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  • richardmitnick 9:00 am on March 5, 2019 Permalink | Reply
    Tags: , , Biology, Eva Lincoln, For 10 weeks Lincoln was immersed in hands-on oceanographic research as a SURF student working under Dr. Susanne Menden-Deuer professor at URI’s Graduate School of Oceanography and a leading expert , Lincoln presented her research on single-cell herbivores or ‘microzooplankton’ at the annual SURF conference this past July. For her work she was honored by Rhode Island Commerce Secretary Stefan , , SURF-Summer Undergraduate Research Fellowship, The data collected will help scientists on board better understand how quickly plankton- the base of the marine food web- grow and die, The RV Endeavor the University of Rhode Island’s research vessel, , With SURF you are in the middle of a research lab learning all sorts of techniques and interacting with faculty graduate students and post-docs,   

    From University of Rhode Island: Women in STEM- “Ways of the Ocean Scientist” Eva Lincoln 

    From University of Rhode Island

    No writer credit

    Eva Lincoln (left) prepares plankton samples aboard the R/V Endeavor with Dr. Gayantonia Franze and undergraduate Anna Ward. Photo: Miraflor Santos/WHOI

    This past summer, Eva Lincoln was working in an unfamiliar place: a boat at the edge of the continental shelf, facing 12-foot swells and waking up at 2 a.m. to process water samples with tiny specks of phytoplankton in them. And she loved it.

    “Sleep was relative,” laughs Lincoln, a senior at Rhode Island College. “Our daily routine was, once we got to a station, to take water samples from the CTD (an instrument to measure salinity, temperature and depth profiles in the ocean), and place these water samples in our incubator. It was our job to make sure everything got done on time and that we handled the samples carefully.”

    For 10 weeks, Lincoln was immersed in hands-on, oceanographic research as a SURF student, working under Dr. Susanne Menden-Deuer, professor at URI’s Graduate School of Oceanography and a leading expert on plankton ecology.

    “She gave me the reins and said, ‘I want you to figure out what aspects of oceanography you find interesting, and then we can build a project from there,’” says Lincoln.

    At the end of her SURF experience, Lincoln was invited by Menden-Deuer to conduct research aboard the R/V Endeavor.

    The RV Endeavor, the University of Rhode Island’s research vessel. Photo courtesy of the Inner Space Center

    Working with a fellow undergraduate, Lincoln filtered the water samples over 24-hour and then 12-hour periods in order to achieve the most accurate chlorophyll readings. The data collected will help scientists on board better understand how quickly plankton, the base of the marine food web, grow and die.

    “It is a privilege to provide students with the opportunity to explore their own research interests, and Eva’s experience was the real thing,” notes Menden-Deuer. “With access to the high-caliber research environment at GSO, students like Eva quickly attain a high degree of proficiency, and as oceanographers, we gain a new colleague with a unique perspective.”

    Eva explains her summer research at the annual SURF Conference to RI Secretary of Commerce Stefan Pryor and Christine Smith, Managing Director of Innovation at RI Commerce. Photo: Michael Salerno/URI

    Functioning as a researcher on board a ship was an entirely separate, and important, lesson for Lincoln.

    “At the dock, we had to make sure we had all of the equipment needed,” she explains. “On the first day we had to get up super early, and I was so sick. I had to go back to bed. There is so much that goes into not just the actual science, but preparing for the cruise.”

    The fourth-year RIC student, who also tutors anatomy and physiology at the Community College of Rhode Island, has always had a deeply inquisitive mind, and wanted to know more about plankton interactions in marine food webs.

    “I have always been the pain in the butt kid who asks, ‘Why does that happen?’” she says. ““Plankton are an essential part of the food web and are eaten by so many things. If you add more nutrients to the phytoplankton, does that make them happier and therefore better food for the zooplankton?”

    Dr. Sarah Knowlton, Lincoln’s advisor and chair of physical sciences at RIC, first suggested SURF as a possible research experience, meeting with the undergraduate this past spring to guide her through the application process.

    “With SURF, you are in the middle of a research lab, learning all sorts of techniques and interacting with faculty, graduate students and post-docs,” explains Knowlton. “The experience really builds confidence, and that students can cross institutions and see how things go is so valuable.”

    Lincoln presented her research on single-cell herbivores, or ‘microzooplankton,’ at the annual SURF conference this past July. For her work, she was honored by Rhode Island Commerce Secretary Stefan Pryor at July’s SURF Conference for producing outstanding research.

    The RIC senior knows that she loves the environment and chemistry. Now, Lincoln’s focus is getting accepted to the best-fitting graduate program.

    “You get that little taste of what it is going to be like when you go to graduate school through SURF,” she emphasizes. “I can’t wait to be in graduate school myself.”

    See the full article here .


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    The University of Rhode Island is a diverse and dynamic community whose members are connected by a common quest for knowledge.

    As a major research university defined by innovation and big thinking, URI offers its undergraduate, graduate, and professional students distinctive educational opportunities designed to meet the global challenges of today’s world and the rapidly evolving needs of tomorrow. That’s why we’re here.

    The University of Rhode Island, commonly referred to as URI, is the flagship public research as well as the land grant and sea grant university for the state of Rhode Island. Its main campus is located in the village of Kingston in southern Rhode Island. Additionally, smaller campuses include the Feinstein Campus in Providence, the Rhode Island Nursing Education Center in Providence, the Narragansett Bay Campus in Narragansett, and the W. Alton Jones Campus in West Greenwich.

    The university offers bachelor’s degrees, master’s degrees, and doctoral degrees in 80 undergraduate and 49 graduate areas of study through eight academic colleges. These colleges include Arts and Sciences, Business Administration, Education and Professional Studies, Engineering, Health Sciences, Environment and Life Sciences, Nursing and Pharmacy. Another college, University College for Academic Success, serves primarily as an advising college for all incoming undergraduates and follows them through their first two years of enrollment at URI.

    The University enrolled about 13,600 undergraduate and 3,000 graduate students in Fall 2015.[2] U.S. News & World Report classifies URI as a tier 1 national university, ranking it tied for 161st in the U.S.

