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  • richardmitnick 3:12 pm on January 17, 2017 Permalink | Reply
    Tags: , , Chemistry, , , The most successful phyla have species that live on land and have a skeleton and are parasites, Three Ways to Be a Winner in the Game of Evolution,   

    From U Arizona: “Three Ways to Be a Winner in the Game of Evolution” 

    U Arizona bloc

    University of Arizona

    1
    Jellyfish, polyps and the like belong to a phylum called Cnidaria, one of about 30 major groups that make up the animal kingdom. (Photo: Chai Seamaker/Shutterstock)

    A new UA study reveals the key traits associated with high species diversity: The most successful phyla have species that live on land, have a skeleton and are parasites.

    A new study by University of Arizona biologists helps explain why different groups of animals differ dramatically in their number of species, and how this is related to differences in their body forms and ways of life.

    For millennia, humans have marveled at the seemingly boundless variety and diversity of animals inhabiting the Earth. So far, biologists have described and catalogued about 1.5 million animal species, a number that many think might be eclipsed by the number of species still awaiting discovery.

    All animal species are divided among roughly 30 phyla, but these phyla differ dramatically in how many species they contain, from a single species to more than 1.2 million in the case of insects and their kin. Animals have incredible variation in their body shapes and ways of life, including the plantlike, immobile marine sponges that lack heads, eyes, limbs and complex organs, parasitic worms that live inside other organisms (nematodes, platyhelminths), and phyla with eyes, skeletons, limbs and complex organs that dominate the land in terms of species numbers (arthropods) and body size (chordates).

    Amid this dazzling array of life forms, one question has remained as elusive as it is obvious: Why is it that some groups on the evolutionary tree of animals have branched into a dizzying thicket of species while others split into a mere handful and called it a day?

    From the beginnings of their discipline, biologists have tried to find and understand the patterns underlying species diversity. In other words, what is the recipe that allows a phylum to diversify into many species, or, in the words of evolutionary biologists, to be “successful”? A fundamental but unresolved problem is whether the basic biology of these phyla is related to their species numbers. For example, does having a head, limbs and eyes allow some groups to be more successful and thus have greater species numbers?

    2
    A simplified evolutionary tree of six representative animal phyla, illustrating differences in body form, habitat, and species numbers among them. (Image: T. Jezkova/Shutterstock/Aaron Ambos/J. Wiens)

    3
    This colorful chocolate chip sea star, along with sea cucumbers and sea urchins, belongs to the Echinoderms, the only phylum with a five-symmetrical body plan. (Photo: Ethan Daniels/Shutterstock)

    n the new study, Tereza Jezkova and John Wiens, both in the University of Arizona’s Department of Ecology and Evolutionary Biology, have helped resolve this problem. They assembled a database of 18 traits, including traits related to anatomy, reproduction and ecology. They then tested how each trait was related to the number of species in each phylum, and how quickly species in each phylum multiplied over time (diversification). The results are published in the journal American Naturalist.

    Jezkova and Wiens found that just three traits explained most variation in diversification and species numbers among phyla: the most successful phyla have a skeleton (either internal or external), live on land (instead of in the ocean) and parasitize other organisms. Other traits, including those that might seem more dramatic, had surprisingly little impact on diversification and species numbers: Evolutionary accomplishments such as having a head, limbs and complex organ systems for circulation and digestion don’t seem to be primary accessories in the evolutionary “dress for success.”

    “Parasitism isn’t correlated with any of the other traits, so it seems to have a strong effect on its own,” Wiens said.

    He explained that when a host species splits into two species, it takes its parasite population(s) with it.

    “You can have a number of parasite species living inside the same host,” he said. “For example, there could be 10 species of nematodes in one host species, and if that host species splits into two, there are 20 species of nematodes. So that really multiplies the diversity.”

    The researchers used a statistical method called multiple regression analysis to tease out whether a trait such as parasitic lifestyle is a likely driver of species diversification.

    “We tested all these unique traits individually,” Wiens explained. “For example, having a head, having eyes, where the species in a phylum tend to live, whether they reproduce sexually or asexually, whether they undergo metamorphosis or not. And from that we picked six traits that each had a strong effect on their own. We then fed those six traits into a multiple regression model. And then we asked, ‘What combination of traits explains the most variation without including any unnecessary variables?’ — and from that we could reduce it down to three key variables.”

    The authors point out that the analysis does not make any assumptions about the fossil record, which is not a true reflection of past biodiversity, as it does not reveal most soft-bodied animals or traits like a parasitic lifestyle.

    “We wanted to know what explains the pattern of diversity in the species we see today,” Wiens said. “Who are the winners, and who are the losers?”

    Marine biodiversity is in jeopardy from human activities such as acidification from carbon emissions, posing an existential threat to many marine animals, Wiens said.

