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  • richardmitnick 10:13 am on March 9, 2017 Permalink | Reply
    Tags: , , , Embryos can be repaired, in vitro fertilization, Triple helix, Yale   

    From Yale: “Gene editing opens the door to a “revolution” in treating and preventing disease” 

    Yale University bloc

    Yale University

    March 8, 2017
    John Dent Curtis

    Today, in vitro fertilization provides a way for couples to avoid passing potentially disease-causing genes to their offspring. A couple will undergo genetic screening. Tests will determine whether their unborn children are at risk. If embryos created through IVF show signs of such a genetic mutation, they can be discarded.

    Flash forward a few years, and, instead of being discarded, those embryos can be repaired with new gene editing technologies. And those repairs will affect not only those children, but all their descendants.

    “This is definitely new territory,” said Pasquale Patrizio, M.D., director of the Yale Fertility Center and Fertility Preservation Program. “We are at the verge of a huge revolution in the way disease is treated.”

    We are at the verge of a huge revolution in the way disease is treated.”
    Pasquale Patrizio, M.D., director of the Yale Fertility Center and Fertility Preservation Program

    In a move that seems likely to help clear the path for the use of gene editing in the clinical setting, on February 14 the Committee on Human Gene Editing, formed by the National Academy of Medicine and the National Academy of Sciences, recommended that research into human gene editing should go forward under strict ethical and safety guidelines. Among their concerns were ensuring that the technology be used to treat only serious diseases for which there is no other remedy, that there be broad oversight, and that there be equal access to the treatment. These guidelines provide a framework for discussion of technology that has been described as an “ethical minefield” and for which there is no government support in the United States.

    A main impetus for the committee’s work appears to be the discovery and widespread use of CRISPR-Cas9, a defense that bacteria use against viral infection. Scientists including former Yale faculty member Jennifer Doudna, Ph.D., now at the University of California, Berkeley, and Emmanuelle Charpentier, Ph.D., of the Max Planck Institute for Infection Biology in Berlin, discerned that the CRISPR enzyme could be harnessed to make precision cuts and repairs to genes. Faster, easier, and cheaper than previous gene editing technologies, CRISPR was declared the breakthrough of the year in 2015 by Science magazine, and has become a basic and ubiquitous laboratory research tool. The committee’s guidelines, said scientists, physicians, and ethicists at Yale, could pave the way for thoughtful and safe use of this and other human gene editing technologies. In addition to CRISPR, the committee described three commonly used gene editing techniques; zinc finger nucleases, meganucleases, and transcription activator-like effector nucleases.

    Patrizio, professor of obstetrics, gynecology, and reproductive sciences, said the guidelines are on the mark, especially because they call for editing only in circumstances where the diseases or disabilities are serious and where there are not alternative treatments. He and others cited such diseases as cystic fibrosis, sickle cell anemia, and thalassemia as targets for gene editing. Because they are caused by mutations in a single gene, repairing that one gene could prevent disease.

    Peter Glazer, M.D. ’87, Ph.D. ’87, HS ’91, FW ’91, chair and the Robert E. Hunter Professor of Therapeutic Radiology and professor of genetics, said, “The field will benefit from guidelines that are thoughtfully developed. This was a step in the right direction.”

    The panel recommended that gene editing techniques should be limited to deal with genes proven to cause or predispose to specific diseases. It should be used to convert mutated genes to versions that are already prevalent in the population. The panel also called for stringent oversight of the process and for a prohibition against use of the technology for “enhancements,” rather than to treat disease. “As physicians, we understand what serious diseases are. Many of them are very well known and well characterized on a genetic level,” Glazer said. “The slippery slope is where people start thinking about modifications in situations where people don’t have a serious disorder or disease.”

    Mark Mercurio, M.D., professor of pediatrics (neonatology), and director of the Program for Biomedical Ethics, echoed that concern. While he concurs with the panel’s recommendations, he urged a clear definition of disease prevention and treatment. “At some point we are not treating, but enhancing.” This in turn, he said, conjures up the nation’s own medical ethical history, which includes eugenics policies in the early 20th century that were later adopted in Nazi Germany. “This has the potential to help a great many people, and is a great advance. But we need to be cognizant of the history of eugenics in the United States and elsewhere, and need to be very thoughtful in how we use this technology going forward,” he said.

    The new technology, he said, can lead to uncharted ethical waters. “Pediatric ethics are more difficult,” Mercurio said. “It is one thing to decide for yourself–is this a risk I’m willing to take—and another thing to decide for a child. It is another thing still further, which we have never had to consider, to decide for future generations.”

    Myron Genel, M.D., emeritus professor of pediatrics and senior research scientist, served on Connecticut’s stem cell commission and four years on the Health and Human Services Secretary’s Advisory Committee on Human Research Protections. He believes that Connecticut’s guidelines on stem cell research provide a framework for addressing the issues associated with human gene editing. “There is a whole regulatory process that has been evolved governing the therapeutic use of stem cells,” he said. “There are mechanisms that have been put in place for effective local oversight and national oversight for stem cell research.”

    Although CRISPR has been the subject of a bitter patent dispute between Doudna and Charpentier and The Broad Institute in Cambridge, Mass., a recent decision by the U.S. Patent Trial and Appeal Board in favor of Broad is unlikely to affect research at Yale and other institutions. Although Broad, an institute of Harvard and the Massachusetts Institute of Technology, can now claim the patent, universities do not typically enforce patent rights against other universities over research uses.

    At Yale, scientists and physicians noted that gene editing is years away from human trials, and that risks remain. The issue now, said Glazer, is “How do we do it safely? It is never going to be risk-free. Many medical therapies have side effects and we balance the risks and benefits.” Despite its effectiveness, CRISPR is also known for what’s called “off-target risk,” imprecise cutting and splicing of genes that could lead to unforeseen side effects that persist in future generations. “CRISPR is extremely potent in editing the gene it is targeting,” Glazer said. “But it is still somewhat promiscuous and will cut other places. It could damage a gene you don’t want damaged.”

    Glazer has been working with a gene editing technology called triple helix that hijacks DNA’s own repair mechanisms to fix gene mutations. Triple helix, as its name suggests, adds a third strand to the double helix of DNA. That third layer, a peptide nucleic acid, binds to DNA and provokes a natural repair process that copies a strand of DNA into a target gene. Unlike CRISPR and other editing techniques, it does not use nucleases that cut DNA. “This just recruits a process that is natural. Then you give the cell this piece of DNA, this template that has a new sequence,” Glazer said, adding that triple helix is more precise than CRISPR and leads to fewer off-target effects, but is a more complex technology that requires advanced synthetic chemistry.

    Along with several scientists across Yale, Glazer is studying triple helix as a potential treatment for cystic fibrosis, HIV/AIDS, spherocytosis, and thalassemia.