  • richardmitnick 11:37 am on March 4, 2019 Permalink | Reply
    Tags: "How Creatures End Up Miles Below the Surface of Earth and Maybe Mars Too", An inevitable and most interesting question that arises is this: If there was robust and adaptable life on early Mars might it have been transported underground in water too?, At the Kopanang mine they had found the roundworm Poikilolaimus oxycercusin in water about a mile underground. What appeared to be the same nematode was also collected from the the Vaal river a few mi, “M. parvella does not have a hibernation stage and cannot survive in fresh water thus it must have been and must be in brackish water all the time” Borgonie said. “The question is did this happe, Biology, , Ecosystems can survive in scalding temperatures in the absence of sunlight at high pressure and without oxygen. Yet they have been found as far down as almost three miles below the surface though in f, H. mephisto, , , Recent reports of another nematode species unaffiliated with South African mines suggests just how robust and adaptable individuals can be — in this case regarding deep freeze hibernation., Round worm Poikilolaimus oxycercus, Salese and colleagues explored 24 deep enclosed craters in the northern hemisphere of Mars with floors lying roughly 4000 meters (2.5 miles) below Martian ‘sea level’ (a level that given the plane, Some potential early Martian life could have migrated into the more protected depths is often discussed as a plausible if at this point untestable possibility   

    From Many Worlds: “How Creatures End Up Miles Below the Surface of Earth, and Maybe Mars Too” 

    NASA NExSS bloc


    Many Words icon

    From Many Worlds

    Marc Kaufman

    Poikilolaimus oxycercus is a microscopic nematode, or roundworm, found alive and well more than a mile below the surface in South Africa, where its ancestors had lived for hundreds or thousands of years. (Gaetan Borgonie)

    When scientists speculate about possible life on Mars, they generally speak of microbial or other simple creatures living deep below the irradiated and desiccated surface. While Mars long ago had a substantial period that was wetter and warmer when it also had a far more protective atmosphere, the surface now is considered to be lethal.

    But the suggestion that some potential early Martian life could have migrated into the more protected depths is often discussed as a plausible, if at this point untestable possibility. In this scenario, some of that primitive subsurface life might even have survived the eons in their buried, and protected, environments.

    This thinking has gotten some support in the past decade with the discovery of bacteria and nematodes (roundworms) found as far down as three miles below the surface of South Africa, in water dated as being many thousands or millions years old. The lifeforms have been discovered by a team that has regularly gone down into the nation’s super-hot gold and platinum mines to search for life coming out of boreholes in the rock face of deep mine tunnels.

    Borgonie setting up a water collector for a borehole at the Driefontein mine in the Witwatersrand Basin of South Africa. (Courtesy of Borgonie)

    Now a new paper [below] describes not only the discovery of additional deep subsurface life, but also tries to explain how the distant ancestors of the worms and bacteria and algae might have gotten there.

    Their conclusion: many were pulled down when fractures opened in the aftermath of earthquakes and other seismic events. While many lifeforms were swept down, only a small percentage were able to adapt, evolve and thus survive.

    The is how Gaetan Borgonie, lead author of the paper in Scientific Reports, explained it to me via email:

    “After the discovery of multicellular animals in the deep subsurface up to 3.8 km (2.5 miles) in South Africa everyone was baffled and asked the question how did they get that deep? This question more or less haunted us for more than a decade as we were unable to get our head around it.

    “However during the decade as we made more observations of multicellular organisms we captured in borehole water we found that these were nearly all animals associated with fresh water and not the soil. This indicated the passage to the deep was from a fresh water source on the surface and that animals did not crawl all the way down through the topsoil over millennia.”

    This makes sense because the deepest soil inhabitants live at about six feet below the surface, said Borgonie, formerly of the University of Ghent in Belgium and now with ELi, a Belgian nonprofit that studies extreme life. So another route to their deep subterranean homes was necessary.

    One of six hibernating nematodes found in biofilms from a borehole in the Kopanang mine. Four of the six in this “dauer” or survival state were taken, placed in a petri dish and came back to active life. Several were mated with worms of the same Poikilolaimus oxycercus species and the offspring survived. (Gaetan Borgonie)

    Borgonie and his team conducted a variety of tests — seismic, geological, genetic — but one stands out as most conclusive.

    At the Kopanang mine, they had found the roundworm Poikilolaimus oxycercusin in water about a mile underground. What appeared to be the same nematode was also collected from the the Vaal river, a few miles from the mine.

    The two appeared to be genetically similar, but the best test was to see if they could successfully reproduce. And the answer was that they could.

    It was a smoking gun, though not necessarily a common one. Nematodes from other surfaces and subsurfaces were placed together and were not able to produce young that survived. As explained in the Scientific Reports paper, this may be a function of the once companionable subsurface nematodes having adapted to their environment in ways that broke their connections with surface nematodes of the same species.

    While nematodes can hibernate for long periods in what is called their dauer stage, when they wake up they survive for only 20 to 30 days. Their lines, however, can last in the subsurface for those very long periods.

    Tunnels in South Africa’s Beatrix mine close to where H. mephisto was found. The deeper one goes in the mine, the hotter it gets. And yet life survives in the fracture water and other often tiny pockets of liquid. (Gaetan Borgonie)

    The nematodes collected and tested for this most recent article were but a small part of the zoo of creatures that have been collected from deep underground in South Africa’s Witwatersrand Basin. There was also algae, fungi, bacteria, a crustaceans and even a few insects, the paper reports. The bacteria is important for the nematodes in particular because they are a food source.

    These ecosystems survive in scalding temperatures, in the absence of sunlight, at high pressure and without oxygen. Yet they have been found as far down as almost three miles below the surface, though in far more isolated conditions at that depth.

    Borgonie with Esta van Heerden, who helped gain access to South African mines for researchers including Borgonie and Princeton University geomicrobiologist Tullis Onstott more than a decade ago is part of their research team. She is founder of the mine water remediation company iwatersolutions and was formerly a professor with the University of the Free State in Bloemfontein, where she was a specialist in extremophiles. (Courtesy of Borgonie)

    The age of that life is difficult to determine. While methods exist to determine the age of the fracture water, scientists cannot definitively say when the lifeforms arrived. Still, Borgonie reports that the worms found at the Kopanang mine had been present for between 3,000 and 12,000 years, or rather their ancestors had been there.