    “Many unique products of animal evolution live only in the oceans and could easily be lost, so groups that have survived for hundreds of millions of years could disappear in our lifetime, which is terrible,” he said. “Many of the animals’ phyla that are losers in terms of present-day species numbers tend to be in the ocean, and because of human activity, they may go completely extinct.”

    The study also suggests that man-made extinction may wage a heavy toll on Earth’s biodiversity because of the effect of secondary extinctions, Wiens explained.

    “When a species goes extinct, all its associated species that live in it or on it are likely to go extinct as well,” he said.

    See the full article here .

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    U Arizona campus

    The University of Arizona (UA) is a place without limits-where teaching, research, service and innovation merge to improve lives in Arizona and beyond. We aren’t afraid to ask big questions, and find even better answers.

    In 1885, establishing Arizona’s first university in the middle of the Sonoran Desert was a bold move. But our founders were fearless, and we have never lost that spirit. To this day, we’re revolutionizing the fields of space sciences, optics, biosciences, medicine, arts and humanities, business, technology transfer and many others. Since it was founded, the UA has grown to cover more than 380 acres in central Tucson, a rich breeding ground for discovery.

    Where else in the world can you find an astronomical observatory mirror lab under a football stadium? An entire ecosystem under a glass dome? Visit our campus, just once, and you’ll quickly understand why the UA is a university unlike any other.

     
  • richardmitnick 12:44 pm on January 10, 2017 Permalink | Reply
    Tags: , , Chemistry, Origin of the Elements in the Solar System,   

    From SDSS: “Origin of the Elements in the Solar System” 

    SDSS Science blog bloc

    Science Blog from the SDSS

    January 9, 2017
    Jennifer Johnson

    “The nitrogen in our DNA, the calcium in our teeth, the iron in our blood, the carbon in our apple pies were made in the interiors of collapsing stars. We are made of starstuff.” — Carl Sagan

    This is an evocative statement. It gets at the heart of the matter. However, it leaves out all the different ways that stars make the elements. It is not just collapsing stars, it is merging stars, burping stars, exploding stars, and the start of the Universe itself.

    Below is the latest version of an evolving periodic table color-coded by the origin of the elements in the Solar System. An original version of this was made by Inese Ivans and me in 2008 and refined and improved by Anna Frebel. Versions highlighting different aspects of the physical processes are available on Inese Ivans’ website.

    1
    My current version of the periodic table, color-coded by the source of the element in the solar system. Elements with more than one source have the approximate amount due to each process indicated by the amount of area. Tc, Pm, and the elements beyond U do not have long-lived or stable isotopes. I have ignored the elements beyond U in this plot, but not including Tc and Pm looked weird, so I have included them in grey.

    For this version, I tried to avoid the technical terms and jargon used in the origin. I also updated the sources of the heavy elements to reflect the current semi-consensus. This graphic draws on an enormous amount of labor from astronomers and physicists. In an upcoming blog post, I will give details on my sources and assumptions for interested parties. Note that this is for the solar system. There will be additional versions showing what this plot would look like if you were in the early Universe, or if you consider the origin of the elements on the Earth, etc.

    However, the main point of this blog post is to present the chart and address the following question:

    Why does your version have different information than the well-known Wikipedia entry?

    3
    Wikipedia version, based on the original from Northern Arizona Meteorite Laboratory.

    Here is a discussion of the some of the differences between the Wikipedia version and mine. In many cases, the Wikipedia graphic is presenting information that is flat-out wrong. I am trying to avoid going into all details in this single blog post. The underlined phrases below represent possible topics for future blog posts where I (or colleagues I coerce bribe ask) in more detail, including why we think we are on the right track.

    I will assume that “Large Stars” and “Small Stars” are “High-Mass Stars” and “Low-Mass Stars”, respectively. It does not make sense to think of nucleosynthesis origin having to do with the radius of the stars. As this wonderful graphic from NASA’s Chandra website shows, all stars at the end of their lives swell up to red giant and supergiant stars.

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    Wonderful graphic from NASA’s Chandra website

    In its death throes, a low-mass star can have a much larger radius than normal high-mass star. Note that the original source cited by the Wikipedia article just has the chart, with no additional information or links that I can find.

    High-mass stars end their lives (at least some of the time) as core-collapse supernovae. Low-mass stars usually end their lives as white dwarfs. But sometimes white dwarfs that are in binary systems with another star get enough mass from the companion to become unstable and explode as so-called Type-Ia supernovae. Which “supernova” is being referred to in the Wikipedia graphic is not clear. The interpretation that makes the graphic the least wrong is the “supernova” here means “Type Ia Supernovae” or “exploding white dwarfs” as I call them. I will assume that “Large Stars” refers to the production in high-mass stars both during their lives and during the explosion that spews products of their nuclear fusion into the interstellar gas. It would also be possible to think that “Supernovae” refers to both massive star core-collapse supernovae and exploding white dwarfs. In this case, “Large Stars” could mean that massive stars make it before they explode and the supernovae is just the mechanism for kicking out. These categories are therefore 1) confusing and 2) incorrect no matter how you slice it.

