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  • richardmitnick 3:03 pm on April 11, 2019 Permalink | Reply
    Tags: , Helical Carotenoid Protein, , Optogenetics, Photoprotection,   

    From Michigan State University: “MSU researchers discover light absorbing protein in cyanobacteria” 

    Michigan State Bloc

    From Michigan State University

    April 11, 2019

    Igor Houwat
    MSU-DOE Plant Research Laboratory office
    (517) 353-2223
    houwatig@msu.edu

    1

    Cyanobacteria are tiny, hardy organisms. Each cell is 25 times smaller than a human hair. Their collective ability to do photosynthesis is why we have air to breathe and a diverse and complex biosphere.

    Scientists are interested in what makes cyanobacteria great at photosynthesis. Some want to isolate and copy successful processes which would then be repurposed for human usage, like in medicine or for renewable energy.

    One of these processes is photoprotection. It includes a network of proteins that detect surrounding light levels and protect cyanobacteria from damages caused by overexposure to bright light.

    The lab of Cheryl Kerfeld at Michigan State University recently discovered a family of proteins, the Helical Carotenoid Protein, or HCP, that are the evolutionary ancestors of today’s photoprotective proteins. Although ancient, HCP still live on alongside their modern descendants.

    This discovery has opened new avenues to explore photoprotection and for the first time, the Kerfeld lab structurally and biophysically characterizes one of these proteins. They call it HCP2. The study is in the journal BBA-Bioenergetics.

    Structurally, the HCP2 is a monomer when isolated in a solution, but in its crystallized form, it curiously shows up as a dimer.

    “We don’t think that the dimer is the protein’s form when it is in the cyanobacteria,” says Maria Agustina Dominguez-Martin, a post-doc in the Kerfeld lab. “Most likely, HCP2 binds to a yet unknown partner. The dimer situation during crystallization is artificial, because the only available molecules in the environment are others like itself.”

    The scientists try to determine HCP2s functions. It is a good quencher of reactive oxygen species, damaging byproducts of photosynthesis. But since many other proteins can do that as well, Dominguez-Martin doesn’t think that is HCP2’s main function.

    “We have yet to identify a primary function,” Dominguez-Martin says. “The difficulty is that the HCP family is a recent discovery, so we don’t have much basis for comparison.”

    The ability to detect light is key for applications, especially in biotech. One promising area is optogenetics, a technology that uses light to control living cells. Optogenetics systems are like light switches that activate predetermined functions when struck by a light source.

    HCP2 could play a part in such applications. But this is all far down the road.

    “There are 9 evolutionary families of HCP to explore,” Dominguez-Martin said. “That adds up to hundreds of variants with possibly distinctive functions that we have yet to discover. With that in mind, we’re characterizing other proteins from the HCP family to expand our available data set.”

    Because these proteins likely play a role in photoprotection, they may represent a system that scientists could engineer for “smart photoprotection,” reducing wasteful photoprotection which would then help photosynthetic organisms become more efficient.

    See the full article here .


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    Michigan State University (MSU) is a public research university located in East Lansing, Michigan, United States. MSU was founded in 1855 and became the nation’s first land-grant institution under the Morrill Act of 1862, serving as a model for future land-grant universities.

    MSU pioneered the studies of packaging, hospitality business, plant biology, supply chain management, and telecommunication. U.S. News & World Report ranks several MSU graduate programs in the nation’s top 10, including industrial and organizational psychology, osteopathic medicine, and veterinary medicine, and identifies its graduate programs in elementary education, secondary education, and nuclear physics as the best in the country. MSU has been labeled one of the “Public Ivies,” a publicly funded university considered as providing a quality of education comparable to those of the Ivy League.

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  • richardmitnick 5:52 pm on December 17, 2017 Permalink | Reply
    Tags: , , Dheeraj Roy, Existing theories about memory formation and storage are wrong or at least incomplete, Light-Triggered Genes Reveal the Hidden Workings of Memory, Nobel laureate Susumu Tonegawa, Optogenetics, , The brain creates multiple copies of memories at once — even though it hides the long-term copy from our awareness at first, Tracking Memories Cell by Cell   

    From Quanta: “Light-Triggered Genes Reveal the Hidden Workings of Memory” 

    Quanta Magazine
    Quanta Magazine

    December 14, 2017
    Elizabeth Svoboda

    1
    Eero Lampinen for Quanta Magazine

    Neuroscientists gained several surprising insights into memory this year, including the discovery that the brain creates multiple copies of memories at once — even though it hides the long-term copy from our awareness at first.

    Nobel laureate Susumu Tonegawa’s lab is overturning old assumptions about how memories form, how recall works and whether lost memories might be restored from “silent engrams.”

    Susumu Tonegawa’s presence announces itself as soon as you walk through the door of the Massachusetts Institute of Technology’s Picower Institute for Learning and Memory. A three-foot-high framed photograph of Tonegawa stands front and center in the high-ceilinged lobby, flanked by a screen playing a looping rainbow-hued clip of recent research highlights.

    The man in the portrait, however, is anything but a spotlight-seeker. Most days, he’s ensconced in the impenetrable warren of labs and offices that make up Picower’s fifth floor. His hair, thick and dark in the photo, is now a subdued silver, and today, a loosely draped blue cardigan replaces the impeccable suit jacket. His accommodating, soft-spoken manner belies his reputation as a smasher of established dogma, or at least as a poker of deep and abiding holes.

    Along with his MIT neuroscientist colleague Dheeraj Roy and others, Tonegawa is upending basic assumptions in brain science. Early this year, he reported that memory storage and retrieval happen on two different brain circuits, not on the same one as was long thought. His team also showed that memories of an event form at the same time in the brain’s short-term and long-term storage areas, rather than moving to long-term storage later on. Most recently (and tantalizingly), his lab demonstrated what could someday be a way to bring currently irretrievable memories back into conscious awareness.

    Tonegawa, now MIT’s Picower Professor of Biology and Neuroscience, first carved out his maverick identity back in the 1980s. While at the Basel Institute for Immunology in Switzerland, he published a theory — first seen as heretical, then brilliant — that immune cells reshuffle their DNA to create millions of different antibodies from a small number of genes. His discovery won him the Nobel Prize in 1987, which explains the oversized lobby portrait. Most researchers would have stayed in the field and basked in the attention, but Tonegawa left immunology behind entirely. He spent the next couple of decades reinventing himself as a master of memory’s workings at the cellular level.

    Despite his professional stature, Tonegawa is no TED-circuit regular or fount of startup concepts. Instead of selling his ideas or his persona, he prefers to let his data speak for themselves. And they do, perhaps more loudly than some of his colleagues would like. “The way he continues to disrupt and innovate is really striking,” said Sheena Josselyn, a neuroscientist at Toronto’s Hospital for Sick Children who also studies memory formation. “He tackles the tough questions. He doesn’t do something that is easy and expected.”

    Tracking Memories Cell by Cell

    Upon meeting Tonegawa, I sensed that he considers his fame a slightly cumbersome side effect of his vocation. The day I visited his office, he was immersed in research banter with a colleague, breaking away only reluctantly to revisit his own journey. The whole immunology sideline, he told me, was something of an accident — his real love has always been molecular biology, and immunology was a fascinating expression of that. He ended up at Basel mostly because his U.S. work permit had run out. “Immunology was a transient interest for me,” he said. “I wanted to do something new.”

    2
    After making Nobel Prize-winning contributions to immunology, Susumu Tonegawa, now a professor of biology and neuroscience at the Massachusetts Institute of Technology, focused his passion for molecular biology on the brain. Tonegawa Lab.

    That “something” turned out to be neuroscience, which Francis Crick and other well-known biologists were touting as the wave of the future. In the late 1980s and early ’90s, researchers knew relatively little about how the cellular and molecular workings of the brain underpin its capabilities, and nothing excited Tonegawa more than mapping unexplored territory.