    Borgonie and his colleagues had earlier discovered the first multicellular creature at great depth, Halicephalobus mephisto, in mine fracture water .6 to 3 miles down. That discovery, announced in 2011, helped establish that the deep subsurface was more able to support life, even complex life, than expected.

    Often the creatures were living in biofilms, loose collections of bacteria and other life held together in the water by secretions that encase them.

    Another aspect of the deep subsurface nematode story involves specimen found in salty stalactites at the Beatrix gold mine. The worms identified, Monhystrella parvella, are associated with salty environments and so the group inferred that the water and creatures may have come from a sea. There were such seas in what is now South Africa, but it was very long ago.

    “M. parvella does not have a hibernation stage and cannot survive in fresh water, thus it must have been and must be in brackish water all the time,” Borgonie said. “The question is did this happen long ago when that area of South Africa was covered by a sea or did it happen via the salt pans surrounding the Beatrix mine?

    “There is no way to know for now. But the fact is and remains that you have a worm in the subsurface in the middle of South Africa that can only survive in salty water.”

    Recent reports of another nematode species, unaffiliated with South African mines, suggests just how robust and adaptable individuals can be — in this case regarding deep freeze hibernation.

    The longest recorded nematode hibernation was 39 years until Russian scientists announced the discovery of frozen nematodes in deep Siberian permafrost. The worms had been asleep for 42,000 and 34,000 years respectively. A Science Alert article raises the possibility of contamination as an issue, but the scientists maintain they took all possible precautions and are convinced the frozen hibernations were as recorded.

    Using an electron microscope, we see the inside of a stalactite in the Beatrix gold mine, about 1 mile below the surface. The nematodes are of the species Monhystrella parvella. (Gaetan Borgonie)

    That the South African deep subsurface life appears now to have come from the surface — via seismic fractures that could bring rushes or trickles of water filled with life many miles down — does have possible implications for Mars. While no signs of early life on Mars have been discovered, research in recent years has proven that the planet once had substantial water and warmer temperatures. In other words, conditions that might be hospitable to life.

    That theory of a once quite watery Mars was taken a significant step further last week in an article in the Journal of Geophysical Research — Planets , which found evidence of an earlier planet-wide groundwater system. Such a system had been predicted before by models, but now there was significant hard evidence that it had indeed existed.

    “Early Mars was a watery world, but as the planet’s climate changed this water retreated below the surface to form pools and ‘groundwater’,” says lead author Francesco Salese of Utrecht University, the Netherlands.

    “We traced this water in our study — as its scale and role is a matter of debate — and we found the first geological evidence of a planet-wide groundwater system on Mars.”

    Salese and colleagues explored 24 deep, enclosed craters in the northern hemisphere of Mars, with floors lying roughly 4000 meters (2.5 miles) below Martian ‘sea level’ (a level that, given the planet’s lack of seas, is arbitrarily defined on Mars based on elevation and atmospheric pressure).

    The scientists found features on the floors of these craters that could only have formed in the presence of water. Many craters contain multiple features, all at depths of 2.5 to 3 miles – indicating that these craters once contained pools and flows of water that changed and receded over time.

    Researchers said flow channels, pool-shaped valleys and fan-shaped sediment deposits seen in dozens of kilometers-deep craters in Mars’ northern hemisphere would have needed water to form. (European Space Agency)

    So an inevitable and most interesting question that arises is this: If there was robust and adaptable life on early Mars, might it have been transported underground in water too?

    The planet does have seismic activity — some are called Marsquakes — that can open fractures. It seems plausible that if life existed in water on the Martian surface, it would have flowed or trickled down fractures and other porous features to substantial depths.

    Given this hypothetical, many would have died but some may have lived and adapted. Rather like what can be seen on Earth in the South African mines.

    With this possibility in mind, the Borgonie paper recommends that the presence of surface fractures be kept in mind when landing sites are chosen on other planets or moons.

    See the full article here .


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    About Many Worlds
    There are many worlds out there waiting to fire your imagination.

    Marc Kaufman is an experienced journalist, having spent three decades at The Washington Post and The Philadelphia Inquirer, and is the author of two books on searching for life and planetary habitability. While the “Many Worlds” column is supported by the Lunar Planetary Institute/USRA and informed by NASA’s NExSS initiative, any opinions expressed are the author’s alone.

    This site is for everyone interested in the burgeoning field of exoplanet detection and research, from the general public to scientists in the field. It will present columns, news stories and in-depth features, as well as the work of guest writers.

    About NExSS

    The Nexus for Exoplanet System Science (NExSS) is a NASA research coordination network dedicated to the study of planetary habitability. The goals of NExSS are to investigate the diversity of exoplanets and to learn how their history, geology, and climate interact to create the conditions for life. NExSS investigators also strive to put planets into an architectural context — as solar systems built over the eons through dynamical processes and sculpted by stars. Based on our understanding of our own solar system and habitable planet Earth, researchers in the network aim to identify where habitable niches are most likely to occur, which planets are most likely to be habitable. Leveraging current NASA investments in research and missions, NExSS will accelerate the discovery and characterization of other potentially life-bearing worlds in the galaxy, using a systems science approach.
    The National Aeronautics and Space Administration (NASA) is the agency of the United States government that is responsible for the nation’s civilian space program and for aeronautics and aerospace research.

    President Dwight D. Eisenhower established the National Aeronautics and Space Administration (NASA) in 1958 with a distinctly civilian (rather than military) orientation encouraging peaceful applications in space science. The National Aeronautics and Space Act was passed on July 29, 1958, disestablishing NASA’s predecessor, the National Advisory Committee for Aeronautics (NACA). The new agency became operational on October 1, 1958.

    Since that time, most U.S. space exploration efforts have been led by NASA, including the Apollo moon-landing missions, the Skylab space station, and later the Space Shuttle. Currently, NASA is supporting the International Space Station and is overseeing the development of the Orion Multi-Purpose Crew Vehicle and Commercial Crew vehicles. The agency is also responsible for the Launch Services Program (LSP) which provides oversight of launch operations and countdown management for unmanned NASA launches. Most recently, NASA announced a new Space Launch System that it said would take the agency’s astronauts farther into space than ever before and lay the cornerstone for future human space exploration efforts by the U.S.

