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Evolution, Fertility, Pregnancy, Research, Science, Stanford News, Stem Cells, Videos

Viral RNA essential for human development, say Stanford researchers

Viral RNA essential for human development, say Stanford researchers

Viruses are tricky, but we humans may be trickier still. Stanford stem cell biologists Vittorio Sebastiano, PhD, and Jens Durruthy-Durruthy, PhD, published a study today in Nature Genetics indicating that the genetic remnants of ancient viral infections that still linger in our genome are essential to early human embryonic development.

As Sebastiano explained in our release:

We’re starting to accumulate evidence that these viral sequences, which originally may have threatened the survival of our species, were co-opted by our genomes for their own benefit. In this manner, they may even have contributed species-specific characteristics and fundamental cell processes, even in humans.

The researchers, who talk about their work in the video above, relied on a new RNA sequencing technique to investigate the expression of what are called long-intergenic noncoding, or lincRNAs. These molecules don’t contain protein-making instructions, but instead affect the expression of other genes. They’ve been implicated in many important biological processes, including the acquisition of a developmental state called pluripotency that is necessary for a fertilized egg to develop into the cells and tissues of a growing fetus.

More from our release:

They identified more than 2,000 previously unknown RNA sequences, and found that 146 are specifically expressed in embryonic stem cells. They homed in on the 23 most highly expressed sequences, which they termed HPAT1-23, for further study. Thirteen of these, they found, were made up almost entirely of genetic material left behind after an eons-ago infection by a virus called HERV-H.

[…] After identifying HPAT1-23 in embryonic stem cells, Sebastiano and his colleagues studied their expression in human blastocysts — the hollow clump of cells that arises from the egg in the first days after fertilization. They found that HPAT2, HPAT3 and HPAT5 were expressed only in the inner cell mass of the blastocyst, which becomes the developing fetus. Blocking their expression in one cell of a two-celled embryo stopped the affected cell from contributing to the embryo’s inner cell mass. Further studies showed that the expression of the three genes is also required for efficient reprogramming of adult cells into induced pluripotent stem cells.

I can’t stop marveling at the close ties we have with viruses. It makes me think of the words of Michael Corleone in The Godfather: “Keep your friends close, and your enemies closer.” As Durruthy-Durruthy told me, “It’s fascinating to imagine how, during the course of evolution, primates began to recycle these viral leftovers into something that’s beneficial and necessary to our development.”

Previously: My baby, my… virus? Stanford researchers find viral proteins in human embryonic cellsMastermind or freeloader? Viral proteins in early human embryos leave researchers puzzled  and Species-specific differences among placentas due to long-ago viral infection, say Stanford researchers
Video by Christopher Vaughan/Stanford Institute for Stem Cell Biology and Regenerative Medicine

Humor, Medical Education, Stanford News, Videos

“Dear Future Doctor, here’s a few things you’ll need to know”: Med students release parody video

"Dear Future Doctor, here's a few things you'll need to know": Med students release parody video

Ready for the first-ever musical parody produced by Stanford medical students? Filmed on campus last month and released this afternoon, Dear Future Doctor features a group of mostly first-years singing and dancing to the tune of one of Meghan Trainor’s recent hits. Featuring characters like the Late Doctor, the Greedy Doctor and the Celebrity Doctor, the song also – in the words of producer/writer/editor/first-year student Gun Ho Lee – aims to teach a lesson “on what the future doctor is NOT to do.”

The song “is meant to be a satire of the 21st century American medical system,” director/writer/ second-year student Joshua Wortzel elaborates. “In her song, Meghan Trainor pokes fun at some of the unfortunate aspects of modern courtship and gender norms” – and Dear Future Doctor, in turn, pokes fun at some of the things that “we medical students learn about becoming doctors.”