    Dying low-mass stars (aka “Small Stars”) make substantial amounts of the heavy elements, including most of the Pb in the solar system. There should be a lot of yellow in the bottom half of the diagram. I don’t understand agree that Cr and Mn are made only in “Large Stars”, but Fe is made in both “Large Stars” and “Supernovae”. Basically all the iron in the Universe is made in explosive nucleosynthesis. The iron that massive stars make right before they explode as supernova is all destroyed/collapsed in the remnant. And so on.
    The information for Li is incorrect. 6Li is indeed made by cosmic rays (fast-moving nuclei) hitting other nuclei and breaking them apart. But most of the far more common 7Li isotope is without question made in low-mass stars and spewed out out into the Universe as the star dies. Some 7Li is also made in the Big Bang and a small fraction by cosmic ray fission.
    This post does not need to be any longer, but I would like to end by pointing out a difference between the Wikipedia graphic and my graphic caused by the fact that we still don’t know everything. A fraction of the heavy elements, including most of the Au, are formed in the “rapid neutron-capture process“. Where that happens is currently in dispute. It could be in massive star supernovae close to the forming neutron-star. More recently, there is compelling evidence that most of the r-process happens when two neutron stars spiral together and merge. That is why “merging neutron stars” is a category in my chart, but “Supernovae” takes the role in the Wikipedia chart.

    The Source of it all

    Here is the original version, done with markers:

    6
    This is what happens when you give two astronomers who are tired of reminding everyone about which elements go with which process a periodic table, a set of markers, and time when they should have been listening to talks. A heartful thanks to Inese Ivans for coming up with this idea.

    See the full article here .

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    After nearly a decade of design and construction, the Sloan Digital Sky Survey saw first light on its giant mosaic camera in 1998 and entered routine operations in 2000. While the collaboration and scope of the SDSS have changed over the years, many of its key principles have stayed fixed: the use of highly efficient instruments and software to enable astronomical surveys of unprecedented scientific reach, a commitment to creating high quality public data sets, and investigations that draw on the full range of expertise in a large international collaboration. The generous support of the Alfred P. Sloan Foundation has been crucial in all phases of the SDSS, alongside support from the Participating Institutions and national funding agencies in the U.S. and other countries.

    The Sloan Digital Sky Survey has created the most detailed three-dimensional maps of the Universe ever made, with deep multi-color images of one third of the sky, and spectra for more than three million astronomical objects.

    In its first five years of operations, the SDSS carried out deep multi-color imaging over 8000 square degrees and measured spectra of more than 700,000 celestial objects. With an ever-growing collaboration, SDSS-II (2005-2008) completed the original survey goals of imaging half the northern sky and mapping the 3-dimensional clustering of one million galaxies and 100,000 quasars. SDSS-II carried out two additional surveys: the Supernova Survey, which discovered and monitored hundreds of supernovae to measure the expansion history of the universe, and the Sloan Extension for Galactic Understanding and Exploration (SEGUE), which extended SDSS imaging towards the plane of the Galaxy and mapped the motions and composition of more than a quarter million Milky Way stars.

    SDSS-III (2008-2014) undertook a major upgrade of the venerable SDSS spectrographs and added two powerful new instruments to execute an interweaved set of four surveys, mapping the clustering of galaxies and intergalactic gas in the distant universe (BOSS), the dynamics and chemical evolution of the Milky Way (SEGUE-2 and APOGEE), and the population of extra-solar giant planets (MARVELS).

    The latest generation of the SDSS (SDSS-IV, 2014-2020) is extending precision cosmological measurements to a critical early phase of cosmic history (eBOSS), expanding its revolutionary infrared spectroscopic survey of the Galaxy in the northern and southern hemispheres (APOGEE-2), and for the first time using the Sloan spectrographs to make spatially resolved maps of individual galaxies (MaNGA).

    This is the “Science blog” of the SDSS. Here you’ll find short descriptions of interesting scientific research and discoveries from the SDSS. We’ll also update on activities of the collaboration in public engagement and other arenas. We’d love to see your comments and questions about what you read here!

    You can explore more on the SDSS Website.

     
  • richardmitnick 9:23 am on December 15, 2016 Permalink | Reply
    Tags: , , , Chemistry, , , X-ray crystallography,   

    From Stanford: “Masters of Crystallization” 

    Stanford University Name
    Stanford University

    March 24, 2016 [Stanford just put this in social media 12.14.16.]
    Glennda Chui

    When molecules won’t crystallize and technology confounds, who you gonna call?

