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Bioengineering, Ethics, Genetics, In the News, Research, Science

Are at-home gene splicing kits a good idea? Stanford researchers weigh in

Are at-home gene splicing kits a good idea? Stanford researchers weigh in

chemist_stick_figure_by_wrpigeekAs demonstrated by the Foldscope, the uber-affordable microscope developed by Stanford bioengineer Manu Prakash, PhD — there is real fervor for bringing easy, do-it-yourself science to the masses. But what if that at-home science allows novices to dabble in some serious stuff, like splicing genes?

One Bay Area scientist has done just that: He’s marketing a $130 gene-editing kit that could bring the popular technology CRISPR into kitchens, basements and garages nationwide.

This particular kit isn’t particularly dangerous, according to a recent article in the San Jose Mercury News:

The kit has limited applications. His altered bacteria and yeast, quite harmless, lead brief and fairly dull lives. They can’t do much except change color, fragrance or live in inhospitable places. Then they die.

But two Stanford experts — infectious disease researcher David Relman, MD, and bioethicist Hank Greely, JD — agree it could place powerful technology in the hands of people who might not use it responsibly.

“I do not think that we want an unregulated, non-overseen community of freelance practitioners of this technology,” Relman told the Mercury News.

Regulation, or control, might not be possible, though, Greely cautioned. “You’ve got guys with B.S. degrees, in a garage,” he said in the article.

Kit developer Josiah Zayner doesn’t have a garage. But one version of the kit has already sold out.

Previously: CRISPR critters and CRISPR conundrums, Foldscope inventor named one of the world’s top innovators under 35 by Technology Review and Manu under the microscope
Image by WRPIgeek

Bioengineering, Immunology, Public Health, Research

Working towards a lifelong, universal flu vaccine

Working towards a lifelong, universal flu vaccine

4919795171_771ae41b50_b_flickr_BlakePatterson_300x247To prepare for holiday socializing, I always roll up my sleeve to get an annual flu shot. I would much rather share food and gifts than a virus with my friends and family. And I don’t want to spend my precious vacation time sick.

However, seasonal flu vaccines are not always effective. There are thousands of strains of influenza virus and each can mutate over the course of the flu season. Seasonal vaccines only protect against a few of the most likely strains. As a result, flu-associated deaths range from 3,000 to 49,000 Americans per flu season, according to the U.S. Centers for Disease Control and Prevention.

Scientists have long sought a lifelong vaccine that would be effective against any variety of influenza, and they are now making significant progress towards this goal.

I recently spoke with Ian Wilson, PhD, a leading structural and computational biologist at the Scripps Research Institute, about his team’s universal flu vaccine research. He told me:

Our research has identified a good target for such a vaccine on a protein called hemagglutinin (HA) that is present on the surface of all influenza viruses. The HA protein has two major components: the head portion, which mutates and varies from strain to strain, and the stem, which is similar across most flu strains. We know that the HA stem is the virus’s most vulnerable spot, and provokes the greatest breadth of immune response. So a synthetic version of the stem was designed, called a mini-HA that mimicked the HA stem.

A key part of Wilson’s flu research took place at the Stanford Synchrotron Radiation Lightsource at SLAC National Accelerator Laboratory, where the scientists used a technique called x-ray crystallography to look at the atomic structure of the mini-HA at each stage of its development. I wrote a recent news article about their efforts.

Though this is important research, more work needs to be done. “We still need to perform human trials and also want to develop a vaccine that protects against all types of influenza that cause human pandemics,” Wilson said.

Jennifer Huber, PhD, is a science writer with extensive technical communications experience as an academic research scientist, freelance science journalist, and writing instructor.

Previously: Working to create a universal flu vaccineScience Friday-style podcast explains work toward a universal flu vaccine and Experts and 8-year-olds agree: It’s worth getting a flu shot
Photo by Blake Patterson

Applied Biotechnology, Bioengineering, Stanford News, Videos

Manu under the microscope

Manu under the microscope

Warning: This video could change the way you look at the world.

So if you’re willing, take the deep dive into this New Yorker magazine video and story, which capture the curiosity-driven magic of Stanford bioengineering inventor Manu Prakash, PhD, and his low-cost microscope, called the Foldscope.

