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  • richardmitnick 10:54 am on November 15, 2018 Permalink | Reply
    Tags: "Searching for ocean microbes", , Bermuda Atlantic Time Series, , Cyverse, DNA Databank of Japan, European Bioinformatics Institute, Hawaiian Ocean Time Series, Hurwitz Lab-University of Arizona, iMicrobe platform, National Center for Biotechnology Information, National Microbiome Collaborative, , Planet Microbe, , The Hurwitz Lab corrals big data sets into a more searchable form to help scientists study microorganisms, Woods Hole Oceanographic Institution   

    From Science Node: “Searching for ocean microbes” 

    Science Node bloc
    From Science Node

    07 Nov, 2018
    Susan McGinley

    How one lab is consolidating ocean data to track climate change.

    Courtesy David Clode/Unsplash.

    Scientists have been making monthly observations of the physical, biological, and chemical properties of the ocean since 1988. Now, thanks to the Hurwitz Lab at the University of Arizona (UA), researchers around the world have greater access than ever before to the information collected at these remote ocean sites.

    U Arizona bloc

    Led by Bonnie Hurwitz, assistant professor of biosystems engineering at UA, the Hurwitz Lab corrals big data sets into a more searchable form to help scientists study microorganisms – bacteria, fungi, algae, viruses, protozoa – and how they relate to each other, their hosts and the environment.

    Sample collection. Bonnie Hurwitz next to the metal pod that serves as the main chamber for the Alvin submersible that scientists operate to collect samples from the deepest parts of the ocean not accessible to people. Courtesy Stefan Sievert, Woods Hole Oceanographic Institution.

    The lab is building a data infrastructure on top of Cyverse to integrate and build information from diverse data stores in collaboration with the broader cyber community. The goal is to give people the ability to use data sets that span a range of storage servers, all in one place.

    “One of the exciting things my lab is funded for is Planet Microbe, a three-year project through the National Science Foundation (NSF), to bring together genomic and environmental data sets coming from ocean research cruises,” Hurwitz said.

    “Samples of water are taken using an instrument called a CTD that measures salinity, temperature, depth, and other features to create a scan of ocean conditions across the water column.”

    As the CTD descends into the ocean, bottles are triggered at different depths to collect water samples for a variety of experiments including sequencing the DNA/RNA of microbes. The moment each sample leaves the ship is often the last time these valuable and varied data appear together.

    The first phase of the project focuses on the Hawaiian Ocean Time Series and the Bermuda Atlantic Time Series. At both locations, samples are collected across an ocean transect at a variety of depths across the water column, from surface to deep ocean.

    A CTD device that measures water conductivity (salinity), temperature and depth is mounted underneath a set of water bottles used for collecting samples at varying depths in a column of water. Courtesy Tara Clemente, University of Hawaii.

    The readings taken at each level stream out to data banks around the world. Different labs conduct the analyses, but the Hurwitz lab reunites all of the data sets, including data from these long-term ecological sites used for monitoring climate and changes in the oceans.

    “Oceanographers have different tool kits. They are collecting data on ship to observe both the ocean environment and the genetics of microbes to understand the role they play in the ocean,” Hurwitz said. “We are including these data in a very simple web-based platform where users can run their own analyses and data pipelines to use the data in new ways.”

    While still in year one of the project, the first data have just been released under the iMicrobe platform, which connects users with computational resources for analyzing and visualizing the data.

    The platform’s bioinformatics tools let researchers analyze the data in new ways that may not have originally been possible when the data were collected, or to compare these global ocean data sets with new data as it becomes available.

    “We’re plumbers, actually, creating the pipelines between the world’s oceanographic data sets. We’re trying to enable scientists to access data from the world’s oceans,” Hurwitz said.

    A larger mission

    In addition to their Planet Microbe work, Hurwitz and her team work with the three entities that store and sync all of the world’s “omics” (genomics, proteomics) data – the European Bioinformatics Institute, the National Center for Biotechnology Information and the DNA Databank of Japan, and others.

    “We are working with the National Microbiome Collaborative, a national effort to bring together the world’s data in the microbiome sciences, from human to ocean and everything in between,” Hurwitz said.

    “Having those data sets captured and searchable is great,” said Hurwitz. “They are so big they can’t be housed in any one place. The infrastructure allows you to search across these areas.”

