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  • richardmitnick 12:40 pm on November 22, 2017 Permalink | Reply
    Tags: , Biology, , , Sangeeta Bhatia,   

    From Brown: Women in STEM- “Building a Better Way” Sangeeta Bhatia 

    Brown University
    Brown University

    November/December 2017
    Louise Sloan

    1
    Sangeeta Bhatia. Geordie Wood

    ____________________________________________________________________________________________

    Be Recognized for Who You Are

    Sangeeta Bhatia ’90 may not have had many role models to look up to as a woman engineer, but that doesn’t mean she didn’t learn a lot of lessons along the way. Here’s some of her advice for people from any group that has been historically underrepresented in the field.

    STAY CONFIDENT. Being one of the only women or people of color in your field is difficult. Keep focused on your strengths. Bhatia says she struggled with “imposter syndrome.” “There’s this feeling that you don’t belong, and you’re always second guessing yourself. That does diminish with time.”

    TAKE THAT MEETING. With famous scientists or engineers, Bhatia learned to ask questions or strike up a conversation about the person’s most recent paper. The collaboration that led to one of her most important breakthroughs was a result of following up on a colleague’s offer of an introduction. Worst case, making connections can make a dull meeting more interesting. “Okay, I’m at a conference,” she’d tell herself; “Who are the people I want to meet? What the heck? Let’s meet them.”

    SPEAK UP EARLY ON. In business meetings, Bhatia says, often “I was the only woman, only engineer, only person of color.” And she looked young. “One thing I quickly realized was that I needed to make a comment or ask an insightful question pretty early in the convening of a group.” It wasn’t her personal style to do this, but, she realized, “there are times where you’ve got a group of really high-powered people together, and you’re there for an hour, and nobody knows who you are. You have something important to add. You have to make it clear early in the conversation why you’re at the table.”

    IDENTIFY MENTORS. When Bhatia and Theresia Gouw ’90 were seniors and looked into what made some women stay in engineering while so many others left, they found that what the women who’d stayed all had in common was mentors—whether that was a professor, parents, or a family friend. Bhatia concedes it’s hard to force these relationships. It’s clear that her mentors came not just through luck but also through her own efforts in cultivating relationships with key people around her and following up on any advice and opportunities.

    STUDY SUCCESS. Identify your weaknesses and look around at who is doing that thing well. Bhatia says she was comfortable expressing her ideas one-on-one, and as a professor she also became comfortable speaking to a lecture hall. But groups of between 10 and 30 people in faculty meetings or on advisory boards felt awkward to her. “I started studying it and looking at who is really effective in this setting. How have they managed to be effective? At what points are they choosing to speak up? What offline work have they done to grease this conversation so that by the time they speak up, they’re able to carry the room? I made kind of a project of it, trying to figure it out, because I realized I wasn’t actually naturally good at that.”

    BE YOUR OWN BOSS. “This is something Theresia has taught me, which is that one of the answers to diversity is to create your own organization, put yourself at the top, make the culture that you want it to be.
    ____________________________________________________________________________________________
    3
    Lego characters designed by Maia Weinstock ’99, Photo by Erik Gould
    Lego minifigures, like engineers, are disproportionately
 male. But Sangeeta Bhatia ’90 has her own, custom-made in 2015 by Maia Weinstock ’99. It’s a fitting tribute to the engineer, physician, biotech entrepreneur, and mom who takes tiny pieces and puts them together in unexpected ways.

    Bhatia is literally a soccer mom when she’s not coming up with incredible scientific breakthroughs. Her husband, Jagesh Shah, coaches their daughters’ teams. But take heart, mere mortals. “My car is a mess; it smells like a dead animal right now,” she has admitted. “I don’t cook. At all.”

    Bhatia does a lot of things a little differently. She has used microfabrication, the technology behind microchips, to grow human liver cells outside the body. This has allowed drug companies to test toxicity on these “micro livers” in the lab and to hope that they can someday manufacture whole human livers for transplant patients. She is a senior scientist at a top institution, but instead of spending nights and weekends at the lab, she insists on balance so that, for example, Wednesdays are “Mommy Day” spent with her kids.

    Her very presence in the field of bioengineering as an engaging, stylish woman of color is de facto doing things differently. “Many people still have this image of an engineer as a kind of nerdy guy, interested in taking things apart,” Bhatia said in an October 2015 speech at Brown celebrating the groundbreaking of the new engineering building (it just opened this fall). “Someone who stays up all night playing video games and eating Doritos, with very few social skills. Right?”

    Bhatia, a petite figure in a sleeveless top and capri pants, her toenails a chic shade of blue, is not that guy. She took a gap year after Brown in which she backpacked and taught aerobics. She does classical Indian dance to relax—she thinks that’s what caught the attention of Brown’s admission office—and, with husband Jagesh Shah, a professor at Harvard, she runs her kids’ elementary school science fair. She’s literally a soccer mom—Shah coaches their daughters’ teams. But take heart, mere mortals. “My car is a mess; it smells like a dead animal right now,” she admitted to Nova ScienceNOW when they profiled her in 2009. “I don’t cook. At all.”

    What she does do, with the team she’s assembled at her lab at MIT, is figure out which sequences of amino acids can get into a tumor, then put them on synthetic materials that are way smaller than the diameter of a human hair, and use that to detect cancer. They’ve managed to grow the dormant version of malaria in a dish so drugs can be tested in vitro before being tested in humans. They’ve also prototyped breathalyzer and urine tests for cancer.

    Bhatia has been elected to the National Academy of Sciences and the National Academy of Inventors, and she was one of the youngest women ever elected to the National Academy of Engineering. She’s won prestigious national prizes and awards, including the Lemelson-MIT Prize, known as the “Oscar for inventors.” In addition to having her own lab, the Laboratory for Multiscale Regenerative Technologies, she recently launched The Marble Center for Cancer Nanomedicine at MIT. The prize for cleanest car in the Boston area can probably wait.

    The door to her future was in the Biomed Center

    Bhatia, who was born and raised in Boston, got interested in bioengineering at Brown when, in order to get to her human physiology lab, she had to walk past a door in the Biomed Center that was labeled “artificial organs.” That sounded cool to her, so one day she knocked on the door. “I begged them to let me intern,” she says. She spent the summer working on using electricity-producing plastics (piezoelectrics) to enhance nerve regeneration and became hooked on the field that is now called tissue engineering. After Brown and that post-undergrad gap year, in which she also worked for a pharmaceutical company pressing pills (“it was really boring”), she started grad school at MIT.

    Her parents approved. Bhatia’s father was an engineer, and her mother was one of the first women in India to earn an MBA. They considered three careers acceptable: doctor, engineer, or entrepreneur. So when Bhatia said she wanted to pursue a PhD because bioengineering bosses seemed to have them, her father, who felt PhDs are often impractical, asked, “When are you going to start a company?”

    It took a few years. In 2008 she launched Hepregen to bring the artificial liver technology to the commercial market, and she started Glympse Bio in 2015 to commercialize the urine-test diagnostics, with investment from her Brown roommate, longtime friend, and venture capitalist Theresia Gouw ’90. “We are scheduled to start, we hope, our first clinical trials next year,” Bhatia says, “It’s like having another child.”

    Bhatia’s work producing artificial livers started in her second year at MIT, when she joined the lab of Mehmet Toner, a biomedical engineer who was trying to develop a device that would use human liver cells to process the blood of patients with liver failure. Bhatia set out to figure out how to get liver cells to grow outside the body. She tried and failed for two years. Then she had a breakthrough.

    In the body, liver cells don’t just grow on their own, Bhatia explains. They grow in a particular structure—a community, she calls it—with connective tissue cells. But just throwing both types of cells into a petri dish didn’t work. Instead, Bhatia hit on the idea of creating the right structure for these cells by using microfabrication techniques designed to create computer chips. Instead of putting tiny circuits on a chip, she etched a glass culture dish with the geometric configuration in which liver cells grow in the body. Success: the liver cells, organized in the right way and supported by connective tissue cells, could live for several weeks outside the body. Today, pharmaceutical companies around the world use Bhatia’s micro livers, grown from human liver cells, to test whether or not their drugs are toxic to humans before they try them on actual people.