This deceptively simple invention is a bookmark-looking assembly made of folded cardstock, a tiny glass bead and a photo battery, that can take you on a fantastic voyage into the microcosmos.

Last year Prakash shipped free Foldscopes around the world, and created a cult-like following of people sharing their microscopic discoveries. The New Yorker article goes on to describe some of the ways that people are using this invention:

The Foldscope performs most of the functions of a high-school lab microscope, but its parts cost less than a dollar. Last year, with a grant from Gordon Moore’s philanthropic foundation (Moore co-founded Intel), Prakash and some of his graduate students launched an experiment in mass microscopy, mailing fifty thousand free Foldscopes to people in more than a hundred and thirty countries, who had volunteered to test the devices. At the same time, they created Foldscope Explore, a Web site where recipients of the kits can share photos, videos, and commentary. A plant pathologist in Rwanda uses the Foldscope to study fungi afflicting banana crops. Maasai children in Tanzania examine bovine dung for parasites. An entomologist in the Peruvian Amazon has happened upon an unidentified species of mite. One man catalogues pollen; another tracks his dog’s menstrual cycle.

If you’d like to explore with your own Foldscope, you’ll have to be patient. Prakash is still in the planning process of manufacturing and distribution. In the meantime, you can put your name on the round-two waiting list at foldingmicroscope@gmail.com.

Previously: Foldscope beta testers share the wonders of the microcosmosStanford microscope inventor invited to first White House Maker Faire, The pied piper of cool science tools and Stanford bioengineer develops a 50-cent paper microscope
Video by Sky Dylan-Robbins

Bioengineering, Evolution, Research, Science, Stanford News, Technology

Fast-forwarding evolution to select suitable proteins

Fast-forwarding evolution to select suitable proteins

4286076672_2763323a1e_zNature churns out new versions of proteins in response to environment changes or random mutations. Sometimes the new versions work better than old. Other times, not.

But now, Stanford researchers have developed a super speedy technique to test millions of versions of a certain protein to see which one works best.

A Stanford news release explains:

The researchers call their tool µSCALE, or Single Cell Analysis and Laser Extraction.

The “µ” stands for the microcapillary glass slide that holds the protein samples. The slide is roughly the size and thickness of a penny, yet in that space a million capillary tubes are arrayed like straws, open on the top and bottom.

The microcapillary glass slide, roughly the size and thickness of a penny, holds the protein samples.

The power of µSCALE is how it enables researchers to build upon current biochemical techniques to run a million protein experiments simultaneously, then extract and further analyze the most promising results.

The research was led by Jennifer Cochran, PhD, associate professor of bioengineering and Thomas Baer, PhD, executive director of the Stanford Photonics Research Center.

The system is easy to use with numerous applications, Baer said.

“Evolution, the survival of the fittest, takes place over a span of thousands of years, but we can now direct proteins to evolve in hours or days,” Cochran said in the release.

Previously: Proteins from pond scum revolutionize neuroscience, Study shows toothed whales have persisted millions of years without two common antiviral proteins and Computing our evolution
Photo by Alexander Boden

Bioengineering, Imaging, Neuroscience, Research, Stanford News

Brain radio: Switching nerve circuit’s firing frequency radically alters alertness levels in animal models

Brain radio: Switching nerve circuit's firing frequency radically alters alertness levels in animal models

brain radioIt’s a kick to consider that a part of the brain could act like a radio, with different stations operating at different frequencies, playing different kinds of music and variously attracting or repelling different “listening audiences.” A new study by Stanford neuroscientist Jin Hyung Lee, PhD, and her colleagues has isolated a brain circuit linking just such a “transmission station” in the midbrain to various “listener” regions in the forebrain.

The findings have clear therapeutic potential. In a news release about the research, I wrote:

In a case study published in 2007, [researchers] demonstrated that electrically stimulating the central portion of the thalamus — a deep-brain relay station routing inputs from the senses to myriad cognitive-processing centers throughout the cerebral cortex — could restore consciousness in a patient who’d been in a minimally conscious state for six years.

“But there was no way to know how it worked,” Lee told me.