    Going deep. Hurwitz and Amy Apprill, associate scientist at Woods Hole Oceanographic Institution, in front of the human-piloted Alvin submersible. Deep-water samples are collected using the pod’s robotic arm because the pressure of the water is too intense for divers. Courtesy Stefan Sievert, Woods Hole Oceanographic Institution.

    “If we want to start looking at things together in a holistic manner, we need to be able to remotely access data that are not on our servers. We are essentially indexing the world’s data and becoming a search engine for microbiome sciences.”

    By reconnecting ‘omics data with environmental data from oceanographic cruises, Hurwitz and her team are speeding up discoveries into environmental changes affecting the marine microbes that are responsible for producing half the air that we breathe.

    These data can be used in the future to predict how our oceans respond to change and to specific environmental conditions.

    “Our researchers can not only use a $30 million supercomputer at XSEDE (Extreme Science and Engineering Discovery Environment) supported by the NSF for running analyses, they also have access to modern big data architectures through a simple computer interface.”

    “We’re trying to understand where all the data are and how we can sync them,” Hurwitz said. “How data are structured and assembled together has been like the Wild West. We’re figuring it out.”

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    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 1:30 pm on September 24, 2018 Permalink | Reply
    Tags: , , OOI-Ocean Observatories Initiative, , Regional Cabled Array, , , Woods Hole Oceanographic Institution   

    From University of Washington: “NSF awards contract to carry OOI into the next decade and beyond” 

    U Washington

    From University of Washington

    September 19, 2018
    Hannah Hickey

    The seafloor cable extends off the coast of Oregon and allows real-time communication with the deep sea. University of Washington

    The National Science Foundation announced that it has awarded a coalition of academic and oceanographic research organizations a five-year, $220 million contract to operate and maintain the Ocean Observatories Initiative.

    The coalition, led by the Woods Hole Oceanographic Institution, with direction from the NSF and guidance from the OOI Facilities Board, will include the University of Washington, Oregon State University and Rutgers, The State University of New Jersey.


    The OOI is an advanced system of integrated, scientific platforms and sensors that measure physical, chemical, geological and biological properties and processes from the seafloor to the sea surface in key coastal and open-ocean sites of the Atlantic and Pacific. as designed to address critical questions about the Earth–ocean system, including climate change, ecosystem variability, ocean acidification, plate-scale seismicity, submarine volcanoes and carbon cycling with the goal of better understanding the ocean and our planet. All OOI data are freely available online.

    Each institution will continue to operate and maintain the portion of OOI assets for which it is currently responsible: the UW will operate the Regional Cabled Array that extends across the Juan de Fuca tectonic plate and overlying ocean; OSU will operate the Endurance Array off the coast of Washington and Oregon; WHOI will operate the Pioneer Array off the Northeast U.S. coast and the Global Arrays in the Irminger Sea off the southern tip of Greenland and at Station Papa in the Gulf of Alaska; and Rutgers will operate the cyberinfrastructure system that ingests and delivers data for the initiative. In addition, WHOI will serve as the home of a new OOI Project Management Office.

    “We at NSF are proud of our continuing investment in 24/7 streaming data from the ocean and coupled Earth systems,” said William Easterling, NSF assistant director for geosciences. “From underwater volcanoes to ocean currents, OOI enables cutting-edge scientific discoveries and makes big data accessible to classrooms at all levels. These data are key to addressing everyday challenges, such as better storm predictions and management of our coastal resources.”

    The OOI officially launched in 2009, when the NSF and the Consortium for Ocean Leadership signed a cooperative agreement to support the construction and initial operation of OOI’s cabled, coastal and global arrays. The launch represented the culmination of work begun decades earlier, when ocean scientists in the 1980s envisioned a collection of outposts in the ocean that would gather data around the clock, in real- and near-real time for years on end, and enhance the scientific community’s ability to observe complex oceanographic processes that occur and evolve over time scales ranging from seconds to decades, and spatial scales ranging from inches to miles.

    An arm of the ocean robot ROB Jason installs a seafloor fluid sampler on the Pacific Northwest’s Regional Cabled Array in summer 2017.UW/OOI-NSF/WHOI, V17

    The OOI currently supports more than 500 autonomous instruments on the seafloor and on moored and free-swimming platforms that are serviced during regular, ship-based expeditions to the array sites. Data from each instrument is transmitted to shore, where it is freely available to users worldwide, including members of the scientific community, policy experts, decision-makers, educators and the general public.