    Tonegawa’s venture into brain science wasn’t a complete turnabout, though, because he brought some of his investigative techniques with him. He had been using transgenic (genetically modified) mice in his immunology studies, knocking out particular genes and observing the physical effects, and he used a similar approach to uncover the biological basis of learning and memory. In an early MIT study, he bred mice that did not produce a particular enzyme thought to be important in cementing long-term memories. Although the behavior of the mutant mice seemed mostly normal, further testing showed that they had deficiencies in spatial learning, confirming the enzyme’s key role in that process.

    With that high-profile result, Tonegawa was off and running. About 10 years ago, he was able to take his work to a new level of precision in part by employing a technique called optogenetics. Developed by the Stanford University bioengineer Karl Deisseroth and others, the technique involves modifying the genes of lab animals so that their cells express a light-sensitive protein called channelrhodopsin, derived from green algae. Researchers can then activate these cells by shining light on them through optical fibers. Tonegawa and his colleagues use optogenetics to generate neural activity on command in specified regions of the brain.

    This method has allowed Tonegawa to show that existing theories about memory formation and storage are wrong, or at least incomplete. This past summer, along with Roy and other colleagues, he reported that — contrary to neuroscience dogma — the neural circuit in the brain structure called the hippocampus that makes a particular memory is not the same circuit [Cell] that recalls the memory later. Instead, retrieving a memory requires what the scientists call a “detour circuit” in the hippocampus’s subiculum, located just off the main memory-formation circuit.

    To illustrate the discovery for me, Roy called up an image of a magnified brain slice in the lab. “What you’re looking at is the hippocampus section of a mouse,” he said. He gestured to a dense cloud of glowing green neurons in the upper right — the subiculum itself — and explained that his team had genetically engineered the mouse to produce channelrhodopsin only in the subiculum’s neurons. He and his team could then activate or deactivate these subiculum neurons with piped-in laser light, leaving the surrounding neurons unaffected.

    4
    Studies have shown that the hippocampus (red) is essential for creating new memories. But short-term recall of those memories depends on a “detour circuit” involving a specialized area called the subiculum (green). Dheeraj Roy/Tonegawa Lab, MIT.

    Armed with this biological switch, the researchers turned the subiculum neurons on and off to see what would happen. To their surprise, they saw that mice trained to be afraid when inside a certain cage stopped showing that fear when the subiculum neurons were turned off. The mice were unable to dredge up the fearful memory, which meant that the subiculum was needed for recall. But if the researchers turned off the subiculum neurons only while teaching the fearful association, the mice later recalled the memory with ease. A separate part of the hippocampus must therefore have encoded the memory. Similarly, when the team turned the main hippocampal circuit on and off, they found that it was responsible for memory formation, but not for recall.

    To explain why the brain would form and recall memories using different circuits, Roy framed it in part as a matter of expediency. “We think these parallel circuits help us quickly update memories,” he said. If the same hippocampal circuit were used for both storage and retrieval, encoding a new memory would take hundreds of milliseconds. But if one circuit adds new information while the detour circuit simultaneously calls up similar memories, it’s possible to apply past knowledge to your current situation much more quickly. “Now you can update on the order of tens of milliseconds,” Roy said.

    That difference might prove crucial to creatures in danger, for whom a few hundred milliseconds could mean the difference between getting away from a predator scot-free and becoming its dinner. The parallel circuits may also help us integrate present information with older memories just as speedily: Memories of a new conversation with your friend Shannon, for instance, can be added seamlessly to your existing memories of Shannon.

    Reassessing How Memories Form

    In addition to revealing that different mechanisms control memory formation and recall, Tonegawa, Roy and their colleague Takashi Kitamura (who recently moved from MIT to the University of Texas Southwestern Medical Center) have shown that memory formation itself is unexpectedly complex. Their work concerned the brain changes involved in the transformation of short-term memories to long-term memories. (In mouse experiments, short-term memory refers to recollections of events from within the past few days — what is sometimes called recent memory to distinguish it from more transient neural impressions that flicker out after only minutes or hours. Long-term memory holds events that happened on the order of two weeks or more ago.)

    For decades in neuroscience, the most widely accepted model posited that short-term memories form rapidly in the hippocampus and are later transferred to the prefrontal cortex near the brain’s surface for long-term storage. But Tonegawa’s team recently reported in Science that new memories form at both locations at the same time.

    The road to that discovery started back in 2012, when Tonegawa’s lab came up with a way to highlight brain cells known as engram cells, which hold a unique memory. He knew that when mice take in new surroundings, certain genes activate in their brains. His team therefore linked the expression of these “experiential-learning” genes in the mice to a channelrhodopsin gene, so that the precise cells that activated during a learning event would glow. “You can demonstrate those are the cells really holding this memory,” Tonegawa said, “because if you reactivate only those neurons with laser light, the animal behaves as if recalling that memory.”

    5
    In this magnified slice of brain tissue enhanced with an optogenetic protein, the green glow shows which engram cells in the hippocampus stored a short-term memory. Dheeraj Roy, Tonegawa Lab/MIT.

    In the new Science study, the team used this technique to create mice whose learning cells would respond to light. They herded each mouse into a special cage and delivered a mild electric shock to its foot, leading the mouse to form a fearful memory of the cage. A day later, they returned each mouse to the cage and illuminated its brain to activate the brain cells storing the memory.

    As expected, hippocampal cells involved in short-term memory responded to the laser light. But surprisingly, a handful of cells in the prefrontal cortex responded as well. Cortical cells had formed memories of the foot shock almost right away, well ahead of the anticipated schedule.

    Yet the researchers noticed that even though the cortical cells could be activated early on with laser light, they did not fire spontaneously when the mice returned to the cage where the foot shock happened. The researchers called these cortical cells “silent engrams” because they contained the memory but did not respond to a natural recall cue. Over the next couple of weeks, however, these cells seemingly matured and became integral for recalling the memory.

    “The dynamic is, the hippocampal engram is active [at first] and goes down, and the prefrontal-cortex engram is silent at the beginning and slowly becomes active,” Tonegawa said. This detailed understanding of how memories are laid down and stored could inform the development of drugs that aid formation of new memories.

    7
    Lucy Ikkanda-Reading/Quanta Magazine

    Some in the neuroscience community, however, think it’s prudent to be cautious in interpreting the significance of findings like these. Last year, Tonegawa’s MIT colleagues Andrii Rudenko and Li-Huei Tsai emphasized that engram science is still so new that we don’t know exactly how engram cells might work together, nor which cells contain which parts of memories. “In these early days of functional memory engram investigation,” they wrote BMC Biology, “we still do not have satisfactory answers to many important questions.”

    Tonegawa has asserted that brains contain silent engrams that could potentially be externally activated — an idea that strikes a few neuroscientists as overblown even as it excites others, according to Josselyn. “It really forces the scientific community to either update our thinking or try experiments to challenge that,” she said.

    Bringing Silent Memories to Life

    Despite the uncertainty that surrounds it, the silent-engram concept offers us the fascinating prospect of gaining access to hidden memories — a prospect that Roy, in particular, continues to explore. In October, he published a paper with Tonegawa [PNAS]that generated a flurry of excited emails from scientists and nonscientists alike. One of the paper’s blockbuster findings was that, at least in mice, it was possible to awaken silent engrams without using a laser light or optical fibers.

    8
    Dheeraj Roy, a postdoctoral associate at MIT, has collaborated with Tonegawa on several recent studies that have overturned old ideas about how memory works. Vicky Roy.