Now, in a set of experiments published in eLife, she and her associates have used precisely targeted stimulation and recording techniques to show that forcing a set of nerve cells in the central thalamus to fire at 40 or 100 times a minute induces a state of arousal: Rats that were fast asleep wake up and start roving around and exploring their environments. Switch the same nerve cells to a firing frequency of 10 times a minute, and the same rats immediately go into a state of deep unconsciousness more akin to a coma or a petit mal seizure (a transient state of behavioral arrest) than to restful sleep.

In addition to these behavioral effects, forcing those central-thalamic nerve cells to fire at different rates causes distinct structures elsewhere in the brain to rev up or slack off. In a sense, firing at 100 times a minute was like blasting heavy-metal music – some forebrain regions leapt into the mosh pit, some ran for cover – while 10 times a minute (the easy-listenin’ channel?) variously appealed to or turned off different brain areas.

You can’t do that with a drug.

Continue Reading »

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

Bioengineering, Cancer, Imaging, Public Safety, Research, Stanford News, Technology

A new way to scan for plastic explosives could someday detect cancerous tumors

A new way to scan for plastic explosives could someday detect cancerous tumors

14591799636_128fbe50ee_zSci-fi shows and superhero films are full of gadgets and beings that have the power to remotely scan their environment for hidden things. For us mere mortals this superability may sound unachievable, but now Stanford engineers are working to develop a safe and portable way to detect concealed objects by scanning with microwaves and ultrasound.

As this Stanford Report story explains, the idea began with a challenge posed by the Defense Advanced Research Projects Agency: Design a way to detect buried plastic explosives from a safe distance without touching the surface of the ground.

A team of electrical engineers led by assistant professor Amin Arbabian, PhD, and research professor Pierre Khuri-Yakub, PhD, took up the challenge, paying homage to the scanning device made popular by sci-fi show Star Trek in the process. They created a tricorder-like device that senses the ultrasonic waves created by objects as they expand and contract when warmed by electromagnetic energy (e.g., light and microwaves).

Here’s the really interesting part: Because everything expands and contracts when heated — but not at identical rates — this scanning tool could have medical applications as well. For example, blood vessels that sprout from cancerous tumors absorb heat differently than surrounding tissue. So, blood vessels radiating from tumors could appear as “ultrasound hotspots” when scanned with the tricorder device.

The team is working to make this device ready to detect the presence of tumors and other health anomalies sometime within the next decade or so.

Previously: Beam me up! Detecting disease with non-invasive technology and Tiny size, big impact: Ultrasound powers miniature medical implant
Photo by Joe Haupt

Bioengineering, Science, Stanford News

Stanford bioengineer Karl Deisseroth wins 2016 Breakthrough Prize in Life Sciences

Stanford bioengineer Karl Deisseroth wins 2016 Breakthrough Prize in Life Sciences

Karl D at Clark - big

Updated 11-9-15: Lloyd Minor, MD, dean of Stanford’s medical school, provided comment last evening on Karl Deisseroth’s win. “The human brain has been called the most complicated object in the universe, but that hasn’t daunted Karl’s quest to understand it,” said Lloyd Minor, MD, dean of the School of Medicine. “If anything it seems the challenge has inspired him to develop techniques to see inside this most important of black boxes. This passion to understand the mind, combined with his intelligence and creativity, led to his pioneering role in creating optogenetics.”

***

11-8-15: We just learned that Stanford Medicine’s Karl Deisseroth, MD, PhD, has received the $3 million 2016 Breakthrough Prize in Life Sciences, an award designed to “honor transformative advances toward understanding living systems and extending human life.” Deisseroth was given the prize for his work in optogenetics, a technique using light to control the activity of the brain.

The award was presented tonight at a private black-tie, red-carpet ceremony in nearby Mountain View, Calif. “The suffering of the mentally ill and the mysteries of the brain are so deep that, to make progress, we need to take big risks and even blind leaps,” Deisseroth said after accepting his award from actress Kate Hudson. “The members of my lab have taken a leap: borrowing genes from microbes to control the brain.”

Congratulations, Dr. Deisseroth!