    1
    Macromolecular Structure Knowledge Center at Stanford’s Shriram Center. From left: Ted Li, T.J. Lane, MSKC Director Marc C. Deller, Nick Cox, Timothy Rhorer, Zachary Rosenthal.

    2
    Researcher Ted Li examines a sample tray full of protein crystals under a microscope. Photo: SLAC National Accelerator Laboratory.

    Biology isn’t just for biologists anymore. That’s nowhere more apparent than in the newly furnished lab in room 097 of the Shriram Center basement, where flasks of bacterial and animal cells, snug in their incubators, are churning out proteins destined for jobs they may not have done in nature.

    Researchers who use this lab span a broad range of backgrounds and interests: Chemists searching for novel antibiotics. Chemical engineers developing biofuels. Doctors seeking new treatments for diabetes.

    Most of these highly skilled researchers have one thing in common: They have no idea how to grow the proteins and other large biomolecules that are essential to their research or how to prepare those proteins for X-ray studies that will reveal their structure and function.

    That’s where Marc Deller comes in.

    “I’m the lab manager, scientist, lab cleaner — I do everything, and I help people who don’t know how to use the equipment,” says Deller, who arrived in August to establish and direct the Macromolecular Structure Knowledge Center (MSKC). “I’m pretty much unboxing things every day and trying to get things plugged in.”

    With a doctorate from Oxford and years of protein-wrangling experience, he’s here to help Stanford faculty and students grow, purify and crystallize proteins and other big biomolecules so they can be probed with the SSRL synchrotron or the LCLS X-ray laser at SLAC National Accelerator Laboratory, just up the hill.

    SLAC/SSRL
    SLAC SSRL Tunnel
    “SLAC/SSRL

    SLAC/LCLS
    SLAC/LCLS

    SLAC jointly funds the center with Stanford ChEM-H, an interdisciplinary institute aimed at understanding human biology at a chemical level, and the services offered at MSKC augment help available from the expert staff at the SLAC X-ray facilities.

    X-ray crystallography has been a revolutionary tool for understanding how living things work, revealing the structures of more than 100,000 proteins, nucleic acids and their complexes over the past few decades and fueling the development of numerous life-saving medications.

    But it’s not always easy, as chemistry graduate student Ted Li can attest. The protein he’s studying — a natural catalyst found in soil bacteria that scientists hope to turn into an antibiotic factory — “is very resistant to crystallization. It’s very floppy and doesn’t want to pack,” says Li, who works in the lab of Chaitan Khosla, professor of chemistry and of chemical engineering. “So I need to find a way to force them to do that. Most of the things I’m doing these days are completely new to me, and Marc is my main mentor. He’ll actually go with me to SLAC and guide me in how to collect my data.”

    In its first six months, MSKC has already helped scientists with two dozen research projects, and Deller is eager to round up more. “From my experience of doing this for 20 years,” he says, “making the protein is definitely a bottleneck.”

    See the full article here .

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    Leland and Jane Stanford founded the University to “promote the public welfare by exercising an influence on behalf of humanity and civilization.” Stanford opened its doors in 1891, and more than a century later, it remains dedicated to finding solutions to the great challenges of the day and to preparing our students for leadership in today’s complex world. Stanford, is an American private research university located in Stanford, California on an 8,180-acre (3,310 ha) campus near Palo Alto. Since 1952, more than 54 Stanford faculty, staff, and alumni have won the Nobel Prize, including 19 current faculty members

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  • richardmitnick 3:18 pm on December 9, 2016 Permalink | Reply
    Tags: , Biofilms, , , Chemistry,   

    From Caltech: “Protein Disrupts Infectious Biofilms” 

    Caltech Logo

    Caltech

    12/08/2016

    Lori Dajose
    (626) 395-1217
    ldajose@caltech.edu

    Many infectious pathogens are difficult to treat because they develop into biofilms, layers of metabolically active but slowly growing bacteria embedded in a protective layer of slime, which are inherently more resistant to antibiotics. Now, a group of researchers at Caltech and the University of Oxford have made progress in the fight against biofilms. Led by Dianne Newman, the Gordon M. Binder/Amgen Professor of Biology and Geobiology, the group identified a protein that degrades and inhibits biofilms of Pseudomonas aeruginosa, the primary pathogen in cystic fibrosis (CF) infections.

    The work is described in a paper in the journal Science that will appear online December 8.