    While Bhatia worked in Toner’s lab, she started taking the year’s worth of medical school classes at Harvard that her biomedical engineering program required. Fascinated, she added even more med school classes. Then after she finished up her bioengineering PhD, she transferred into Harvard Medical School as a third-year med student—a foray into one of her other parentally approved career paths. But she still threw her hat in the ring for academic gigs and later that year accepted a junior professor position at UC San Diego. So in 1999, her fourth year of medical school, she multitasked, working at both a hospital (“for inspiration”) and a research lab (“where my heart is”). The combination remains crucial for her work, Bhatia says. “Over my career, I have always looked to the clinic to recognize what the real unmet medical needs are,” she explains.

    In 2005, after six years in San Diego, Bhatia returned with Shah and their first daughter to Boston to accept a professorship at MIT.

    How to build a kinder, gentler top academic lab

    When Bhatia was in grad school she looked “up the pipeline” to the lives of research scientists and engineers, and she didn’t like what she saw. When she popped into the lab one Saturday night at 3 am, her colleagues were still working. When she thought about her future, she says, “I realized I didn’t want to be there every Saturday night.” So when she set up her own lab at MIT, she prioritized excellence but she had other key concerns.

    As with the liver cells she studies, she feels people thrive best in a community and with support. For her own sake and to enhance the success of her lab, Bhatia makes it a priority to hire people who aren’t just great at what they do but can also get along well with others. Like some high-tech entrepreneurs, she encourages them to both work hard and live a balanced life—and to spend 20 percent of their work time “tinkering” on creative projects that may or may not pan out. (The breathalyzer test for cancer came out of one of these “submarine” projects, so called because they’re hidden from Bhatia unless they succeed.) Bhatia’s lab manager, Lian-Ee Ch’ng, says the lab, a warren-like series of rooms on the fourth floor of MIT’s Koch Institute for Integrative Cancer Research, feels very different from others she has worked in. “Sangeeta has a very personal touch,” Ch’ng says.

    Thirty people work in Bhatia’s lab, including a research director, scientists, and the grad students. It looks like any top facility, with row after row of workstations and separate rooms for incubators, specialized microscopes, ultra-low-temperature freezers, and massive tanks of liquid nitrogen. They have a 3-D printer and, perhaps the most high-tech piece of equipment in the lab, Ch’ng says, the Pannoramic 250, a high-speed, five-color slide scanner that produces beautiful digital images of the cells on a microscope slide.

    It looks like a place built for workaholics, where it would be easy to keep your head down and your focus on yourself. But Bhatia doesn’t allow it. She sets a tone of collegiality, Ch’ng says, which really makes a difference: “People talk to each other.”

    There’s an inherent tension, Bhatia admits, in bringing together excellent, ambitious people and also prioritizing work-life balance, community, and citizenship. “They’re not all exactly the same thing,” she says. But this combination of priorities may be an important reason why the Bhatia lab has a staff that’s about half female. “I have an orientation that attracts young moms,” she says. Her male staff members who have kids are probably able to be better dads, too.

    “I think Sangeeta’s a wonderful role model for women,” then-grad student Geoffrey Von Maltzahn told Nova. “But she’s a terrific role model for anybody. One of the hardest things in life is to make a clear distinction between how much time you’re going to dedicate to your work and how much time you’re going to dedicate to your family and your friends. She’s able to manage that with a sense of ease that I think is inspirational, independent of whether you’re a man or a woman.”

    However, when Bhatia started working from home on Wednesdays so that she could pick up her daughters from school, she felt it was professionally risky. So at first she called it “working off campus.” Now, everyone knows it’s “Mommy Wednesday.” She makes a point of modeling work-life balance to show that it can be done without sacrificing success.

    She’s also purposely using her visibility as a top scientist to be a role model for women in engineering. “There are not a lot of engineers that look like me, still.” Yet when she first got to Brown, she didn’t see what all the “diversity” fuss was about. “I looked around the classroom and thought that there were plenty of women.”

    Then, when she was a senior, she and her friend Theresia Gouw looked around again, and there were many fewer women—only seven in a class of 100. “We realized that we had just witnessed the so-called disproportionate attrition, the leaky pipeline.”

    Bhatia started reading about the subtle bias and the feeling of “not belonging” that discourages many women from pursuing the field. She and Gouw surveyed the other women who stayed in engineering and found that “every one of them had had mentors or parents who encouraged them.”

    As a newcomer to MIT, and as one of the few women engineering graduate students, Bhatia got a clear taste of that “not belonging” feeling when a thermodynamics professor asked her, on the first day, if she was in the right class. At first, Bhatia says she did what she could to downplay her femininity, wearing pants and not much makeup, trying to disappear. But later, she realized she had to be visible to make a difference and help patch up that leaky pipeline. So she makes a point of speaking openly and specifically about being a woman engineer.

    Bhatia thinks her attitude stems from the orientation towards public service she got in college. “I think that’s very Brown,” she says. “Not just noticing, but taking action.” But she says that her commitment to gender and other types of diversity also happens to be good business. “Just look at the metrics,” she points out. “Quality of ideas, return on investment, time to profitability, every objective metric has shown to be improved with diversity.”

    Though living a balanced life was important to Bhatia, she feared the consequences on her career. “I said to myself, ‘This is a tradeoff I’m willing to make. If it means I’m not at the top of my field, that’s absolutely a decision I’m making with my eyes open.’”

    Instead, she found that her choice to have a life outside the lab had the opposite effect: it helped her excel. “You have to find a way to sustain your energy and your creative spirit,” she says. As many workplace productivity studies have shown, having downtime increases productivity, and Bhatia is no exception to this rule. “I feel like if I worked the way that I thought I was supposed to, I actually think I wouldn’t be as productive. For me it’s helpful to come in and out of those worlds.”

    The tiniest tools 
on earth

    Bhatia’s still working with livers, but microfabrication is now old technology. Much of her current work uses nanotechnology: “You make materials so tiny that they can circulate in the body,” she explains.

    It’s with these insanely small tools that Bhatia set out to find better ways to diagnose and treat cancer. While still at UC San Diego, she began collaborating with renowned cancer researcher Erkki Ruoslahti, who had figured out how to engineer viruses so they’d home in on tumors. Bhatia replicated that, not with viruses but with materials, such as quantum dots (qdots), little semiconductor crystals that are more than ten thousand times smaller than the width of a strand of human hair.

    Bhatia coated qdots with peptide sequences that would allow them to enter tumor cells. Then she injected the qdots into mice that had cancer. Sure enough, the qdots homed in on the tumors. In 2002, Bhatia and Ruoslahti published a paper on their findings. “A lot of people say it was one of the first of its kind in what later became this field of nanomedicine,” Bhatia says.

    The urine test for cancer was an outgrowth of that work—and a happy accident. In the Bhatia lab, they were trying to make “smart contrast agents,” materials that would light up in tumors and thus show up on an MRI. “That was when the students noticed that whenever the animals were tumor-bearing, the bladder would light up,” Bhatia says. “Then we realized we didn’t need an MRI at all, that we had created this kind of urine diagnostic.” All they had to do was create a paper test to detect the biomarker that appeared in the urine and voilà, an inexpensive and relatively noninvasive test for cancer.

    “We think it’s a platform technology,” says Bhatia, who is investigating the use of this type of diagnostic with other diseases, including liver disease, which could help patients avoid expensive and invasive biopsies. The test works great in mice, so their biggest hurdle is to work with the FDA so that it can be tested on people.

    The “blue-sky” goal

    One of Bhatia’s dreams is to create a functioning human liver made outside the body that can be implanted into it. That goal is still far away, but it’s getting closer. In June, she published a paper that explained her group’s successful attempt to grow working livers in mice.

    Building on her micro liver technology, they used a 3-D printer to produce tiny liver “seeds” that they populated with a community of liver cells and helper cells. The configuration, they thought, would allow the cells to respond to regeneration cues—the liver being one of the only organs in the body that can regenerate.

    They implanted these seeds in mice with failing livers—and the lab-created livers grew 50 times larger in the mice’s bodies. They also looked a lot like real livers and performed liver functions. Making a liver for a human obviously requires many more cells than making one for a mouse, though.

    “We think you probably need about 10 billion cells to get up to clinically relevant tissue, which is a lot and too many to print practically in a reasonable amount of time,” Bhatia says. “We have a long way to go.”

    In the meantime, they have found another use for the micro livers: testing malaria drugs. “There’s a really elusive dormant form of vivax malaria that can hide out in a liver,” Bhatia explains. The only drug that’s been known to clear this dormant form of the disease is primaquine, which has been around since World War II. But it can cause blood damage in patients, and some strains of the dormant malaria have developed resistance to it. “There’s been a big push for new drugs since 2008, when the World Health Organization announced a new malaria eradication campaign,” Bhatia says.