Bioengineering, Events, Mental Health, Research, Stanford News, Videos

Stanford’s Karl Deisseroth talks about the work he was “destined to do”

Stanford's Karl Deisseroth talks about the work he was "destined to do"

Earlier this week we announced the exciting news that Stanford bioengineer Karl Deisseroth, MD, PhD, had won a $3 million 2016 Breakthrough Prize in Life Sciences. Before he took the stage to accept his award during a star-studded Academy Awards-like ceremony Sunday evening, the video above was shown to highlight the significance of his work. One of Deissoroth’s quotes:

There are deep questions about the brain that may never be answered, but we’re making headway with optogenetics… We’re headed down a path that gets us to understanding [questions like] why does one person feel the way they do and why does it create a disease when they do a particular way, and what can be done to correct it?

Noting that the suffering of people with psychiatric disease “is a very, very serious and pervasive matter,” he also says “the nature of the illnesses – their complexity, the amount of suffering and the mystery – has made this what I was destined to do.”

Previously: Stanford bioengineer Karl Deisseroth wins 2016 Breakthrough Prize in Life SciencesInside the brain of optogenetics pioneer Karl DeisserothLightning strikes twice: Optogenetics pioneer Karl Deisseroth’s newest technique renders tissues transparent, yet structurally intact and An in-depth look at the career of Stanford’s Karl Deisseroth, “a major name in science”
Video courtesy of National Geographic Channel

Aging, Events, Stanford News, Videos

Former medical school dean discusses learning and longevity at Stanford 125 event

Former medical school dean discusses learning and longevity at Stanford 125 event

The year-long celebrations for Stanford University’s 125th anniversary are in full swing, and Philip Pizzo, MD, former dean of Stanford’s medical school, recently helped kick off the festivities. Earlier this month, he and experts in the fields of psychology, computer science, education, physics and the humanities drew a crowd of more than 550 people to Stanford’s Cemex Auditorium to discuss the theme “Thinking Big About Learning.”

In his talk, Pizzo, founding director of the Stanford Distinguished Careers Institute, explored the topics of learning, aging and longevity and how traditional views of education and career (learn when young and do the same job for life) no longer apply now that people are living and working longer than ever.

If you missed the event, you can watch video of Pizzo’s talk here. Other videos from the symposium, including talks from Stanford psychology professor Carol Dweck, PhD, and Jeremy Bailenson, PhD, director of the Virtual Human Interaction Lab, are available on the Stanford 125 website.

Previously: Living long and living well: A conversation on longevity at Medicine XA look at aging and longevity in this “unprecedented” time in history and Living loooooooonger: A conversation on longevity


In the News, Research, Science, Stanford News, Videos

Brain cell spheres offer new tool to study disease

Brain cell spheres offer new tool to study disease

Earlier this year my colleague reported on some pretty neat work from the labs of psychiatrist Sergiu Pasca, MD, and neurobiologist Ben Barres, MD, PhD. Researchers there figured out how to create spheres of neuronal cells resembling the cerebral cortex, making functional human brain tissue available for the first time to study neuropsychiatric diseases such as autism and schizophrenia. In an article today the Associated Press highlighted this work, with Malcolm Ritter writing:

It’s part of a larger movement over the past few years to create “organoids,” miniature versions of the body’s organs or key parts of organs. Goals include studying disease, testing possible treatments and perhaps supplying replacements for transplants. Scientists have made organoids representing the intestine, prostate, kidney, thyroid, retina and liver.

This overall organoid approach “is a major change in the paradigm in terms of doing research with human tissues rather than animal tissues that are substitutes. … It’s truly spectacular,” says Arnold Kriegstein, who studies the brain at the University of California, San Francisco.

Pasca talks more about the work in the AP video above; Stanford ethicist Hank GreelyJD, also weighs in.

Previously: Brain cell spheres in a lab dish mimic human cortex, Stanford study says

Patient Care, Stanford News, Videos

A new tool to treat atrial fibrillation

A new tool to treat atrial fibrillation

The first time Susan Klein’s heart stopped, and then started again, she was very frightened. But she didn’t run for the phone to call a doctor. Klein had a pretty good idea of what had happened: Six other women in her immediately family had experienced heart palpitations, or, what they called “the little mouse running around their chest,” Klein said. “I had a history — and it was to be expected in my family.”