    1
    Crystal structure of the PodA protein complex with three molecules of 1-hydroxyphenazine, the reaction product, bound in the active sites.
    Credit: Kyle Costa/Caltech

    “Pseudomonas aeruginosa causes chronic infections that are difficult to treat, such as those that inhabit burn wounds, diabetic ulcers, and the lungs of individuals living with cystic fibrosis,” Newman says. “In part, the reason these infections are hard to treat is because P. aeruginosa enters a biofilm mode of growth in these contexts; biofilms tolerate conventional antibiotics much better than other modes of bacterial growth. Our research suggests a new approach to inhibiting P. aeruginosa biofilms.”

    The group targeted pyocyanin, a small molecule produced by P. aeruginosa that produces a blue pigment. Pyocyanin has been used in the clinical identification of this strain for over a century, but several years ago the Newman group demonstrated that the molecule also supports biofilm growth, raising the possibility that its degradation might offer a new route to inhibit biofilm development.

    To identify a factor that would selectively degrade pyocyanin, Kyle Costa, a postdoctoral scholar in biology and biological engineering, turned to a milligram of soil collected in the courtyard of the Beckman Institute on the Caltech campus. From the soil, he isolated another bacterium, Mycobacterium fortuitum, that produces a previously uncharacterized small protein called pyocyanin demethylase (PodA).

    Adding PodA to growing cultures of P. aeruginosa, the team discovered, inhibits biofilm development.

    “While there is precedent for the use of enzymes to treat bacterial infections, the novelty of this study lies in our observation that selectively degrading a small pigment that supports the biofilm lifestyle can inhibit biofilm expansion,” says Costa, the first author on the study. The work, Costa says, is relevant to anyone interested in manipulating microbial biofilms, which are common in natural, clinical, and industrial settings. “There are many more pigment-producing bacteria out there in a wide variety of contexts, and our results pave the way for future studies to explore whether the targeted manipulation of analogous molecules made by different bacteria will have similar effects on other microbial populations.”

    While it will take several years of experimentation to determine whether the laboratory findings can be translated to a clinical context, the work has promise for the utilization of proteins like PodA to treat antibiotic-resistant biofilm infections, the researchers say.

    “What is interesting about this result from an ecological perspective is that a potential new therapeutic approach comes from leveraging reactions catalyzed by soil bacteria,” says Newman. “These organisms likely co-evolved with the pathogen, and we may simply be harnessing strategies other microbes use to keep it in check in nature. The chemical dynamics between microorganisms are fascinating, and we have so much more to learn before we can best exploit them.”

    The paper is titled Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms. In addition to Costa and Newman, other co-authors include Caltech graduate student Nathaniel Glasser and Professor Stuart Conway of the University of Oxford. The work was funded by the National Institutes of Health’s National Institute of Allergy and Infectious Diseases, the National Science Foundation, the Howard Hughes Medical Institute, the Molecular Observatory at the Beckman Institute at Caltech, the Gordon and Betty Moore Foundation, and the Sanofi-Aventis Bioengineering Research Program at Caltech.

    See the full article here .

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    The California Institute of Technology (commonly referred to as Caltech) is a private research university located in Pasadena, California, United States. Caltech has six academic divisions with strong emphases on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. “The mission of the California Institute of Technology is to expand human knowledge and benefit society through research integrated with education. We investigate the most challenging, fundamental problems in science and technology in a singularly collegial, interdisciplinary atmosphere, while educating outstanding students to become creative members of society.”
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  • richardmitnick 1:31 pm on December 6, 2016 Permalink | Reply
    Tags: American Association for the Advancement of Science, , , Chemistry, FSU, , Yan-Yan Hu   

    From FSU: Women in STEM – “FSU chemistry professor wins prestigious women in science award” 

    FSU bloc

    Florida State University

    December 5, 2016
    Kathleen Haughney

    1
    Assistant Professor of Chemistry Yan-Yan Hu. No image credit

    A Florida State University chemistry professor has won a prestigious award from the American Association for the Advancement of Science that recognizes promising female scientists in the early stages of their career.

    Assistant Professor of Chemistry Yan-Yan Hu will receive the 2017 Marion Milligan Mason Award along with $50,000 to help fund her research endeavors. The other four awardees are from Duke University, University of Texas at Austin, Johns Hopkins University and Stanford University.

    “It was such a surprise and honor,” Hu said. “And I think it’s a tribute to all my colleagues at Florida State University and the National High Magnetic Field Laboratory who have welcomed, guided and supported my research group and me. I’m at the best place with the best resources and best people for what we do.”

    Hu was hired by Florida State University in 2014 as part of a cluster of faculty dedicated to studying energy and materials. She focuses on fundamental chemistry that is critical to energy conversion and storage technologies.

    She plans to use the award to help fund some of her graduate students as they pursue research on interface chemistry of organic-inorganic composite materials for energy and health.

    In addition to outlining the research proposal, Hu received nomination letters from FSU Associate Vice President of Research Ross Ellington, Department of Chemistry Chair Tim Logan, Professor of Chemistry Alan Marshall and University of Cambridge Professor Clare Grey.