    Adele Ricciardi, a student in her sixth year of the M.D./Ph.D. program, is working with Glazer and other faculty on use of triple helix to make DNA repairs in utero. She also supports the panel’s decision, but believes that more public discussion is needed to allay fears of misuse of the technology. In a recent presentation to her lab mates, she noted that surveys show widespread public concern about such biomedical advances. One study found that most of those surveyed felt it should be illegal to change the genes of unborn babies, even to prevent disease.

    “There is, I believe, a misconception of what we are using gene editing for,” Ricciardi said. “We are using it to edit disease-causing mutations, not to improve the intelligence of our species or get favorable characteristics in babies. We can improve quality of life in kids with severe genetic disorders.”

    See the full article here .

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    Yale University Campus

    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

  • richardmitnick 3:15 pm on March 7, 2017 Permalink | Reply
    Tags: , Wimps axions and neutralinos, , Yale   

    From Yale: Women in STEM – “Yale-led team puts dark matter on the map” Priyamvada Natarajan 

    Yale University bloc

    Yale University

    March 1, 2017

    Jim Shelton

    Professor Priyamvada Natarajan

    Detailed map of reconstructed dark matter clump distributions in a distant galaxy cluster, obtained from the Hubble Space Telescope Frontier Fields data. The unseen matter in this map is comprised of a smooth heap of dark matter on which clumps form. No image credit.

    A Yale-led team has produced one of the highest-resolution maps of dark matter ever created, offering a detailed case for the existence of cold dark matter — sluggish particles that comprise the bulk of matter in the universe.

    The dark matter map is derived from Hubble Space Telescope Frontier Fields data of a trio of galaxy clusters that act as cosmic magnifying glasses to peer into older, more distant parts of the universe, a phenomenon known as gravitational lensing.

    Yale astrophysicist Priyamvada Natarajan led an international team of researchers that analyzed the Hubble images. “With the data of these three lensing clusters we have successfully mapped the granularity of dark matter within the clusters in exquisite detail,” Natarajan said. “We have mapped all of the clumps of dark matter that the data permit us to detect, and have produced the most detailed topological map of the dark matter landscape to date.”

    Scientists believe dark matter — theorized, unseen particles that neither reflect nor absorb light, but are able to exert gravity — may comprise 80% of the matter in the universe. Dark matter may explain the very nature of how galaxies form and how the universe is structured. Experiments at Yale and elsewhere are attempting to identify the dark matter particle; the leading candidates include axions and neutralinos.

    “While we now have a precise cosmic inventory for the amount of dark matter and how it is distributed in the universe, the particle itself remains elusive,” Natarajan said.

    Dark matter particles are thought to provide the unseen mass that is responsible for gravitational lensing, by bending light from distant galaxies. This light bending produces systematic distortions in the shapes of galaxies viewed through the lens. Natarajan’s group decoded the distortions to create the new dark matter map.

    Significantly, the map closely matches computer simulations of dark matter theoretically predicted by the cold dark matter model; cold dark matter moves slowly compared to the speed of light, while hot dark matter moves faster. This agreement with the standard model is notable given that all of the evidence for dark matter thus far is indirect, said the researchers.

    The high-resolution simulations used in the study, known as the Illustris suite, mimic structure formation in the universe in the context of current accepted theory. A study detailing the findings appeared Feb. 28 in the journal Monthly Notices of the Royal Astronomical Society.

    Other Yale researchers involved in the study were graduate students Urmila Chadayammuri and Fangzhou Jiang, faculty member Frank van den Bosch, and former postdoctoral fellow Hakim Atek. Additional co-authors came from institutions worldwide: Mathilde Jauzac from the United Kingdom and South Africa; Johan Richard, Eric Jullo, and Marceau Limousin from France; Jean-Paul Kneib from Switzerland; Massimo Meneghetti from Italy; and Illustris simulators Annalisa Pillepich, Ana Coppa, Lars Hernquist, and Mark Vogelsberger from the United States.

    The research was supported in part by grants from the National Science Foundation, the Science and Technology Facilities Council, and NASA via the Space Telescope Institute HST Frontier Fields initiative.

    The study can be found online.

    See the full article here .

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    Yale University Campus

    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

  • richardmitnick 11:27 am on March 6, 2017 Permalink | Reply
    Tags: , COSINE-100 Dark Matter Experiment - Yale University, DAMA/LIBRA at Gran Sasso, , , Laboratori Nazionali del Gran Sasso in Italy, , Women in STEM - "Meet the South Pole’s Dark Matter Detective" Reina Maruyama, Yale   

    From Nautilus: Women in STEM – “Meet the South Pole’s Dark Matter Detective” Reina Maruyama 



    Matthew Sedacca

    Reina Maruyama wasn’t expecting her particle detector to work buried deep in ice. She was wrong.

    In the late 1990s, a team of physicists at the Laboratori Nazionali del Gran Sasso in Italy began collecting data for DAMA/LIBRA, an experiment investigating the presence of dark matter particles.

    Gran Sasso LABORATORI NAZIONALI del GRAN SASSO, located in the Abruzzo region of central Italy

    DAMA/LIBRA at Gran Sasso
    DAMA/LIBRA at Gran Sasso

    The scientists used a scintillation detector to spot the weakly interactive massive particles, known as WIMPs, thought to constitute dark matter. They reported seeing an annual modulation in the number of “hits” that the detector receives. This was a potential sign that the Earth is moving through the galaxy’s supposed halo of dark matter—something that few, if any, researchers could claim.

    Reina Maruyama’s job, at a detector buried two-kilometers deep in the South Pole, is to determine whether or not these researchers’ findings are actually valid. Previously, Maruyama worked at the South Pole to detect neutrinos, the smallest known particle. But when it came to detecting dark matter, especially with using detectors buried under glacial ice, she was initially skeptical of the task. In those conditions, she “couldn’t imagine having it run and produce good physics data.”

    Contrary to Maruyama’s expectations, the detector’s first run went smoothly. Their most recent paper, published in Physical Review D earlier this year, affirmed the South Pole as a viable location for experiments detecting dark matter. The detector, despite the conditions, kept working. At the moment, however, “DM-Ice17,” as her operation is known, is on hiatus, with the team having relocated to Yangyang, South Korea, to focus on COSINE-100, another dark matter particle detector experiment, and continue the search for the modulation seen in DAMA/LIBRA.

    COSINE-100 Dark Matter Experiment – Yale University

    The shielding structure of COSINE-100 includes 3 cm of copper, 20 cm of lead, and 3 cm of 37 plastic scintillator panels for cosmic ray muon tagging. 18 5-inch PMTs are attached to the copper box to observe scintillation light from liquid scintillator, and each plastic scintillator has a 2-inch PMT attached on one side (top panels have a PMT on each side). http://cosine.yale.edu/about-us/cosine-100-experiment.