Klein’s palpitations, however, became so frequent and debilitating that, even with medication, she didn’t have enough breath to make it across a street. By then, of course, she knew that her diagnosis was officially atrial fibrillation, an irregular heartbeat most often called afib. More than two million people in the United States and an estimated 30 million worldwide suffer from what is the most common type of heart rhythm disorder. Before I interviewed Klein this year for a Stanford Health Care video, I was naïve about the seriousness of afib and the challenge of treating it with any certainty of full recovery.

Afib symptoms can include shortness of breath, weakness, fatigue, heart palpitations, light-headedness, and chest or abdominal pain. Some patients with afib feel no symptoms – making it more difficult to diagnose the disease early enough to prevent its most serious consequences: an increased risk of heart failure and a five-times-more-likely incidence of stroke. Afib accounts for about 15 percent of strokes in the United States.

Afib in some people can be managed with medications. Those didn’t work for Klein. Ablation, the standard interventional procedure, often had to be done more than once or even several times. That wasn’t good enough for Klein. “To spend six to seven hours under general anesthetic with only a 40 percent success rate? I wasn’t satisfied,” she said.  Then she heard about Sanjiv Narayan, MD, PhD, a Stanford doctor with a very particular specialty: cardiac electrophysiology. Narayan, who now directs Stanford’s atrial fibrillation program and its electrophysiology research, had long been interested in detecting the points of electrical chaos in the heart that cause afib.

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Aging, Behavioral Science, Neuroscience, Stanford News, Videos

Decisions, decisions: How our decision making changes with age

Decisions, decisions: How our decision making changes with age

Research in neuroscience, psychology, business and economics tells us that a plethora of influences can alter the decisions we make. The author explored some of these factors in a Worldview Stanford course and wrote about them in a Stanford story package, Decisions, Decisions. This post is part of a series on what she learned. 

Without revealing my age, I will simply say that I am beyond the teenage years, when risks fail to register and decisions are dominated by reward. But it turns out the person I was then shaped how my brain makes decisions today.

Kathleen Fitzpatrick, MD, a child psychiatrist, says that during our teenage years dramatic changes take place in the brain. Wiring we don’t use dies off and wiring we use heavily flourishes and multiplies, creating new connections and with it new behaviors.

In my story about how age alters decision-making I write:

During this time of brain circuit upheaval, adolescents weigh the pros and cons of decisions differently from adults. They overestimate the rewards of a decision (Fun! Friends!) but don’t accurately estimate possible risks (grounding, police).

Our teenage behaviors shape which of those new connections remain. If a behavior is rewarded, those pathways are strengthened. A failed behavior fades into a distant, embarrassing memory.

Read the story for more about both the teenage brain and also the way our decision-making shifts as we get older. Hint: we become less worried, which is something to look forward to.

Previously: Exploring the science of decision making and Exploring the intelligence-gathering and decision-making processes of infants
Video courtesy of Worldview Stanford

Emergency Medicine, Global Health, Health Policy, Stanford News, Videos

A look at “India’s medical miracle,” the largest ambulance service in the world

A look at "India's medical miracle," the largest ambulance service in the world

A patient in shock arrives via ambulance at Gandhi Hospital in Hyderabad, India with a gaping wound in his right hand, blood spattered on his blue jeans and T-shirt. Emergency medical technicians wheel him into a dark room in the government-run hospital, where clinicians move quickly to irrigate the wound and pump fluids into the man, who appears to be in his 20s.

With luck, the patient might survive. Ten years ago, he would not have had a chance.

Thanks to some passionate philanthropists, businessmen and medical experts, India today has what we have long taken for granted in the United States: a modern, emergency 911-type system and a cadre of trained emergency responders who have helped save an estimated 1.4 million lives. Begun in 2005, it is now the largest ambulance service in the world and serves more than 750 million people in cities and villages across the Indian sub-continent.

