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  • richardmitnick 3:19 pm on June 19, 2018 Permalink | Reply
    Tags: Biology, , ,   

    From World Community Grid (WCG): “Microbiome Immunity Project Researchers Create Ambitious Plans for Data” 

    New WCG Logo


    From World Community Grid (WCG)

    By: Dr. Tomasz Kościółek and Bryn Taylor
    University of California San Diego
    19 Jun 2018

    The Microbiome Immunity Project researchers—from Boston, New York, and San Diego—met in person a few weeks ago to make plans that include a 3D map of the protein universe and other far-ranging uses for the data from the project.

    The research team members pictured above are (from left to right): Vladimir Gligorijevic (Simons Foundation’s Flatiron Institute), Tommi Vatanen (Broad Institute of MIT and Harvard), Tomasz Kosciolek (University of California San Diego), Rob Knight (University of California San Diego), Rich Bonneau (Simons Foundation’s Flatiron Institute), Doug Renfrew (Simons Foundation’s Flatiron Institute), Bryn Taylor (University of California San Diego), Julia Koehler Leman (Simons Foundation’s Flatiron Institute). Visit the project’s Research Participants page for additional team members.

    During the week of May 28, researchers from all Microbiome Immunity Project (MIP) institutions (University of California San Diego, Broad Institute of MIT and Harvard, and the Simons Foundation’s Flatiron Institute) met in San Diego to discuss updates on the project and plan future work.

    Our technical discussions included a complete overview of the practical aspects of the project, including data preparation, pre-processing, grid computations, and post-processing on our machines.

    We were excited to notice that if we keep the current momentum of producing new structures for the project, we will double the universe of known protein structures (compared to the Protein Data Bank) by mid-2019! We also planned how to extract the most useful information from our data, store it effectively for future use, and extend our exploration strategies.

    We outlined three major areas we want to focus on over the next six months.

    Structure-Aided Function Predictions

    We can use the structures of proteins to gain insight into protein function—or what the proteins actually do. Building on research from MIP co-principal investigator Richard Bonneau’s lab, we will extend their state-of-the-art algorithms to predict protein function using structural models generated through MIP. Using this new methodology based on deep learning, akin to the artificial intelligence algorithms of IBM, we hope to see improvements over more simplistic methods and provide interesting examples from the microbiome (e.g., discover new genes creating antibiotic resistance).

    Map of the Protein Universe

    Together we produce hundreds of high-quality protein models every month! To help researchers navigate this ever-growing space, we need to put them into perspective of what we already know about protein structures and create a 3D map of the “protein universe.” This map will illustrate how the MIP has eliminated the “dark matter” from this space one structure at a time. It will also be made available as a resource for other researchers to explore interactively.

    Structural and Functional Landscape of the Human Gut Microbiome

    We want to show what is currently known about the gut microbiome in terms of functional annotations and how our function prediction methods can help us bridge the gap in understanding of gene functions. Specifically, we want to follow up with examples from early childhood microbiome cohorts (relevant to Type-1 diabetes, or T1D) and discuss how our methodology can help us to better understand T1D and inflammatory bowel disease.

    The future of the Microbiome Immunity Project is really exciting, thanks to everyone who makes our research possible. Together we are making meaningful contributions to not one, but many scientific problems!

    See the full article here.

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Ways to access the blog:

    World Community Grid (WCG) brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”
    WCG projects run on BOINC software from UC Berkeley.

    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing.

    BOINC WallPaper


    My BOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Microbiome Immunity Project

    FightAIDS@home Phase II

    FAAH Phase II

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding




    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation

    IBM – Smarter Planet

  • richardmitnick 4:44 pm on June 16, 2018 Permalink | Reply
    Tags: , , Biology, , , New type of photosynthesis discovered   

    From Imperial College London: “New type of photosynthesis discovered” 

    Imperial College London
    From Imperial College London

    15 June 2018
    Hayley Dunning

    Colony of cells where colours represent chlorophyll-a and -f driven photosynthesis. Dennis Nuernberg

    The discovery changes our understanding of the basic mechanism of photosynthesis and should rewrite the textbooks.

    It will also tailor the way we hunt for alien life and provide insights into how we could engineer more efficient crops that take advantage of longer wavelengths of light.

    The discovery, published today in Science, was led by Imperial College London, supported by the BBSRC, and involved groups from the ANU in Canberra, the CNRS in Paris and Saclay and the CNR in Milan.

    The vast majority of life on Earth uses visible red light in the process of photosynthesis, but the new type uses near-infrared light instead. It was detected in a wide range of cyanobacteria (blue-green algae) when they grow in near-infrared light, found in shaded conditions like bacterial mats in Yellowstone and in beach rock in Australia.

    As scientists have now discovered, it also occurs in a cupboard fitted with infrared LEDs in Imperial College London.

    Photosynthesis beyond the red limit

    The standard, near-universal type of photosynthesis uses the green pigment, chlorophyll-a, both to collect light and use its energy to make useful biochemicals and oxygen. The way chlorophyll-a absorbs light means only the energy from red light can be used for photosynthesis.

    Since chlorophyll-a is present in all plants, algae and cyanobacteria that we know of, it was considered that the energy of red light set the ‘red limit’ for photosynthesis; that is, the minimum amount of energy needed to do the demanding chemistry that produces oxygen. The red limit is used in astrobiology to judge whether complex life could have evolved on planets in other solar systems.

    However, when some cyanobacteria are grown under near-infrared light, the standard chlorophyll-a-containing systems shut down and different systems containing a different kind of chlorophyll, chlorophyll-f, takes over.

    Cross-section of beach rock (Heron Island, Australia) showing chlorophyll-f containing cyanobacteria (green band) growing deep into the rock, several millimetres below the surface. Dennis Nuernberg

    Until now, it was thought that chlorophyll-f just harvested the light. The new research shows that instead chlorophyll-f plays the key role in photosynthesis under shaded conditions, using lower-energy infrared light to do the complex chemistry. This is photosynthesis ‘beyond the red limit’.

    Lead researcher Professor Bill Rutherford, from the Department of Life Sciences at Imperial, said: “The new form of photosynthesis made us rethink what we thought was possible. It also changes how we understand the key events at the heart of standard photosynthesis. This is textbook changing stuff.”

    Preventing damage by light

    Another cyanobacterium, Acaryochloris, is already known to do photosynthesis beyond the red limit. However, because it occurs in just this one species, with a very specific habitat, it had been considered a ‘one-off’. Acaryochloris lives underneath a green sea-squirt that shades out most of the visible light leaving just the near-infrared.

    The chlorophyll-f based photosynthesis reported today represents a third type of photosynthesis that is widespread. However, it is only used in special infrared-rich shaded conditions; in normal light conditions, the standard red form of photosynthesis is used.

    It was thought that light damage would be more severe beyond the red limit, but the new study shows that it is not a problem in stable, shaded environments.

    Co-author Dr Andrea Fantuzzi, from the Department of Life Sciences at Imperial, said: “Finding a type of photosynthesis that works beyond the red limit changes our understanding of the energy requirements of photosynthesis. This provides insights into light energy use and into mechanisms that protect the systems against damage by light.”

    These insights could be useful for researchers trying to engineer crops to perform more efficient photosynthesis by using a wider range of light. How these cyanobacteria protect themselves from damage caused by variations in the brightness of light could help researchers discover what is feasible to engineer into crop plants.

    Textbook-changing insights

    More detail could be seen in the new systems than has ever been seen before in the standard chlorophyll-a systems. The chlorophylls often termed ‘accessory’ chlorophylls were actually performing the crucial chemical step, rather than the textbook ‘special pair’ of chlorophylls in the centre of the complex.