    Dark Matter?Data visuals from COSINE-100, a dark matter experiment in Yangyang, South Korea. Reina Maruyama

    Nautilus sat down with Maruyama at Yale this past January to talk about the potential nature of dark matter, the variety of ways scientists use to search for it, and what it’s like working in the South Pole.

    What do the scientists behind DAMA claim to have discovered?

    What this experiment with DAMA has seen is that in June, the velocity is odd. The sun and Earth are going in the same direction; in December, the velocities are in opposite directions, at about a 10 percent difference. That means in June we expect this signature to occur more frequently than in December. DAMA claims to have seen this annual modulation signature. People started to think about: “Well what is it that DAMA is seeing? Could it be some sort of environmental effect?” We don’t know. They’ve looked at their data, and they’ve argued against every possibility that people have come up with. One thing that the dark matter community has asked them to do is actually release their data, but so far they have refused to do that.

    The original idea of DM-Ice was to go to the southern hemisphere where the seasonal variation is opposite in phase, so if we continue to see the signal, then it would be really hard to attribute that signal to something seasonal. If we don’t see anything, then there is something in their data that they don’t understand.

    University of Wisconsin–Madison, DM-Ice collaborators

    So what is dark matter?

    We don’t know what it is. We know it exerts gravity. This is why we call it matter. We see evidence from it: in how stars move around in a galaxy, and galaxies around each other. When we look out at distant stars and galaxies, we can see light being bent around something that exerts gravity, even on photons, but we don’t see any light, x-rays, or clues of things existing.

    What we saw was that the speed of the rotating objects are much faster than what you would expect for something like that. So that seems to indicate there is more mass between these objects. You can do that by adding a clump of mass between. That’s what we see: not specific objects, but dark matter diffusely spread out all over, typically surrounding galaxies. There must be dark matter inside the orbit of our sun so that we can move at the speed that we are. That means we are going through this halo of dark matter, riding along with the sun and the earth.

    What can we do to prove that dark matter is causing these changes?

    Let’s just pick a volume, your coffee, right there. We are hypothesizing that if dark matter is WIMPs, then there’s a very small possibility that the WIMPs going at 300 kilometers per second could interact with the coffee nuclei. If that happens in our detectors, we can actually see a nucleus being kicked by a WIMP. That’s how a lot of particle detectors work: Either there are some energy transfers to the electrons, or there is some energy transfer into the nuclei, and then we detect the electrons or light emitted from that, or sound waves. If those occur at the right energy, with the right frequency, then we can say maybe we see dark matter in our detectors.

    When there is a knock into a nucleus you can actually collect two different kinds of signals: the charge and photon emissions. When nuclei get kicks, it transfers some of that energy into electrons, and then the electrons move around, and that process emits light, and in some of that, electrons can be collected, and that is a signal. You need some sort of mass, and you need to be able to tell if a nucleus got a kick. The most efficient way to do that is to have a detector that is also the target, where the nuclei is. You want some big volume to increase the likeliness this can occur. DAMA is using sodium iodide detectors. These are very sensitive experiments, and a lot of these can actually tell the difference between an initial electron kick versus an initial nuclear kick. The electron kicks actually occur much more often in these detectors, so you can reject those as background and just keep the nuclear kicks.

    Newer technologies are much more sensitive to nuclear kicks than sodium iodide. Every other experiment that has tried to look for a signature like this has not seen anything. They see nuclear kicks, but mostly attributable to neutrons. They cannot definitively say that this must be dark matter.

    Gamma Ray Shield, or Bath tub?Maruyama said, “We put detectors inside when we need to shield them from gamma rays that are present in a typical room. The box is made of lead bricks.” NO image credit.

    How did you come up with the design for your experiments?

    With DM-Ice, we wanted to be as similar to DAMA as possible: We want sodium iodide, and we want it to be low-background. So we need shielding around it to block the detector from gamma rays and cosmic rays. The only thing that’s changing should be the dark matter. It turns out the South Pole is actually a pretty good environment. You have an entire continent of ice, which is very stable. Once you go two and a half kilometers into the ice, nothing is changing. Ice at the South Pole, it’s super clean.

    Then you need to start worrying about practical things like: Can you get there, and do you have infrastructure to run the experiment? Is it affordable, do you have the right people to do this with? That starts to narrow down the site and the environment. You end up with the a few places in the world you could do this, and then maybe you want to partner with somebody else so that you can afford a bigger detector, and more, better infrastructure that’s more stable. That is the thinking process. Then you have to convince your colleagues in the field that this is a really good idea and need to share a pot of resources available to all U.S. funds. That’s the thought-process behind the experiment.

    What’s it like working in the South Pole?

    First you have to get approved to go, but that’s pretty competitive. A lot of people want to go and so if you have a good reason to go, you go. Before you go, you need to get medical clearance. You get checked out. It’s a remote location. They want to make sure you’re not gonna get sick while you’re there. So you spend one or two nights in Christchurch, New Zealand. You meet a lot of other people who might be going with you: engineers, geologists, biologists, other scientists, firemen, cooks, and bus drivers; a lot of really engaged and very passionate people.

    When you get to the South Pole, you have take it slow, even though you’re excited and working, it’s 10,000 feet, so they ask you to take it easy your first few days. You enter through what looks like a restaurant-refrigerator door. Keep the cold out kind of thing. Very comfortable, get your own room, dormitory-style living. Water is very precious. All of the energy is provided by jet fuel. So airplanes fly in and siphon off the fuel except for what’s needed for to get back. And there’s a power station where they generate electricity. They get water by melting the ice, and it’s a very expensive process. You get like two-minute showers twice a week. It’s on the honor system. That’s what it’s like living in the station.

    What are some problems that you faced when working down there?

    It’s 24/7 sunlight. So the sun circles above your head. Because you’re there to get things done, it’s hard to know when to stop working. But before you know it, it’s two in the morning, and the sun’s bright and shining. So you have to make sure you get enough sleep and ready to work the next day. That was a challenge for me.

    So when you’re not on site what are you doing in terms of research?

    We might have a small-scale detector here and do stress tests on it. Physicists love to tinker: How we can improve these detectors? What if we changed the temperature a lot? How can we make this detector even quieter so that we can look for even smaller signals, or a signal that exists that looks even bigger? People like to say things like we’re looking for a needle in a haystack, so can we reduce the haystack? Can we change the color of the haystack so that the needle looks even more visible?

    What’s the future for DM-Ice?

    Right now there is no drilling happening at the South Pole. We’ll keep pushing to do that experiment. In the meantime, the detector is buried and frozen into the ice, so we might as well just keep it running. We’re focusing on the Korean effort. What we can do there is look for the signal. If we continue to see the same signal, we can try to look for other correlations and cross them off on our own. If we cannot find other causes for it, I think the case for DAMA becomes stronger. Then DAMA’s signal is not specific to DAMA.