    NASA science is focused on better understanding Earth through the Earth Observing System, advancing heliophysics through the efforts of the Science Mission Directorate’s Heliophysics Research Program, exploring bodies throughout the Solar System with advanced robotic missions such as New Horizons, and researching astrophysics topics, such as the Big Bang, through the Great Observatories [Hubble, Chandra, Spitzer, and associated programs. NASA shares data with various national and international organizations such as from the [JAXA]Greenhouse Gases Observing Satellite.

  • richardmitnick 10:28 am on March 4, 2019 Permalink | Reply
    Tags: , Biology, , Directed evolution, Engineer synthetic nanoparticles as optical biosensors, , ,   

    From École Polytechnique Fédérale de Lausanne: “Directed evolution builds nanoparticles” 

    EPFL bloc

    From École Polytechnique Fédérale de Lausanne

    Nik Papageorgiou

    Directed evolution is a powerful technique for engineering proteins. EPFL scientists now show that it can also be used to engineer synthetic nanoparticles as optical biosensors, which are used widely in biology, drug development, and even medical diagnostics such as real-time monitoring of glucose.

    The 2018 Nobel Prize in Chemistry went to three scientists who developed the method that forever changed protein engineering: directed evolution. Mimicking natural evolution, directed evolution guides the synthesis of proteins with improved or new functions.

    First, the original protein is mutated to create a collection of mutant protein variants. The protein variants that show improved or more desirable functions are selected. These selected proteins are then once more mutated to create another collection of protein variants for another round of selection. This cycle is repeated until a final, mutated protein is evolved with optimized performance compared to the original protein.

    Now, scientists from the lab of Ardemis Boghossian at EPFL, have been able to use directed evolution to build not proteins, but synthetic nanoparticles. These nanoparticles are used as optical biosensors – tiny devices that use light to detect biological molecules in air, water, or blood. Optical biosensors are widely used in biological research, drug development, and medical diagnostics, such as real-time monitoring of insulin and glucose in diabetics.

    “The beauty of directed evolution is that we can engineer a protein without even knowing how its structure is related to its function,” says Boghossian. “And we don’t even have this information for the vast, vast majority of proteins.”

    Her group used directed evolution to modify the optoelectronic properties of DNA-wrapped single-walled carbon nanotubes (or, DNA-SWCNTs, as they are abbreviated), which are nano-sized tubes of carbon atoms that resemble rolled up sheets of graphene covered by DNA. When they detect their target, the DNA-SWCNTs emit an optical signal that can penetrate through complex biological fluids, like blood or urine.

    General principle of the directed evolution approach applied to the nanoparticle DNA-SWCNT complexes. The starting complex is a DNA-SWCNT with a dim optical signal. This is evolved through directed evolution: (1) random mutation of the DNA sequence; (2) wrapping of the SWCNTs with the DNA and screening of the complex’s optical signal; (3) selection of the DNA-SWCNT complexes exhibiting an improved optical signal. After several cycles of evolution, we can evolve DNA-SWCNT complexes that show enhanced optical behavior. Credit: Benjamin Lambert (EPFL)

    Using a directed evolution approach, Boghossian’s team was able to engineer new DNA-SWCNTs with optical signals that are increased by up to 56% – and they did it over only two evolution cycles.

    “The majority of researchers in this field just screen large libraries of different materials in hopes of finding one with the properties they are looking for,” says Boghossian. “In optical nanosensors, we try to improve properties like selectivity, brightness, and sensitivity. By applying directed evolution, we provide researchers with a guided approach to engineering these nanosensors.”

    The study [Chemical Communications] shows that what is essentially a bioengineering technique can be used to more rationally tune the optoelectronic properties of certain nanomaterials. Boghossian explains: “Fields like materials science and physics are mostly preoccupied with defining material structure-function relationships, making materials that lack this information difficult to engineer. But this is a problem that nature solved billions of years ago – and, in recent decades, biologists have tackled it as well. I think our study shows that as materials scientists and physicists, we can still learn a few pragmatic lessons from biologists.”

    SNSF AP Energy Grant

    See the full article here .


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    EPFL campus

    EPFL is Europe’s most cosmopolitan technical university. It receives students, professors and staff from over 120 nationalities. With both a Swiss and international calling, it is therefore guided by a constant wish to open up; its missions of teaching, research and partnership impact various circles: universities and engineering schools, developing and emerging countries, secondary schools and gymnasiums, industry and economy, political circles and the general public.

  • richardmitnick 5:27 pm on February 20, 2019 Permalink | Reply
    Tags: , , , Biology, , Photo Essay- Underground Lab science in many fields, ,   

    From Sanford Underground Research Facility: “Science impact” 

    SURF logo
    Sanford Underground levels

    From Sanford Underground Research Facility

    Erin Broberg
    Matthew Kapust, photographer

    Sanford Lab’s dedication to science, research and development and engineering, as well as its innovative approach to education, make it a world-leading science facility.

    Dark matter science impacts

    The LZ experiment is the upgraded successor to the highly successful Large Underground Xenon (LUX) experiment. LUX held world-leading sensitivity for approximately three and a half years over most of the WIMP-mass region. The LZ experiment was one of two direct-search, next-generation dark matter experiments selected for funding by DOE’s Office of High Energy Physics (HEP).

    LZ involves a collaboration of 250 scientists, engineers and technicians from 38 institutions, including five U.S. National Labs. LZ expects to achieve a projected sensitivity level up to 100 times better than the final LUX search result for weakly interacting massive particles (WIMPs), the leading dark matter particle candidate.

    Currently in the construction and installation phase, LZ is expected to begin operations in late 2019. The collaboration will perform a direct search for dark matter using 10 tonnes of liquid xenon within an ultra-pure titanium cryostat that will be surrounded by a new liquid scintillator veto system. The entire experiment will be immersed in a 72,000-gallon tank filled with ultra-pure water.

    Neutrino science impacts

    Beginning with Dr. Ray Davis’ groundbreaking neutrino research (1965-1992), the drifts at Sanford Lab are dedicated to refining knowledge about neutrinos and other research.