    This indicates that this pattern holds for the other types of photosynthesis, which would change the textbook view of how the dominant form of photosynthesis works.

    Dr Dennis Nürnberg, the first author and initiator of the study, said: “I did not expect that my interest in cyanobacteria and their diverse lifestyles would snowball into a major change in how we understand photosynthesis. It is amazing what is still out there in nature waiting to be discovered.”

    Peter Burlinson, lead for frontier bioscience at BBSRC – UKRI says, “This is an important discovery in photosynthesis, a process that plays a crucial role in the biology of the crops that feed the world. Discoveries like this push the boundaries of our understanding of life and Professor Bill Rutherford and the team at Imperial should be congratulated for revealing a new perspective on such a fundamental process.”

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    Imperial College London

    Imperial College London is a science-based university with an international reputation for excellence in teaching and research. Consistently rated amongst the world’s best universities, Imperial is committed to developing the next generation of researchers, scientists and academics through collaboration across disciplines. Located in the heart of London, Imperial is a multidisciplinary space for education, research, translation and commercialisation, harnessing science and innovation to tackle global challenges.

  • richardmitnick 12:21 pm on June 15, 2018 Permalink | Reply
    Tags: , Biology, Retinal,   

    From SLAC Lab: “Scientists Make the First Molecular Movie of One of Nature’s Most Widely Used Light Sensors” 

    From SLAC Lab

    June 14, 2018
    Glennda Chui

    A molecular movie based on experimental data shows the retinal molecule, in green, changing shape along with parts of its surrounding protein pocket, in pink, when hit by light. The changing numbers are distances in angstroms. One angstrom is one ten-billionth of a meter. That’s roughly the diameter of the smallest atoms. (Paul Scherrer Institute, Andy Freeberg/SLAC)

    The X-ray laser movie shows what happens when light hits retinal, a key part of vision in animals and photosynthesis in microbes. The action takes place in a trillionth of an eye blink.

    Scientists have made the first molecular movie of the instant when light hits a sensor that’s widely used in nature for probing the environment and harvesting energy from light. The sensor, a form of vitamin A known as retinal, is central to a number of important light-driven processes in people, animals, microbes and algae, including human vision and some forms of photosynthesis, and the movie shows it changing shape in a trillionth of an eye blink.

    “To my knowledge, nobody has measured changes in a retinal biosensor so quickly and so accurately,” said Jörg Standfuss, a biologist at the Paul Scherrer Institute (PSI) in Switzerland who led the research at the Department of Energy’s SLAC National Accelerator Laboratory. “And the fact that we saw just the opposite of what we intuitively expected was spectacular and surprising to us.”

    The team carried out their experiments at the lab’s Linac Coherent Light Source (LCLS) X-ray laser and reported the results today in Science.


    Comming soon (A really bad attempt at lab humor. In fact, it will be a while).

    SLAC/LCLS II projected view

    In the past, scientists had to fill the gaps in their knowledge about retinal’s behavior by making inferences based on theory and computer simulations, said Mark Hunter, a staff scientist at LCLS and paper co-author. But in this study, “LCLS’s super-short pulses allowed us to collect data on where the atoms actually were in space and how that changed over time,” he said, “so it gave us a much more direct visualization of molecules in motion.”

    Colorful Lakes and Arching Cats

    Retinal is so central to human vision – it’s named for the retina at the back of the eye – that scientists have been studying it for nearly a century, steadily building a more detailed picture of how it works. It’s also used in the burgeoning field of optogenetics to turn groups of nerve cells on and off, revealing how the brain works and how things go wrong in conditions like depression, stroke and addiction.

    The retinal studied in this experiment came from salt-loving microbes that use it to harvest energy from the sun. (Fun fact: Purple and orange-red pigments in these microbes give the briny waters they live in, from San Francisco Bay salt ponds to Senegal’s Lake Retba, their incredibly vivid colors.)

    Retinal does its job while snuggled deep into a pocket of specialized proteins in the membrane of the cell. When hit by light, the retinal changes shape – in this case it curves, like a cat arching its back. This creates a signal that’s transmitted by the protein into the cell’s interior, initiating photosynthesis or vision.

    Scientists thought retinal set off the signal by pushing on the protein pocket as it changed shape. But the LCLS experiments found just the opposite: The pocket actually changed shape first, creating space for the retinal to perform its arching-cat maneuver. Nearby water molecules also moved aside and made room, Standfuss said. It all took place within 200 to 500 femtoseconds, or millionths of a billionth of a second. That’s about a trillionth of the blink of an eye, making this one of the fastest chemical reactions known in living things.

    “In retrospect, this makes a lot of sense,” Standfuss said. “We always say seeing is believing in structural biology, and in this case it’s very true. The molecular movie we made makes it so obvious what’s going on that you can immediately grasp it. This solves a very important piece of the puzzle of how retinal works that people have been wondering about.”

    The protein pocket’s initial movements are triggered by small changes in electrical charge that rearrange certain chemical bonds, he said. These movements guide the retinal’s response and make it much more efficient, which is why it requires only a few photons of light and why nature can use that light so effectively.

    In this pair of molecular movies we see the retinal molecule (in the middle of each frame) and parts of its surrounding protein pocket with their shapes defined by their electron clouds (blue lines). The top frame shows the retinal molecule from the side, and the bottom one shows it from the top as it curves in response to light. (Paul Scherrer Institute)

    Catching Molecules in Action

    How can you watch something so small that happens so fast? The X-ray laser was key, Standfuss said. LCLS produces brilliant pulses of X-ray laser light that scatter off the electrons in a sample and reveal how its atoms are arranged. Like a camera with an extreme zoom lens and ultrafast shutter speed, the X-ray laser can also make snapshots of molecules moving, breaking apart and interacting with each other.

    In this case, the researchers looked at samples of retinal snuggled into pockets of bacteriorhodopsin, a purple protein found in simple microbes like those in the salt ponds.

    After years of effort, PSI postdoctoral researcher Przemyslaw Nogly, the lead author of the report, found ways to pack these retinal-protein pairs into thousands and thousands of tiny but well-ordered crystals. One after another, crystals were hit with light from an optical laser – a stand-in for sunlight – followed by X-ray laser pulses to record the response. Then Nogly and the team boiled down data into 20 snapshots and assembled them into stop-action movies that show the retinal moving in sync with its protein pocket.

    Proteins like bacteriorhodopsin that sit in cell membranes are notoriously difficult to study because it’s so hard to form them into crystals for X-ray experiments, Hunter said. But scientists have learned that they crystallize more readily when embedded in a fatty, toothpaste-like sludge that mimics their natural environment, and that’s how these crystals were formed and delivered into the X-ray beam.

    The researchers were also able to detect “protein quakes,” vibrations that release some of the energy deposited by the light flashes. These had been predicted by theory and came off as expected.

    Standfuss said he has spent most of his career studying retinal and its role in vision, which involves slightly different shape changes in the protein-embedded molecule. “I really hope that we can now study the same reaction in many different systems,” he said. “Now that we see for the first time how it works in one particular bacterial protein, I want to understand how it works in the human eye as well.”

    LCLS researchers Sergio Carbajo, Jason Koglin, Matthew Seaberg and Thomas Lane were co-authors of this study. Other contributors came from PSI, the University of Gothenburg in Sweden, the Fritz Haber Center for Molecular Dynamics at the Hebrew University of Jerusalem, the RIKEN SPring-8 Center and Kyoto University in Japan, the Center for Free-Electron Laser Science at DESY in Germany and Arizona State University. Major funding came from the European Horizon 2020 Program, the Swedish Research Council and the Swiss National Science Foundation.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    SLAC Campus
    SLAC is a multi-program laboratory exploring frontier questions in photon science, astrophysics, particle physics and accelerator research. Located in Menlo Park, California, SLAC is operated by Stanford University for the DOE’s Office of Science.