    The question the team asked themselves, Roy said, was whether they could make hidden memories permanently active with a noninvasive treatment. A cellular protein called PAK1 stimulates the growth of dendritic spines, or protrusions, that allow communication between neurons, and Roy had a hunch that this protein — when transported into brain cells — might help bring silent engrams back into direct awareness. “Can we artificially put [in] more of one gene that would make more protrusions?” he asked, excitedly noting that this approach might be simpler than optogenetics.

    To test this possibility, the researchers first gave mild shocks to mice in a cage while also suppressing their ability to make the proteins that normally cement long-term memories. When these mice returned to the same cage later on, they showed no fear, indicating that they did not naturally recall the shock in response to a cue. Yet laser light could still switch on the mice’s fearful response, which meant the memory was still there in silent-engram form.

    When the team injected these mice with the PAK1 gene to make them overproduce the protein, the animals froze up spontaneously when entering the dreaded cage. They were recalling the memory of the cage all on their own: The silent engram was coming to life. When PAK1 is administered, “you just wait four days, [and] they recover it with natural cues,” Roy said. In the future, he added, a therapeutic injection of PAK1 molecules that enter the brain’s memory cells could awaken people’s silent memories as well.

    “So it would just be an injected protein?” I asked.

    “That’s right — one molecular transporter that has one protein. People already have ways to put proteins into brain cells. I don’t think we’re that far [away] anymore.”

    It’s amazing to think that all of our minds hold hundreds or thousands of silent memories that are just waiting for the right activation to re-emerge into conscious awareness. If Roy’s findings hold true in humans, the retrieval of hidden memories might someday be as easy to initiate as getting a flu shot. “What would happen if you did that to a normal person? What would come flooding back?” I asked. “What would that experience be like?”

    “Very sci-fi, even for me,” Roy said. “My family says, ‘Is this all real?’ I say, ‘Yeah, I’m not lying to you!’”

    A few minutes later, back in Tonegawa’s office, I posed more or less the same question to him. Reactivating silent engrams could allow people with memory issues — like Alzheimer’s sufferers, soldiers who have survived explosive blasts and concussed athletes in contact sports — to regain memories that have become inaccessible. (To be sure, these people would often need to get such treatments early, before their conditions progressed and too many brain cells died.) Roy and Tonegawa’s past research [PubMed] suggests that people with cognitive difficulties have many stored memories that they simply can’t recall. But what about the rest of us who just want to mine our memories, to excavate what’s buried deep within?

    Tonegawa paused to consider. “It could be these silent memories could come out,” he said. “If you artificially increase the spine density, inject enzymes which promote spine formation, then the silent engram can be converted to active engram.”

    When I pressed him further, though, he exuded caution. It was as if he was used to hearing people like me run away with the possibilities and wanted to tamp down my expectations. Even though his lab successfully reactivated mice’s silent engrams after a few days, that’s no guarantee that silent engrams last very long, he said. And once the cells that encode particular memories die off from old age or dementia, it might be game over, no matter what kind of proteins you inject. Tonegawa pointed to Roy, who was sitting across from him. “I won’t remember his name.”

    His patience seemed to be running out. The contrarian in him, I could tell, wanted to assert that he was a student of the essential nature of things, not a pursuer of drug patents or quick cures or even the ideal of perfect recall. “I know a joke,” he said cryptically. “Not injecting protein or genes, but I keep an external brain. I hold the information in that brain.” He pointed to Roy again — the person he counts on to remember things he can’t. “The only thing I have to do is have a relationship with that person,” he explained. It’s comforting, in a way, to know that the wizard of tracing and unlocking memories also believes that no brain is an island. “It’s better,” he said, “not to memorize everything.”

    See the full article here .

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    Formerly known as Simons Science News, Quanta Magazine is an editorially independent online publication launched by the Simons Foundation to enhance public understanding of science. Why Quanta? Albert Einstein called photons “quanta of light.” Our goal is to “illuminate science.” At Quanta Magazine, scientific accuracy is every bit as important as telling a good story. All of our articles are meticulously researched, reported, edited, copy-edited and fact-checked.

     
  • richardmitnick 5:59 pm on December 15, 2017 Permalink | Reply
    Tags: , , How the prefrontal cortex is contributing to social behavior, Humans spend the majority of our time on social interactions, , New avenues of treatment for disorders that have social behavior deficits from autism to schizophrenia or dementia, Optogenetics, PNI-Princeton Neuroscience Institute,   

    From Princeton University: “Hope for autism: Optogenetics shines light on social interactions” 

    Princeton University
    Princeton University

    Dec. 14, 2017
    Liz Fuller-Wright

    1
    From left: HeeJae Jang, Malavika Murugan, Ilana Witten and their colleagues have identified a neural substrate for social learning in mice, with possible relevance to disorders like autism.
    Photo by Danielle Alio, Office of Communications.

    Ilana Witten didn’t set out to study spatial learning. She thought she was investigating how mice socialize — but she discovered that in mouse brains, the social and the spatial are inextricably linked.

    “The data had to be screaming at us for a while before we realized what was really going on,” said Witten, an assistant professor of psychology and the Princeton Neuroscience Institute (PNI). “I think it’s pretty exciting, because it’s a different way to think about how the prefrontal cortex is contributing to social behavior.” In addition, she said, the data suggest new avenues of treatment for disorders that have social behavior deficits, from autism to schizophrenia or dementia.

    “This research could help us understand autism better,” said Malavika Murugan, a PNI postdoctoral research fellow and the lead author on their Dec. 14 paper in the journal Cell.

    Most previous research on social behavior has focused on the brain’s circuits for hardwired behaviors, like aggression, sex, or mothering. Finding a neural substrate for social learning provides a different perspective into social behavior, with possible relevance to disorders such as autism, which are thought to involve abnormalities in the same brain circuitry studied in this work.

    In the future, the researchers are interested in examining how the neural substrates of social and spatial learning differ in mouse models of autism. This may shed light on the question of whether autism stems from physical causes or deficits in social learning.

    “It’s pretty exciting to see a mechanism that supports a simple form of learning about something as cool as social behavior,” Witten said. “Learning is a process of changing. Learning means that the circuit can change over time … that there could be more hope to find behavioral or other types of interventions.”

    2
    When mice socialize in non-aggressive, non-sexual situations, they often begin by sniffing each other, as seen here, before moving on to grooming behaviors. Photo by Danielle Alio, Office of Communications.

    Witten and her colleagues “are taking the best possible approach to this question by delving deep into the fundamentals of circuity that encodes and modulates social interaction,” said Karl Deisseroth, the D.H. Chen Professor of Bioengineering and of Psychiatry and Behavioral Sciences at Stanford University, who is also an investigator with the Howard Hughes Medical Institute. “New basic understanding of social circuitry is welcome, since our ability to treat disordered social/communication function (as seen in autism, for example) is severely limited.”

    In their experiments, Witten and her team gave two mice a chance to socialize in a cage that limited the mobility of one of the mice (the “social target”), so the test mouse could choose whether or not to go to the target for friendly behaviors like sniffing and grooming. Later, the test mouse was reintroduced to the test cage. When the researchers used optogenetics, a biological technique which involves the use of light to control neurons, to inhibit the key social-spatial pathway they had identified in the brain, the test mouse wandered freely through the space. When they didn’t inhibit that circuit, the test mouse preferred to spend time where it remembered socializing with the other mouse.

    In other words, the test mouse had learned where the fun hangout spot was, and chose to return. Humans engage in this sort of social-spatial association all the time, Witten noted, whether it’s visiting the hottest new club or returning to a mall, a coffee shop, a park, or another spot where we remember spending quality time with friends.

    When the “cool kids” turn an otherwise dull spot into an exciting social destination, that’s a real-life example of what Witten observed with her mice: “The social target can change the value of a location,” she said.