    The Majorana Demonstrator Project has been collecting physics data since 2017. Recently published results are competitive with world-leading experiments and highlight the exceptional energy resolution and low backgrounds that have been achieved through the shielding offered at Sanford Lab.

    The MJD project invested significant resources to produce the world’s purest copper. In parallel with ongoing MJD operations, specific elements—such as electronics upgrades and copper electroforming—are being pursued at Sanford Lab in the context of R&D for the next-generation neutrinoless double-beta decay experiment called the Large Enriched Germanium Experiment for Neutrinoless bb Decay (LEGEND). LEGEND-200 physics data collection is expected to begin in 2021. Extraordinary levels of material radiopurity will be required to reach the LEGEND-1000 background goal.

    The work done at Sanford Lab, including depth and ultra-pure materials, have been instrumental in refining the search and preparing for the next generations.

    223 acres
    Surface footprint

    The local footprint of the facility includes 223 acres on the surface. Facilities at both the Yates and Ross surface campuses offer researchers administrative support, office space, communications and education and public outreach. The Waste Water Treatment Plant handles and processes waste materials and a warehouse for shipping and receiving.

    370 miles
    Underground footprint
    Of the 370 total miles of underground space, Sanford Lab maintains approximately 12 for science at various levels, including the 300, 800, 1700, 2000, 4100, and 4850 levels. The Davis Campus on the 4850 Level is a world-class laboratory space that houses experiment for neutrinoless double-beta decay and dark matter.

    The CASPAR experiment, led by SD Mines, studies stellar nuclear fusion reactions, especially neutron production for slow neutron-capture nucleosynthesis (s-process). Accelerator components were relocated from the University of Notre Dame in 2015, and since the first beam in May 2017 and the first operations event in July 2017, accelerator commissioning has continued. Advanced commissioning data were obtained starting in February 2018 using the domain of interest for stellar CNO reactions.

    “Researchers at CASPAR are engaging a community of researchers. Although Notre Dame and SD Mines are at the core, the collaboration continues to reach out to other research groups to build interest. One of the biggest impacts in South Dakota is the number of grad students participating in the Physics Ph.D. program in the state.” —Jaret Heise


    Low-background counting impacts

    The BHUC houses a low-background counting facility where components for physics experiments, including current and future Sanford Lab experiments, can be assayed. There has been significant interest in the BHUC low-background counting facility from many groups, including the Sub Electron Noise Skipper-CCD Experimental Instrument (SENSEI) experiment, which aims to search for low-mass dark matter using ~100 g of silicon CCD sensors, and the Germanium Internal Charge Amplification for Dark Matter Searches (GeICA) project.

    Six high-purity germanium detectors are currently operating at the facility, with installation of an additional germanium detector expected in 2019. These low-background counters have been instrumental in characterizing materials for the LZ experiment for the past several years.

    “The campus at Sanford Lab is an ideal location for these counters. Not only does its depth create a shield for the detectors, but it’s in the thick of major physics experiments—it’s where the action is.” —Kevin Lesko, senior scientist at Lawrence Berkley National Lab (Berkeley Lab) who manages the measurement and control of backgrounds

    Geology research impacts

    The SIGMA-V experiment, led by Lawrence Berkeley National Lab (Berkeley Lab), is a significant effort within the earth science field. SIGMA-V mobilized in October 2017, drilling a set of eight horizontal holes (each nearly 200 feet long) on the 4850L.

    Members of the SIGMA-V experiment are continuing to explore enhanced or engineered geothermal systems (EGS) by building on results obtained from a previous experiment that was hosted at SURF between 2016 and 2017. Both groups drilled new holes as field demonstration sites in support of DOE flagship EGS effort called the Frontier Observatory for Research in Geothermal Energy (FORGE). SIGMA-V is testing the validation of thermal-hydrological mechanical-chemical (THMC) modeling approaches, as well as novel monitoring tools.

    Biology opportunities

    Important questions in life science, such as the conditions of life, the extent of life and ultimately the rules of life, are also being addressed underground at SURF. Generally, these programs have a small footprint in existing spaces and require only modest support from the facility. Biology researchers take full advantage of SURF’s footprint by gathering samples from a number of underground levels and areas with different temperatures and geologic mineralogies. Various groups focus on the diversity of life, including rock-hosted microbial ecosystems, and engineering applications such as improvements to biofuel production.


    The Sanford Underground Research Facility offers a variety of environments in which engineers can test real-world applications and new technologies. And the rich history of the Homestake Mine, which includes a vast archive of core samples, allows engineers to better understand how to excavate caverns for new experiments.

    Sanford Lab’s dedication to science, research and development and engineering, as well as its innovative approach to education, make it a world-leading science facility.

    The Sanford Underground Research Facility supports world-leading research in particle and nuclear physics and other science disciplines. While still a gold mine, the facility hosted Ray Davis’s solar neutrino experiment, which shared the 2002 Nobel Prize in Physics. His work is a model for other experiments looking to understand the nature of the universe.

    The Facility’s depth, rock stability and history make it ideal for sensitive experiments that need to escape cosmic rays. The impacts on science can be seen worldwide.

    Our science as national priority

    In 2014, the Department of Energy’s High Energy Physics Advisory Panel (HEPAP) committee prioritized physics experiments, giving neutrino and dark matter projects high-priority. Sanford Lab houses two of the five experiments named in the Particle Physics Project Prioritization Panel (P-5) Report: LUX-ZEPLIN (LZ) and LBNF/DUNE.

    In 2015, a similar report done by the Department of Energy’s Nuclear Science Advisory Committee (NSAC) committee prioritized the ton-scale neutrinoless double-beta decay experiment, which aligns with the objectives of the Majorana Demonstrator Project.

    International investment and cooperation

    Sanford Lab hosts a variety of research projects in many disciplines. Researchers from around the globe use the facility to learn more about our universe, life underground and the unique geology of the region.

    The site also allows scientists to share and foster growth within the science community and encourages cooperation between many countries and institutions.

    We now have several hundred researchers from dozens of institutions around the world.