    The UW operates the largest single piece of the OOI, the Regional Cabled Array: cables from Newport, Oregon, that bring high power and high-bandwidth internet to an observatory that spans the seafloor and water above. The equipment was built and installed by the UW starting in 2011 and became fully operational in 2016. It includes more than 140 instruments and six tethered robots laden with instruments that collect data from about 9,500 feet beneath the ocean’s surface to the near-surface environments.

    Two UW undergraduates help graduate student Theresa Whorley (left) work on instruments retrieved from the seafloor during a summer 2017 maintenance cruise.Mitch Elend/University of Washington/V17

    The new grant will fund refresh and maintenance of the Regional Cabled Array infrastructure, data evaluation, and five annual cruises. The main hardware will continue to be maintained and upgraded by the UW’s Applied Physics Laboratory, and will continue to incorporate sensors from local companies Sea-Bird Scientific of Bellevue and Paroscientific of Redmond.

    Just before its official commissioning, the Regional Cabled Array in April 2015 captured first-of-its-kind data of an underwater volcanic eruption that included more than 8,000 earthquakes over a 24-hour period, a roughly 7-foot collapse of the seafloor and more than 30,000 explosive events. The data evolution of the eruption was the focus of several papers [Science]. One of those authors is now using real-time observations to predict that the underwater volcano’s next eruption, which also will be monitored, will occur in early 2022.

    “At one of the meetings, an NSF officer said: ‘If you build it, they will come.’ That’s what we’re seeing,” said UW principal investigator and oceanography professor Deborah Kelley. “The real-time capability and power supply are key because they let us have a permanent, 24/7 presence on the seafloor and throughout the water column and we are now able to respond to events in near-real time. We have significant expansion capabilities and are excited to continue gathering fundamental measurements in the ocean.”

    The number of instruments attached to the observatory is growing. William Wilcock, a UW professor of oceanography, has received two NSF grants that include funding for a new instrument now monitoring seismic activity and deformation of the seafloor, and another geophysical instrument to be installed next year on the underwater volcano, Axial Seamount. An award from Germany’s national research agency resulted in the installation this past summer of two high-resolution sonars to image methane gas plumes that are bubbling up from the seafloor at a highly active area called Southern Hydrate Ridge.

    “We are looking at some of the most biologically productive and geologically active regions in the world, and we’ve never had so many co-registered sensors in these dynamic environments. With these data, collected on time scales from seconds to years, we hope to discover important links about how the ocean works and evolves,” Kelley said.

    “We now have the capability to examine in real time the impacts of large storms and low-oxygen events on ocean biology and chemistry, offshore earthquakes and underwater eruptions, and to share these data and discoveries with a global community of users.”

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.
    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

  • richardmitnick 7:25 am on November 14, 2017 Permalink | Reply
    Tags: ABISS project - deep-sea technologies that could be a model for exploring oceans on the moons of Jupiter and Saturn, , Peter Girguis professor of organismic and evolutionary biology, Woods Hole Oceanographic Institution   

    From Harvard Gazette: “Launching a space mission from the deepest ocean” 

    Harvard University
    Harvard Gazette

    November 9, 2017
    Alvin Powell

    Peter Girguis, professor of organismic and evolutionary biology, is collaborating with NASA to develop deep-sea technology to search for life on the solar systems’ ocean moons. Kris Snibbe/Harvard Staff Photographer

    NASA-backed scientists hope project advances plans to search moons for extraterrestrial life.

    Scientists from Harvard and the Woods Hole Oceanographic Institution are collaborating on deep-sea technologies that could be a model for exploring oceans on the moons of Jupiter and Saturn.

    The ABISS project aims to create an autonomous ocean-floor observatory equipped to kick into high gear when something interesting happens, switching on cameras and sophisticated sensors and wirelessly alerting researchers hundreds of miles away.

    All that sounds good to NASA. The agency is funding the project as it grapples with the likelihood that the search for extraterrestrial life will lead underwater, from the dry terrain of Mars to ice-encrusted oceans on Jupiter’s Europa, Saturn’s Enceladus, and other moons.