    See the full article here .

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    Welcome to Nautilus. We are delighted you joined us. We are here to tell you about science and its endless connections to our lives. Each month we choose a single topic. And each Thursday we publish a new chapter on that topic online. Each issue combines the sciences, culture and philosophy into a single story told by the world’s leading thinkers and writers. We follow the story wherever it leads us. Read our essays, investigative reports, and blogs. Fiction, too. Take in our games, videos, and graphic stories. Stop in for a minute, or an hour. Nautilus lets science spill over its usual borders. We are science, connected.

  • richardmitnick 4:47 pm on February 2, 2017 Permalink | Reply
    Tags: , , , Yale, Yale scientists identify key defect in brain tumor cells   

    From Yale: “Yale scientists identify key defect in brain tumor cells” 

    Yale University bloc

    Yale University

    February 1, 2017

    Ziba Kashef

    © stock.adobe.com

    In a new study, Yale researchers identified a novel genetic defect that prevents brain tumor cells from repairing damaged DNA. They found that the defect is highly sensitive to an existing FDA-approved drug used to treat ovarian cancer — a discovery that challenges current practice for treatment of brain tumors and other cancers with the same genetic defect, said the scientists.

    The study was published on Feb. 1 by Science Translational Medicine.

    Certain malignant brain tumors and leukemias have mutations in genes known as IDH1 and IDH2. The mutations render the cancers sensitive to treatment with radiation therapy or chemotherapy, significantly increasing the survival time for patients with the mutations. To better understand this sensitivity, a cross-disciplinary team of researchers led by Yale created models of the mutation in cell cultures.

    The researchers tested several existing cancer drugs on the mutated cell lines. They found that tumor cells with the mutant genes were particularly sensitive to a drug, olaparib, recently approved for the treatment of hereditary ovarian cancer. The drug caused a 50-fold increase in brain tumor cell death.

    Known as a PARP inhibitor, the drug acts on a defect in the DNA repair mechanism in the brain tumor cells, they said.

    These findings run counter to current practices in oncology. “Our work at Yale has practice-changing implications, as our data suggest an entirely new group of tumors can be targeted effectively with DNA repair inhibitors, and that possibly these patients currently are not being treated with the most optimal approaches,” said senior author Dr. Ranjit Bindra, assistant professor of therapeutic radiology and of experimental pathology.

    Co-senior author Dr. Peter Glazer, professor of therapeutic radiology and of genetics, noted, “Our work raises serious caution regarding current therapeutic strategies that are aimed at blocking mutant IDH1 and IDH2 protein function, as we believe the DNA repair defect should be exploited rather than blocked.”

    Based on these studies, the authors are designing a clinical trial to test whether DNA repair inhibitors, such as olaparib, are active against IDH1- and IDH2-mutant tumors. They anticipate that this trial will be open for enrollment later in 2017.

    “The opportunity to translate Yale science directly into the clinic is just so exciting, as it shows our ability to pivot seamlessly between the bench and the bedside, which is a key mission of our cancer center,” says Bindra.

    Co-first authors are Parker Sulkowski and Chris Corso. Additional authors are Nathaniel Robinson, Susan Scanlon, Karin Purshouse, Hanwen Bai, Yanfeng Liu, Ranjini Sundaram, Denise Hegan, Nathan Fons, Gregory Breuer, Yuanbin Song, Ketu Mishra-Gorur, Henk de Feyter, Robin de Graaf, Yulia Surovtseva, and Maureen Kachman. Bindra and Glazer are inventors on a related patent application.

    This research was supported by the National Institutes of Health (NIH), the American Cancer Society, the Cure Search for Children’s Cancer Research Foundation, and the Connecticut Department of Public Health.

    See the full article here .

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    Yale University Campus

    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

  • richardmitnick 2:34 pm on January 30, 2017 Permalink | Reply
    Tags: Debra Fischer, EXPRES spectrometer, SCIENCE LINE, , Yale   

    From Yale via Science Line: Women in STEM: “Breaking limits in science and life” Debra Fischer 

    Yale University bloc

    Yale University



    January 18, 2017
    Cici Zhang

    Debra Fischer, a Yale astronomer, hopes to find Earth-like planets outside our solar system, especially those close enough to reach by unmanned spacecraft. [Image Credit: Flickr user NASA | CC BY-NC-ND 2.0]

    A planet, Debra Fischer likes to tell her Yale students, “is a billion times fainter than the star.” Speaking from experience, she’s been searching for distant planets in the vastness of space for almost two decades and has been finding them with impressive regularity.

    Listening to Fischer lecturing undergraduates in an amphitheater classroom, you immediately recognize her as an engaging explainer and committed teacher. But she’s much more: a female pioneer in a testosterone-infused field, a social activist in science, and a cutting-edge researcher finishing a new machine that may soon rock the field of planet-hunting.

    Back in her sunlit office in a converted 19th-century mansion on Yale’s Science Hill, Fischer explains that downstairs, her graduate students are building the most precise spectrometer ever used in exoplanet research.

    Spectrometers are crucial tools for planet hunters like Fischer, who use them to measure the wavelengths of light from distant stars. Periodic changes in starlight wavelengths suggest an orbiting planet is tugging the star — bluer as the star moves towards us, redder away.

    In August, this technique helped astronomers find an Earth-like planet orbiting our nearest star neighbor, the red dwarf star Proxima Centauri. Fischer is sure that many more discoveries will be made soon with the help of more powerful tools like the ultrasensitive $5 million spectrometer she’s building, known as EXPRES, for EXtreme PREcision Spectrometer.

    “I’ve spent twenty years trying to get to this point,” Fischer says. “Now I can take everything that I’ve learned, thought about, worked on and struggled with, put them into this instrument which is going be better than anything that’s been built before.”

    With the help of better instruments like EXPRES, Fischer says, it may only be a matter of time until we find nearby exoplanets capable of harboring life. “We just need to figure out what we can do to push the limits [of our observational power],” she says.

    Represented here as an artist’s conception, the planet Proxima Centauri b excites a lot of people because it is just slightly larger than Earth and is only 4.2 light years away. [Image Credit: Flickr user European Southern Observatory | CC BY 2.0]

    A youthful-looking 63, Fischer is the mother of three grown children. She lives in New Haven, Connecticut with her husband Ed and two Australian shepherds, Radar and Rocket. For two decades, she’s been hunting exoplanets — and finding hundreds of them, including the first multi-planet system ever discovered.

    Fischer is now one of few prominent women astronomers in the United States, says Didier Queloz, a professor of astrophysics at the University of Cambridge and Geneva University. He believes Fischer’s success comes from her openness to new ideas. Fischer is well aware of “key technical developments to improve the stability and the precision of the machine she is building,” says Queloz.