    For example, for the first time in its history, CERN is investing in an experiment outside of the European Union with its $90 million commitment to LBNF/DUNE in the form of ProtoDUNE. The ProtoDUNE detectors have already recorded physics results. Additionally, the UK committed $88 million to the project.

    CERN ProtoDune

    Cern ProtoDune


    Local impact

    Building laboratory spaces deep underground at Sanford Lab created new opportunities for higher education in South Dakota. In 2012, the Board of Regents authorized a joint Ph.D. physics program at the South Dakota School of Mines and Technology in Rapid City and the University of South Dakota in Vermillion. Since then, dozens of students have participated in the program and worked on experiments at Sanford Lab. In 2017, each university saw their first students complete the program.

    To date, there are 27 ongoing research projects housed at Sanford Lab, 24 of which include students and faculty from universities across South Dakota.

    The Black Hills State University Underground Campus (BHUC) provides a space for students from across the state to preform interdisciplinary research underground. While physics students contribute to large-scale physics experiments by working in the low background counting facility, students from other disciplines can work on research in two areas adjoining the counting cleanroom.

    “Biology students can study microbes in situ, and geology students can study the unique rock formations of the Black Hills,” said Briana Mount, director of the BHUC.

    Additionally, a National Science Foundation (NSF) program, Research Experience for Undergraduates (REU), gives students from around the country, opportunities to pursue research through the underground campus.


    Global footprint

    Competition for underground laboratory space is fierce. With the completion of the Long-Baseline Neutrino Facility (LBNF) construction, Sanford Lab will host approximately 25 percent of the total volume of underground laboratory space in the world.

    Surf-Dune/LBNF Caverns at Sanford

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

    The sheer amount of space (7,700 acres underground) and existing infrastructure make the site highly attractive for future experiments in a variety of disciplines.

    Global footprint depth

    Sanford Lab is the deepest underground lab in the U.S. at 1,490 meters. The average rock overburden is approximately 4300 meters water equivalent for existing laboratories on the 4850 Level. The underground laboratory space has a strong track record of meeting experiment needs.


    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    About us.
    The Sanford Underground Research Facility in Lead, South Dakota, advances our understanding of the universe by providing laboratory space deep underground, where sensitive physics experiments can be shielded from cosmic radiation. Researchers at the Sanford Lab explore some of the most challenging questions facing 21st century physics, such as the origin of matter, the nature of dark matter and the properties of neutrinos. The facility also hosts experiments in other disciplines—including geology, biology and engineering.

    The Sanford Lab is located at the former Homestake gold mine, which was a physics landmark long before being converted into a dedicated science facility. Nuclear chemist Ray Davis earned a share of the Nobel Prize for Physics in 2002 for a solar neutrino experiment he installed 4,850 feet underground in the mine.

    Homestake closed in 2003, but the company donated the property to South Dakota in 2006 for use as an underground laboratory. That same year, philanthropist T. Denny Sanford donated $70 million to the project. The South Dakota Legislature also created the South Dakota Science and Technology Authority to operate the lab. The state Legislature has committed more than $40 million in state funds to the project, and South Dakota also obtained a $10 million Community Development Block Grant to help rehabilitate the facility.

    In 2007, after the National Science Foundation named Homestake as the preferred site for a proposed national Deep Underground Science and Engineering Laboratory (DUSEL), the South Dakota Science and Technology Authority (SDSTA) began reopening the former gold mine.

    In December 2010, the National Science Board decided not to fund further design of DUSEL. However, in 2011 the Department of Energy, through the Lawrence Berkeley National Laboratory, agreed to support ongoing science operations at Sanford Lab, while investigating how to use the underground research facility for other longer-term experiments. The SDSTA, which owns Sanford Lab, continues to operate the facility under that agreement with Berkeley Lab.

    The first two major physics experiments at the Sanford Lab are 4,850 feet underground in an area called the Davis Campus, named for the late Ray Davis. The Large Underground Xenon (LUX) experiment is housed in the same cavern excavated for Ray Davis’s experiment in the 1960s.
    LUX/Dark matter experiment at SURFLUX/Dark matter experiment at SURF

    LBNL LZ project will replace LUX at SURF [see below]

    In October 2013, after an initial run of 80 days, LUX was determined to be the most sensitive detector yet to search for dark matter—a mysterious, yet-to-be-detected substance thought to be the most prevalent matter in the universe. The Majorana Demonstrator experiment, also on the 4850 Level, is searching for a rare phenomenon called “neutrinoless double-beta decay” that could reveal whether subatomic particles called neutrinos can be their own antiparticle. Detection of neutrinoless double-beta decay could help determine why matter prevailed over antimatter. The Majorana Demonstrator experiment is adjacent to the original Davis cavern.

    LUX’s mission was to scour the universe for WIMPs, vetoing all other signatures. It would continue to do just that for another three years before it was decommissioned in 2016.

    In the midst of the excitement over first results, the LUX collaboration was already casting its gaze forward. Planning for a next-generation dark matter experiment at Sanford Lab was already under way. Named LUX-ZEPLIN (LZ), the next-generation experiment would increase the sensitivity of LUX 100 times.

    SLAC physicist Tom Shutt, a previous co-spokesperson for LUX, said one goal of the experiment was to figure out how to build an even larger detector.
    “LZ will be a thousand times more sensitive than the LUX detector,” Shutt said. “It will just begin to see an irreducible background of neutrinos that may ultimately set the limit to our ability to measure dark matter.”
    We celebrate five years of LUX, and look into the steps being taken toward the much larger and far more sensitive experiment.

    Another major experiment, the Long Baseline Neutrino Experiment (LBNE)—a collaboration with Fermi National Accelerator Laboratory (Fermilab) and Sanford Lab, is in the preliminary design stages. The project got a major boost last year when Congress approved and the president signed an Omnibus Appropriations bill that will fund LBNE operations through FY 2014. Called the “next frontier of particle physics,” LBNE will follow neutrinos as they travel 800 miles through the earth, from FermiLab in Batavia, Ill., to Sanford Lab.