    “One of the things we learn [with] ABISS is how exploration like this can be done remotely,” said Mary Voytek, NASA’s senior scientist for astrobiology. “We’re not going to be sending ships out there. We’re going to be sending something that will be able to penetrate the ice and then, once below the surface of the ice, will be into the ocean and … will have to operate remotely and autonomously.”

    ABISS, which stands for autonomous biogeochemical instrument for in situ studies, is led by Harvard biologist Peter Girguis with Woods Hole colleagues Norman Farr and Clifford Pontbriand. Girguis said the project seeks to harness advances in robotics, big data, and telecommunications to advance ocean exploration, here and out there.

    Earth’s oceans are mysterious, hard to get to, and hostile to sustained exploration. The sea floor is miles below the surface, with temperatures just above freezing, crushing pressure, and total darkness. Communication is difficult because water blocks the radio waves that make surface communications comparatively effortless.

    Girguis and his Woods Hole colleagues are developing a new method to transmit information through ocean waters using light. Kris Snibbe/Harvard Staff Photographer

    Just as in space exploration, Girguis noted, terrestrial oceanographers are looking for life. Though some 2 million species of marine animals have been identified, there are an estimated 18 million still to be found, he said. They live in the deep ocean, starting a half-mile below the illuminated surface.

    “We really know so little about our oceans,” Girguis said. “Eighty percent of our planet’s living space is in the deep sea, by volume.”

    Interest in extraterrestrial oceans was piqued by the Cassini spacecraft’s 13-year tour of Saturn’s moons, during which it observed plumes of water vapor shooting from the icy surface of Enceladus. Europa, thought to have an ice-covered ocean, is the focus of the planned Europa Clipper, which would focus instruments on the moon’s surface during dozens of fly-bys sometime after 2020.

    Plenty of work remains for the three-year ABISS project. This past summer, Girguis and Pontbriand spent a week off the California coast aboard the E.V. Nautilus, a research ship run by explorer Robert Ballard’s Ocean Exploration Trust, tackling challenges in communications. Scientists working underwater usually communicate via cumbersome cables to the mother ship or wireless acoustic technology akin to sonar. The acoustic signals can transmit over long distances, but with very limited bandwidth, similar to that offered by dial-up computer modems. (“You can forget pictures,” Girguis said.)

    Girguis and Pontbriand tested an alternative, developed in 2005 at Woods Hole, that uses light to transmit information at broadband speeds. The optical modem’s range is limited by water’s ability to absorb light, but in the clear water of the ocean floor, it can transmit images and video 100 meters. The test sought to integrate the optical modem with cameras and other gear on the ABISS observatory.

    “We’re really excited to have the opportunity to use our technology to get the experiment going,” Pontbriand said.

    Other goals of the project, Girguis said, include improving battery life in hopes of an observatory that can operate a year or more without needing service. Another major objective is to make sensors as energy-efficient as possible and get them to communicate with each other. Ultimately, Girguis said, he’d like the ABISS chemical sensor to run all the time, waking the microbial sensor to gather additional data when methane or other life molecules are detected.

    Girguis isn’t certain that life will be found elsewhere in the solar system, but has no trouble imagining plausible scenarios. Some microbes can survive a journey through space’s vacuum, he noted, and Earth’s bombardment by meteors and comets provides a mechanism for rocks carrying them to be blasted into space. Pontbriand, meanwhile, isn’t sold that the devices he’s had a hand in building one day might be deployed in a search for extraterrestrial life.

    “It does seem farfetched, even to me,” Pontbriand said. “But it would be great to see it happen.”

    The ideal ABISS observatory would be able to provide long-term data gathering anywhere, Girguis and Pontbriand said. Information — including bandwidth-gobbling images and video – would be transferred to an untethered robotic sub. The sub would rise to the surface and transmit to a nearby boat, satellite, or spacecraft, which would then convey the data to labs.

    “In order to do exploration of this kind, we need to understand the strategy for exploration or science operations,” said NASA’s Voytek. “Projects like ABISS start teaching us what that’s like: What are the limitations? What are the things we need to further develop?”

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Harvard University campus
    Harvard is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best known landmark.

    Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

    • stewarthoughblog 11:05 pm on November 14, 2017 Permalink | Reply

      While STEM is being promoted at Harvard with a high priority and funding, don’t forget the original motto of the university, “Christo et Ecclesiae,” which the present motto “Veritas” complements.

      The possible exploration of remote moons may reveal some interesting science. Any prospect of fossil or living organisms is only satisfied by Earth based organisms. No non-Earth-based life will be found. Developing better battery and transmitters could be of significant value in many areas and worth the funding.


  • richardmitnick 9:51 pm on March 2, 2017 Permalink | Reply
    Tags: , , , Woods Hole Oceanographic Institution   

    From Carnegie: “Melting temperature of Earth’s mantle depends on water” 

    Carnegie Institution for Science
    Carnegie Institution for Science

    A joint study between Carnegie and the Woods Hole Oceanographic Institution has determined that the average temperature of Earth’s mantle beneath ocean basins is about 110 degrees Fahrenheit (60 Celsius) higher than previously thought, due to water present in deep minerals. The results are published in Science.

    Earth’s mantle, the layer just beneath the crust, is the source of most of the magma that erupts at volcanoes. Minerals that make up the mantle contain small amounts of water, not as a liquid, but as individual molecules in the mineral’s atomic structure. Mid-ocean ridges, volcanic undersea mountain ranges, are formed when these mantle minerals exceed their melting point, become partially molten, and produce magma that ascends to the surface. As the magmas cool, they form basalt, the most-common rock on Earth and the basis of oceanic crust. In these oceanic ridges, basalt can be three to four miles thick.

    An image of one of the team’s lab mimicry experiments, which was conducted in a capsule made of gold-palladium alloy. The black boxes highlight the locations of olivine grains, and the dark pits in the olivines are actual measurements for the water content of the olivine. The peridotite is the super fine-grained matrix. Image is courtesy of Emily Sarafian.

    Studying these undersea ranges can teach scientists about what is happening in the mantle, and about the Earth’s subsurface geochemistry.

    One longstanding question has been a measurement of what’s called the mantle’s potential temperature. Potential temperature is a quantification of the average temperature of a dynamic system if every part of it were theoretically brought to the same pressure. Determining the potential temperature of a mantle system allows scientists better to understand flow pathways and conductivity beneath the Earth’s crust. The potential temperature of an area of the mantle can be more closely estimated by knowing the melting point of the mantle rocks that eventually erupt as magma and then cool to form the oceanic crust.

    In damp conditions, the melting point of peridotite, which melts to form the bulk of mid-ocean ridge basalts, is dramatically lower than in dry conditions, regardless of pressure. This means that the depth at which the mantle rocks start to melt and well up to the surface will be different if the peridotite contains water, and beneath the oceanic crust, the upper mantle is thought to contain small amounts of water—between 50 and 200 parts per million in the minerals of mantle rock.

    So lead author Emily Sarafian of Woods Hole, Carnegie’s Erik Hauri, and their team set out to use lab experiments in order to determine the melting point of peridotite under mantle-like pressures in the presence of known amounts of water.

    “Small amounts of water have a big effect on melting temperature, and this is the first time experiments have ever been conducted to determine precisely how the mantle’s melting temperature depends on such small amounts of water,” Hauri said.

    They found that the potential temperature of the mantle beneath the oceanic crust is hotter than had previously been estimated.

    “These results may change our understanding of the mantle’s viscosity and how it influences some tectonic plate movements,” Sarafian added.

    The study’s other co-authors are Glenn Gaetani and Adam Sarafian, also of Woods Hole.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    Carnegie Institution of Washington Bldg

    Andrew Carnegie established a unique organization dedicated to scientific discovery “to encourage, in the broadest and most liberal manner, investigation, research, and discovery and the application of knowledge to the improvement of mankind…” The philosophy was and is to devote the institution’s resources to “exceptional” individuals so that they can explore the most intriguing scientific questions in an atmosphere of complete freedom. Carnegie and his trustees realized that flexibility and freedom were essential to the institution’s success and that tradition is the foundation of the institution today as it supports research in the Earth, space, and life sciences.

    6.5 meter Magellan Telescopes located at Carnegie’s Las Campanas Observatory, Chile.
    6.5 meter Magellan Telescopes located at Carnegie’s Las Campanas Observatory, Chile

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