  • richardmitnick 12:38 pm on May 20, 2018 Permalink | Reply
    Tags: , , Biology, ,   

    From Astrobiology Magazine: “How primordial life on Earth might have replicated itself” 

    Astrobiology Magazine

    From Astrobiology Magazine

    May 20, 2018

    Liquid brine containing replicating RNA molecules is concentrated in the cracks between ice crystals, as seen with an electron microscope. Credit: Philipp Holliger, MRC LMB

    Scientists have created a new type of genetic replication system which demonstrates how the first life on Earth – in the form of RNA – could have replicated itself. The scientists from the Medical Research Council (MRC) Laboratory of Molecular Biology say the new RNA utilises a system of genetic replication unlike any known to naturally occur on Earth today.

    A popular theory for the earliest stages of life on Earth is that it was founded on strands of RNA, a chemical cousin of DNA. Like DNA, RNA strands can carry genetic information using a code of four molecular letters (bases), but RNA can be more than a simple ‘string’ of information. Some RNA strands can also fold up into three-dimensional shapes that can form enzymes, called ribozymes, and carry out chemical reactions.

    If a ribozyme could replicate folded RNA, it might be able to copy itself and support a simple living system.

    Previously, scientists had developed ribozymes that could replicate straight strands of RNA, but if the RNA was folded it blocked the ribozyme from copying it. Since ribozymes themselves are folded RNAs, their own replication is blocked.

    Now, in a paper published today in the journal eLife, the scientists have resolved this paradox by engineering the first ribozyme that is able to replicate folded RNAs, including itself.

    Normally when copying RNA, an enzyme would add single bases (C, G, A or U) one at a time, but the new ribozyme uses three bases joined together, as a ‘triplet’ (e.g. GAU). These triplet building blocks enable the ribozyme to copy folded RNA, because the triplets bind to the RNA much more strongly and cause it to unravel – so the new ribozyme can copy its own folded RNA strands.

    The scientists say that the ‘primordial soup’ could have contained a mixture of bases in many lengths – one, two, three, four or more bases joined together – but they found that using strings of bases longer than a triplet made copying the RNA less accurate.

    Dr Philipp Holliger, from the MRC Laboratory of Molecular Biology and senior author on the paper, said: “We found a solution to the RNA replication paradox by re-thinking how to approach the problem – we stopped trying to mimic existing biology and designed a completely new synthetic strategy. It is exciting that our RNA can now synthesise itself.

    “These triplets of bases seem to represent a sweet spot, where we get a nice opening up of the folded RNA structures, but accuracy is still high. Notably, although triplets are not used in present-day biology for replication, protein synthesis by the ribosome – an ancient RNA machine thought to be a relic of early RNA-based life – proceeds using a triplet code.

    “However, this is only a first step because our ribozyme still needs a lot of help from us to do replication. We provided a pure system, so the next step is to integrate this into the more complex substrate mixtures mimicking the primordial soup – this likely was a diverse chemical environment also containing a range of simple peptides and lipids that could have interacted with the RNA.”

    The experiments were conducted in ice at -7°C, because the researchers had previously discovered that freezing concentrates the RNA molecules in a liquid brine in tiny gaps between the ice crystals. This also is beneficial for the RNA enzymes, which are more stable and function better at cold temperatures.

    Dr Holliger added: “This is completely new synthetic biology and there are many aspects of the system that we have not yet explored. We hope in future, it will also have some biotechnology applications, such as adding chemical modifications at specific positions to RNA polymers to study RNA epigenetics or augment the function of RNA.”

    Dr Nathan Richardson, Head of Molecular and Cellular Medicine at the MRC, said: “This is a really exciting example of blue skies research that has revealed important insights into how the very beginnings of life may have emerged from the ‘primordial soup’ some 3.7 billion years ago. Not only is this fascinating science, but understanding the minimal requirements for RNA replication and how these systems can be manipulated could offer exciting new strategies for treating human disease.”

    See the full article here .

    Please help promote STEM in your local schools.


    Stem Education Coalition

  • richardmitnick 8:17 pm on May 9, 2018 Permalink | Reply
    Tags: , APOE ε4 allele, , Biology, ,   

    From Vanderbilt University: “Study provides robust evidence of sex differences with Alzheimer’s gene” 

    Vanderbilt U Bloc

    From Vanderbilt University

    May. 7, 2018
    Tom Wilemon
    (615) 322-4747

    The APOE gene, the strongest genetic risk factor for Alzheimer’s disease, may play a more prominent role in disease development among women than men, according to new research from the Vanderbilt Memory and Alzheimer’s Center.

    The research confirmed recent studies that carrying the APOE ε4 allele has a greater association with Alzheimer’s disease among women compared to men, and went one step further by evaluating its association with amyloid and tau levels.

    The study published May 7 in JAMA Neurology adds to mounting evidence that the higher prevalence of Alzheimer’s disease among women may not simply be a consequence of living longer.

    Almost two-thirds of Americans with Alzheimer’s are women. The research, based on a meta-analysis of both cerebral spinal fluid (CSF) samples from study volunteers from four datasets and autopsy findings from six datasets of Alzheimer-diseased brains, is the most robust evidence to date that the APOE gene may play a greater role in women than men in developing Alzheimer’s pathology, said Timothy Hohman, PhD, assistant professor of Neurology and the study’s lead author.

    “In Alzheimer’s disease, we have not done enough to evaluate whether or not sex is a contributing factor to the neuropathology,” Hohman said. “We haven’t fully evaluated sex as a biological variable. But there is good reason to expect in older adulthood that there would be hormonal differences between the sexes that could impact disease.”

    The study looked at whether APOE in men and women was primarily associated with the amyloid pathway — the proteins that form plaques in the brain — or with the tau pathway — the proteins that form tangles in the brain.

    The association with the amyloid pathway was the same in men and women. However, the APOE association was much greater for women with the tau pathway. This is opposite of what researchers expected because of APOE’s established role in amyloid processing.

    “The prevailing hypothesis of disease in Alzheimer’s is that amyloid comes online first and downstream is where we see tau changes that ultimately drive neurodegenerative changes,” Hohman said.

    Further analysis revealed that the sex difference with tau levels was present in amyloid-positive individuals — those with higher levels of amyloid plaque as determined by their CSF amyloid levels. The research suggests that APOE may modulate risk for neurodegeneration in a sex-specific manner, particularly in the presence of amyloidosis.

    The greater association with tau occurred in CSF samples, but not with the autopsy datasets.

    The reason for the contradiction between CSF samples and autopsy datasets could be because Braak staging — the method for quantifying the degree of tau tangle pathology at autopsy — measures a different aspect of tau pathology than what is measured in CSF .

    “The way Braak staging works is you are actually looking at where in the cortex you see tangles at autopsy,” Hohman explained. “So it is not a measure of how many tangles are there. It is a measure of where those tangles are located.”

    Another possibility is that CSF tau may be an indicator of a more general neurodegenerative process that is not specific to tangle pathology.

    “This study is at least moving toward bringing sex as a biological variable into our analyses and thinking about sex differences. Do we see differences in disease that could tell us something about the biology of the disease and could help both sexes in terms of coming up with treatment approaches? I think that the right treatment approach for a female above the age of 65 may end up being different than what it is for a male. Really the only way to find out is to look.”

    The research was supported by the National Institutes of Health, the Alzheimer’s Disease Genetics Consortium (funded by the National Institute on Aging) and the Vanderbilt Memory and Alzheimer’s Center.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Commodore Cornelius Vanderbilt was in his 79th year when he decided to make the gift that founded Vanderbilt University in the spring of 1873.