    What makes the EXPRES spectrometer unique is its targeted precision. To find more planets like Earth, Fischer says, we need to be able to detect wobbles ten times subtler than we are currently capable of picking up with the spectrometer that found the planet Proxima Centauri b.

    “Earth only induces a velocity wiggle of 10-centimeter per second on the sun,” says Fischer. To detect a signal almost as weak as Earth’s, she aims to push the precision limit of EXPRES down to 20-centimeter per second from the current 100-centimeter per second.

    Next fall, Fischer will install EXPRES on the Discovery Channel Telescope in Arizona.

    Discovery Channel Telescope at Lowell Observatory, Happy Jack AZ, USA
    Discovery Channel Telescope at Lowell Observatory, Happy Jack AZ, USA

    “She is willing to try something new and risky and harder,” says Sara Seager, a professor of planetary science at MIT and a 2013 MacArthur Fellow. “That’s the only way to make progress.”

    Fischer is used to taking risks. When she studied for her master’s degree in physics at San Francisco State University in the early 1990s, there were never more than two women in any of her classes — often there were none at all.

    But later, as she pursued her doctorate at the University of California, Santa Cruz, there were two women on the astronomy faculty: Sandra Faber and Jean Brodie. “It was unheard of,” says Fischer. “You don’t say this out loud, but subconsciously it’s registering: yeah, this is a place where I could be.”

    Last summer, when Fischer organized a meeting about exoplanet instrumentation at Yale, she made a point of inviting women to chair sessions and give talks. But in the end, only 14 percent of attendees were women. “It was really disappointing,” Fischer says, especially when a male NASA project manager told her it’s because the field is technical and women don’t like instrumentation.

    MIT’s Seager has seen improvement over the years. More and more women are working as postdocs and junior faculty members in astronomy, she says, and a “relatively large number” — “large” is not yet the right word — have reached the highest level in academia, full professor, like herself and Fischer.

    With EXPRES, she hopes to find Earth-like exoplanets in nearby star systems as part of her 100 Earths Project. But there’s no guarantee the machine will meet those ambitious expectations. EXPRES, and Fischer, might fail — which is why many of her colleagues admire her so much.

    There was plenty of competitive machismo in exoplanet hunting, especially in the early 2000s when discoveries were coming fast and astronomers were jockeying for credit. “I hate to be gender biased on this, but it was hard for me. And I think for many people who are sensitive — they would not like that environment,” Fischer says.

    Fischer’s willingness to speak up also manifested itself in 2013, when she led a boycott of a NASA meeting — risking her future career and funding. After learning from Ji Wang, her then-postdoctoral fellow, that six Chinese researchers including Wang were banned from the meeting, Fischer went on Facebook and called out the space agency. It wasn’t fair to ban “people who are doing incredibly innovative work,” she explains.

    At the time, Wang says, some colleagues worried that Fischer’s outspokenness could imperil her research support, but Fischer says she had no regrets. Although the boycott “caused a big problem and a lot of people were unhappy with me,” she says, getting people to like her is not her priority. “The first thing for me is making the world a more just, more fair place.” In the end, the meeting organizer backed off, and Wang and the other Chinese researchers were allowed to attend.

    Wang is now a postdoctoral associate at the California Institute of Technology. When Fischer comes to California, he catches up with her and sometimes takes her out for dim sum.

    “Although one man or one woman cannot change the entire attitude of the government,” Wang says, individual actions matter. He says Fischer not only taught him how to be a successful scientist but also “how to be a decent human being.”

    Speaking of the future as a step-by-step process, Fischer quotes Isaac Newton: “‘If I see further than others it is because I stood on the shoulders of giants.’ We can see further than others now because of the work that the astronomers who came before us did.”

    Fischer thinks now is the time for her to be that “shoulder” for her students. “One thing I can do in my career is to figure out how to push the spectrometer’s precision to the limit” of 10-centimeters per second, says Fischer. “As my students are climbing up onto my shoulder, they will find 100 nearby stars that have Earth-like planets, and they will figure out if there is life out there.”

    “That’s not hundreds of years away. That’s the next generation.”

    See the full article here .

    Please help promote STEM in your local schools.

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    Yale University Campus

    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

  • richardmitnick 8:26 am on January 3, 2017 Permalink | Reply
    Tags: , , , , , Multi-fractal temporally weighted detrended fluctuation analysis, Searching a sea of ‘noise’ to find exoplanets — using only data as a guide, Yale   

    From Yale: “Searching a sea of ‘noise’ to find exoplanets — using only data as a guide” 

    Yale University bloc

    Yale University

    December 20, 2016

    Jim Shelton

    (Illustration by Michael S. Helfenbein)

    Yale researchers have found a data-driven way to detect distant planets and refine the search for worlds similar to Earth.

    The new approach, outlined in a study published Dec. 20 in The Astronomical Journal, relies on mathematical methods that have their foundations in physics research. Rather than trying to filter out the signal “noise” from stars around which exoplanets are orbiting, Yale scientists studied all of the signal information together to understand the intricacies within its structure.

    “It requires nothing but the data itself, which is a game changer,” said senior author John Wettlaufer, the A.M. Bateman Professor of Geophysics, Mathematics and Physics at Yale. “Moreover, it allows us to compare our findings with other, traditional approaches and improve whatever modeling assumptions they use.”

    The search for exoplanets — planets found outside our own solar system — has increased dramatically in recent years. The effort is motivated, in part, by a desire to discover Earth analogs that might also support life.

    Scientists have employed many techniques in this effort, including pulsar timing, direct imaging, and measuring the speed at which stars and galaxies move either toward or away from Earth. Yet each of these techniques, individually or in combination, presents challenges.

    Primarily, those challenges have to do with eliminating extraneous data — noise — that doesn’t match existing models of how planets are expected to behave. In this traditional interpretation of noise, searches can be hampered by data that obscures or mimics exoplanets.

    Wettlaufer and his colleagues decided to look for exoplanets in the same way they had sorted through satellite data to find complex changes in Arctic sea ice. The formal name for the approach is “multi-fractal temporally weighted detrended fluctuation analysis” (MF-TWDFA). It sifts data at all time scales and extracts the underlying processes associated with them.

    “A key idea is that events closer in time are more likely to be similar than those farther away in time,” Wettlaufer said. “In the case of exoplanets, it is the fluctuations in a star’s spectral intensity that we are dealing with.”

    The use of multi-fractals in science and mathematics was pioneered at Yale by Benoit B. Mandelbrot and Katepalli Sreenivasan. For expertise in the search for exoplanets, the researchers consulted with Yale astrophysicist Debra Fischer, who has pioneered many approaches in the field.

    The researchers confirmed the accuracy of their methodology by testing it against observations and simulation data of a known planet orbiting a star in the constellation Vulpecula, approximately 63 light years from Earth.