    In his nomination letter, Ellington wrote Hu’s work ethic was “beyond reproach” and said she was the “poster child” for the university’s energy and materials initiative due to her close collaboration with other experts in the Department of Chemistry and at the MagLab.

    Logan added that Hu was an “outstanding young scientist.”

    “She is an exemplary role model for women in science and actively mentors female undergraduate and graduate students through FSU’s Women in Math, Science and Engineering program,” Logan said. “We are extremely pleased to have someone of her caliber on our faculty.”

    Hu will accept her award at a ceremony in Washington, D.C., in December.

    See the full article here .

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    One of the nation’s elite research universities, Florida State University preserves, expands, and disseminates knowledge in the sciences, technology, arts, humanities, and professions, while embracing a philosophy of learning strongly rooted in the traditions of the liberal arts.

    FSU’s welcoming campus is located on the oldest continuous site of higher education in Florida, in a community that fosters free inquiry and embraces diversity, along with championship athletics, and a prime location in the heart of the state capital.
    FAST FACTS

    Founded in 1851; oldest continuous site of higher education in Florida

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  • richardmitnick 5:45 pm on December 5, 2016 Permalink | Reply
    Tags: , Chemistry, , Designer Crystals for Drug Advancements, Metallic Organic Frameworks (MOFs)   

    From CSIRO: “Designer Crystals for Drug Advancements “ 

    CSIRO bloc

    Commonwealth Scientific and Industrial Research Organisation

    6 December 2016
    Mr Chris Still
    Chris.Still@csiro.au
    +61 3 9545 2267

    1
    A chaotic MOF. No image credit

    A breakthrough in chemistry led by Australian scientists could revolutionise healthcare by fast-tracking the development of vaccines and tiny devices that give real-time information about a patient’s condition.

    Collaborating with teams in Japan, Austria, Monash University and The University of Adelaide, CSIRO scientists led by Dr Paolo Falcaro have found a way to harness the potential of designer crystals known as Metallic Organic Frameworks (MOFs) – the most porous materials on the planet.

    MOFs have so many holes inside that a single teaspoon of the powdery material has the same surface area as a football field.

    Since their discovery in 1999, they have been used in an array of fields including pharmaceutics, electronics and horticulture.

    Although the novel materials exert a powerful appeal for scientists, one of the roadblocks to realising the full potential of MOFs is their erratic structure, which makes it difficult to integrate them into functional devices.

    “We’ve found a way to control the structure of MOFs and align them in one direction, creating a MOF film,” CSIRO scientist Dr Aaron Thornton, co-author of the paper published today in Nature Materials said.

    “Having the MOFs in alignment means they conduct a current far better, opening up more electrical uses such as implantable medical devices that give real-time information about someone’s health.

    “It also gives researchers more control in the development of vaccines, which will fast-track the process.

    “MOFs could also be structured in such a way that they’d only react with certain compounds or elements – for example, miners could wear clothes impregnated with a layer of MOFs that tell them when dangerous gases are building up.

    “The possibilities are endless.”

    Once the hard work was complete the scientists had to prove that the MOFs were in alignment.

    This was achieved by placing a polarisable fluorescent molecule in aligned MOFs.

    If the MOFs were all in perfect alignment then they would only be able to make them light up along the one axis, in line with the MOFs so you could turn the light on or off by rotating the film.

    CSIRO has already used MOFs to develop a molecular shell to protect and deliver drugs and vaccines, a ‘solar sponge’ that can capture and release carbon dioxide emissions and plastic material that gets better with age.

    Find out how we’ve been applying these clever MOF crystals to other industries, including potential opportunities for your business – MOFs – next generation smart materials.

    See the full article here .

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    CSIRO campus

    CSIRO, the Commonwealth Scientific and Industrial Research Organisation, is Australia’s national science agency and one of the largest and most diverse research agencies in the world.

     
  • richardmitnick 8:25 am on October 30, 2016 Permalink | Reply
    Tags: , Chemistry, , Scientists just accidentally discovered a process that turns CO2 directly into ethanol   

    From Science Alert: “Scientists just accidentally discovered a process that turns CO2 directly into ethanol” 

    ScienceAlert

    Science Alert

    1
    Billy Wilson/Flickr

    Converting pollution into fuel.

    If scientists can figure out how to convert atmospheric carbon dioxide into fuel – and do it at an industrial scale – it would, quite literally, change the world. Last month, we hit the highest levels of atmospheric CO2 in 4 million years, and it’s now permanent, meaning we’ll never be able to drop to ‘safe’ levels again.

    But if we can turn CO2 into a fuel source, we can at least slow things down a bit, and now researchers have developed a process that can achieve this with a single catalyst.