    The $1 million that he gave to endow and build the university was the commodore’s only major philanthropy. Methodist Bishop Holland N. McTyeire of Nashville, husband of Amelia Townsend who was a cousin of the commodore’s young second wife Frank Crawford, went to New York for medical treatment early in 1873 and spent time recovering in the Vanderbilt mansion. He won the commodore’s admiration and support for the project of building a university in the South that would “contribute to strengthening the ties which should exist between all sections of our common country.”

    McTyeire chose the site for the campus, supervised the construction of buildings and personally planted many of the trees that today make Vanderbilt a national arboretum. At the outset, the university consisted of one Main Building (now Kirkland Hall), an astronomical observatory and houses for professors. Landon C. Garland was Vanderbilt’s first chancellor, serving from 1875 to 1893. He advised McTyeire in selecting the faculty, arranged the curriculum and set the policies of the university.

    For the first 40 years of its existence, Vanderbilt was under the auspices of the Methodist Episcopal Church, South. The Vanderbilt Board of Trust severed its ties with the church in June 1914 as a result of a dispute with the bishops over who would appoint university trustees.

    kirkland hallFrom the outset, Vanderbilt met two definitions of a university: It offered work in the liberal arts and sciences beyond the baccalaureate degree and it embraced several professional schools in addition to its college. James H. Kirkland, the longest serving chancellor in university history (1893-1937), followed Chancellor Garland. He guided Vanderbilt to rebuild after a fire in 1905 that consumed the main building, which was renamed in Kirkland’s honor, and all its contents. He also navigated the university through the separation from the Methodist Church. Notable advances in graduate studies were made under the third chancellor, Oliver Cromwell Carmichael (1937-46). He also created the Joint University Library, brought about by a coalition of Vanderbilt, Peabody College and Scarritt College.

    Remarkable continuity has characterized the government of Vanderbilt. The original charter, issued in 1872, was amended in 1873 to make the legal name of the corporation “The Vanderbilt University.” The charter has not been altered since.

    The university is self-governing under a Board of Trust that, since the beginning, has elected its own members and officers. The university’s general government is vested in the Board of Trust. The immediate government of the university is committed to the chancellor, who is elected by the Board of Trust.

    The original Vanderbilt campus consisted of 75 acres. By 1960, the campus had spread to about 260 acres of land. When George Peabody College for Teachers merged with Vanderbilt in 1979, about 53 acres were added.

    wyatt centerVanderbilt’s student enrollment tended to double itself each 25 years during the first century of the university’s history: 307 in the fall of 1875; 754 in 1900; 1,377 in 1925; 3,529 in 1950; 7,034 in 1975. In the fall of 1999 the enrollment was 10,127.

    In the planning of Vanderbilt, the assumption seemed to be that it would be an all-male institution. Yet the board never enacted rules prohibiting women. At least one woman attended Vanderbilt classes every year from 1875 on. Most came to classes by courtesy of professors or as special or irregular (non-degree) students. From 1892 to 1901 women at Vanderbilt gained full legal equality except in one respect — access to dorms. In 1894 the faculty and board allowed women to compete for academic prizes. By 1897, four or five women entered with each freshman class. By 1913 the student body contained 78 women, or just more than 20 percent of the academic enrollment.

    National recognition of the university’s status came in 1949 with election of Vanderbilt to membership in the select Association of American Universities. In the 1950s Vanderbilt began to outgrow its provincial roots and to measure its achievements by national standards under the leadership of Chancellor Harvie Branscomb. By its 90th anniversary in 1963, Vanderbilt for the first time ranked in the top 20 private universities in the United States.

    Vanderbilt continued to excel in research, and the number of university buildings more than doubled under the leadership of Chancellors Alexander Heard (1963-1982) and Joe B. Wyatt (1982-2000), only the fifth and sixth chancellors in Vanderbilt’s long and distinguished history. Heard added three schools (Blair, the Owen Graduate School of Management and Peabody College) to the seven already existing and constructed three dozen buildings. During Wyatt’s tenure, Vanderbilt acquired or built one-third of the campus buildings and made great strides in diversity, volunteerism and technology.

    The university grew and changed significantly under its seventh chancellor, Gordon Gee, who served from 2000 to 2007. Vanderbilt led the country in the rate of growth for academic research funding, which increased to more than $450 million and became one of the most selective undergraduate institutions in the country.

    On March 1, 2008, Nicholas S. Zeppos was named Vanderbilt’s eighth chancellor after serving as interim chancellor beginning Aug. 1, 2007. Prior to that, he spent 2002-2008 as Vanderbilt’s provost, overseeing undergraduate, graduate and professional education programs as well as development, alumni relations and research efforts in liberal arts and sciences, engineering, music, education, business, law and divinity. He first came to Vanderbilt in 1987 as an assistant professor in the law school. In his first five years, Zeppos led the university through the most challenging economic times since the Great Depression, while continuing to attract the best students and faculty from across the country and around the world. Vanderbilt got through the economic crisis notably less scathed than many of its peers and began and remained committed to its much-praised enhanced financial aid policy for all undergraduates during the same timespan. The Martha Rivers Ingram Commons for first-year students opened in 2008 and College Halls, the next phase in the residential education system at Vanderbilt, is on track to open in the fall of 2014. During Zeppos’ first five years, Vanderbilt has drawn robust support from federal funding agencies, and the Medical Center entered into agreements with regional hospitals and health care systems in middle and east Tennessee that will bring Vanderbilt care to patients across the state.

    studentsToday, Vanderbilt University is a private research university of about 6,500 undergraduates and 5,300 graduate and professional students. The university comprises 10 schools, a public policy center and The Freedom Forum First Amendment Center. Vanderbilt offers undergraduate programs in the liberal arts and sciences, engineering, music, education and human development as well as a full range of graduate and professional degrees. The university is consistently ranked as one of the nation’s top 20 universities by publications such as U.S. News & World Report, with several programs and disciplines ranking in the top 10.

    Cutting-edge research and liberal arts, combined with strong ties to a distinguished medical center, creates an invigorating atmosphere where students tailor their education to meet their goals and researchers collaborate to solve complex questions affecting our health, culture and society.

    Vanderbilt, an independent, privately supported university, and the separate, non-profit Vanderbilt University Medical Center share a respected name and enjoy close collaboration through education and research. Together, the number of people employed by these two organizations exceeds that of the largest private employer in the Middle Tennessee region.
    Related links

  • richardmitnick 2:57 pm on May 8, 2018 Permalink | Reply
    Tags: , , Biology, , , , ,   

    From Symmetry: “Leveling the playing field” 

    Symmetry Mag
    From Symmetry

    Photo by Eleanor Starkman

    Ali Sundermier

    [When I read this article, my first reaction was that this is all worthless. I have been running a series in this blog which highlights “Women in STEM” in all of the phases that the expression implies. The simple fact is that there is and continues to be and will continue to be gender bias in the physical sciences (and probably elsewhere, but this is my area of choice). This is certainly unfair to women, but it is also unfair to all of mankind. We are losing a lot of great and powerful minds and voices as we try to push the future of knowledge and quality of life for all. So I am doing the post. But in all fields men need to call on and respect women if things are to improve. I personally see no evidence of this. As long as women only get to talk to women there will be no progress.]

    Conferences for Undergraduate Women in Physics aims to encourage more women and gender minorities to pursue careers in physics and improve diversity in the field.

    Nicole Pfiester, an engineering grad student at Tufts University, says she has been interested in physics since she was a child. She says she loves learning how things work, and physics provides a foundation for doing just that.