    Sahil Agarwal, a graduate student in the Yale Program in Applied Mathematics, is first author. Fabio Del Sordo, a joint postdoctoral fellow at Yale and in Stockholm, is co-author.

    Grants from NASA and the Swedish Research Council helped to fund the research, as did a Royal Society Wolfson Research Merit Award.

    See the full article here .

    Please help promote STEM in your local schools.

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    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

  • richardmitnick 10:57 am on September 23, 2016 Permalink | Reply
    Tags: , , , , , , , Yale   

    From Yale via Vox: “Why physicists really, really want to find a new subatomic particle” 

    Yale University bloc

    Yale University



    Sep 21, 2016
    Brian Resnick

    The latest search for a new particle has fizzled. Scientists are excited, and a bit scared.

    Particle physicists are begging nature to reveal the secrets of the universe. The universe isn’t talking back. FABRICE COFFRINI/AFP/Getty Images

    Particle physicists are rather philosophical when describing their work.

    “Whatever we find out, that is what nature chose,” Kyle Cranmer, a physics professor at New York University, tells me. It’s a good attitude to have when your field yields great disappointments.

    For months, evidence was mounting that the Large Hadron Collider, the biggest and most powerful particle accelerator in the world, had found something extraordinary: a new subatomic particle, which would be a discovery surpassing even the LHC’s discovery of the Higgs boson in 2012, and perhaps the most significant advance since Einstein’s theory of relativity.

    CERN/LHC Map
    CERN LHC Grand Tunnel
    CERN LHC particles
    LHC at CERN

    And yet, nature had other plans.

    In August, the European Organization for Nuclear Research (CERN) reported that the evidence for the new particle had run thin. What looked like a promising “bump” in the data, indicating the presence of a particle with a unique mass, was just noise.

    But to Cranmer — who has analyzed LHC data in his work — the news did not equate failure. “You have to keep that in mind,” he says. “Because it can feel that way. It wasn’t there to be discovered. It’s like being mad that someone didn’t find an island when someone is sailing in the middle of the ocean.”

    What’s more, the LHC’s journey is far from over. The machine is expected to run for another 20 or so years. There will be more islands to look for.

    “We’re either going to discover a bunch of new particles or we will not,” Cranmer says. “If we find new particles, we can study them, and then we have a foothold to make progress. And if we don’t, then [we’ll be] staring at a flat wall in front figuring out how to climb it.”

    This is a dramatic moment, one that could provoke “a crisis at the edge of physics,” according to a New York Times op-ed. Because if the superlative LHC can’t find answers, it will cast doubt that answers can be found experimentally.

    From here, there are two broad scenarios that could play out, both of which will vastly increase our understanding of nature. One scenario will open up physics to a new world of understanding about the universe; the other could end particle physics as we know it.

    The physicists themselves can’t control the outcome. They’re waiting for nature to tell them the answers.

    Why do we care about new subatomic particles anyway?

    A graphic showing traces of collision of particles at the Compact Muon Solenoid (CMS) experience is pictured with a slow speed experience at Universe of Particles exhibition of the the European Organization for Nuclear Research (CERN) on December 13, 2011, in Geneva. FABRICE COFFRINI/AFP/GettyImages

    The LHC works by smashing together atoms at incredibly high velocities. These particles fuse and can form any number of particles that were around in the universe from the Big Bang onward.

    When the Higgs boson was confirmed in 2012, it was a cause for celebration and unease.

    CERN CMS Higgs Event
    CERN CMS Higgs Event

    CERN ATLAS Higgs Event
    CERN ATLAS Higgs Event

    The Higgs was the last piece of a puzzle called the standard model, which is a theory that connects all the known components of nature (except gravity) together in a balanced, mathematical equation.

    The Standard Model of elementary particles (more schematic depiction), with the three generations of matter, gauge bosons in the fourth column, and the Higgs boson in the fifth.
    The Standard Model of elementary particles (more schematic depiction), with the three generations of matter, gauge bosons in the fourth column, and the Higgs boson in the fifth

    The Higgs was the final piece that had been theorized to exist but never seen.

    After the Higgs discovery, the scientists at the LHC turned their hopes in a new direction. They hoped the accelerator could begin to find particles that had never been theorized nor ever seen. It was like going from a treasure hunt with a map to chartering a new ocean.

    They want to find these new subatomic particles because even though the standard model is now complete, it still can’t answer a lot of lingering questions about the universe. Let’s go through the two scenarios step by step.

    Scenario 1: There are more subatomic particles! Exciting!

    If the LHC finds new subatomic particles, it lend evidence to a theory known as supersymmetry. Supersymmetry posits that all the particles in the standard model must have a shadow “super partner” that spins in a slightly different direction.

    Standard model of Supersymmetry DESY
    Standard model of Supersymmetry DESY

    Scientists have never seen one of these supersymmetrical particles, but they’re keen to. Supersymmetry could neatly solve some of the biggest problems vexing physicists right now.

    Such as:

    1) No one knows what dark matter is

    One of these particles could be what scientists call “dark matter,” which is theorized to make up 27 percent of the universe. But we’ve never seen dark matter, and that leaves a huge gaping hole in our understanding of the how the universe formed and exists today.

    “It could be that one particle is responsible for dark matter,” Cranmer explains. Simple enough.

    2) The Higgs boson is much too light

    The Higgs discovery was an incredible triumph, but it also contained a mystery to solve. The boson — at 126 GeV (giga electron volts) — was much lighter than the standard model and the math of quantum mechanics suggests it should be.

    Why is that a problem? Because it’s a wrinkle to be ironed out in our understanding of the universe. It suggests the standard model can’t explain everything. And physicists want to know everything.

    “Either nature is sort of ugly, which is entirely conceivable, and we just have to live with the fact that the Higgs boson mass is light and we don’t know why,” Ray Brock, a Michigan State University physicist who has worked on the LHC, says, “or nature is trying to tell us something.”

    It could be that a yet-to-be-discovered subatomic particle interacts with the Higgs, making it lighter than it ought to be.

    3) The standard model doesn’t unify the forces of the universe

    There are four major forces that make the universe tick: the strong nuclear force (which holds atoms together), the weak nuclear force (what makes Geiger counters tick), electromagnetism (you’re using it right now, reading this article on an electronic screen), and gravity (don’t look down.)

    Scientists aren’t content with the four forces. They, for decades, have been trying to prove that the universe works more elegantly, that, deep down, all these forces are just manifestations of one great force that permeates the universe.

    Physicists call this unification, and the standard model doesn’t provide it.

    “If we find supersymmetry at the LHC, it is a huge boost to the dream that three of the fundamental forces we have [all of them except gravity] are all going to unify,” Cranmer says.

