine in the Department of Medicine. Participants have the option of taking the course for CME credit.

Previously: Side effects of long-term antibiotic use linked to oxidative stress, New method may speed identification of antibiotic targets, Harnessing evolutionary forces to develop more effective methods for treating superbugs and Norway’s strategy for fighting drug-resistant bacteria
Photo by Iqbal Osman1

History, In the News, Science

Museum sheds some light on early electric medical devices

Museum sheds some light on early electric medical devices

electric fishThis Wired.com story on the 20th century medical devices housed at the Bakken Museum had me at “electric torpedo fish.”

As the story explains, we’ve experimented with the possible medical applications of electricity since 1st century AD when Roman physician Scribonius Largus applied electric torpedo fish to his patients as a therapy for headaches, gout, or hemorrhoids.

We’ve refined our use of electricity for medicine a bit over the years. The Bakken Museum in Minneapolis showcases some of our progress in this field.

From the piece:

The museum’s collection, which also includes some 11,000 books and scientific manuscripts dating back to the 13th century, focuses on the use of electromagnetism in medicine.

Assistant curator Adrian Fischer (below) compiled this selection of some of the Bakken’s more rare and unusual devices, such as the Garceau Nerve Stimulator (above) that was made sometime between 1940 and 1970. Fischer says the documentation accompanying this device suggests it was used to stimulate the cerebral cortex during brain surgery, for example, to help surgeons pinpoint the source of a patient’s epileptic seizures.

Holly MacCormick is a writing intern in the medical school’s Office of Communication & Public Affairs. She is a graduate student in ecology and evolutionary biology at University of California-Santa Cruz.

Previously: The history of biotech in seven bite-sized chunksA low-cost way to keep premature babies warm and well and Stanford engineers create wireless, self-propelled medical device that swims through blood stream
Photo by BioDivLibrary

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