    “We discovered somewhat by accident that this material worked,” said one of the team, Adam Rondinone, from the US Department of Energy’s Oak Ridge National Laboratory.

    “We were trying to study the first step of a proposed reaction when we realised that the catalyst was doing the entire reaction on its own.”

    Rondinone and his colleagues had put together a catalyst using carbon, copper, and nitrogen, by embedding copper nanoparticles into nitrogen-laced carbon spikes measuring just 50-80 nanometres tall. (1 nanometre = one-millionth of a millimetre.)

    When they applied an electric current of just 1.2 volts, the catalyst converted a solution of CO2 dissolved in water into ethanol, with a yield of 63 percent.

    This result was surprising for a couple of reasons: firstly, because it’s effectively reversing the combustion process using a very modest amount of electricity, and secondly, it was able to do this while achieving a relatively high yield of ethanol – they were expecting to end up with the significantly less desirable chemical, methanol.

    As Colin Jeffrey explains for New Atlas, this type of electrochemical reaction usually results in a mix of several different products in small amounts, such as methane, ethylene, and carbon monoxide – none of which are in particularly high demand.

    Instead, the team got usable amounts of ethanol, which the US needs billions of gallons of each year to add to gasoline.

    “We’re taking carbon dioxide, a waste product of combustion, and we’re pushing that combustion reaction backwards with very high selectivity to a useful fuel,” Rondinone said in a press statement.

    “Ethanol was a surprise – it’s extremely difficult to go straight from carbon dioxide to ethanol with a single catalyst.”

    This certainly isn’t the first attempt to convert CO2 pollution into something we can actually use – researchers around the world have been figuring out ways to turn it into things like methanol, formate, and hydrocarbon fuel.

    This one team working in Iceland wants to turn it all into solid rock so we can just bury it and forget about it.

    But all of these methods, while promising, are dishing up an end product that the world doesn’t really need right now. Sure, we could adjust our cars and energy plants to run on hydrocarbon fuel if it was cheap and efficient enough to produce from CO2, but we’re certainly not there yet.

    Ethanol, on the other hand – well, the US is already blending most of its gasoline with 10 to 15 percent ethanol content.

    The researchers explain that they were able to achieve such high yields because the nanostructure of the catalyst was easy to manipulate and adjust to get the desired results.

    “By using common materials, but arranging them with nanotechnology, we figured out how to limit the side reactions and end up with the one thing that we want,” said Rondinone. “They are like 50-nanometre lightning rods that concentrate electrochemical reactivity at the tip of the spike.”

    The team says that since the catalyst is made from inexpensive materials, and can operate at room temperature with modest electrical requirements, it could be scaled up for industrial level use.

    But with so many CO2 conversion projects in the works right now that are aiming to do the same thing, we’ll have to remain cautiously optimistic until they can show real results in the field.

    Let’s hope someone ultimately figures it out, because with a drastically expanding population, we’re only going to be needing more energy, and we’re only going to be pumping more pollution into the atmosphere. A ‘two birds with one stone’ solution would change everything – particularly if we can integrate it with solar and wind farms.

    “A process like this would allow you to consume extra electricity when it’s available to make and store as ethanol,” Rondinone said. “This could help to balance a grid supplied by intermittent renewable sources.”

    The results have been published in ChemistrySelect.


    Access mp4 video here.

    See the full article here .

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  • richardmitnick 10:20 am on October 22, 2016 Permalink | Reply
    Tags: , Chemistry, , From greenhouse gas to usable ethanol, ,   

    From Science Node: “From greenhouse gas to usable ethanol” 

    Science Node bloc
    Science Node

    19 Oct, 2016
    Morgan McCorkle

    ORNL scientists find a way to use nano-spike catalysts to convert carbon dioxide directly into ethanol.

    In a new twist to waste-to-fuel technology, scientists at the Department of Energy’s Oak Ridge National Laboratory (ORNL) have developed an electrochemical process that uses tiny spikes of carbon and copper to turn carbon dioxide, a greenhouse gas, into ethanol. Their finding, which involves nanofabrication and catalysis science, was serendipitous.


    Access mp4 video here .
    Serendipitous science. Looking to understand a chemical reaction, scientists accidentally discovered a method for converting combustion waste products into ethanol. The chance discovery may revolutionize the ability to use variable energy sources. Courtesy ORNL.

    “We discovered somewhat by accident that this material worked,” said ORNL’s Adam Rondinone, lead author of the team’s study published in ChemistrySelect. “We were trying to study the first step of a proposed reaction when we realized that the catalyst was doing the entire reaction on its own.”

    The team used a catalyst made of carbon, copper and nitrogen and applied voltage to trigger a complicated chemical reaction that essentially reverses the combustion process. With the help of the nanotechnology-based catalyst which contains multiple reaction sites, the solution of carbon dioxide dissolved in water turned into ethanol with a yield of 63 percent. Typically, this type of electrochemical reaction results in a mix of several different products in small amounts.