    4) Supersymmetry would lead to more particle hunting

    If scientists find one new particle, supersymmetry means they’ll find many more. That’s exciting. “It’s not going to be just one new particle that we discovered, and yay!” Cranmer says. “We’re going to be finding new forces, or learn something really deep about the nature of space and time. Whatever it is, it’s going to be huge.”

    Scenario 2: There are no new subatomic particles. Less exciting! But still interesting. And troubling.

    The LHC is going to run for around another 20 years, at least. There’s a lot of time left to find new particles, even if there is no supersymmetry. “This is what always blows my mind,” Brock says. “We’ve only taken about 5 percent of the total planned data that the LHC is going to deliver until the middle 2020s.”

    But the accelerator also might not find anything. If the new particles aren’t there to find, the LHC won’t find them. (Hence, the notion that physicists are looking for “what nature chose.”)

    But again, this doesn’t represent a failure. It will actually yield new insights about the universe.

    “It would be a profound discovery to find that we’re not going to see anything else,” Cranmer says.

    1) For one, it would suggest that supersymmetry isn’t the answer

    If supersymmetry is dead, then theoretical physicists will have to go back to the drawing board to figure out how to solve the mysteries left open by the standard model.

    “If we’re all coming up empty, we would have to question our fundamental assumptions,” Sarah Demers, a Yale physicist, tells me. “Which is something we’re trying to do all the time, but that would really force us.”

    2) The answers exist, but they exist in a different universe

    If the LHC can’t find answers to questions like “why is the Higgs so light?” scientists might grow to accept a more out-of-the-box idea: the multiverse.

    That’s the idea where there are tons of universes all existing parallel to one another. It could be that “in most of [the universes], the Higgs boson is really heavy, and in only in very unusual universes [like our own] is the Higgs boson so light that life can form,” Cranmer says.

    Basically: On the scale of our single universe, it might not make sense for the Higgs to be light. But if you put it together with all the other possible universes, the math might check out.

    There’s a problem with this theory, however: If heavier Higgs bosons exist in different universes, there’s no possible way to observe them. They’re in different universes!

    “Which is why a lot of people hate it, because they consider it to be anti-science,” Cranmer says. “It might be impossible to test.”

    3) The new subatomic particles do exist, but the LHC isn’t powerful enough to find them

    In 20 years, if the LHC doesn’t find any new particles, there might be a simple reason: These particles are too heavy for the LHC to detect.

    This is basic E=mc2 Einstein: The more energy in the particle accelerator, the heavier the particles it can create. The LHC is the most powerful particle accelerator in the history of man, but even it has its limits.

    So what will physicists do? Build an even bigger, even smashier particle collider? That’s an option. There are currently preliminary plans in China for a collider double the size of the LHC.

    Building a bigger collider might be a harder sell for international funding agencies. The LHC was funded in part because of the quest to confirm the Higgs. Will governments really spend billions on a machine that may not yield epic insights?

    “Maybe we were blessed as a field that we always had a target or two to shoot for. We don’t have that anymore,” says Markus Klute, an MIT physicist stationed at CERN in Europe. “It’s easier to explain to the funding agencies specifically that there’s a specific endpoint.”

    The LHC will keep running for the foreseeable future. But it could prove a harder task to make the case to build a new collider.

    Either way, these are exciting times for physics

    Dean Mouhtaropoulos/Getty Images

    “I think we have had a tendency to be prematurely depressed,” Demers says. “It’s never a step backward to learn something new,” even if the news is negative. “Ruling out ideas teaches us an incredible amount.”

    And she says that even if the LHC can never find another particle, it can still produce meaningful insights. Already, her colleagues are using it to help determine why there’s so much more matter than antimatter in the universe. And she reminds me the LHC can still teach us more about the mysterious Higgs. We will be able to measure it to a more precise degree.

    Brock, the MSU physicist, notes that since the 1960s, physicists have been chasing the standard model. Now they don’t quite know what they’re chasing. But they know it will change the world.

    “I can’t honestly say in all those 40 years, I’ve been exploring,” Brock says. “I’ve been testing the standard model. The Higgs boson was the last missing piece. Now, we have to explore.”

    See the full article here .

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    Yale University Campus

    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

  • richardmitnick 8:23 pm on September 12, 2016 Permalink | Reply
    Tags: , , Type 1 diabetes, Yale   

    From Yale: “How gut microbes may trigger type 1 diabetes” 

    Yale University bloc

    Yale University

    September 12, 2016

    Ziba Kashef

    © stock.adobe.com

    Research on the tiny microbes that live in our gut has yielded clues to understanding a growing number of medical conditions. A new Yale-led study explores the link between gut microbes and type 1 diabetes.

    The research team studied specific immune cells, CD8 T cells, in a mouse model. They found that a protein in the gut bacteria had a similar molecular structure to a protein in pancreatic cells that produce insulin. The researchers referred to the similarity as “molecular mimicry” and found that this mimicry triggered the immune cells to attack the pancreatic cells, accelerating diabetes.

    The finding may have significant implications for this chronic disease. “A change in the gut microbiome could be factor in the development of type 1 diabetes,” said Li Wen, senior author and senior research scientist in endocrinology. Presence of similar bacteria that could act as a mimic in the individuals who are susceptible to type 1 diabetes may be an additional indicator of the disease risk, Wen noted.

    The study was published in the Journal of Experimental Medicine.

    See the full article here .

    Please help promote STEM in your local schools.

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    Yale University Campus

    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

  • richardmitnick 11:39 am on September 2, 2016 Permalink | Reply
    Tags: , , , , , Sterling Chemistry Lab reopens as a catalyst for cutting-edge science, Yale   

    From Yale: “Sterling Chemistry Lab reopens as a catalyst for cutting-edge science” 

    Yale University bloc

    Yale University

    August 31, 2016

    Jim Shelton

    President Salovey addresses the crowd at the SCL ribbon-cutting event. (Photo by Michael Marsland)

    From its gleaming, glass-enclosed teaching labs to the powerful mechanical hubs located in the basement and penthouse, the new Sterling Chemistry Lab (SCL) has all the right elements to be a citadel of science for the next century.

    The 93-year-old building has been transformed from the inside out, and Yale officials celebrated with a grand reopening on Aug. 30. Hundreds of students, faculty, and staff gathered to tour SCL’s new teaching labs, hear more about the building’s history and envision scientific discoveries yet to come.

    “The center of gravity of this campus is shifting north,” Yale President Peter Salovey said at the ribbon cutting, noting the construction of Yale’s newest residential colleges nearby and the resurgence of investment in Science Hill.

    “We are at a moment here at Yale when we will take the excellent science, research, and education we do on campus, especially Science Hill, and move it to a truly outstanding level,” Salovey said. “We should want nothing less for students and for faculty.”