    Fermilab LBNE

    U Washington Majorana Demonstrator Experiment at SURF

    The MAJORANA DEMONSTRATOR will contain 40 kg of germanium; up to 30 kg will be enriched to 86% in 76Ge. The DEMONSTRATOR will be deployed deep underground in an ultra-low-background shielded environment in the Sanford Underground Research Facility (SURF) in Lead, SD. The goal of the DEMONSTRATOR is to determine whether a future 1-tonne experiment can achieve a background goal of one count per tonne-year in a 4-keV region of interest around the 76Ge 0νββ Q-value at 2039 keV. MAJORANA plans to collaborate with GERDA for a future tonne-scale 76Ge 0νββ search.

    LBNL LZ project at SURF, Lead, SD, USA


    CASPAR is a low-energy particle accelerator that allows researchers to study processes that take place inside collapsing stars.

    The scientists are using space in the Sanford Underground Research Facility (SURF) in Lead, South Dakota, to work on a project called the Compact Accelerator System for Performing Astrophysical Research (CASPAR). CASPAR uses a low-energy particle accelerator that will allow researchers to mimic nuclear fusion reactions in stars. If successful, their findings could help complete our picture of how the elements in our universe are built. “Nuclear astrophysics is about what goes on inside the star, not outside of it,” said Dan Robertson, a Notre Dame assistant research professor of astrophysics working on CASPAR. “It is not observational, but experimental. The idea is to reproduce the stellar environment, to reproduce the reactions within a star.”

  • richardmitnick 12:31 pm on December 18, 2018 Permalink | Reply
    Tags: , Biology, , , , , Planetary HAZE (PHAZER) chamber   

    From JHU HUB: “Alien imposters: Planets with oxygen don’t necessarily have life, study finds” 

    Johns Hopkins

    From JHU HUB

    Chanapa Tantibanchachai

    Chao He shows off the lab’s PHAZER setup. Image credit: Chanapa Tantibanchachai

    In their search for life in solar systems near and far, researchers have often accepted the presence of oxygen in a planet’s atmosphere as the surest sign that life may be present there. A new Johns Hopkins study, however, recommends a reconsideration of that rule of thumb.

    Simulating in the lab the atmospheres of planets beyond the solar system, researchers successfully created both organic compounds and oxygen, absent of life.

    The findings, published Dec. 11 by the journal ACS Earth and Space Chemistry, serve as a cautionary tale for researchers who suggest the presence of oxygen and organics on distant worlds is evidence of life there.

    A CO2-rich planetary atmosphere exposed to a plasma discharge in Sarah Hörst’s lab. Image credit: Chao He

    “Our experiments produced oxygen and organic molecules that could serve as the building blocks of life in the lab, proving that the presence of both doesn’t definitively indicate life,” says Chao He, assistant research scientist in the Johns Hopkins University Department of Earth and Planetary Sciences and the study’s first author. “Researchers need to more carefully consider how these molecules are produced.”

    Oxygen makes up 20 percent of Earth’s atmosphere and is considered one of the most robust biosignature gases in Earth’s atmosphere. In the search for life beyond Earth’s solar system, however, little is known about how different energy sources initiate chemical reactions and how those reactions can create biosignatures like oxygen. While other researchers have run photochemical models on computers to predict what exoplanet atmospheres might be able to create, no such simulations to his knowledge have before now been conducted in the lab.

    The research team performed the simulation experiments in a specially designed Planetary HAZE (PHAZER) chamber in the lab of Sarah Hörst, assistant professor of Earth and planetary sciences and the paper’s co-author. The researchers tested nine different gas mixtures, consistent with predictions for super-Earth and mini-Neptune type exoplanet atmospheres; such exoplanets are the most abundant type of planet in our Milky Way galaxy. Each mixture had a specific composition of gases such as carbon dioxide, water, ammonia, and methane, and each was heated at temperatures ranging from about 80 to 700 degrees Fahrenheit.

    He and the team allowed each gas mixture to flow into the PHAZER setup and then exposed the mixture to one of two types of energy, meant to mimic energy that triggers chemical reactions in planetary atmospheres: plasma from an alternating current glow discharge or light from an ultraviolet lamp. Plasma, an energy source stronger than UV light, can simulate electrical activities like lightning and/or energetic particles, and UV light is the main driver of chemical reactions in planetary atmospheres such as those on Earth, Saturn, and Pluto.

    After running the experiments continuously for three days, corresponding to the amount of time gas would be exposed to energy sources in space, the researchers measured and identified resulting gasses with a mass spectrometer, an instrument that sorts chemical substances by their mass to charge ratio.

    The research team found multiple scenarios that produced both oxygen and organic molecules that could build sugars and amino acids—raw materials for which life could begin—such as formaldehyde and hydrogen cyanide.

    “People used to suggest that oxygen and organics being present together indicates life, but we produced them abiotically in multiple simulations,” He says. “This suggests that even the co-presence of commonly accepted biosignatures could be a false positive for life.”

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    About the Hub
    We’ve been doing some thinking — quite a bit, actually — about all the things that go on at Johns Hopkins. Discovering the glue that holds the universe together, for example. Or unraveling the mysteries of Alzheimer’s disease. Or studying butterflies in flight to fine-tune the construction of aerial surveillance robots. Heady stuff, and a lot of it.

    In fact, Johns Hopkins does so much, in so many places, that it’s hard to wrap your brain around it all. It’s too big, too disparate, too far-flung.

    We created the Hub to be the news center for all this diverse, decentralized activity, a place where you can see what’s new, what’s important, what Johns Hopkins is up to that’s worth sharing. It’s where smart people (like you) can learn about all the smart stuff going on here.

    At the Hub, you might read about cutting-edge cancer research or deep-trench diving vehicles or bionic arms. About the psychology of hoarders or the delicate work of restoring ancient manuscripts or the mad motor-skills brilliance of a guy who can solve a Rubik’s Cube in under eight seconds.

    There’s no telling what you’ll find here because there’s no way of knowing what Johns Hopkins will do next. But when it happens, this is where you’ll find it.

    Johns Hopkins Campus

    The Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

    The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

    What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

  • richardmitnick 3:02 pm on December 14, 2018 Permalink | Reply
    Tags: , Biology, In the Ediacaran period complex organisms including soft-bodied animals up to a meter long sprang to life in deep ocean waters, ,   

    From Stanford University: “Stanford researchers unearth why deep oceans gave life to the first big, complex organisms” 

    Stanford University Name
    From Stanford University

    December 12, 2018
    Josie Garthwaite
    (650) 497-0947

    In the beginning, life was small.