    What Bhatia’s team has been able to do is grow this dormant strain of malaria in their micro livers, allowing drugs to be tested against it. “Now we’re trying to molecularly describe it, which has never been done,” she says.

    The malaria work came about because a lab member, graduate student Nil Gural, wanted to work on the untreatable form of the disease. “When she came, we had never grown [the dormant strain] before. We had no access to it.” Gural, who is originally from Turkey, said she was willing to live in Bangkok for a while to get it going.

    Gural has now been working on this for a couple of years, going back and forth from Boston to Bangkok. The work is going really well, Bhatia says. The lab is working with Medicine for Malaria Ventures, the organization that is coordinating the effort to develop new drugs that will work on the dormant stage of the disease. Given that there are about 212 million malaria cases that cause nearly half a million deaths each year, according to the World Health Organization, it’s research that has great potential for positive impact.

    Bhatia says her commitment to malaria work comes out of her entrepreneurial instincts as shaped by Brown. “My professional work has started out in what I would say is a very high-tech place,” she says, “and that’s growing 3-D livers. That’s probably going to be an expensive solution for patients with liver failure. The same thing for our cancer work. We’re working on really, really, really cutting-edge but still expensive ideas.”

    Expensive ideas are, of course, where the profit lies for an entrepreneur. But Bhatia says Brown taught her to look beyond profit to ask, “What can you do to make the world a better place?” For Bhatia, that’s finding global health applications for her work, such as taking the micro livers and using them to help eradicate malaria, or using the nanotechnology the lab comes up with to create inexpensive paper-based diagnostic urine tests for lung, colon, and ovarian cancers, allowing patients to be tested and even treated right on the spot, including in remote areas of developing countries where follow-up can be next to impossible. That’s still a dream, but as she said in her Spring 2017 TED Talk, “We already have this working in mice.”

    Half of Bhatia’s staff crowds into her office every Friday—it switches back and forth between the cancer and liver groups. It’s a medium-sized office with a desk, a small table, and a small couch. Behind her desk is a large framed print of something that looks like a lush white flower in full bloom. It’s actually a genetically engineered colony of yeast. Her Lego figure is perched on a window sash, and below it an unusual clock keeps the time. Six metal figures in the clock itself appear to hoist a seventh who hangs below, though every time the seventh figure gets almost to the top, it falls down again. Her husband gave it to her as a present when she got tenure. “What he said was, ‘Look at all these people helping you climb. You’re leading a team and they’re helping you achieve your vision.”

    “I was like, that’s nice, but once you get tenure”—the figure plummets to the bottom again as if to illustrate her point—“you climb the next ladder.”

    Fifteen people assemble in this space that would comfortably seat half as many. “They sit on the floor and the table,” Bhatia says. “We keep saying maybe we should move to the conference room but I think they like the intimacy of barreling into my office for 90 minutes.” The group uses the time to talk about early results of experiments and to “cross-fertilize.”

    “I’m continually reinforcing that,” Bhatia says. “Otherwise they don’t talk to each other.” Science is a lot of failure, she adds. “You have to think of all different ways to keep your team energized and excited and engaged. The best way is if they’re constantly learning.”

    Bhatia has improved and perhaps saved many lives already, thanks to the drugs that now are not tested in humans if they are toxic to micro livers. An off-the-shelf liver or a urine test for cancer or liver disease could also be lifesaving.

    But when asked what she’s proudest of, she says it’s her students, because she gets to be what she calls a “multiplier.” She trains her grad students and post-docs in a way of working and a way of thinking, and then they go out into the world. “I feel like they’ve all gone on to do really interesting things,” Bhatia says. “One of them is a venture capitalist and serial entrepreneur. He built a bunch of companies. Some of them are professors training their own students. There’s a lot of them out there. It’s the most amazing thing to feel like you’ve played a role in that.”

    See the full article here .

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    With its talented and motivated student body and accomplished faculty, Brown is a leading research university that maintains a particular commitment to exceptional undergraduate instruction.

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    Undergraduates pursue bachelor’s degrees in more than 70 concentrations, ranging from Egyptology to cognitive neuroscience. Anything’s possible at Brown—the university’s commitment to undergraduate freedom means students must take responsibility as architects of their courses of study.

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  • richardmitnick 2:20 pm on November 18, 2017 Permalink | Reply
    Tags: , Biology, , , Stanford University-Engineering,   

    From Stanford University – Engineering: “An advance in stem-cell development could help lead to new therapies” 

    Stanford University Name
    Stanford University – Engineering

    November 02, 2017
    Andrew Myers

    1
    Stem cells hold the promise of being able to cure ills ranging from spinal cord injuries to cancers. | Image by: luismmolina/Getty Images

    In many ways, stem cells are the divas of the biological world. On the one hand, these natural shapeshifters can transform themselves into virtually any type of cell in the body. In that regard, they hold the promise of being able to cure ills ranging from spinal cord injuries to cancers.

    On the other hand, said associate professor of materials science and engineering Sarah Heilshorn, stem cells, like divas, are also mercurial and difficult to work with.

    “We just don’t know how to efficiently and effectively grow massive numbers of stem cells and keep them in their regenerative state,” Heilshorn said. “This has prevented us from making more progress in creating therapies.”

    Until now, that is. In a recent paper in Nature Materials, Heilshorn described a solution to the dual challenges of growing and preserving neural stem cells in a state where they are still able to mature into many different cell types. The first challenge is that growing stem cells in quantity requires space. Like traditional farming, it is a two-dimensional affair. If you want more wheat, corn or stem cells, you need more surface area. Culturing stem cells, therefore, requires a lot of relatively expensive laboratory real estate, not to mention the energy and nutrients necessary to pull it all off.

    The second challenge is that once they’ve divided many times in a lab dish, stem cells do not easily remain in the ideal state of readiness to become other types of cells. Researchers refer to this quality as “stemness.” Heilshorn found that for the neural stem cells she was working with, maintaining the cells’ stemness requires the cells to be touching.

    Heilshorn’s team was working with a particular type of stem cell that matures into neurons and other cells of the nervous system. These types of cells, if produced in sufficient quantities, could generate therapies to repair spinal cord injuries, counteract traumatic brain injury or cure some of the most severe degenerative disorders of the nervous system, like Parkinson’s and Huntington’s diseases.

    Seeking stemness

    Heilshorn’s solution involves the use of better materials in which to grow stem cells. Her lab has developed new polymer-based gels that allow the cells to be grown in three dimensions instead of two. This new 3-D process takes up less than 1 percent of the lab space required by current stem cell culturing techniques. And because cells are so tiny, the 3-D gel stack is just a single millimeter tall, roughly the thickness of a dime.

    “For a 3-D culture, we need only a 4-inch-by-4-inch plot of lab space, or about 16 square inches. A 2-D culture requires a plot four feet by four feet, or about 16 square feet,” more than 100-times the space, according to first author Chris Madl, a recent doctoral graduate in bioengineering from Heilshorn’s lab

    In addition to the dramatic savings of lab space, the new process demands fewer nutrients and less energy, as well.

    The gels the team developed allow the stem cells to remodel the long molecules and maintain physical contact with one another to preserve critical communication channels between cells. “The simple act of touching is key to communication between stem cells and to maintaining stemness. If stem cells can’t remodel the gels, they can’t touch one another,” Madl explained.

    “The stem cells don’t exactly die if they can’t touch, but they lose that ability to regenerate that we really need for therapeutic success,” Heilshorn added.

    Striking results

    This need for neural stem cell to remodel their environment differs from what Heilshorn has found in working with other types of stem cells. For those cells, it is the stiffness of the gels – not the ability to remodel – that is the key factor in maintaining stemness. It is as if for these other types of stem cells, gels must mimic the rigidity of the tissue in which the cells will eventually be transplanted. Not so with neural progenitors, said Heilshorn.

    “Neural cell stemness is not sensitive to stiffness and that was a big surprise to us,” she said.

    The result was so striking and unexpected that Heilshorn, at first, didn’t believe her own results. The lab ended up testing three entirely different gels to see if their conclusion held, an unusual supplementary step in this kind of research. With each new material, they saw that those that could be remodeled produced quality stem cells; those that could not be remodeled had a negative effect on stemness.