    But when Pfiester began pursuing a degree in physics as an undergraduate at Purdue University in 2006, she had a hard time feeling like she belonged in the male-dominated field.

    “In a class of about 30 physics students,” she says, “I think two of us were women. I just always stood out. I was kind of shy back then and much more inclined to open up to other women than I was to men, especially in study groups. Not being around people I could relate to, while it didn’t make things impossible, definitely made things more difficult.”

    In 2008, two years into her undergraduate career, Pfiester attended a conference at the University of Michigan that was designed to address this very issue. The meeting was part of the Conferences for Undergraduate Women in Physics, or CUWiP, a collection of annual three-day regional conferences to give undergraduate women a sense of belonging and motivate them to continue in the field.

    Pfiester says it was amazing to see so many female physicists in the same room and to learn that they had all gone through similar experiences. It inspired her and the other students she was with to start their own Women in Physics chapter at Purdue. Since then, the school has hosted two separate CUWiP events, in 2011 and 2015.

    “Just seeing that there are other people like you doing what it is you want to do is really powerful,” Pfiester says. “It can really help you get through some difficult moments where it’s really easy, especially in college, to feel like you don’t belong. When you see other people experiencing the same struggles and, even more importantly, you see role models who look and talk like you, you realize that this is something you can do, too. I always left those conferences really energized and ready to get back into it.”

    CUWiP was founded in 2006 when two graduate students at the University of Southern California realized that only 21 percent of US undergraduates in physics were women, a percentage that dropped even further in physics with career progression. In the 12 years since then, the percentage of undergraduate physics degrees going to women in the US has not grown, but CUWiP has. What began as one conference with 27 attendees has developed into a string of conferences held at sites across the country, as well as in Canada and the UK, with more than 1500 attendees per year. Since the American Physical Society took the conference under its umbrella in 2012, the number of participants has continued to grow every year.

    The conferences are supported by the National Science Foundation, the Department of Energy and the host institutions. Most student transportation to the conferences is almost covered by the students’ home institutions, and APS provides extensive administrative support. In addition, local organizing committees contribute a significant volunteer effort.

    “We want to provide women, gender minorities and anyone who attends the conference access to information and resources that are going to help them continue in science careers,” says Pearl Sandick, a dark-matter physicist at the University of Utah and chair of the National Organizing Committee for CUWiP.

    Some of the goals of the conference, Sandick says, are to make sure people leave with a greater sense of community, identify themselves more as physicists, become more aware of gender issues in physics, and feel valued and respected in their field. They accomplish this through workshops and panels featuring accomplished female physicists in a broad range of professions.

    Before the beginning of the shared video keynote talk, attendees at each CUWiP site cheer and wave on video. This gives a sense of the national scale of the conference and the huge number of people involved.
    Courtesy of Columbia University

    “Often students come to the conference and are very discouraged,” says past chair Daniela Bortoletto, a high-energy physicist at the University of Oxford who organizes CUWiP in the UK. “But then they meet these extremely accomplished scientists who tell the stories of their lives, and they learn that everybody struggles at different steps, everybody gets discouraged at some point, and there are ups and downs in everyone’s careers. I think it’s valuable to see that. The students walk out of the conference with a lot more confidence.”

    Through CUWiP, the organizers hope to equip students to make informed decisions about their education and expose them to the kinds of career opportunities that are open to them as physics majors, whether it means going to grad school or going into industry or science policy.

    “Not every student in physics is aware that physicists do all kinds of things,” says Kate Scholberg, a neutrino physicist at Duke and past chair. “Everybody who has been a physics undergrad gets the question, ‘What are you going to do with that?’ We want to show students there’s a lot more out there than grad school and help them expand their professional networks.”

    They also reach back to try to make conditions better for the next generations of physicists.

    At the 2018 conference, Hope Marks, now a senior at Utah State University majoring in physics, participated in a workshop in which she wrote a letter to her high school physics teacher, who she says really sparked her interest in the field.

    “I really liked the experiments we did and talking about some of the modern discoveries of physics,” she says. “I loved how physics allows us to explore the world from particles even smaller than atoms to literally the entire universe.”

    The workshop was meant to encourage high school science and math teachers to support women in their classes.

    One of the challenges to organizing the conferences, says Pat Burchat, an observational cosmologist at Stanford University and past chair, is to build experiences that are engaging and accessible for undergraduate women.

    “The tendency of organizers is naturally to think about the kinds of conferences they go to,” says Burchat says, “which usually consist of a bunch of research talks, often full of people sitting passively listening to someone talk. We want to make sure CUWiP consists of a lot of interactive sessions and workshops to keep the students engaged.”

    Candace Bryan, a physics major at the University of Utah who has wanted to be an astronomer since elementary school, says one of the most encouraging parts of the conference was learning about imposter syndrome, which occurs when someone believes that they have made it to where they are only by chance and don’t feel deserving of their achievements.

    “Science can be such an intimidating field,” she says. “It was the first time I’d ever heard that phrase, and it was really freeing to hear about it and know that so many others felt the same way. Every single person in that room raised their hand when they asked, ‘Who here has experienced imposter syndrome?’ That was really powerful. It helped me to try to move past that and improve awareness.”

    Women feeling imposter syndrome sometimes interpret their struggles as a sign that they don’t belong in physics, Bryan says.

    “It’s important to support women in physics and make sure they know there are other women out there who are struggling with the same things,” she says.

    “It was really inspirational for everyone to see how far they had come and receive encouragement to keep going. It was really nice to have that feeling after conference of ‘I can go to that class and kill it,’ or ‘I can take that test and not feel like I’m going to fail.’ And if you do fail, it’s OK, because everyone else has at some point. The important thing is to keep going.”

    See the full article here .

    Please help promote STEM in your local schools.

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    Stem Education Coalition

    Symmetry is a joint Fermilab/SLAC publication.

  • richardmitnick 1:27 pm on May 7, 2018 Permalink | Reply
    Tags: , Biology, , Elysia chlorotica,   

    From Rutgers University: “Solar-Powered Sea Slugs Shed Light on Search for Perpetual Green Energy” 

    Rutgers smaller
    Our Great Seal.

    From Rutgers University

    May 2, 2018

    Todd Bates


    The sea slug Elysia chlorotica steals millions of green-colored plastids, which are like tiny solar panels, from algae.
    Photo: Karen N. Pelletreau/University of Maine

    Near-shore animal becomes plantlike after pilfering tiny solar panels and storing them in its gut.

    In an amazing achievement akin to adding solar panels to your body, a northeast sea slug sucks raw materials from algae to provide its lifetime supply of solar-powered energy, according to a study by Rutgers University–New Brunswick and other scientists.

    “It’s a remarkable feat because it’s highly unusual for an animal to behave like a plant and survive solely on photosynthesis,” said Debashish Bhattacharya, senior author of the study and distinguished professor in the Department of Biochemistry and Microbiology at Rutgers–New Brunswick. “The broader implication is in the field of artificial photosynthesis. That is, if we can figure out how the slug maintains stolen, isolated plastids to fix carbon without the plant nucleus, then maybe we can also harness isolated plastids for eternity as green machines to create bioproducts or energy. The existing paradigm is that to make green energy, we need the plant or alga to run the photosynthetic organelle, but the slug shows us that this does not have to be the case.”

    The sea slug Elysia chlorotica, a mollusk that can grow to more than two inches long, has been found in the intertidal zone between Nova Scotia, Canada, and Martha’s Vineyard, Massachusetts, as well as in Florida. Juvenile sea slugs eat the nontoxic brown alga Vaucheria litorea and become photosynthetic – or solar-powered – after stealing millions of algal plastids, which are like tiny solar panels, and storing them in their gut lining, according to the study published online in the journal Molecular Biology and Evolution.