    Like mice, humans spend the majority of our time on social interactions, Witten said.

    “Social interactions are some of the most rewarding interactions that mammals have,” she said. “They drive all sorts of different forms of learning, the simplest being what we found here: spatial learning, contextual learning.”

    Witten and her research team performed optogenetic experiments with the mice to isolate precisely which circuits of the brain are involved in social-spatial learning. Previous research had identified that the prelimbic cortex, part of the prefrontal cortex, has three “downstream” channels into the nucleus accumbens, the amygdala, and the ventral tegmental area. Witten’s team determined that only the pathway between the prefrontal cortex and the nucleus accumbens is linked to the social-spatial learning they observed.

    Some key discoveries were made by the undergraduate researchers who make up four of the paper’s 13 co-authors, Witten said: Varun Bhave, Class of 2019; HeeJae Jang, Class of 2017; Michelle Park, Class of 2016; and Josh Taliaferro, Class of 2015.

    “Ilana really takes care and time to mentor undergraduates regardless of their academic background,” said Jang.

    Jang, who concentrated in physics, joined Witten’s lab in her junior year. “At that time, I had not taken a single neuroscience class, but Ilana very generously gave me an opportunity,” she said.

    Jang did her senior thesis with Witten, and after two years of nights and weekends in the lab, she chose to continue as a research specialist in Witten’s lab after graduation, while she prepares for medical school. “I highly recommend the Witten lab to undergrads and senior thesis writers,” Jang said.

    This work at Princeton was funded by Pew, McKnight and Sloan Foundation grants to Witten; the National Institute of Health (DP2 DA035149-01 and 5R01MH106689-02 to Witten and 1F32MH112320-01A1 to Julia Cox, a postdoctoral research fellow in PNI); a Simons Collaboration on the Global Brain Postdoctoral Fellowship to Murugan; a National Science Foundation Graduate Research Fellowship Program grant to Nathan Parker, a graduate student in PNI); and National Alliance for Research on Schizophrenia and Depression Young Investigator Awards from the Brain & Behavior Research Foundation to Witten and Alexander Nectow, a visiting associate research scholar in PNI. Witten is also a New York Stem Cell Foundation—Robertson Investigator.

    See the full article here .

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    About Princeton: Overview

    Princeton University is a vibrant community of scholarship and learning that stands in the nation’s service and in the service of all nations. Chartered in 1746, Princeton is the fourth-oldest college in the United States. Princeton is an independent, coeducational, nondenominational institution that provides undergraduate and graduate instruction in the humanities, social sciences, natural sciences and engineering.

    As a world-renowned research university, Princeton seeks to achieve the highest levels of distinction in the discovery and transmission of knowledge and understanding. At the same time, Princeton is distinctive among research universities in its commitment to undergraduate teaching.

    Today, more than 1,100 faculty members instruct approximately 5,200 undergraduate students and 2,600 graduate students. The University’s generous financial aid program ensures that talented students from all economic backgrounds can afford a Princeton education.

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  • richardmitnick 2:17 pm on July 11, 2017 Permalink | Reply
    Tags: Amygdala, Kay Tye, , Neurons, Optogenetics, ,   

    From MIT Tech Review: Women in STEM – “How the Brain Seeks Pleasure and Avoids Pain” Kay Tye 

    MIT Technology Review
    M.I.T Technology Review

    June 27, 2017
    Amanda Schaffer

    1
    Neuroscientist Kay Tye

    As a child, Kay Tye was immersed in a life of science. “I grew up in my mom’s lab,” she says. At the age of five or six, she earned 25 cents a box for “restocking” bulk-ordered pipette tips into boxes for sterilization as her mother, an acclaimed biochemist at Cornell University, probed the genetics of yeast. (Tye’s father is a theoretical physicist known for his work on cosmic inflation and superstring theory.)

    Today, Tye runs her own neuroscience lab at MIT. Under large black lights reminiscent of a fashion shoot, she and her team at the Picower Institute for Learning and Memory can observe how mice behave when particular brain circuits are turned on or off. Nearby, they can record the mice’s neural activity as the animals move toward a particular stimulus, like sugar water, or away, if they’re crossing a floor that delivers mild electric shocks. Elsewhere, they create brain slices to test in vitro, since these samples retain their physiological activity, even outside the body, for up to eight hours.

    Tye has been at the forefront of efforts to pinpoint the sources of anxiety and other emotions in the brain by analyzing how groups of neurons work together in circuits to process information. In particular, her work has contributed to a profound shift in researchers’ understanding of the amygdala, a brain area that has been thought of as central to fear responses: she has found that signaling in the amygdala can in fact reduce anxiety as well as increase it. To gain such insights, she has also made crucial advances in a technique, called optogenetics, that allows researchers to activate or suppress particular neural circuits in lab animals using light. Optogenetics was developed by Stanford neuroscientist and psychiatrist Karl ­Deisseroth, and it represented a breakthrough in efforts to determine the role of specific parts of the brain. While Tye was working in his laboratory as a postdoc, she demonstrated, for the first time, that it was possible to pinpoint and control specific groups of neurons that were sending signals to specific target neurons.

    2
    No image caption or credit.

    This fine-grained approach is important because drugs that treat conditions like anxiety currently do not target specific circuits, let alone individual neurons; rather, they operate throughout the brain, which often leads to undesirable side effects. Tye’s research may eventually help open the door to drugs that affect only specific neural circuits, reducing anxiety with fewer side effects.

    Such work has earned formal accolades, including a Presidential Early Career Award for Scientists and Engineers from President Obama, a Freedman Prize for neuroscience, and a TR35 award, recognizing outstanding researchers under the age of 35. Tye has also won high praise from others in her field who admire the creative breadth of her ambition. “She’s not afraid to ask the most fundamental questions, the ones most other scientists shy away from,” says Sheena Josselyn of the University of Toronto and the Hospital for Sick Children Research Institute.

    The questions she takes on involve emotions and phenomena that loom large in human experience, such as reward-seeking, loneliness, and compulsive overeating. Her goal is to understand their neural basis—to bridge the gap between brain, as understood by neuroscientists, and the mind, as conceived more expansively by psychiatrists, psychologists, and other students of human behavior.

    Would-be novelist

    Though it might seem as if Tye was born to be a scientist, she says her choice of career was anything but inevitable. In high school, she was ambivalent about science and gravitated instead toward writing; she wrote plays, short stories, and poetry. “In my mind, I was going to be a novelist,” she recalls.

    Still, while applying to college, she included MIT on her list, partly to humor her parents, Bik-Kwoon Tye and Henry Tye, both of whom had earned PhDs there in 1974. And when she received an acceptance letter, her father found it hard to disguise his feelings as his eyes welled with tears. “I’d never in my life seen my dad cry,” she says. She decided that she ought to give scientific learning a more dedicated try. She also convinced herself (with parental encouragement) that focusing on the natural world would give her more to write about down the road.

    As a freshman at MIT, Tye joined the lab of Suzanne Corkin, who was working with H.M., one of the most famous patients in the history of neuroscience. H.M., whose name was revealed to be Henry Molaison upon his death in 2008, suffered from profound amnesia after a lobotomy to treat seizures; studying his condition allowed researchers to probe the neural underpinnings of memory. One of Tye’s roles in the group was to make H.M. a peanut butter and jelly sandwich for lunch. He would eat it and then, moments later, with crumbs still on his face, ask, “Did we have lunch yet?”

    3
    Researchers troubleshoot behavioral boxes in which mice learn to form positive and negative associations with sounds. No image credit.

    “It made me appreciate that these basic functions, like memory, that are so key to who we are have biological substrates in the brain,” she says. Neuroscience can be intimidating and filled with jargon, she adds. But the experience with H.M., along with an inspiring introductory psychology class taught by Steven Pinker, “made it seem worth it to slog through the all-nighters” to understand the biological mechanisms behind psychological constructs.