I saw the system in action first-hand in August when I traveled to India, together with about 10 other faculty and staff from Stanford’s School of Medicine, including Dean Lloyd Minor, MD, to celebrate its 10th anniversary amid much color and fanfare. I was there to write a story about the new system for Stanford Medicine magazine.

Begun in August 2005 in the south Indian metropolis of Hyderabad, the service, known as GVK EMRI (Emergency Management and Research Institute), is operated as a public-private partnership, providing its services free of charge, mostly to the very poor. It is a remarkable achievement, given the diversity of India, with its 29 states and more than 120 major languages, and the bureaucracy and corruption that can sometimes impede progress in this vast country of 1.2 billion souls.

“It’s hard to fathom what this system has done in 10 years,” S.V. Mahadevan, MD, interim chair of Stanford’s Department of Emergency Medicine, told me while stationed in one of EMRI’s ambulances. “It could be regarded as one of the most important advances in global medicine in the world today.”

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Emergency Medicine, Pregnancy, Research, Surgery, Videos

Self-propelled powder moves against blood flow to staunch bleeding in hard-to-reach areas

Self-propelled powder moves against blood flow to staunch bleeding in hard-to-reach areas

If you nick your skin, it’s easy to stop the bleeding by applying a coagulant powder directly to the cut. Yet, bleeding wounds inside the body are beyond the reach of such blood-stopping powders.

Now, Christian Kastrup, PhD, an assistant professor at the University of British Columbia, and a team of researchers, biochemical engineers and emergency physicians, have developed a way to clot internal wounds by creating a self-propelled powder that moves against the flow of blood.

“Bleeding is the number one killer of young people, and maternal death from postpartum hemorrhage can be as high as one in 50 births in low resource settings so these are extreme problems,” Kastrup explained in a UBC press release. “People have developed hundreds of agents that can clot blood but the issue is that it’s hard to push these therapies against severe blood flow, especially far enough upstream to reach the leaking vessels. Here, for the first time, we’ve come up with an agent that can do that.”

To give blood-clotting powder a push, Kastrup and his colleagues added calcium carbonate to the coagulant powder. The carbonate forms porous micro-particles that latch onto the clotting agent (tranexamic acid). As the particles release carbon dioxide gas, fizzing and moving like mini-antacid tablets, they launch the clotting agent toward the source of bleeding.

More rigorous testing and development needs to be done before this agent is ready for use in humans, as the press release and study explain. But it’s possible that in the near future this powder could be used to treat otherwise unreachable cuts such as those in postpartum hemorrhages, sinus operations and internal combat wounds.

Previously: New obstetric hemorrhage tool kit released todayIn poorest countries, increase in midwives could save lives of mothers and their babiesTeen benefited by Stanford surgeon’s passion for trauma care
Video courtesy of UBC

Imaging, Neuroscience, NIH, Research, Videos

Video reconstruction reveals stunning detail within a tiny section of brain

Video reconstruction reveals stunning detail within a tiny section of brain

Important discoveries in science are often called “big” breakthroughs, yet much of the information that makes these “aha” moments possible is found in the most diminutive of details. So it seems fitting that our first glimpse into the inner workings of the mammalian cerebral cortex arises from a tidbit of brain no bigger than a grain of sand.

For the first time, researchers have created a digital reconstruction of part of a mammalian cerebral cortex — the “rind” of the brain, about two to three dimes thick, that plays a central role in functions like memory, thought, language and consciousness.

This digitized rendering was created by NIH grantee Jeff Lichtman, MD, PhD, and his colleagues as part of the Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Francis Collins, MD, PhD, director of the National Institutes of Health, offers more details on how the film was made over on the NIH Director’s blog.

Previously: Exercise and your brain: Stanford research highlighted on NIH Director’s blogProcess that creates transparent brain named one of year’s top scientific discoveries and How CLARITY offers an unprecedented 3-D view of the brain’s neural structure

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