    Photosynthesis is when algae and plants use sunlight to create chemical energy (sugars) from carbon dioxide and water. The brown alga’s plastids are photosynthetic organelles (like the organs in animals and people) with chlorophyll, a green pigment that absorbs light.

    YouTube video of the sea slug Elysia chlorotica by Mary S. Tyler and Mary E. Rumpho

    This particular alga is an ideal food source because it does not have walls between adjoining cells in its body and is essentially a long tube loaded with nuclei and plastids, Bhattacharya said. “When the sea slug makes a hole in the outer cell wall, it can suck out the cell contents and gather all of the algal plastids at once,” he said.

    Based on studies of other sea slugs, some scientists have argued that they steal and store plastids as food to be digested during hard times, like camels that store fat in their humps, Bhattacharya said. This study showed that’s not the case for solar-powered Elysia chlorotica.

    This microscopic image shows stolen algal plastids (in green) and lipids from algae (in yellow) inside the sea slug’s digestive system.
    Photo: Karen N. Pelletreau/University of Maine

    “It has this remarkable ability to steal these algal plastids, stop feeding and survive off the photosynthesis from the algae for the next six to eight months,” he said.

    The team of Rutgers and other scientists used RNA sequencing (gene expression) to test their solar energy supply hypothesis. The data show that the slug responds actively to the stolen plastids by protecting them from digestion and turning on animal genes to utilize the algal photosynthetic products. Their findings mirror those found in corals that maintain dinoflagellates (also algae) – as intact cells and not stolen plastids – in symbiotic relationships.

    Whereas Elysia chlorotica stores plastids, the algal nuclei that are also sucked in don’t survive, and scientists still don’t know how the sea slug maintains the plastids and photosynthesis for months without the nuclei that are normally needed to control their function, Bhattacharya said.

    The study’s coauthors include Pavel Vaysberg, a former undergrad in biotechnology in the School of Environmental and Biological Sciences; Dana C. Price, associate research professor in the Department of Plant Biology; and researchers from the University of Queensland in Australia, University of Maine and University of Connecticut.

    See the full article here .

    Follow Rutgers Research here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition


    Rutgers, The State University of New Jersey, is a leading national research university and the state’s preeminent, comprehensive public institution of higher education. Rutgers is dedicated to teaching that meets the highest standards of excellence; to conducting research that breaks new ground; and to providing services, solutions, and clinical care that help individuals and the local, national, and global communities where they live.

    Founded in 1766, Rutgers teaches across the full educational spectrum: preschool to precollege; undergraduate to graduate; postdoctoral fellowships to residencies; and continuing education for professional and personal advancement.

    As a ’67 graduate of University college, second in my class, I am proud to be a member of

    Alpha Sigma Lamda, National Honor Society of non-tradional students.

  • richardmitnick 10:25 am on May 3, 2018 Permalink | Reply
    Tags: A Series of New Videos for Users, , Biology, ,   

    From EMSL: “A Series of New Videos for Users” 



    at PNNL

    EMSL recently posted a collection of eight new videos on its YouTube channel and website to help users improve their research.

    The short videos – around two minutes each – feature EMSL scientists describing how certain capabilities can advance users’ projects, particularly those relevant to DOE Office of Biological and Environmental Research.

    Featured scientists and capabilities include:

    Amir Ahkami and Kim Hixson – Plant Sciences Laboratory
    Mark Engelhard – X-ray Photoelectron Spectrometer
    Libor Kovarik – Environmental Transmission Electron Microscope
    Scott Lea – Helium Ion Microscope
    Malak Tfaily – 21 Tesla FTICR Mass Spectrometer
    Tamas Varga – X-ray Computed Tomography
    Zheming Wang – Sum-frequency Generation Vibrational Spectroscopy
    Zihua Zhu – Time of Flight Secondary Ion Mass Spectrometry

    Or check out all the videos under EMSL’s “Accelerate Your Research” YouTube playlist.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    EMSL campus

    Welcome to EMSL. EMSL is a national scientific user facility that is funded and sponsored by DOE’s Office of Biological & Environmental Research. As a user facility, our scientific capabilities – people, instruments and facilities – are available for use by the global research community. We support BER’s mission to provide innovative solutions to the nation’s environmental and energy production challenges in areas such as atmospheric aerosols, feedstocks, global carbon cycling, biogeochemistry, subsurface science and energy materials.

    A deep understanding of molecular-level processes is critical to gaining a predictive, systems-level understanding of the impacts of aerosols and terrestrial systems on climate change; making clean, affordable, abundant energy; and cleaning up our legacy wastes. Visit our Science page to learn how EMSL leads in these areas, through our Science Themes.

    Team’s in Our DNA. We approach science differently than many institutions. We believe in – and have proven – the value of drawing together members of the scientific community and assembling the people, resources and facilities to solve problems. It’s in our DNA, since our founder Dr. Wiley’s initial call to create a user facility that would facilitate “synergism between the physical, mathematical, and life sciences.” We integrate experts across disciplines; experiment with theory; and our user program proposal calls with other user facilities.

    We proudly provide an enriched, customized experience that allows users to connect with our people and capabilities in an environment where we focus on solving problems. We collaborate with researchers from academia, government labs and industry, and from nearly all 50 states and from other countries.

  • richardmitnick 9:52 pm on April 29, 2018 Permalink | Reply
    Tags: , , Biology, , , , , , , , ,   

    From Symmetry : “Putting the puzzle together” 

    Symmetry Mag

    [While this article was written for a journal specializing in Physics, everything in it is true for all Basic and Applied Science. Soemwhere in my archives is an article from Natural History Magazine by Stephen Jay Gould in which he states that many new scientific ideas arise out of the existence of the devices built by technicians for the last experimental project. So it will be with the HL-LHC and the ILC.]

    11/21/17 [in social media today]
    Ali Sundermier

    Photos by Fermilab and CERN

    Successful physics collaborations rely on cooperation between people from many different disciplines.

    So, you want to start a physics experiment. Maybe you want to follow hints of an as yet unseen particle. Or maybe you want to learn something new about a mysterious process in the universe. Either way, your next step is to find people who can help you.

    In large science collaborations, such as the ATLAS and CMS experiments at the Large Hadron Collider; the Deep Underground Neutrino Experiment (DUNE); and Fermilab’s NOvA, hundreds to thousands of people spread out across many institutions and countries keep things operating smoothly. Whether they’re senior scientists, engineers, technicians or administrators, each of them has an important role to play.

    CERN/ATLAS detector

    CERN CMS detector


    CERN/LHC Map

    FNAL LBNF/DUNE from FNAL to SURF, Lead, South Dakota, USA

    FNAL DUNE Argon tank at SURF

    Surf-Dune/LBNF Caverns at Sanford

    SURF building in Lead SD USA

    CERN LHC Tunnel

    CERN LHC particles

    FNAL NOvA Near Detector

    FNAL/NOvA experiment map

    Think of it like a jigsaw puzzle: This list will give you an idea about how their work fits together to create the big picture.

    Dreaming up the experiment

    Many particle physics experiments begin with a fundamental question. Why do objects have mass? Or, why is the universe made of matter?

    When scientists encounter these big, seemingly inscrutable questions, part of their job is to identify possible ways to answer them. A large part of this is breaking down the big questions into a program of smaller, answerable questions.

    In the case of the LHC, scientists who wondered about things such as undiscovered particles and the origin of mass designed a 27-kilometer particle collider and four giant detectors to learn more.

    Each scientist in a collaboration brings their own unique perspective and skill set to the table, whether it’s providing an understanding of the physics or offering expertise in operations or detector design.

    CERN/ALICE Detector

    CERN/LHCb detector

    (ATLAS and CMS detectors are depicted above.]