    Next up on Heilshorn’s research agenda is to create gels that can be injected directly from the lab dish into the body. The possibilities have her feeling optimistic about stem cell therapies again. For a time, she said, it felt as if the field had hit a wall, as initial excitement for regeneration gave way to uninspiring results in the clinic. With her new finding, she said, it feels like new things may be just around the corner.

    “There’s this convergence of biological knowledge and engineering principles in stem cell research that has me hopeful we might finally actually solve some big problems,” she said.

    See the full article here .

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  • richardmitnick 12:09 pm on November 15, 2017 Permalink | Reply
    Tags: A Speed Gun for Photosynthesis, A type of optical sensor that if the science bears out will be able to estimate the rate of photosynthesis, , Biology, , , SIF - Solar Induced Fluorescence, Specially designed sap flow sensors, Such aDevice would revolutionize agriculture forestry and the study of Earth’s climate and ecosystems   

    From NIST: “A Speed Gun for Photosynthesis” 


    NIST

    1
    The NIST forest in Gaithersburg, Maryland. Credit: R. Press/NIST

    November 03, 2017 [NIST is not always quick to social media]
    Rich Press

    On a recent sunny afternoon, David Allen was standing by a third-floor window in a research building at the National Institute of Standards and Technology (NIST), holding in his hands a device that looked like a cross between a video camera and a telescope. The NIST campus is in suburban Gaithersburg, Maryland, but looking out the window, Allen could see 24 hectares (60 acres) of tulip tree, oak, hickory and red maple—a remnant of the northeastern hardwood forest that once dominated this landscape.

    Allen mounted the device on a tripod and pointed it out the window at the patch of forest below. The device wasn’t a camera, but a type of optical sensor that, if the science bears out, will be able to estimate the rate of photosynthesis—the chemical reaction that enables plants to convert water, carbon dioxide (CO2) and sunlight into food and fiber—from a distance.

    That measurement is possible because when plants are photosynthesizing, their leaves emit a very faint glow of infrared light. That glow is called Solar Induced Fluorescence, or SIF, and in recent years, optical sensors for measuring it have advanced dramatically. The sensor that Allen had just mounted on a tripod was one of them.

    “If SIF sensors end up working well,” Allen said, “I can imagine an instrument that stares at crops or a forest and has a digital readout on it that says how fast the plant is growing in real time.”

    Such a device would revolutionize agriculture, forestry and the study of Earth’s climate and ecosystems.

    2
    NIST scientist David Allen and Boston University Ph.D. student Julia Marrs aim a SIF sensor at a specific tree in the NIST forest.
    Credit: R. Press/NIST

    Allen is a NIST chemist whose research involves remote sensing—the technology that’s used to observe Earth from outer space. Remote sensing allows scientists to track hurricanes, map terrain, monitor population growth and produce daily weather reports. The technology is so deeply embedded in our everyday lives that it’s easy to take for granted. But each type of remote sensing had to be developed from the ground up, and the SIF project at NIST shows how that’s done.

    Some satellites are already collecting SIF data, but standards are needed to ensure that those measurements can be properly interpreted. NIST has a long history of developing standards for satellite-based measurements, and Allen’s research is aimed at developing standards for measuring SIF. Doing that requires a better understanding of the biological processes that underlie SIF, and for that, Allen teamed up with outside scientists.

    At the same time that Allen was aiming a SIF sensor through that third-floor window, a team of biologists from Boston University and Bowdoin College was in the NIST forest measuring photosynthesis up close. A pair of them spent the day climbing into the canopy on an aluminum orchard ladder. Once there, they would use a portable gas exchange analyzer to measure photosynthesis directly based on how much CO2 the leaf pulled out of the air. They also measured SIF at close range.

    3
    Boston University ecologist Lucy Hutyra (left) works at the forest edge alongside plant physiological ecologist Barry Logan (center) and ecologist Jaret Reblin, both of Bowdoin College in Brunswick, Maine. They measured photosynthesis directly, as well as temperature, humidity, and other environmental variables. Credit: R. Press/NIST

    Other scientists checked on specially designed sap flow sensors they had installed on the trunks of trees to measure the movement of water toward the leaves for photosynthesis.

    “We’re measuring the vital signs of the trees,” said Lucy Hutyra, the Boston University ecologist who led the team of scientists on the ground. The idea was to use those ground measurements to make sense of the SIF data collected from a distance.

    “If we measure an increase in photosynthesis at the leaf, we should see a corresponding change in the optical signal,” Hutyra said.

    4
    After directly measuring photosynthesis in an individual leaf using a field portable gas exchange analyzer, scientists preserved a small sample of leaf tissue in liquid nitrogen. They would later analyze that tissue in the lab to measure levels of chlorophyll and other pigments. Credit: R. Press/NIST

    The research was also taking place at still a higher level. That afternoon, Bruce Cook and Larry Corp, scientists with NASA’s G-LiHT project, flew over the NIST forest in a twin-turboprop plane that carried multiple sensors, including a SIF sensor and Light Detection and Ranging (LiDAR) sensors that mapped the internal structure of the forest canopy. The aircraft made six parallel passes over the forest at about 340 meters (1,100 feet, slightly above the minimum safe altitude allowed by FAA regulations), the instruments peering out from a port cut into the belly of the aircraft.

    That gave the scientists three simultaneous measurements to work with: from the ground, from the window above the forest and from the air. They’ll spend months correlating the data.

    “It’s tricky, because when you go from the leaf level to the forest level, you often get different results,” Allen said. For instance, at the forest level, the SIF signal is affected by the variations in the canopy, including its contours and density. “We’re still studying those effects.”

    5
    At the airport in Gaithersburg, Maryland, NASA earth scientist Bruce Cook (left), leader of the Goddard LiDAR, Hyperspectral, and Thermal (G-LiHT) project, shows David Allen and Julia Marrs the sensor array in the bottom of the aircraft. Credit: R. Press/NIST

    Currently, there is no reliable way to measure photosynthesis in real time over a wide area. Instead, scientists measure how green an area is to gauge how much chlorophyll is present—that’s the molecule that supports photosynthesis and gives leaves their color. But if a plant lacks water or nutrients, it may be green even if the photosynthetic machinery is switched off.

    SIF may be a much better indicator of active photosynthesis. When plants are photosynthesizing, most of the light energy absorbed by the chlorophyll molecule goes into growing the plant, but about two to five percent of that energy leaks away as SIF. The amount of leakage is not always proportional to photosynthesis, however. Environmental variables also come into play.

    The NIST forest is a test bed for understanding how all those variables interrelate. In addition to SIF data and the vital signs of trees, the scientists are collecting environmental data such as temperature, relative humidity and solar irradiance. They’re also figuring out the best ways to configure and calibrate the SIF instruments.

    “We’d like to see robust, repeatable results that make sense,” Allen said. “That will allow us to scale up from the leaf level, to the forest level, to the ecosystem level, and to estimate photosynthesis from measurements made at any of those scales.”

    Making SIF scalable is a key part of the measurement standard that Allen is working to create, and it will go from the ground level to measurements made from outer space.

    6
    A corner of the NIST forest shot by NASA scientists, and the plane that carried them and their G-LiHT airborne imaging system.
    Credit: Bruce Cook, Larry Corp/NASA (left); David Allen/NIST

    Using SIF to measure photosynthesis in real time would allow farmers to use only as much irrigation and fertilizer as their crops need, and only when they need it. Forest managers would be able to know how fast their timber is growing without having to tromp through the woods with a tape measure. Environmental managers would be able to monitor the recovery of damaged or deforested habitats after a drought or forest fire.

    And scientists would have a powerful new tool for studying how plants help regulate the amount of CO2 in the atmosphere.

    Humans add CO2 to the atmosphere when they burn fossil fuels, and land-based plants remove roughly a quarter of that CO2 through photosynthesis. But the environmental factors that affect that process are not well understood, mainly because scientists haven’t had a good way to measure the uptake of CO2 at the ecosystem level. SIF measurements, and the standards for interpreting them accurately, might help solve that problem.

    “CO2 exchange by plants is one of the most important biological processes on the planet,” Allen said, “and SIF will give us a new way to see that process in action.”

    See the full article here.