    Still, after graduation, Tye wanted to make sure she was “looking around,” thinking about who she was and who she wanted to be. So she spent a year backpacking in Australia, where she worked on a farm, lived in a yoga ashram, taught yoga, camped out on the beach, and worked on a novel. She found that writing was “hard and lonely.” She enjoyed teaching yoga but didn’t see it as a satisfying career path.

    “I came out of that year surprisingly ready to go to grad school,” she says. Diving back into the academic world, she initially struggled to find a lab that would accept her and almost dropped out after her first year. But she found a mentor in Patricia Janak, who became her advisor, and earned a PhD in neuroscience at the University of California, San Francisco, in 2008.

    A surprise in the amygdala

    In 2009, Tye joined Deisseroth’s lab at Stanford. Deisseroth had already developed optogenetics, which gave researchers a much more precise way to identify the contributions of individual neurons within a circuit. Along with others in the lab, Tye used optogenetics to probe the connection between two parts of the amygdala, an almond-shaped region that is crucial to anxiety and fear. She first identified neurons in one area (known as the basolateral amygdala) that formed connections to neurons in another amygdalar area (known as the central nucleus) by sending out projections of nerve fibers. When she stimulated those basolateral amygdala neurons, she was able to reduce anxiety in mice. That is, she could cause the animals to spend more time in open spaces and less time cowering to the side. This was surprising, because when researchers stimulated the amygdala as a whole, the mice’s behavior grew more anxious.

    At first, everyone asked, “Are you sure you’re using the tool right? What’s going on?” she recalls. But after meticulous validation, in 2011, Tye and the group published their results in Nature, showing that some circuitry within the amygdala helps to calm animals down. This paper also represented a breakthrough in optogenetic technique. For the first time, researchers were able to zero in on and manipulate a specific part of a brain circuit: particular groups of neurons communicating with known target neurons. The technique, known as optogenetic projection-specific manipulation, is now considered one of the key tools of neuroscience.

    In 2012, Tye came to MIT as an assistant professor of brain and cognitive sciences at the Picower, continuing her work on anxiety. While setting up her lab, she targeted neurons within the amygdala that seemed to have the opposite effect on mouse anxiety, causing it to increase. These brain cells are also located in the basolateral amygdala, but they send projections to a nearby region known as the ventral hippocampus. When Tye stimulated this circuit using optogenetics, the mice avoided open spaces, apparently suffering from anxiety. (When she inhibited the connections from forming, the animals hung out in the open again, their anxiety seemingly alleviated.) Tye proposed that neighboring neurons in the amygdala can have opposite effects on animals’ behavior, depending on the targets to which they send signals.

    4
    Tye lab grad students Chris Leppla and Caitlin Vander Weele and postdocs Praneeth Namburi and Stephen Allsop. No image credit.

    Threats and rewards

    At the time, most researchers studying the amygdala still tended to focus mainly on its role in fear. Yet Tye suspected that activity in this part of the brain might encode a stimulus as either rewarding or threatening, good or bad, helping individuals decide how to respond. “There are many stimuli we encounter in our daily lives that are ambiguous,” says Conor ­Liston of the Brain and Mind Research Institute at Weill Cornell. “A social interaction, for example, can be either threatening or rewarding, and we need brain circuits devoted to differentiating which is which.”

    By looking at the relative strength of the currents passing through two glutamate receptors known to indicate synaptic strength, Tye discovered that different neural connections in mice were reinforced depending on whether a particular stimulus was linked to a reward or a threat. When mice learned to associate a sound with a treat of sugar, she found stronger synaptic input to the neurons in the basolateral amygdala that were sending information to the nucleus accumbens, which is part of the brain’s reward circuitry. On the other hand, when mice learned to associate the sound with mild electric shocks to their feet, input signals grew stronger in circuits leading from the basolateral amygdala to the centromedial amygdala, which is involved in pain and fear. In addition, she demonstrated a trade-off: when one of these circuits grew more active, the other grew less so. In other words, she had found how the brain encodes information that allows mice to differentiate between stimuli that are rewarding and those that are potentially harmful. The results were published in Nature in 2015.

    In recent work, Tye also probed the circuitry involved in making split-second decisions when both threatening and rewarding cues are present at the same time. She and her team focused this time on connections between the amygdala and the prefrontal cortex, an area responsible for higher-order thinking. (Specifically, they examined interactions between the basolateral amygdala and the prelimbic medial prefrontal cortex.) Using optogenetics and other techniques, they showed that this circuitry was active when the animals were simultaneously exposed to a potential sugar treat and a potential electric shock and had to make a decision about how to behave. Her results, which appeared in April in Nature Neuroscience, help illuminate how animals figure out what to do in the face of complex and sometimes contradictory cues.

    5
    Grad student Caitlin Vander Weele examines magnified images of brain slices to verify that a calcium sensor is targeting a specific type of neuron. No image credit.

    Cravings and compulsions

    As a graduate student, Tye had worked with researchers focused on addiction, but she was more interested in natural rewards, like sugar, than in substances that are regularly abused. In 2012, New York City mayor Michael Bloomberg announced a plan to limit the portion size of sodas sold in movie theaters, stadiums, and fast-food restaurants. Tye found herself wondering what exactly, at a brain level, causes people to crave sugary treats, above and beyond the normal drive to satisfy hunger.

    So she delved into the neural circuitry. In a paper published in 2015 in Cell, she and her team focused on neurons in the lateral hypothalamus (LH), a brain area involved in drives like hunger, and studied their projections into another region, called the ventral tegmental area (VTA), known to play a role in both motivation and addiction. Using optogenetics, she and her team showed that turning on specific LH-VTA connections caused the mice to gorge on sugar, while turning them off reduced the compulsive overeating.

    On her desktop, Tye loads a video demonstration featuring a mouse with a cable for light transmission attached to its brain. The video shows the mouse moving around, casually at first. Then, when the laser light is turned on to activate specific neurons in the LH-VTA circuit, the animal becomes frantic, running and licking the floor. Soon after, it brings its empty paws up to its mouth and does a pantomime of tasting and nibbling. “It engages in this complicated motor sequence and pretends to eat, which is crazy because there’s no food,” says Tye. In other words, turning the circuit on causes the animal to behave compulsively. Turning it off has the opposite effect.

    Crucially, though, while switching off this circuit prevents compulsive behavior, it does not affect normal eating. That is, it is possible to define a brain-based difference between at least some healthy and unhealthy drives to eat. This suggests that it might be possible to develop targeted drugs or even some form of biofeedback that might someday help people reduce unhealthy cravings without blocking ordinary hunger.

    Another recent finding, about loneliness, arose serendipitously from a project that postdoc Gillian Matthews had begun as a graduate student at Imperial College London with Mark Ungless. ­Matthews noticed that mice that had been isolated for 24 hours during experiments displayed stronger neural signaling in the brain’s dorsal raphe nucleus, which participates in reward signaling—and actively sought out the company of other mice. After she moved to Tye’s lab at MIT, Matthews and Tye developed the theory that the animals were craving interaction. In further experiments, they used optogenetics to turn off the signaling pathway in the dorsal raphe nucleus. Mice subjected to this treatment did not seem to seek out additional social interaction following time by themselves.

    Ultimately, Tye hopes that she and her team can speak to fundamental human questions, like why some people prefer to spend more time alone while others crave greater social contact.

    A lab without drama

    Though Tye’s lab is interested in the origins of phenomena like fear and compulsion, it is notable for its own lack of tension and conflict. Stephen Allsop, a postdoc who has worked with her for five years (several of which were spent as a graduate student), says that she stresses close collaboration among team members and oversees an upbeat, supportive culture: “It’s amazing how little drama we have in this lab.”