    Perfecting the design

    Once scientists have an idea about the experiment they want to do and the approach they want to take, it’s the job of the engineers to turn the concepts into pieces of hardware that can be built, function and meet the experiment’s requirements.

    For example, engineers might have to figure out how the experiment should be supported mechanically or how to connect all the electrical systems and make signals available in a detector.

    In the case of NOvA [depicted above], which investigates neutrino oscillations, scientists needed a detector that was huge and free of dense materials, which made conventional construction techniques unworkable. They had to work with engineers who could understand plastic as a building material so they could be confident about using it to build a gigantic, free-standing structure that fit the requirements.

    Keeping things running

    Technicians come in when the experimental apparatus and instrumentation are being built and often have complementary knowledge about what they’re working on. They build the hardware and coordinate the integration of components. It’s their work that, in the end, pulls everything together so the experiment functions.

    Once the experiment is built, technicians are responsible for keeping everything humming along at top performance. When physicists notice things going wrong with the detectors, the technicians usually have first eyes on it. It’s a vital task, since every second counts when it comes to collecting data.

    Doing the heavy lifting

    When designing and constructing the experiment, the scientists also recruit postdocs and grad students, who do the bulk of the data analysis.

    Grad students, who are still working on their PhDs, have to balance their own coursework with the real-world experiment, learning their way around running simulations, analyzing data and developing algorithms. They also make sure that every part of the detector is working up to par. In addition, they may work in instrumentation, developing new instruments and electronics.

    Postdocs, on the other hand, have already worked on experiments and obtained their PhDs, so they typically assume more of a leadership role in these collaborations. Part of their role is to guide the grad students in a sort of apprenticeship.

    Postdocs are often in charge of certain types of analysis or detector operations. Because they’ve worked on previous experiments, they have a tool kit and experience to draw on to solve problems when they crop up.

    Postdocs and grad students often work with technicians and engineers to ensure everything is properly built.

    Making the data accessible

    The LHC produces about 25 petabytes of data every year, or 25 billion megabytes. If the average size of an MP3 is about one megabyte per minute, then it would take almost 50,000 years to play 25 petabytes of songs. In physics collaborations, computer scientists and engineers have to organize the computing networks to ensure against bottlenecks or traffic jams when this massive amount of data is shared.

    They also maintain the software framework, which takes care of data handling and archiving. Say a scientist wants to know what happened on Feb. 27, 2015, at 3 a.m. Computing experts have to be able to go into the data catalogue and find, among the petabytes of data, where that event is stored.

    Sorting out the logistics

    One often overlooked group is the administrators.

    It’s up to the administrators to sequence all the different projects so they get the funds they need to make progress. They sort the logistics to make sure the right people are in the right places working on the right things.

    Administrators manage a group of people who are constantly coming and going. Is someone traveling to a site from a different institution? The administrators make sure that people get connected, work out itineraries and schedule where visiting scientists will live and work.

    Administrators also organize collaboration meetings, transfer money, and procure and ship equipment.

    Translating discoveries to the public

    While every single person involved in an experiment has a responsibility to effectively communicate with others, it can be challenging to communicate about research in a way that’s relatable to people from different backgrounds. That’s where the professional communicators come in.

    Communicators can translate a paper full of jargon and complicated science into a fascinating story that the rest of the world can get excited about.

    In addition to doing outreach for the public and writing press releases and pitching stories for the media, communicators offer coaching to people in a scientific collaboration on how to relay the science to a general audience, which is important for generating public interest. [Everyone involved need to remember that all of this work is publicly funded with tax dollars, except in places like China where it is virtually the same thing.]

    [One of the main reasons I started this blog was that I found out that 30% of the scientists on the LHC are USA scientists and the US press does not write about science except the rare person like Dennis Overbye of the New York Times. I had seen the PBS video Creation of the Universe by Timothy Ferris (music by Brian Eno); The PBS video The Atom Smashers, centered on but not limited to the Tevatron at Fermilab and hints of what was to come in Europe in stead of Waxahachie, Texas; and The Big Bang Machine, with (Sir) Brian Cox, all about the LHC, with a nod back to the Tevatron. Someone at Quantum Diaries put me on to the Greybook which lists every institution in the world processing data from the LHC. I collected as much of their social media as I could and that was my start. Of course by now my source list has grown considerably and my subjects have also increased.]

    Fitting the pieces

    Now that you know many of the pieces that must fall into place for a large physics collaboration to be successful, also know that none of these roles is performed in a vacuum. For an experiment to work, there must be a synergy of tasks: Each relies on the success of the others. Now go start that experiment!

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Symmetry is a joint Fermilab/SLAC publication.

  • richardmitnick 9:39 am on April 23, 2018 Permalink | Reply
    Tags: $100 million gift to Brown will name Carney Institute for Brain Science which it is hoped will advance discoveries and cures, , Biology, , ,   

    From Brown University: “$100 million gift to Brown will name Carney Institute for Brain Science, advance discoveries and cures” 

    Brown University
    Brown University

    [This post is dedicated to EJM and EBM]

    April 18, 2018
    No writer credit

    Brown U Carney Institute for Brain Science

    No image credit.

    A new $100 million gift to Brown University’s brain science institute from alumnus Robert J. Carney and Nancy D. Carney will drive an ambitious agenda to quicken the pace of scientific discovery and help find cures to some of the world’s most persistent and devastating diseases, such as ALS and Alzheimer’s.

    Carney graduated in Brown’s undergraduate Class of 1961, is a long-serving Brown trustee, and is founder and chairman of Vacation Publications Inc. Previously, he was a founder of Jet Capital Corp., a financial advisory firm, and Texas Air Corp., which owned Continental Airlines and several other airlines. Nancy Doerr Carney is a former television news producer.

    The Carneys’ gift changes the name of the Brown Institute for Brain Science to the Robert J. and Nancy D. Carney Institute for Brain Science, and establishes the institute as one of the best-endowed university brain institutes in the country. Brown President Christina Paxson said the $100 million donation — one of the largest single gifts in Brown’s history — will help establish the University as a leader in devising treatments and technologies to address brain-related disease and injury.

    “This is a signal moment when scientists around the world are poised to solve some of the most important puzzles of the human brain,” Paxson said. “This extraordinarily generous gift will give Brown the resources to be at the forefront of this drive for new knowledge and therapies. We know that discoveries in brain science in the years to come will dramatically reshape human capabilities, and Brown will be a leader in this critical endeavor.”

    The gift will allow the Carney Institute to accelerate hiring of leading faculty and postdoctoral scholars in fields related to brain science, supply seed funding for high-impact new research, and also fund essential new equipment and infrastructure in technology-intensive areas of exploration.

    Core areas of research at the institute include work on brain-computer interfaces to aid patients with spinal injury and paralysis; innovative advances in computational neuroscience to address behavior and mood disorders; and research into mechanisms of cell death as part of efforts to identify therapies for neurodegenerative diseases that include amyotrophic lateral sclerosis (ALS) and Alzheimer’s.

    Carney said he is excited that he and his wife are making their gift at a time when brain science has emerged as one of the fastest growing programs at Brown, both in terms of research and student interest.

    “Nancy and I have long been impressed by the phenomenal research and education of bright young minds that we see at Brown,” Carney said. “We are excited to see the brain institute continue to grow and serve society in ways that are vitally important.”

    VIDEO: Brain Science at Brown. No video credit.

    With up to 45 labs across campus engaged in research at any given time — and 130 affiliated professors in departments ranging from neurology and neurosurgery to engineering and computer science — Brown’s brain science institute already has built a reputation for studying the brain at all scales, said Diane Lipscombe, the director of the institute since 2016 and a professor of neuroscience. From studying genes and circuits, to healthy behavior and psychiatric disorder, the institute’s faculty contribute expertise to routinely produce insights and tools to see, map, understand and fix problems in the nervous system.