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    NIST will be the world’s leader in creating critical measurement solutions and promoting equitable standards. Our efforts stimulate innovation, foster industrial competitiveness, and improve the quality of life.
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  • richardmitnick 1:48 pm on November 10, 2017 Permalink | Reply
    Tags: , Biology, Cryo-electron microscopy (cryo-EM), Cryo-EM lets us examine the machinery of cells at the atomic level, , Pushing the Limits of Lower-Cost Electron Microscopes with Incredible Results,   

    From Scripps: “Pushing the Limits of Lower-Cost Electron Microscopes, with Incredible Results” 

    Scripps
    Scripps Research Institute

    November 10, 2017
    Bonnie Ward
    Madeline McCurry-Schmidt

    From Ebola virus’s deadly machinery to crucial human cell receptors, recent technical breakthroughs in cryo-electron microscopy (cryo-EM) have allowed scientists to obtain unprecedented insights into a variety of molecular structures directly involved in health and disease pathologies.

    In fact, this technology—which gives researchers detailed three-dimensional views of biomolecules in near-native states—recently drew the eye of the Nobel Prize committee, which awarded the 2017 Prize in Chemistry to three founding members of the field of cryo-EM. The field has seen an explosive development over the past few years, both in terms of technical and methodological advances. Nowadays, scientists can reliably use this technique to visualize critical disease-relevant biomolecules, and the 3D structures of solved by cryo-EM are a cornerstone of scientific literature.

    At The Scripps Research Institute (TSRI), Associate Professor Gabriel Lander, Ph.D., leads a team pushing the limits of cryo-EM technology to further improve and expand the utility of this technique. His lab’s most recent work, published in Nature Methods, demonstrates that TSRI researchers—and the scientific community as a whole—can visualize astonishing molecular details of biomolecules that were previously thought to be too small to be resolved. What’s more, they can accomplish this even on less expensive electron microscopes.

    “This work has reshaped the way the EM field views these microscopes,” said Lander. “Hopefully research institutes and universities will realize that, without a massive investment, they can do a lot of this work themselves,” he said.

    In their study, Lander and colleagues showed that resolutions of similar quality could be achieved using the 200-keV transmission electron microscope (TEM) versus the significantly more expensive 300-keV TEM.

    “TSRI was one of the first institutes in the world to purchase this ‘mid-range’ electron microscope, and we have shown that it can be used to solve structures at resolutions that were previously only thought attainable using top-of-the-line ‘Titan Krios’-type microscopes,” said Lander.

    The resolution of a structure is important because higher resolutions provide scientists with clear images of molecular interactions in minute detail that can be confidently applied towards drug development. “Cryo-EM lets us examine the machinery of cells at the atomic level,” said Mark Herzik, Ph.D., the study’s first co-author and a Helen Hay Whitney Foundation postdoctoral fellow in Lander’s lab. “This level of detail can aide researchers in designing drugs based on blocking certain cellular activities for therapeutic purposes,” he said, noting this approach is known as structure-based drug design.

    Lander and his team’s desire to move forward with such research as quickly as possible led to their new discovery.

    TSRI purchased a high-powered 300-keV TEM three years ago and researcher interest quickly grew—and so did the wait list to use the equipment.

    2
    “This is probably one of the best microscope suites in the world,” says Clint Potter, professor at TSRI and co-director of the National Resource for Automated Molecular Microscopy. Shown above is part of the new Titan Krios.(Photo by John Dole.)

    “It took about three months to schedule a 24-hour time slot on the microscope,” said Lander.

    This led TSRI to purchase a mid-level cryo-EM microscope (a 200-keV TEM) for the specific purpose of paring down cellular samples to the best candidates. TSRI bought the intermediate microscope last year, and Lander and his team soon got surprising results.

    “We never expected to be able to resolve structures at this resolution on this microscope,” said Lander. “That really inspired us to try to push the resolution levels even higher. Through very careful sample preparation and microscope alignments, we ended up getting resolutions that were comparable to the higher-end model (300-keV TEM).”

    Based on this discovery, TSRI researchers can now make greater use of cryo-EM. “We’ve essentially doubled the number of microscopes that can turn out high-resolution images 24-7,” said Lander. Together with improved data collection strategies, wait times also have vastly improved, going from three months to approximately one to two weeks for a microscope time slot, he said.

    Along with improving access for TSRI researchers, Lander and his team hope their finding will boost cryo-EM research across the scientific community.

    “Understanding disease, and how to develop therapeutics to effectively treat disease, is predicated on having very detailed structural information,” said study co-author Mengyu Wu, a graduate student in Lander’s lab. “Cryo-EM has become one of the most powerful methods for obtaining these critical insights.”

    See the full article here .

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    The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

    The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

     
  • richardmitnick 8:46 am on November 10, 2017 Permalink | Reply
    Tags: , Biology, Essential amino acid methionine, , , SAMTOR, The mTOR cellular pathway connects nutrition metabolism and disease   

    From MIT: “New player in cellular signaling” 

    MIT News
    MIT Widget

    MIT News

    November 9, 2017
    Nicole Giese Rura | Whitehead Institute

    1
    The mTOR cellular pathway connects nutrition, metabolism, and disease. Image courtey of Steven Lee/Whitehead Institute.

    Researchers have identified a key nutrient sensor in the mTOR pathway that links nutrient availability to cell growth.

    To survive and grow, a cell must properly assess the resources available and couple that with its growth and metabolism — a misstep in that calculus can potentially cause cell death or dysfunction. At the crux of these decisions is the mTOR pathway, a cellular pathway connecting nutrition, metabolism, and disease.

    The mTOR pathway incorporates input from multiple factors, such as oxygen levels, nutrient availability, growth factors, and insulin levels to promote or restrict cellular growth and metabolism. But when the pathway runs amok, it can be associated with numerous diseases, including cancer, diabetes, and Alzheimer’s disease. Understanding the various sensors that feed into the mTOR pathway could lead to novel therapies for these diseases and even aging, as dialing down the mTOR pathway is linked to longer lifespans in mice and other organisms.

    Although the essential amino acid methionine is one of the key nutrients whose levels cells must carefully sense, researchers did not know how it fed into the mTOR pathway — or if it did at all. Now, Whitehead Institute Member David Sabatini and members of his laboratory have identified a protein, SAMTOR, as a sensor in the mTOR pathway for the methionine derivative SAM (S-adenosyl methionine). Their findings are described in the current issue of the journal Science.

    Methionine is essential for protein synthesis, and a metabolite produced from it, SAM, is involved in several critical cellular functions to sustain growth, including DNA methylation, ribosome biogenesis, and phospholipid metabolism. Interestingly, methionine restriction at the organismal level has been linked to increased insulin tolerance and lifespan, similar to the antiaging effects associated with inhibition of mTOR pathway activity. But the connection between mTOR, methionine, and aging remains elusive.

    “There are a lot of similarities between the phenotypes of methionine restriction and mTOR inhibition,” says Sabatini, who is also a Howard Hughes Medical Institute investigator and a professor of biology at MIT. “The existence of this protein SAMTOR provides some tantalizing data suggesting that those phenotypes may be mechanistically connected.”

    Sabatini identified mTOR as a graduate student and has since elucidated numerous aspects of its namesake pathway. He and his lab recently pinpointed the molecular sensors in the mTOR pathway for two key amino acids: leucine and arginine. In the current line of research, co-first authors of the Science paper Xin Gu and Jose Orozco, both graduate students Sabatini’s lab, identified a previously uncharacterized protein that seemed to interact with components of the mTOR pathway. After further investigation, they determined that the protein binds to SAM and indirectly gauges the pool of available methionine, making this protein — SAMTOR — a specific and unique nutrient sensor that informs the mTOR pathway.

    “People have been trying to figure out how methionine was sensed in cells for a really long time,” Orozco says. “I think that this is the first time in mammalian cells a mechanism has been found to describe the way methionine can regulate a major signaling pathway like mTOR.”

    The current research indicates that SAMTOR plays a crucial role in methionine sensing. Methionine metabolism is vital for many cellular functions, and the Sabatini lab will further investigate the potential links between SAMTOR and the extended lifespan and increased insulin sensitivity effects that are associated with low methionine levels.

    “It is very interesting to consider mechanistically how methionine restriction might be associated in multiple organisms with beneficial effects, and identification of this protein provides us a potential molecular handle to further investigate this question,” Gu says. “The nutrient-sensing pathway upstream of mTOR is a very elegant system in terms of responding to the availability of certain nutrients with specific mechanisms to regulate cell growth. The currently known sensors raise some interesting questions about why cells evolved sensing mechanisms to these specific nutrients and how cells treat these nutrients differently.”

    This work was supported by the National Institutes of Health, the Department of Defense, the National Science Foundation, and the Paul Gray UROP Fund.

    See the full article here .