    For the new SCL, that effort required two years of cranes, jackhammers, power saws, and occasional corridor closings. The exterior of the iconic building, designed by architect Williams Adams Delano in a Collegiate Gothic style, remains unchanged. CannonDesign is the architect for the renovation, with HBRA Architects designing the central public corridor areas, and Dimeo Construction guiding the work. SCL renovations encompass 159,000 square feet, of which 31,600 is additional space, and the building will be seeking LEED Gold certification.

    The renovation includes new teaching labs for chemistry, such as this one, as well as labs for physics and biology. (Photo by Michael Marsland)

    “Science is and must be a top priority for Yale,” said Provost Benjamin Polak. “If we think about what great universities will do in the 21st century, they’re going to advance knowledge by their discoveries, they’re going to change the world, and they’re going to move minds. That means science, and Yale has to be part of that — has to lead at that.”

    A trio of teaching labs is central to that goal at the new SCL, both physically and symbolically. Biology teaching labs are located on the second floor, with flexibility allowing for adaptability to a variety of experiments and teaching needs; chemistry teaching labs are on the third floor, with individual venting hoods for each student conducting an experiment and dedicated spaces for teaching general, organic, advanced, and physical chemistry. Physics teaching labs are on the second floor, built with enhanced flexibility for experiments of different durations and sizes.

    “This really is an occasion of coming together,” said Dean of the Faculty of Arts and Sciences (FAS) Tamar Gendler, noting that the renovation merges research and teaching, brings together students and faculty, and involves multiple disciplines. It also combines past and present, knits together different areas of the campus, and blends the abstract with the concrete, Gendler said.

    Scott Miller, the Irénée du Pont Professor of Chemistry, divisional director of sciences for FAS, and former chair of the Department of Chemistry, took note of the many scientific discoveries that have taken place at SCL since 1923. He mentioned Lars Onsager’s work on thermodynamics for irreversible systems; the pioneering chemical biology research of Stuart Schreiber; and emeritus professor Jerome Berson’s research on reactive intermediates.

    “Laboratories are sacred places,” Miller said. “Laboratories are the places where we try very hard to connect observation to explanation; where we try to make things on the basis of our theories and then when we can’t make them the way we’d like to we have to revise our theories. Laboratories are the places where we connect ‘mind to hand.’ These are truly profound things.”

    In order to create teaching labs for today’s students, the SCL renovation involved a major overhaul of the building’s mechanical systems. Prior to renovation, many of the individual labs in SCL required separate services to handle venting, electricity, and other needs. Now there is a centralized system to handle the flow of power, water, and ventilation throughout the building. In addition, SCL has new replacement skylights and windows, switched from steam heat to hot-water baseboards, upgraded its sprinkler system, installed a bigger service elevator, completed masonry work, and conducted structural upgrades.

    The renovation addresses aesthetic needs, as well. Expansive, well-lit corridors connect the labs with communal areas and a landscaped courtyard, for example. Also, the use of glass walls to frame the labs is intended to inspire a more connected, collaborative spirit among students and faculty.

    “I can’t wait to come back in the coming weeks and see students at these benches and classes being taught,” Salovey said.

    See the full article here .

    Please help promote STEM in your local schools.

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    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

  • richardmitnick 9:24 am on August 25, 2016 Permalink | Reply
    Tags: Fetal microcephaly, , Sofosbuvir, Yale,   

    From Yale: “Yale team discovers how Zika virus causes fetal brain damage” 

    Yale University bloc

    Yale University

    August 24, 2016
    Bill Hathaway

    Human neuroepithelial stem cells self-organize into rose-like patterns and express the typical neural stem cell markers nestin (green) and SOX2 (red). They were used to understand how Zika virus infection works and to block its proliferation. No image credit.

    Infection by the Zika virus diverts a key protein necessary for neural cell division in the developing human fetus, thereby causing the birth defect microcephaly, a team of Yale scientists reported Aug. 24 in the journal Cell Reports.

    The findings suggest that Zika virus might be susceptible to existing antiviral drugs that may prevent disruption to the developing nervous system, said the researchers.

    One of the frightening side-effects of Zika virus infection in pregnant women is the risk of fetal microcephaly, in which babies are born with abnormally small brains. The multidisciplinary collaboration of Yale scientists revealed that Zika virus kills stem cells in the brain and disrupts the process of creating brain cells. An analysis shows that the virus diverts a form of the protein TBK1 from its primary job of organizing cell division to the mitochondria, the cell’s power pack, where it helps initiate an immune response. Lacking the protein at the site of cell division, cells die instead of forming new brain cells, resulting in microcephaly. The data suggest this mechanism may also contribute to microcephaly associated with other common congenital viral infections.

    Researchers note that an existing FDA-approved drug, Sofosbuvir, showed promise in preventing Zika virus infection of neural stem cells in laboratory culture and also seems to keep phospho-TBK1 involved in cell division. More study needs to be conducted to prove the efficacy of the drug as a medical therapy for Zika virus, the authors said.

    “There is an urgent need to identify therapeutic approaches to halt Zika infection, especially in pregnant women,” said Marco Onorati, co-first author of the paper and researcher in the lab of senior author Nenad Sestan, professor of neuroscience, comparative medicine, genetics, and psychiatry. “In the interim, we hope these findings can lead to therapies that might minimize the damage caused by this virus.”

    Co-first authors of the paper are Zhen Li, Fuchen Liu, and Andre M.M. Sousa of Yale. Tamas L. Horvath and Brett Lindenbach, also of Yale, are co-senior authors of the work.

    See the full article here .


    There is a new project at World Community Grid [WCG] called OpenZika.
    Zika depiction. Image copyright John Liebler, http://www.ArtoftheCell.com
    Rutgers Open Zika

    WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the OpenZika project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

    This project is directed by Dr. Alexander Perryman a senior researcher in the Freundlich lab, with extensive training in developing and applying computational methods in drug discovery and in the biochemical mechanisms of multi-drug-resistance in infectious diseases. He is a member of the Center for Emerging & Re-emerging Pathogens, in the Department of Pharmacology, Physiology, and Neuroscience, at the Rutgers University, New Jersey Medical School. Previously, he was a Research Associate in Prof. Arthur J. Olson’s lab at The Scripps Research Institute (TSRI), where he ran the day-to-day operations of the FightAIDS@Home project, the largest computational drug discovery project devoted to HIV/AIDS, which also runs on WCG. While in the Olson lab, he also designed, led, and ran the largest computational drug discovery project ever performed against malaria, the GO Fight Against Malaria project, also on WCG.

    Rutgers smaller

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    Please help promote STEM in your local schools.

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    Yale University comprises three major academic components: Yale College (the undergraduate program), the Graduate School of Arts and Sciences, and the professional schools. In addition, Yale encompasses a wide array of centers and programs, libraries, museums, and administrative support offices. Approximately 11,250 students attend Yale.

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