    “We’re taking carbon dioxide, a waste product of combustion, and we’re pushing that combustion reaction backwards with very high selectivity to a useful fuel,” Rondinone said. “Ethanol was a surprise — it’s extremely difficult to go straight from carbon dioxide to ethanol with a single catalyst.”

    The catalyst’s novelty lies in its nanoscale structure, consisting of copper nanoparticles embedded in carbon spikes. This nano-texturing approach avoids the use of expensive or rare metals such as platinum that limit the economic viability of many catalysts.

    “By using common materials, but arranging them with nanotechnology, we figured out how to limit the side reactions and end up with the one thing that we want,” Rondinone said.

    The researchers’ initial analysis suggests that the spiky textured surface of the catalysts provides ample reactive sites to facilitate the carbon dioxide-to-ethanol conversion.

    “They are like 50-nanometer lightning rods that concentrate electrochemical reactivity at the tip of the spike,” Rondinone said.

    Given the technique’s reliance on low-cost materials and an ability to operate at room temperature in water, the researchers believe the approach could be scaled up for industrially relevant applications. For instance, the process could be used to store excess electricity generated from variable power sources such as wind and solar.

    “A process like this would allow you to consume extra electricity when it’s available to make and store as ethanol,” Rondinone said. “This could help to balance a grid supplied by intermittent renewable sources.”

    The researchers plan to refine their approach to improve the overall production rate and further study the catalyst’s properties and behavior.

    ORNL’s Yang Song, Rui Peng, Dale Hensley, Peter Bonnesen, Liangbo Liang, Zili Wu, Harry Meyer III, Miaofang Chi, Cheng Ma, Bobby Sumpter and Adam Rondinone are coauthors on the study.

    The work was supported by DOE’s Office of Science and used resources at the ORNL’s Center for Nanophase Materials Sciences, which is a DOE Office of Science User Facility.

    See the full article here .

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    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

     
  • richardmitnick 3:49 pm on September 26, 2016 Permalink | Reply
    Tags: , Chemistry, , Researchers unlock coveted bond connection   

    From Princeton: “Researchers unlock coveted bond connection” 

    Princeton University
    Princeton University

    September 23 2016
    Tien Nguyen

    Researchers at Princeton University have introduced a long-awaited reaction capable of forming sp3-sp3 bonds whose presence increases a molecule’s complexity and its chances for clinical success as a drug candidate.

    Published in Nature, the study detailed a mild and general method to couple sp3 carbon atoms – carbon centers defined by that fact that only single bonds connect them to their neighbors. Until now, this coveted reaction had resisted chemists’ efforts, even eluding transition metal catalysis, a powerful field that has enabled a staggering range of coupling reactions over the past 50 years.

    1
    General schematic of metallophotoredox catalyzed sp3-sp3 couplings

    “The reaction is a very unique way of approaching how you would join molecules together, and broadly expands the types of carbons you can connect,” said David MacMillan, the James S. McDonnell Distinguished University, Professor of Chemistry and corresponding author on the work.

    Their method revolves around the cooperation of two catalysts, a light-activated iridium catalyst and a nickel-based catalyst. Coined metallaphotoredox catalysis, this process circumvents roadblocks, such as undesired side reactions and an inability to form key intermediates, which had plagued other transition metal mediated attempts. Also, in contrast to previous, specialized versions of the reaction, the researchers’ strategy doesn’t require high temperatures, harsh basic compounds or additional zinc-based molecules.

    The reaction succeeds by enlisting the two catalysts to bring together the molecules forming either side of the final sp3-sp3 bond. The light-activated iridium catalyst converts the commercially available starting compound known as a carboxylic acid into a ready partner. This intermediate is intercepted by the nickel catalyst, which can then incorporate the other chemical partner, called an alkyl halide. Finally, the nickel catalyst excises itself from the compound, releasing the desired product and resetting the cycle.

    The team demonstrated the reaction’s generality as it proceeded smoothly with array of structurally diverse partners. Using this method, they also constructed the antiplatelet drug tirofiban in two steps from simple starting materials using their sp3-sp3 coupling reaction and another metallaphotoredox method recently developed in their lab. This example showcased the utility of their program for drug discovery though it holds potential for other industries as well.

    “That’s what we really care about – inventing reactions that people will use,” MacMillan said. “We really want to do things that are enabling to people all around the world who care about making molecules.”

    See the full article here .

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    Princeton University Campus

    About Princeton: Overview

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

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

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

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

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

    Yale University bloc

    Yale University

    August 31, 2016

    Jim Shelton
    james.shelton@yale.edu
    203-361-8332

    1
    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.

    3
    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 .

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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.

     
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