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  • richardmitnick 5:04 pm on November 9, 2017 Permalink | Reply
    Tags: , Biology, Microtubular highways, Proteins called kinesins and dyneins act like motors and are essentially the cargo trucks in cells, , Rutgers-led research may lead to new treatments for neurodegenerative diseases and nerve injuries., These enzymes are involved in degenerating cells that are crucial for vision as well as neurons, TTLL-11 is an enzyme that puts traffic signs composed of the amino acid glutamate on the microtubule highways to regulate the speed of the protein cargo trucks   

    From Rutgers University: “How to Control Traffic on Cellular Highways 

    Rutgers University
    Rutgers University

    November 8, 2017
    Todd B. Bates
    848-932-0550
    todd.bates@rutgers.edu

    1
    Robert O’Hagan, assistant research professor in the Human Genetics Institute of New Jersey and the Department of Genetics at Rutgers University–New Brunswick, with C. elegans – a microscopic roundworm – in the background. Nick Romanenko/Rutgers University

    Rutgers-led research may lead to new treatments for neurodegenerative diseases and nerve injuries.

    Inside cells, protein “motors” act like trucks on tiny cellular highways to deliver life-sustaining cargoes.

    Now a team led by Rutgers University–New Brunswick researchers has discovered how cells deploy enzymes to place traffic control and “roadway under construction” signs along cellular highways.

    “To stay alive and function, every cell in our body needs to transport cargoes to the place they’re needed inside the cell, in the right amount and at the right time,” said Robert O’Hagan, lead author of a new study and assistant research professor in the Human Genetics Institute of New Jersey and the Department of Genetics at Rutgers University–New Brunswick. “So there has to be a lot of organization in how transport inside the cell is regulated, and now we know a lot more about how that happens.”

    The study, published online today in Current Biology, has implications for future therapies for spinal cord and nerve injuries and neurodegenerative diseases. Co-authors include Malan Silva, who earned a doctorate at Rutgers; Winnie Zhang, Sebastian Bellotti and Yasmin Ramadan, who received bachelor’s degrees at Rutgers; and Professor Maureen M. Barr, who heads the Barr Lab in the Human Genetics Institute of New Jersey and the Department of Genetics in the School of Arts and Sciences.

    The highways inside cells are called microtubules, and proteins called kinesins and dyneins act like motors and are essentially the cargo trucks in cells, O’Hagan said. The motor proteins drive cargoes around microtubule highways, but a central question in cell biology is how intracellular transport and the highway systems are organized. Questions include how the motor proteins know where to go and how fast they need to be.

    The Rutgers-led team studied C. elegans, a microscopic roundworm, and looked at microtubules in cilia – hair-like organelles that protrude from cells and perform sensory tasks. The scientists found that TTLL-11 is an enzyme that puts traffic signs composed of the amino acid glutamate on the microtubule highways to regulate the speed of the protein cargo trucks. CCPP-1 is an enzyme that takes down these glutamate traffic signs when there are too many of them, according to O’Hagan.

    “Working together, they seem to regulate the speed of the motors that move cargoes on the microtubular highways,” he said.

    The scientists also found that the glutamates can also act as a “roadway under construction” sign, changing the highways’ structure, he said.

    2
    Professor of Genetics Maureen M. Barr (left), Assistant Research Professor Robert O’Hagan (center) and Lab Technician Yasmin Ramadan SAS’16 (right) in the Barr Lab. Nick Romanenko/Rutgers University

    Intriguingly, these enzymes are involved in degenerating cells that are crucial for vision, as well as neurons, O’Hagan said. The study suggests that future therapies targeting these enzymes might counter neurodegenerative diseases or nerve damage, including spinal cord injuries, he said.

    “The picture that’s emerging from our and other labs’ research is that, for neurons to regenerate after injury or to survive in the brain, they need to be able to reorganize their microtubular highways and their cargo trucks in order to bring the right cargoes around to rebuild or maintain the cell,” he said.

    “There’s a lot more to be discovered,” he added. “Our next step is to see how this works in the spinal cord in mammals, so we’ve started studies of rat spinal cord neurons.”

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  • richardmitnick 10:21 am on November 6, 2017 Permalink | Reply
    Tags: , Biology, , Kew Gardens Millennium Seed Bank, Newton’s apple seeds, , The apple tree in Isaac Newton’s mother’s orchard where Newton saw the famous apple fall, The next step will be to find suitable welcoming homes for the young trees so that they can help tell the intertwining stories of Newton seed science and space travel, The tree is still flourishing at Woolsthorpe Manor Newton’s home near Grantham 330 years after he wrote his great work Philosophiae Naturalis Principia Mathematica, UK Space Agency Blog   

    From UK Space Agency Blog: “Newton’s apple seeds” 

    UK Space Agency

    UK Space Agency Blog

    6 November 2017
    Steven Watson

    I’ve just met some remarkable seedlings at Wakehurst Place in West Sussex, where Kew Gardens keeps its Millennium Seed Bank. They are the experts when it comes to anything to do with storing and growing plant seeds.

    The seeds in question were flown on the International Space Station with Tim Peake and were collected from the apple tree in Isaac Newton’s mother’s orchard where Newton saw the famous apple fall, which helped him figure out the laws of gravity. Isaac Newton (born in 1643) was a physicist and mathematician who developed the principles of modern physics including the laws of gravity and motion.

    The tree is still flourishing at Woolsthorpe Manor, Newton’s home near Grantham, 330 years after he wrote his great work Philosophiae Naturalis Principia Mathematica, which set out the laws of gravitation on which every space mission depends. This was the great work that Tim Peake’s Principia mission was named after.

    1
    Newton’s apple tree – and the seeds being presented by Dallas Campbell and Jannette Warrener to the Agency’s Head of Education and Skills, Jeremy Curtis.

    The National Trust’s Operations Manager at Woolsthorpe Manor, Jannette Warrener, and her team harvested the seeds and presented them to the UK Space Agency during Grantham’s annual Gravity Fields festival in October 2014. We then delivered them to Wakehurst Place to dry and pack them for their epic journey into space.

    The seeds were delivered to space in SpaceX-8, a cargo supply to the International Space Station, on the 16 April 2016 and spent 198 days in space before returning to Earth with SpaceX-9 on 26 August 2016.

    2
    Tim with seeds on ISS. No image credit.

    On their return from space, the well-travelled seeds then went back to Wakehurst Place where they spent 90 days sitting on a bed of agar jelly at 5°C to simulate the winter cold needed to break dormancy. Spring arrived for them in May 2017 when they were warmed to 15°C and the young seedlings started to emerge.

    Since then they have grown fast and we now have ten healthy young plants. The Kew staff, led by Hugh Pritchard (Head of Comparative Seed Biology) and Anne Visscher (Career Development Fellow), will continue to nurture them until they are large enough to fend for themselves.

    3
    The healthy young apple trees with the Kew team. From left to right: Jannette Warrener, Joanna Walmisley, Jeremy Curtis, Eliana Van Der Schraft, Anne Visscher, Cristina Blandino, David Cleeve, Hugh Pritchard.

    The next step will be to find suitable welcoming homes for the young trees so that they can help tell the intertwining stories of Newton, seed science and space travel. Watch this space for details of how to make your bid to host one of these precious plants.

    See the full article here .

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    At the heart of UK efforts to explore and benefit from space, we are responsible for ensuring that the UK retains and grows a strategic capability in space-based systems, technologies, science and applications. We lead the UK’s civil space programme in order to win sustainable economic growth, secure new scientific knowledge and provide benefit to all citizens.

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  • richardmitnick 2:00 pm on November 2, 2017 Permalink | Reply
    Tags: , Biology, , , , Room for growth: Princeton’s Vertical Farming Project harvests knowledge for a budding industry   

    From Princeton University- “Room for growth: Princeton’s Vertical Farming Project harvests knowledge for a budding industry” 

    Princeton University
    Princeton University

    Nov. 2, 2017
    Morgan Kelly, Princeton Environmental Institute

    1
    Princeton University’s Vertical Farming Project was established as a model vertical farm — which involves growing food crops indoors on stacked shelves — to generate accessible and up-to-date research for the field. For her senior thesis, Princeton senior Jesenia Haynes (above) is analyzing the environmental impacts of growing kale and lettuce in a vertical farm versus a conventional farm. Haynes is one of several student researchers engaged in the Vertical Farming Project, which is part of the Campus as Lab Initiative.
    Video still from Nick Donnoli, Office of Communications

    Princeton University’s Vertical Farming Project began at a conference in 2016 when the topic turned to increasing the crop yield of hydroponic systems — wherein plants are grown indoors without soil by using only water and nutrient solutions — by pressurizing water with extra oxygen in a tank before feeding it to the plants. The idea was on everyone’s lips.