Previously: Inside the brain of optogenetics pioneer Karl Deisseroth, Stanford’s Karl Deisseroth awarded prestigious Albany Prize, Breaking through scientific barriers: Stanford hosts 2015 Breakthrough Prize winners, Lightning 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”
Related: Head lights and Optogenetics earns Stanford professor Karl Deisseroth the Keio prize in medicine
Photo by Steve Fisch

Applied Biotechnology, Bioengineering, Stanford News, Technology

The rocket men and their breathtaking invention

The rocket men and their breathtaking invention

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It’s a gadget straight out of Star Trek — a breath analyzer that may someday quickly and noninvasively detect everything from diabetes to cancers.

In a new Stanford Medicine magazine story, you can read about how three Stanford rocket-combustion experts — Christopher Strand, Victor Miller and Mitchell Spearrin — designed and tested a Breathalyzer-like device to measure toxic ammonia levels in critically ill children, all in about a year.

Breath testing with the human nose has been used in medicine since ancient times. (The rotten-apple smell of acetone is a sign of diabetes. A fishy smell is indicative of liver disease.) The rocket men in the story recognized the opportunity to develop a medical device that could transform this art into a science.

They figured that the technology they used in rocket testing, laser absorption spectroscopy, would be sensitive enough to make measurements of trace compounds in the breath. Just as engineers can use these data to tell if a rocket engine is operating efficiently, they could tell if a human biochemical engine is operating in a healthy range. Their project mentor, Gregory Enns, MD, a biochemical geneticist who diagnoses and treats metabolic diseases at Lucile Packard Children’s Hospital Stanford, helped the team get up to speed on metabolic disorders and remove bureaucratic roadblocks to clinical testing.

What was most inspiring to me about this story was the indefatigable optimism of the engineering team. The rocket men chose the most difficult molecule to measure (ammonia), a disease caused by a rare genetic defect with little commercial potential (hyperammonemia), and a hard-to-test patient population (infants). During the development process, they demonstrated the same mental toughness as abandoned-on-Mars engineer Mark Watney in the film “The Martian“; as each insurmountable technical challenge came up, they did what Watney did: “science the hell out of it.”

Previously: Stanford physicians and engineers showcase innovative health-care solutionsRaising awareness about rare diseases, Extraordinary Measures: a film about metabolic disease
Photo by Misha Gravenor

Bioengineering, Research, Stanford News

Stanford engineers create artificial skin that can signal pressure sensation to brain

Stanford engineers create artificial skin that can signal pressure sensation to brain

skin_news_560x373

A hand without a sense of touch doesn’t really feel like a hand, many amputees describe. It’s more like a pliers that can be manipulated by sending signals from the brain to the prosthetic device. They dream of being able to delicately pick up a glass or to feel the touch of a loved one’s hand.

Stanford chemical engineering professor Zhenan Bao, PhD, and her team have spent a decade trying to help make this dream a reality, by developing a material that mimics skin and its sensory functions. Taking a big step towards this goal, they have now created a skin-like material that can tell the difference between a soft touch and a firm handshake.

Their artificial skin has two layers. The bottom layer acts as a circuit that transports pulses of electricity to nerve cells and translates these signals into biochemical stimuli that the nerve cells can detect. The top layer is a sensing mechanism composed of thin plastic embedded with billions of carbon nanotubes. When pressure is put on the plastic, the nanotubes are squeezed closer together enabling them to conduct electricity. What’s new is that the top layer can now detect pressure over the same range as human skin.

According to a Stanford news release:

This allowed the plastic sensor to mimic human skin, which transmits pressure information to the brain as short pulses of electricity, similar to Morse code. Increasing pressure on the waffled nanotubes squeezes them even closer together, allowing more electricity to flow through the sensor, and those varied impulses are sent as short pulses to the sensing mechanism. Remove pressure, and the flow of pulses relaxes, indicating light touch. Remove all pressure and the pulses cease entirely.

A paper describing Bao’s new research has just been published in Science. As Bao comments in the release, “We have a lot of work to take this from experimental to practical applications. But after spending many years in this work, I now see a clear path where we can take our artificial skin.”

Jennifer Huber, PhD, is a science writer with extensive technical communications experience as an academic research scientist, freelance science journalist, and writing instructor. 

Previously: Stanford researchers develop transparent, stretchable skin-like sensorStretchable solar cells could power electronic ‘super skin’ and Neuroscientists dream big, come up with ideas for prosthetics, mental health, stroke and more
Photo by Bao Lab

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