    “Along with scientific integrity, I make the positive, collaborative, open culture of my research group—and the happiness of the individuals within it—my top priority,” says Tye. “Scientific excellence is a close second.” Strong relationships with professors and mentors are part of the draw of science, she adds.

    Indeed, she says, they are second only to the bonds between parents and children. In 2013, Tye and her husband, Jim Wagner, a software developer, had a daughter, Keeva, who has already accompanied her to conferences around the world. Their son, Jet, was born last year. And the children have found a place in her lab, much as she found a niche in her mother’s (though they have yet to earn paid positions). As she told Nature when Keeva was still an infant: “If my daughter all of a sudden needs to be picked up, I bring her to my lab meeting or meet with people while I bounce her. If she has a total meltdown, then sometimes I have to bail and follow up later.”

    But while she may be easygoing as a parent and a lab leader, Tye finds plenty of drama in neuroscience itself, and she keeps returning to its central questions because they are so enticing. Though she says she reads fewer novels now than she used to, she still seems compelled by the kinds of mysteries a writer might probe: Why does a hero set out on a journey? Why does the chatter in his or her head go awry and lead to gloomy soliloquizing or anxious self-sabotage? Like a novelist, she exhibits tremendous creative breadth. “There is something special about science,” she says. “Your new work is based on what you did previously. And if you’re lucky, you can help shape the future.”

    See the full article here .

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  • richardmitnick 10:36 am on June 28, 2017 Permalink | Reply
    Tags: , , channelrhodopsin-2, , , Optogenetics, Purkinje cells,   

    From U Washington: “Study shines light on brain cells that control movement” 

    U Washington

    University of Washington

    06.26.2017
    Michael McCarthy
    Media contact:
    Leila Gray
    206.685.0381

    1
    In this image of neurons in the cerebellum of the brain, the yellow cells are Purkinje cells in which the channelrhodopsin-2 gene is being produced. Horwitz Lab/UW Medicine

    UW Medicine researchers have developed a technique for inserting a gene into specific cell types in the adult brain in an animal model.

    Recent work shows that the approach can be used to alter the function of brain circuits and change behavior. The study appears in the journal Neuron in the NeuroResources section.

    Gregory Horwitz, associate professor of physiology and biophysics at the University of Washington School of Medicine in Seattle, led the research team. He said that the approach will allow scientists to better understand what roles select cell types play in the brain’s complex circuitry.

    Researchers hope that the approach might someday lead to developing treatments for conditions, such as epilepsy, that might be curable by activating a small group of cells

    “The brain is made up of a mix of many cell types performing different functions. One of the big challenges for neuroscience is finding ways to study the function of specific cell types selectively without affecting the function of other cell types nearby,” Horwitz said. “Our study shows it is possible to selectively target a specific cell type in an adult brain using this technique and affect behavior nearly instantly.”

    In their study, Horowitz and his colleagues at the Washington National Primate Research Center in Seattle inserted a gene into cells in the cerebellum, a small structure located at the back of the brain and tucked under the brain’s larger cerebrum.

    The cerebellum’s primary function is controlling motor movements. Disorders of the cerebellum generally lead to often disabling loss of coordination. Recent research suggests the cerebellum may also be important in learning and may be involved in such conditions as autism and schizophrenia.

    The cells the scientists selected to study are called Purkinje cells. These cells, named after their discoverer, Czech anatomist Jan Evangelista Purkinje, are some of the largest in the human brain. They typically make connections with hundreds of other brain cells.

    “The Purkinje cell is a mysterious cell,” said Horwitz. “It’s one of the biggest and most elaborate neurons and it processes signals from hundreds of thousands of other brain cells. We know it plays a critical role in movement and coordination. We just don’t know how.”

    The gene they inserted, called channelrhodopsin-2, encodes for a light-sensitive protein that inserts itself into the brain cell’s membrane. When exposed to light, it allows ions – tiny charged particles – to pass through the membrane. This triggers the brain cell to fire.

    The technique, called optogenetics, is commonly used to study brain function in mice. But in these studies, the gene must be introduced into the embryonic mouse cell.

    “This ‘transgenic’ approach has proved invaluable in the study of the brain,” Horwitz said. “But if we are someday going to use it to treat disease, we need to find a way to introduce the gene later in life, when most neurological disorders appear.”

    The challenge for his research team was how to introduce channelrhodopsin-2 into a specific cell type in an adult animal. To achieve this, they used a modified virus that carried the gene for channelrhodopsin-2 along with segment of DNA called a promoter. The promoter stimulates the cell to start expressing the gene and make the channelrhodopsin-2 membrane protein. To make sure the gene was expressed only by Purkinje cells, the researchers used a promoter that is strongly active in Purkinje cells, called L7/Pcp2.”

    In their paper, the researchers reported that by painlessly injecting the modified virus into a small area of the cerebellum of rhesus macaque monkeys, the channelrhodopsin-2 was taken up exclusively by the targeted Purkinje cells. The researchers then showed that when they exposed the treated cells to light through a fine optical fiber, they were able stimulate the cells to fire at different rates and affect the animals’ motor control.

    Horwitz said that it was the fact that Purkinje cells express L7/Pcp2 promoter at a higher rate than other cells that made them more likely to produce the channelrhodopsin-2 membrane protein.

    “This experiment demonstrates that you can engineer a viral vector with this specific promoter sequence and target a specific cell type,” he said. “The promoter is the magic. Next, we want to use other promoters to target other cell types involved in other types of behaviors.”

    Horwitz coauthors were: lead author Yasmine El-Shamayleh, a postdoctoral fellow; Yoshiko Kojima, an acting instructor; and Robijanto Soetedjo, a UW School of Medicine research associate professor of physiology and biophysics. All are researchers at the Washington National Primate Research Center.

    This study was funded by National Institutes of Health grants to the researchers; an NIH Office of Research Infrastructure Programs grant to the Washington National Primate Research Center, and a National Eye Institute Center Core Grant for Vision Research to the University of Washington School of Medicine.

    See the full article here .

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    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
  • richardmitnick 6:31 am on September 8, 2016 Permalink | Reply
    Tags: , Karl Deisseroth at Stanford University and Ed Boyden at the Massachusetts Institute of Technology, , Optogenetics, , Zhuo-Hua Pan   

    From SA: “He May Have Invented One of Neuroscience’s Biggest Advances–but You’ve Never Heard of Him” 

    Scientific American

    Scientific American

    September 6, 2016
    Anna Vlasits

    1
    Credit: KIYOSHI TAKAHASE SEGUNDO Getty Images, iStockphoto, Thinkstock

    The next revolution in medicine just might come from a new lab technique that makes neurons sensitive to light. The technique, called optogenetics, is one of the biggest breakthroughs in neuroscience in decades. It has the potential to cure blindness, treat Parkinson’s disease, and relieve chronic pain. Moreover, it’s become widely used to probe the workings of animals’ brains in the lab, leading to breakthroughs in scientists’ understanding of things like sleep, addiction, and sensation.

    So it’s not surprising that the two Americans hailed as inventors of optogenetics are rock stars in the science world. Karl Deisseroth at Stanford University and Ed Boyden at the Massachusetts Institute of Technology have collected tens of millions in grants and won millions in prize money in recent years. They’ve stocked their labs with the best equipment and the brightest minds. They’ve been lauded in the media and celebrated at conferences around the world. They’re considered all but certain to win a Nobel Prize.

    There’s only one problem with this story:

    It just may be that Zhuo-Hua Pan invented optogenetics first.

    1
    Zhuo-Hua Pan

    Even many neuroscientists have never heard of Pan.