    Paul Gauthier knew it was wrong. A plant physiologist, he realized that once the water leaves the tank, it will depressurize and release more oxygen, which reduces photosynthesis.

    “They wanted to provide more oxygen to the roots to increase the yield, but they were doing the opposite of that,” said Gauthier, an associate research scholar in geosciences and the Princeton Environmental Institute. “That’s when I decided to get into the game.”

    In April, Gauthier launched the Vertical Farming Project with support from a High Meadows Foundation Sustainability Fund grant obtained through the Office of Sustainability. The project includes a number of student researchers and is part of the Campus as Lab Initiative. Vertical farming involves growing food crops indoors on stacked shelves. Hydroponics is the most popular form of vertical farming, but the concept is always the same. Sheltered from pests, frost and the scorching sun, plants can grow rapidly, with harvests taking place several times a year. The Princeton farm can produce mature basil in one month, month after month.

    Located in a small windowless room in Moffett Laboratory, Princeton’s vertical farm is used to identify the optimal conditions for growing food indoors. The farm contains about 80 plants. (No tomatoes, for space considerations: “If you give them the right conditions, they’ll grow and grow and grow and never stop,” Gauthier said.) The most successful plants are herbs and leafy greens, which allow for the occasional feast. The project has partnered with an eating club, the Terrace F. Club, which has incorporated the project’s bounty into meals. An Oct. 24 event at Forbes College featured dishes made with lettuce and herbs from the vertical farm and the Princeton Garden Project served alongside produce from a commercial food distributor.

    Gauthier, who has been at the University since 2012 and focuses his research on plant resilience to environmental stress, envisions the Princeton project as an open-source model for vertical farming. Free from having to turn a profit, he and the students involved in the project can experiment with various crops, techniques, technologies and nutrient solutions. Their focus is getting the best harvest with the least amount of resource consumption, then making those data publicly available. They grow less common crops such as edible flowers and wheat. Wheat from the Princeton vertical farm is ready for harvest in 65 days. One of Gauthier’s side projects is to see how much and how economically he can produce flour from a single wheat harvest. He would like to eventually grow citrus and fruit shrubs.

    “We want to create new knowledge in the field,” Gauthier said. “We want to prove that this is sustainable. All the research strengths of Princeton can be combined into this project: sustainability, environmental science, biology and engineering. We hope Princeton will start leading the field by providing new technologies and training students for consulting in this new industry.”

    Paul Gauthier (left), a plant physiologist and an associate research scholar in geosciences and the Princeton Environmental Institute, launched the project in April to identify the optimal conditions for growing various crops with the least amount of water and energy, then make those data publicly available to potential growers. In this video, Gauthier, Haynes and sophomore Seth Lovelace (right) discuss the project’s aims and their individual research interests.
    Video by [not named].

    A field ripe for cultivation

    In recent years, vertical farming has gained traction as a method for producing food for a growing global population that is running short on arable land. Reducing the need for new — or even existing — farmland would go a long way toward preserving natural ecosystems and restoring the ones ravaged by agriculture, according to Dickson Despommier, the Columbia University microbiologist whose 2010 book, The Vertical Farm, helped popularize the topic. Vertical farms reportedly consume up to 95 percent less water than conventional farming by recycling water and they also eliminate the chemical-laden runoff that poisons waterbodies and aquifers.

    The technique also has potential for bringing locally sourced and readily available food to arid and urban areas, which would reduce shipping-related carbon emissions. Several vertical farms are now based in and around New York City, including the world’s largest vertical farm, Newark-based AeroFarms, which produces up to 2 million pounds of produce annually and is headquartered in an old steel mill.

    Gauthier discovered, however, that the industry overall suffers a lack of accessible and up-to-date research on everything from leaf physics to a breakdown of the market. He found very little or outdated peer-reviewed data on nutrient efficiency, automation or sustainable energy and water use. The hydroponic farmers Gauthier has met largely rely on trial-and-error and information from the 1980s. Commercial vertical farms are private businesses that keep their research results to themselves, he said.

    “In science, we know very well how to grow plants hydroponically,” Gauthier said. “The problem is that the public doesn’t know that.”

    Admittedly, vertical farming is not a booming research area, Gauthier said. For instance, there’s little data on growing herbs and leafy greens, which are high-demand crops, he said. Plant and agricultural scientists largely focus on optimizing traditional farming, particularly through the use of genetically modified crops.

    “There’s a difference between what science is doing and what vertical farmers need to know,” Gauthier said.

    3
    The Princeton vertical farm contains about 80 plants. The most successful are herbs and leafy greens, which have been distributed on campus. The Terrace F. Club eating club has incorporated the vertical farm’s harvests into meals. An Oct. 24 event at Forbes College (above) featured salads made with lettuce from the vertical farm (foreground) versus lettuce from a commercial food distributor. Photo by Nick Donnoli, Office of Communications

    Questions keep cropping up

    For her senior thesis, Princeton student Jesenia Haynes is analyzing the environmental impacts of growing kale and lettuce in a vertical farm versus a conventional farm. Her focus is on water and electricity use, the energy costs of producing fertilizer, and the resources that go into shipping and delivering produce to consumers.

    Haynes, who is majoring in ecology and evolutionary biology with a certificate in environmental studies, has been working with Gauthier nearly since the project began. She has gardened since childhood, but her interest in sustainable agricultural was piqued by lectures and classes at Princeton such as ENV 200: “The Environmental Nexus.” While she enjoys growing food, she also is now aware of the obstacles vertical farming poses.

    “The maintenance of the farm for me has been the most challenging part. The biggest problem if you want to reproduce this system on a local scale is having the people to maintain it,” Haynes said. “But with any new initiative, you need to keep improving it. It takes time and effort. We have to keep working to make the process better.”

    In August, Manolya Adan, a graduate student of Gauthier’s based at Imperial College London, visited vertical farms around the United States. Her goal is to build a carbon-footprint model of the entire vertical-farm supply chain. Vertical farms are expanding rapidly, she said — in the past five years, the number in Asia has increased from 23 to 130. (A driving force is the advancement of light-emitting diode, or LED, technology that can provide ample light more efficiently than incandescent lightbulbs. In particular, Gauthier explained, LEDs now incorporate green light, which is essential for secondary plant metabolism.)

    Vertical farms frequently tout the environmental benefits of their trade, but there’s no publicly available information with which anyone can objectively verify those claims, Adan said. “Vertical farming holds a lot of promise, but I want to see what the actual benefit is in terms of reducing our environmental impact,” Adan said. “We want the industry to do well and we need to be sustainable. It’s about helping companies see what they themselves are doing and what they could do better.”

    Operational costs are a significant obstacle facing vertical, Gauthier said — more than 85 percent of vertical farms fail within two years. LEDs, labor and space are expensive, but there is no hard data on what drives these operations to close. Senior Rozalie Czesana, a Woodrow Wilson School of Public and International Affairs major, is preparing to examine the costs associated with running a small vertical farm, together with the feasibility of scaling them up to the community level. Her focus will be on “food deserts,” or areas such as low-income urban neighborhoods that often lack sufficient access to fresh, healthy food.

    Czesana, who established the project’s partnership with the Terrace F. Club, previously conducted a comparative study that examined the speed of growth and average water use of herbs and lettuce in the vertical farm versus a greenhouse. She found that the vertical farm is much more resilient to New Jersey weather — the heat wave in May 2016 killed most of the greenhouse produce despite constant care. She also found that while basil, lettuce and kale do much better in the vertical farm under a certain nutrient concentration, cilantro preferred the greenhouse.

    Sophomore Seth Lovelace, a prospective mathematics major, works with Gauthier to analyze the level of individual nutrients in the solution they feed the plants using a technique called inductively coupled plasma mass spectrometry (ICP-MS). They can then adjust the amount of a certain nutrient based on what a plant uses most, as well as adjust the micronutrients that influence flavor, Lovelace said.

    “We’re really trying to bring metrics to the vertical-farming game. All of our team members are trying to get data so we can make the farm grow better, to help these plants thrive,” Lovelace said. “Interdisciplinary research, when applied to any project, really enhances how the project moves forward. I think the access to this kind of research as an undergrad is amazing.”