    In addition, as the brain institute’s work grows in its breadth, undergraduates continue to take on key roles as researchers, reflecting a distinctive aspect of Brown’s undergraduate curriculum. About a quarter of all Brown undergraduates take Introduction to Neuroscience, demonstrating the excitement in the field.

    “This is a transformative moment that is going to catapult Brown and our brain science institute,” said Lipscombe, who is president-elect of the Society for Neuroscience, the field’s international professional organization. “We will be able to crack the neural codes, push discoveries forward and address some of the largest challenges facing humanity, at the same time training the next generation of brain scientists.”

    Investments like the gift from the Carneys are the “lifeblood to driving innovation and discovery,” Lipscombe said.

    The Carneys’ gift is part of Brown University’s $3-billion BrownTogether comprehensive campaign, which has raised $1.7 billion to date. In total, $148 million has been raised to support research and education in brain science. The gifts support one of the core research priorities defined in Brown’s Building on Distinction strategic plan: understanding the human brain. The study of the brain and its relationship to cognition, behavior and disease is often described as the “last frontier” in biomedical science.

    Leading in research

    The Carney Institute had its start at Brown as the Brain Science Program in 1999, later becoming the Brown Institute for Brain Science. The scope of its work has increased dramatically in recent years, and the institute now has affiliated faculty spanning 19 academic departments, including clinical departments in the Warren Alpert Medical School.

    Since 2011, core faculty members have led projects with more than $116 million in grant funding from federal and other sources. Many of the institute’s researchers have been recognized as pioneering leaders, winning top national awards in recent years. This includes faculty such as Eric Morrow, associate professor of biology and psychiatry, a 2017 winner of a Presidential Early Career Award for Scientists and Engineers.

    Faculty and Student Voices

    Brown’s brain scientists talk about the brain as ‘final frontier’

    We asked researchers at Brown what excites them about brain science, why they chose to conduct research here, and how Brown’s unique approach to collaborative problem-solving is unlocking and explaining the complexity of the brain.

    Full story here.

    The funding from the Carneys’ gift will help support what has become a signature program of Brown’s brain institute over the past decade: cutting-edge efforts to help those who have lost the ability to move and communicate through paralysis to regain those abilities. Research into brain-computer interfaces, part of the BrainGate project, uses tiny micro-electrode arrays implanted into the brain.

    “This is the area of research that said to us, ‘Look what can be done if you pull groups together from a wide range of academic disciplines within and beyond the life sciences to take an integrative approach to big, challenging questions,’” Lipscombe said. “The breakthroughs we have seen in confronting paralysis could not have happened without the integrative approach that is distinctive to the way Brown approaches brain science.”

    The study of neurodegenerative diseases and the growing research field of computational neuroscience are among the other areas in the institute that are poised for further expansion.

    “The general challenge is that, despite 20 or 30 years of focused effort by pharmaceutical companies and labs, we still don’t know why neurons die in neurodegenerative disorders,” Lipscombe said. “ALS is part of a group of disorders that takes people’s lives way too early. We need more research into the basic mechanisms that lead to cell death.”

    Computational neuroscience is an increasingly influential field that employs mathematical models to understand the brain and develops quantitative approaches to diagnosing and treating complex brain disorders.

    Scientists working in computational psychiatry at Brown are thinking about how they can use their work modeling the brain to address psychiatric disease, such as depression.

    “And when you are catalyzing innovative research in areas such as this by bringing together great faculty from different disciplines, having a pool of seed funding is critical to move from exciting ideas to research and discovery,” Lipscombe said. “From there, federal funding follows. Now we can say we have the people, resources and the new research space to support big ideas to address key problems in brain science.”

    A new technology called “trans-Tango” allows scientists to exploit the connections between pairs of neurons to make discoveries in neuroscience. Developing the system required decades of work and a dedicated team of brain scientists at Brown. No image credit.

    The Carney Institute will move into expanded new quarters at 164 Angell Street early next year, after extensive renovation of the building that formerly housed Brown administrative offices. The building will give the institute state-of-the-art shared lab spaces that will further promote collaboration among teams from cognitive neuroscience, computational neuroscience and neuroengineering. These scientists are working on processes such as decoding neural signals, developing new ways to use neural signals in assistive technology, and mining neural data for more accurate predictors of psychiatric illnesses.

    The new location will be in the same building as Brown’s Data Science Initiative and directly across the street from the new home of Brown’s Jonathan M. Nelson Center for Entrepreneurship, stimulating opportunities for collective work that will support discoveries and their impact on society.

    Inspired giving

    The gift from the Carneys is one of three single gifts of $100 million to Brown in its 254-year history. Brown announced in 2004 that New York businessman Sidney E. Frank, a member of the Brown Class of 1942, had pledged $100 million for undergraduate financial aid. A $100 million gift from the Warren Alpert Foundation announced by Brown in 2007 funded research, faculty recruitment, a new building and named Brown’s Warren Alpert Medical School.

    Brown President Christina Paxson (standing, left) joined Robert J. Carney and Nancy D. Carney to celebrate the couple’s generous gift at an event in Houston on April 18. No image credit.

    This wonderful gift from the Carneys is one of the most significant in the long, distinguished history of Brown University,” Brown Chancellor Samuel M. Mencoff said. “The gift represents a substantial long-term investment in what Brown does exceptionally well — bringing together the people and expertise to solve problems and benefit society.”

    The Carneys said they were inspired to make their gift by many previous positive experiences with Brown, as well as the opportunities they saw for the University in brain science.

    “Brown has meant so much to Nancy and me,” Carney said. “We feel extremely fortunate to be able to help expand Brown’s brain institute and carry forward such a significant priority for the University.”

    The Carneys, of Houston, are long-time supporters of Brown, including as the donors of two endowed professorships — the Robert J. and Nancy D. Carney University Professor of Economics and the Robert J. and Nancy D. Carney Assistant Professor of Neuroscience. This spring, Carney will finish his third term as a trustee on the Corporation of Brown University. His volunteerism includes having served as the co-chair of the 50th reunion gift committee for the Class of 1961.

    Former Brown Chancellor Thomas J. Tisch, currently a member of the Corporation’s Board of Fellows, said about the Carneys, “They have always done things worth doing, quietly and with modesty and deep intelligence. Bob and Nancy have a great combined sense of caring and commitment to things important.”

    As part of a celebration in Houston coinciding with the announcement of the Carneys’ gift to the brain science institute, Paxson on behalf of the University conferred honorary Doctor of Humane Letters degrees on both of the Carneys.

    The citation read, in part: “Through your steadfast support of Brown’s ambitions to expand its reach through excellence in teaching and research in particular, you have played a major role in bolstering its reputation as a world-class learning institution.”

    After implantation with the BrainGate brain-computer interface (which originated in a Brown research laboratory) and stimulative electrodes in his arm, a Cleveland man with quadriplegia was able to again move his arm to eat and drink. Cleveland FES Center.

    See the full article here .

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    Located in historic Providence, Rhode Island and founded in 1764, Brown University is the seventh-oldest college in the United States. Brown is an independent, coeducational Ivy League institution comprising undergraduate and graduate programs, plus the Alpert Medical School, School of Public Health, School of Engineering, and the School of Professional Studies.

    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.

    Brown’s vibrant, diverse community consists of 6,000 undergraduates, 2,000 graduate students, 400 medical school students, more than 5,000 summer, visiting and online students, and nearly 700 faculty members. Brown students come from all 50 states and more than 100 countries.

    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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