    Pan, 60, is a vision scientist at Wayne State University in Detroit who began his research career in his home country of China. He moved to the United States in the 1980s to pursue his PhD and never left. He wears wire-rimmed glasses over a broad nose framed by smile-lines in his cheeks. His colleagues describe him as a pure scientist: modest, dedicated, careful.

    Pan was driven by a desire to cure blindness. In the early 2000s, he imagined that putting a light-sensitive protein into the eye could restore vision in the blind—compensating for the death of rods and cones by making other cells light-sensitive.

    That was the germ of the idea of optogenetics—taking a protein that converts light into electrical activity and putting it into neurons. That way, scientists could shine light and stimulate the neurons remotely, allowing them to manipulate brain circuits. Others had experimented with trying to make neurons light-sensitive before, but those strategies hadn’t caught on because they lacked the right light-sensitive protein.

    That all changed with the first molecular description [PNAS] of channelrhodopsin, published in 2003.

    Channelrhodopsin, a protein made by green algae, responds to light by pumping ions into cells, which helps the algae search out sunlight.

    That “was one of the most exciting things in my life,” Pan said. “I thought, wow! This is the molecule we are looking for. This is the light sensor we are looking for.”

    By February 2004, he was trying channelrhodopsin out in ganglion cells—the neurons in our eyes that connect directly to the brain—that he had cultured in a dish. They became electrically active in response to light. Over the moon with excitement, Pan applied for a grant from the National Institutes of Health. The NIH awarded him $300,000, with the comment that his research was “quite an unprecedented, highly innovative proposal, bordering on the unknown.”

    Pan didn’t know it at the time but he was racing against research groups across the United States and around the world to put channelrhodopsin into neurons.

    Deisseroth and Boyden were working at Stanford, where Deisseroth was finishing a postdoc and Boyden was finishing graduate school. At least two other groups were in the game as well, led by Stefan Herlitze and Lynn Landmesser, who were at Case Western Reserve University at the time, and Hiromu Yawo at Tohoku University in Japan.

    And they were by no means the only scientists experimenting with ways to control neurons with light. By 2004, Gero Miesenbock and Richard Kramer had already published articles using other, more complicated molecules for that purpose. But channelrhodopsin was the tool that was about to revolutionize the field.

    The Stanford group had been toying with the idea of controlling neurons with light for quite some time. They had also noticed the paper about the discovery of channelrhodopsin. Deisseroth got in touch with the paper’s author, Georg Nagel, in March 2004 (a month after Pan’s first success getting channelrhodopsin into neurons) and asked if Nagel would collaborate, sharing the channelrhodopsin DNA so Boyden could try it out in neurons. Nagel shared the DNA, and in August 2004, Boyden shined light on a brain neuron in a dish and recorded electrical activity from the channelrhodopsin.

    Pan had done the same thing with retina neurons six months earlier. But then he got scooped.

    ‘We didn’t feel very lucky’

    Boyden, who is now a professor at MIT, was surprised when told by STAT that Pan ran the experiment first.

    “Wow. Interesting. I didn’t know that,” Boyden said.

    “It’s funny to think about how science regards when something is proven,” he added, noting that scientists build on each others’ work, sometimes working together while at other times working in parallel, scrambling onto one another’s shoulders. “There’s both intentional and unintentional teamwork,” he said.

    The Stanford press office said Deisseroth was unavailable. In response to questions provided by STAT, spokesman Bruce Goldman wrote that Pan’s study was “a far cry from the use of optogenetics … to open up a new world of precision neuroscience. That’s the potential revealed in Dr. Deisseroth’s widely cited 2005 publication.”

    Pan said he might have mentioned the timing of his experiment to Boyden once several years ago, but, Pan said, “I didn’t want to take too much time to talk about this because people feel uncomfortable.”

    That sentiment is in keeping with Pan’s wider approach—diligent, reserved, outside the limelight. Wayne State is a small university not known for its scientific research. Pan had gone to a state school for his PhD, then done mostly obscure research for decades. These things may have contributed to what happened next, when he tried to get his invention out into the world: It wasn’t seen as the big advance it was.

    Pan spent the summer of 2004 figuring out how to get the channelrhodopsin protein into a living eye. He settled on the idea of using a virus, which could infect cells in the eye and sneak the channelrhodopsin DNA inside. His colleague, Alexander Dizhoor, a professor at Salus University, engineered the channelrhodopsin DNA to add the gene for a protein that fluoresced green under blue light, so they could track where the channelrhodopsin ended up.

    In July 2004, Pan dosed his first rat with the virus. About five weeks later, he looked at the retinas to see if it had worked. What he saw was a sea of green—thousands of ganglion cells had the green protein coupled to channelrhodopsin in their membranes. And when he stuck an electrode in one of those cells and turned on a lamp, the cell responded with a flurry of electrical activity. The channelrhodopsin was working. It was just a first step, but it was a revolutionary step—indicating that Pan’s method may just be able to restore sight to the blind.

    “Everything turned out beautifully,” Pan said.

    So Pan and Dizhoor wrote a paper about their work and submitted it to Nature on November 25, 2004, according to the submission letter Pan shared with STAT. The editors at Nature suggested they send it on to a more specialized journal called Nature Neuroscience, which rejected it. Early the next year, Pan sent the paper to the Journal of Neuroscience, where it was reviewed but then again rejected.

    Disheartened, Pan set to work revising his paper, and in May 2005 traveled to Fort Lauderdale, Fla. for the Association for Research in Vision and Opthamology conference, where he described his work using channelrhodopsin in neurons. That single lecture, lasting just 15 minutes, would come to be his clearest stake along the timeline of invention.

    It was what came next that would make that stake matter. A few months later, in August of 2005, Nature Neuroscience published a paper about using channelrhodopsin to make neurons sensitive to light. The paper was by Edward Boyden and Karl Deisseroth.

    Pan heard the news from a colleague who emailed him the paper. “I felt terrible. I felt terrible,” Pan said, pausing. “We didn’t feel very lucky.”

    Met with a shrug

    Deisseroth and Boyden’s paper was slightly different than Pan’s. They simply demonstrated that they could use channelrhodopsin to control neurons’ activity in a dish; Pan had waited to publish until he could make it work in a live animal. And Deisseroth and Boyden had shown incredibly precise time control, by turning the light on for just a millisecond. But their technical feat was essentially the same: They had used channelrhodopsin to successfully make neurons in a dish respond to illumination.

    The Stanford paper took a little while to take off, but take off it did. The work jump-started both Deisseroth’s and Boyden’s careers, landing them big money grants and talented students for their labs—Deisseroth at Stanford and Boyden at MIT. The New York Times started writing about Deisseroth’s breakthroughs with optogenetics in 2007, and the citations of the research paper took off exponentially.

    By the time Pan finally managed to publish his paper, in Neuron in April 2006, it was mostly met with a shrug. Richard Kramer, a neuroscientist at UC Berkeley who was also studying vision, remembers, “It wasn’t that creative, it was just ‘Oh look, you can put channelrhodopsin in neurons from the brain, you can also put it in neurons from the retina.’ Was it impressive? No.”

    Those handful of months seem to have made all the difference.

    Why didn’t Pan’s paper get published first? He may never know the answer. After Boyden’s paper came out, Pan wrote to the editor at Nature Neuroscience asking how they could have rejected his paper but published Boyden’s.

    In her response, the editor replied that while the papers were similar, Boyden et al. presented theirs as a new technology rather than as a scientific finding. Pan’s paper, it seemed, was too narrow, only focusing on using channelrhodopsin to restore vision, while Boyden’s paper took the broad view of thinking of channelrhodopsin as a tool for neuroscience in general.