    Gauthier welcomes the student interest. “I want undergrads involved because they are the next generation and the big burden of saving the planet will be on them,” he said. “When they are familiar with this system and know it, they can start thinking outside of the box.

    “The industry is growing for sure and it will be part of our lives in the future,” he said. “That’s what this project is about — understanding this system well enough to expand it.”

    4
    The Oct. 24 “Meet What You Eat” event featured the harvests from Princeton Garden and Vertical Farming projects. From left to right: sophomore Anna Marsh, Garden Project leader; junior Emmy Bender, Garden Project leader; sophomore Laurie Zielinkski; sophomore Natalie Grayson, vertical farm manager; Violette Chamoun, Campus Dining operations manager; Alex Trimble, Campus Dining chef du cuisine; senior Rozalie Czesana, who is conducting an economic analysis for the Vertical Farming Project; Gauthier; and Patrick Caddeau, dean of Forbes College.
    Photo by
    Nick Donnoli, Office of Communications

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    About Princeton: Overview

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    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.

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  • richardmitnick 1:35 pm on November 2, 2017 Permalink | Reply
    Tags: , Biology, , Earth Microbiome Project, , Mapping the Microbiome of … Everything, Massive global research collaboration known as the Earth Microbiome Project catalogues planet’s microbial diversity at unprecedented scale,   

    From UCSD: “Mapping the Microbiome of … Everything” 

    UC San Diego bloc

    UC San Diego

    November 01, 2017
    Heather Buschman

    Massive global research collaboration known as the Earth Microbiome Project catalogues planet’s microbial diversity at unprecedented scale.

    1
    From left, Berkeley Lab researchers Eric Dubinsky, Shi Wang (on left), and Neslihan Tas contributed to the Earth Microbiome Project. LBNL.

    ​In the Earth Microbiome Project, an extensive global team co-led by researchers at University of California San Diego, Pacific Northwest National Laboratory, University of Chicago and Argonne National Laboratory collected more than 27,000 samples from numerous, diverse environments around the globe. They analyzed the unique collections of microbes — the microbiomes — living in each sample to generate the first reference database of bacteria colonizing the planet. Thanks to newly standardized protocols, original analytical methods and open data-sharing, the project will continue to grow and improve as new data are added.

    The paper describing this effort, published November 1 in Nature, was co-authored by more than 300 researchers at more than 160 institutions worldwide.

    2
    Earth Microbiome Project collaborators collect and analyze samples from diverse environments around the world. Top left: Hiking through the rain forest of Puerto Rico to sample soils with students (credit: Krista McGuire, University of Oregon). Top middle: Colobine monkeys in China, whose fecal microbiomes were sampled for this study (credit: Kefeng Niu). Top right: Bat in Belize, whose fecal microbiome was sampled for this study (credit: Angelique Corthals and Liliana Davalos). Bottom Left: Researcher sampling a stream in the Brooks Mountain Range, Alaska (credit: Byron Crump). Bottom middle: Swabbing bird eggshells from Spain (credit: Juan Peralta-Sanchez). Bottom right: Researcher sampling the southernmost geothermal soils on the planet, at summit of Mt. Erebus, Ross Island, Antarctica (credit: S. Craig Cary, Univ. of Waikato, New Zealand).

    The Earth Microbiome Project was founded in 2010 by Rob Knight, PhD, professor at UC San Diego School of Medicine and director of the Center for Microbiome Innovation at UC San Diego; Jack Gilbert, PhD, professor and faculty director of The Microbiome Center at University of Chicago and group leader in Microbial Ecology at Argonne National Laboratory; Rick Stevens, PhD, associate laboratory director at Argonne National Laboratory and professor and senior fellow at University of Chicago; and Janet Jansson, PhD, chief scientist for biology and laboratory fellow at Pacific Northwest National Laboratory. Knight, Gilbert and Jansson are also co-senior authors of the Nature paper and Stevens is a co-author.

    “The potential applications for this database and the types of research questions we can now ask are almost limitless,” Knight said. “Here’s just one example — we can now identify what kind of environment a sample came from in more than 90 percent of cases, just by knowing its microbiome, or the types and relative quantities of microbes living in it. That could be useful forensic information at a crime scene … think ‘CSI.’”

    The goal of the Earth Microbiome Project is to sample as many of the Earth’s microbial communities as possible in order to advance scientific understanding of microbes and their relationships with their environments, including plants, animals and humans. This task requires the help of scientists from all over the globe. So far, the project has spanned seven continents and 43 countries, from the Arctic to the Antarctic, and more than 500 researchers have contributed to the sample and data collection. Project members are using this information as part of approximately 100 studies, half of which have been published in peer-reviewed journals.

    “Microbes are everywhere,” said first author Luke Thompson, PhD, who took on the role of project manager while a postdoctoral researcher in Knight’s lab and is currently a research associate at the National Oceanic and Atmospheric Administration (NOAA). “Yet prior to this massive undertaking, changes in microbial community composition were identified mainly by focusing on one sample type, one region at a time. This made it difficult to identify patterns across environments and geography to infer generalized principles.”

    Project members analyze bacterial diversity among various environments, geographies and chemistries by sequencing the 16S rRNA gene, a genetic marker specific for bacteria and their relatives, archaea. The 16S rRNA sequences serve as “barcodes” to identify different types of bacteria, allowing researchers to track them across samples from around the world. Earth Microbiome Project researchers also used a new method to remove sequencing errors in the data, allowing them to get a more accurate picture of the number of unique sequences in the microbiomes.

    Within this first release of data, the Earth Microbiome Project team identified around 300,000 unique microbial 16S rRNA sequences, almost 90 percent of which don’t have exact matches in pre-existing databases.

    Pre-existing 16S rRNA sequences are limited because they were not designed to allow researchers to add data in a way that’s useful for the future. Project co-author Jon Sanders, PhD, a postdoctoral researcher in Knight’s lab, compares the difference between these other databases and the Earth Microbiome Project to the difference between a phone book and Facebook. “Before, you had to write in to get your sequence listed, and the listing would contain very little information about where the sequence came from or what other sequences it was found with,” he said. “Now, we have a framework that supports all that additional context, and which can grow organically to support new kinds of questions and insights.”

    “There are large swaths of microbial diversity left to catalogue. And yet we’ve ‘recaptured’ about half of all known bacterial sequences,” Gilbert said. “With this information, patterns in the distribution of the Earth’s microbes are already emerging.”

    According to Gilbert, one of the most surprising observations is that unique 16S sequences are far more specific to individual environments than are the typical units of species used by scientists. The diversity of environments sampled by the Earth Microbiome Project helps demonstrate just how much local environment shapes the microbiome. For example, the skin microbiomes of cetaceans (whales and dolphins) and fish are more similar to each other than they are to the water they swim in; conversely, the salt in saltwater microbiomes makes them distinct from freshwater, but they are still more similar to each other than to aquatic animal skin. Overall, the microbiomes of a host, such as a human or animal, were quite distinct from free-living microbiomes, such as those found in water and soil. For example, the free-living microbiomes were far more diverse, in general, than host-associated microbiomes.

    “These global ecological patterns offer just a glimpse of what is possible with coordinated and cumulative sampling,” Jansson said. “More sampling is needed to account for factors such as latitude and elevation, and to track environmental changes over time. The Earth Microbiome Project provides both a resource for the exploration of myriad questions, and a starting point for the guided acquisition of new data to answer them.”

    For more about the Earth Microbiome Project, visit earthmicrobiome.org and follow @earthmicrobiome on Twitter. For the complete list of co-authors and institutions participating in the Earth Microbiome Project, view the full Nature paper .

    The project was funded, in part, by the John Templeton Foundation, W. M. Keck Foundation, Argonne National Laboratory, Australian Research Council, and Extreme Science and Engineering Discovery Environment, which is supported by National Science Foundation (ACI-1053575).

    See the full article here .

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    UC San Diego Campus

    The University of California, San Diego (also referred to as UC San Diego or UCSD), is a public research university located in the La Jolla area of San Diego, California, in the United States.[12] The university occupies 2,141 acres (866 ha) near the coast of the Pacific Ocean with the main campus resting on approximately 1,152 acres (466 ha).[13] Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC San Diego is the seventh oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling about 22,700 undergraduate and 6,300 graduate students. UC San Diego is one of America’s Public Ivy universities, which recognizes top public research universities in the United States. UC San Diego was ranked 8th among public universities and 37th among all universities in the United States, and rated the 18th Top World University by U.S. News & World Report ‘s 2015 rankings.

     
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