    The reviews that other researchers submitted to the Journal of Neuroscience shed some more light on what people thought of Pan’s paper. One reviewer liked it and had some minor suggestions for improvement. The other, in a single long paragraph, said the research was “ambitious” and “very preliminary” and concluded that “there is too little here to entice most neuroscientists.”

    In hindsight, Pan’s coauthor Dizhoor can’t help but laugh while reading that. Reviewers would ultimately greenlight an expanded version of Pan’s paper, in 2006, with minimal revisions.

    But that hasn’t elevated Pan to the optogenetics pantheon. In terms of publication, he was quite late to the party, with three different groups publishing papers about channelrhodopsin before he did. He didn’t share in two big prizes that recently went to Deisseroth and Boyden, the Brain Prize in 2013 (1 million euros split between six inventors of optogenetics) and the Breakthrough Prize in 2015 ($3 million each to Boyden and Deisseroth).

    Since 2005, Deisseroth has been awarded over $18 million in NIH grants for his work on optogenetics, and Boyden has received more than $10 million. Both have other major projects that bring in additional funding to their labs each year. Boyden is a prolific speaker who’s given multiple TED talks; Deisseroth was the subject of an in-depth profile in the New Yorker in 2015.

    Pan, on the other hand, has cumulatively received just over $3 million over the past 10 years and holds one NIH grant—the bare minimum to keep a research program going. Most of the accolades for his work have come from Wayne State University. According to his website, he’s been invited to give a couple of talks—most recently at a technology show in Russia.

    Rules of the invention game

    The whole saga raises the question of what it means to invent something in science. It’s a question that has plagued scientists in recent years—including the ongoing CRISPR patent fight—as research becomes ever more global and the spoils of biotechnology and medical discoveries become ever more valuable.

    The answer, it turns out, shifts depending on context.

    Fellow academics often consider the first scientists to publish a paper on a technique the discoverers or inventors of that technique.

    But that metric can be problematic, as Pan’s experience shows. In a recent essay in the journal eLife, Ronald Vale and Anthony Hyman, two biologists, laid out the problem. They point out that “the delay between the submission of a paper and its publication can range from a few weeks to more than two years,” adding that journals “slow down and create inequities in how knowledge is transferred from the scientist to the worldwide scientific community.”

    And reviewers can be biased toward familiar names or prestigious institutions. Blinded review, in which the author’s name is redacted, has been suggested as a way to minimize that effect, but many scientists are skeptical that it would work, since research is often discussed ahead of time at conferences.

    Vale and Hyman advocate, instead, for scientists to post drafts of their work on “preprint servers” such as bioRxiv before they submit it to journals. If such a server had been widely used by neuroscientists in 2004, Pan could have posted his rejected findings there, staking his claim.

    But whether that would mean he would be on the short list for the Nobel Prize is unclear. Kramer thinks that even if Pan had published on bioRxiv, he’d be shut out because he wasn’t the first to publish a peer-reviewed paper on the technique. That’s what will matter if and when the inventors of optogenetics win the Nobel.

    The legal system doesn’t play by quite the same rules. According to an American Bar Association representative specializing in patent law, to prove precedence for a patent in the early 2000s, most of the time you needed to show both “when someone had actually conceived of the invention—that’s sort of in your mind the lightbulb going off, ‘Aha! I have it!’—and when the invention was reduced to practice—that means you’ve actually done it and you’ve proven that your idea can work.”

    By those standards, a discovery happens at the time of its demonstration in the lab, even before it’s been posted on a preprint server.

    Then there’s the court of public opinion. Scientists are increasingly public personalities, running Twitter accounts and appearing on late-night talk shows.

    “The quality rising to the top is a little more influenced by non-scientific things than it used to be,” said Richard Masland, an emeritus professor at Harvard Medical School, who also holds patents on gene therapy for blindness.

    Being at Wayne State University might have meant that Pan didn’t have the resources to get a high-profile paper published. There’s the actual costs of doing high quality of research, but in addition, senior researchers at top universities usually mentor junior professors, reading their work and helping them take it to the next level.

    Pan agrees that fact may have put him at a disadvantage compared with scientists at prestigious institutions like MIT or Stanford. “Of course, I cannot prove that with evidence,” he said. And Pan’s modesty and non-native language abilities may have kept him from promoting himself as well as Boyden and Deisseroth did.

    “He’s just not as public a speaker and presenter as other people in the field. And this is an important part of the whole game of being able to get out there and sell yourself,” Kramer, the UC Berkeley vision researcher, said.

    That publicity can be self-reinforcing. Landmesser, the Case Western professor who worked on channelrhodopsin in the beginning, said, “I think there’s always a tendency [that] whoever gets there first gets more publicity, let’s put it that way.”

    A university PR video can spawn a national news article, which spurs someone to think of your name in nominations for a nice cash prize, which leads to some TV appearances. The word “inventor” gets used at some point and before you know it you’re Google’s automatic answer to the question “Who invented optogenetics?”

    Ultimately, both Pan and the team of Boyden and Deisseroth won patents for their discoveries.

    Pan’s May 2005 lecture threatened to derail the Boyden-Deisseroth patent for a while—the US patent office rejected it multiple times because Pan’s abstract was published more than a year before they got around to filing.

    Eventually, Deisseroth and Boyden signed a document stating that they had invented this method of using channelrhodopsin privately in the lab before Pan’s conference abstract was published. The relevant patent was issued in March 2016, almost 10 years after they filed.

    Now, Deisseroth is a cofounder and scientific advisor at Circuit Therapeutics, a company developing a wide range of therapies based on optogenetics, presumably using Deisseroth’s patented inventions. (Circuit Therapeutics declined to comment on specifics of their intellectual property licenses.)

    Pan won a patent as well, to use channelrhodopsin to restore vision in the eye. His patent was licensed by RetroSense, which won an award from the Angel Capital Association in 2015. Retrosense—whose CEO in passing told STAT about Pan’s role in the invention of optogenetics—began clinical trials this year to put the algae proteins in blind people using gene therapy. It’s the first application of optogenetics in humans and the first time a non-human gene is being used in a gene therapy trial.

    Right now, there are blind people in Texas walking around with algae DNA and proteins in their eyes. And that was what Pan was in it for all along. “One thing I still feel glad about is that even right now our clinical study is still ahead of anyone,” Pan said.

    But given that there are no gene therapies approved for clinical use in the United States, the road to successfully using optogenetics in humans will likely be a long one. Yang Dan, a professor of neuroscience at UC Berkeley who uses optogenetics to study sleep, isn’t betting on optogenetics cures being in the clinic any time soon. “I believe that these safety checks will take a long, long time,” she said.

    As for the invention itself, some scientists say Pan may not have had the big, award-worthy vision that Deisseroth and Boyden had. Stefan Herlitze, one of the others who was scooped for the first publication about channelrhodopsin in neurons, said, “Of course I have to say, Deisseroth and Boyden, they really developed the field further.”

    Boyden echoed this. “Karl and I were very interested in the general question of how to control cell types in the brain,” he said. “In recent years, we worked to push these molecules to their logical limits.”

    So maybe it doesn’t matter who invented optogenetics, just who has stretched science’s boundaries the furthest.

    Asked whether he deserves the recognition that Boyden and Deisseroth have enjoyed, Pan declined to answer. He later told STAT that Deisseroth “also did a very excellent job, no doubt. But he’s also very lucky because if our paper was ahead of him, the story would be different. We would have gotten more credit.”

    That is about as much as Pan is willing to say about the way his cards fell. Today he’s still in Detroit. He’s been working on new versions of channelrhodopsin that could be used to cure blindness. “My lab is a very small lab,” Pan said, “We’re mainly interested in trying to restore vision.”

    See the full article here .

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    Scientific American, the oldest continuously published magazine in the U.S., has been bringing its readers unique insights about developments in science and technology for more than 160 years.

     
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