    For billions of years, all life on Earth was microscopic, consisting mostly of single cells. Then suddenly, about 570 million years ago, complex organisms including animals with soft, sponge-like bodies up to a meter long sprang to life. And for 15 million years, life at this size and complexity existed only in deep water.

    More than 570 million years ago, in the Ediacaran period, complex organisms including soft-bodied animals up to a meter long sprang to life in deep ocean waters. (Image credit: Peter Trusler)

    Scientists have long questioned why these organisms appeared when and where they did: in the deep ocean, where light and food are scarce, in a time when oxygen in Earth’s atmosphere was in particularly short supply. A new study from Stanford University, published Dec. 12 in the peer-reviewed Proceedings of the Royal Society B, suggests that the more stable temperatures of the ocean’s depths allowed the burgeoning life forms to make the best use of limited oxygen supplies.

    All of this matters in part because understanding the origins of these marine creatures from the Ediacaran period is about uncovering missing links in the evolution of life, and even our own species. “You can’t have intelligent life without complex life,” explained Tom Boag, lead author on the paper and a doctoral candidate in geological sciences at Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth).

    The new research comes as part of a small but growing effort to apply knowledge of animal physiology to understand the fossil record in the context of a changing environment. The information could shed light on the kinds of organisms that will be able to survive in different environments in the future.

    “Bringing in this data from physiology, treating the organisms as living, breathing things and trying to explain how they can make it through a day or a reproductive cycle is not a way that most paleontologists and geochemists have generally approached these questions,” said Erik Sperling, senior author on the paper and an assistant professor of geological sciences.

    Goldilocks and temperature change

    Previously, scientists had theorized that animals have an optimum temperature at which they can thrive with the least amount of oxygen. According to the theory, oxygen requirements are higher at temperatures either colder or warmer than a happy medium. To test that theory in an animal reminiscent of those flourishing in the Ediacaran ocean depths, Boag measured the oxygen needs of sea anemones, whose gelatinous bodies and ability to breathe through the skin closely mimic the biology of fossils collected from the Ediacaran oceans.

    “We assumed that their ability to tolerate low oxygen would get worse as the temperatures increased. That had been observed in more complex animals like fish and lobsters and crabs,” Boag said. The scientists weren’t sure whether colder temperatures would also strain the animals’ tolerance. But indeed, the anemones needed more oxygen when temperatures in an experimental tank veered outside their comfort zone.

    Together, these factors made Boag and his colleagues suspect that, like the anemones, Ediacaran life would also require stable temperatures to make the most efficient use of the ocean’s limited oxygen supplies.

    Refuge at depth

    It would have been harder for Ediacaran animals to use the little oxygen present in cold, deep ocean waters than in warmer shallows because the gas diffuses into tissues more slowly in colder seawater. Animals in the cold have to expend a larger portion of their energy just to move oxygenated seawater through their bodies.

    Shallow waters offered sunlight and food supplies, but the deeper waters where large, complex organisms first evolved provided a refuge from wild swings in temperature. (Image credit: Shutterstock)

    But what it lacked in useable oxygen, the deep Ediacaran ocean made up for with stability. In the shallows, the passing of the sun and seasons can deliver wild swings in temperature – as much as 10 degrees Celsius in the modern ocean, compared to seasonal variations of less than 1 degree Celsius at depths below one kilometer (.62 mile). “Temperatures change much more rapidly on a daily and annual basis in shallow water,” Sperling explained.

    In a world with low oxygen levels, animals unable to regulate their own body temperature couldn’t have withstood an environment that so regularly swung outside their Goldilocks temperature.

    The Stanford team, in collaboration with colleagues at Yale University, propose that the need for a haven from such change may have determined where larger animals could evolve. “The only place where temperatures were consistent was in the deep ocean,” Sperling said. In a world of limited oxygen, the newly evolving life needed to be as efficient as possible and that was only possible in the relatively stable depths. “That’s why animals appeared there,” he said.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Stanford University campus. No image credit

    Stanford University

    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

    Stanford University Seal

  • richardmitnick 10:45 am on December 10, 2018 Permalink | Reply
    Tags: , Biology, Calditol, , Stanford researchers show that a protein in a microbe’s membrane helps it survive extreme environments, , Sulfolobus acidocaldarius   

    From Stanford University: “Stanford researchers show that a protein in a microbe’s membrane helps it survive extreme environments” 

    Stanford University Name
    From Stanford University

    December 5, 2018
    Danielle Torrent Tucker
    (650) 497-9541

    Scientists discovered a protein that modifies a microbe’s membrane and helps it survive in hot, acidic environments, proving a long-standing hypothesis that these structures have a protective effect.

    The microorganism Sulfolobus acidocaldarius lives in extreme environments, such as Emerald Hot Spring in Yellowstone National Park. (Image credit: Rennett Stowe / flickr)

    Within harsh environments like hot springs, volcanic craters and deep-sea hydrothermal vents – uninhabitable by most life forms – microscopic organisms are thriving. How? It’s all in how they wrap themselves.

    Stanford University researchers have identified a protein that helps these organisms form a protective, lipid-linked cellular membrane – a key to withstanding extremely highly acidic habitats.

    Scientists had known that this group of microbes – called archaea – were surrounded by a membrane made of different chemical components than those of bacteria, plants or animals. They had long hypothesized that it could be what provides protection in extreme habitats. The team directly proved this idea by identifying the protein that creates the unusual membrane structure in the species Sulfolobus acidocaldarius.

    The structures of some organisms’ membranes are retained in the fossil record and can serve as molecular fossils or biomarkers, leaving hints of what lived in the environment long ago. Finding preserved membrane lipids, for example, could suggest when an organism evolved and how that may have been the circumstance of its environment. Being able to show how this protective membrane is created could help researchers understand other molecular fossils in the future, offering new evidence about the evolution of life on Earth. The results appeared the week of Dec. 3 in Proceedings of the National Academy of Sciences.

    “Our model is that this organism evolved the ability to make these membranes because it lives in an environment where the acidity changes,” said co-author Paula Welander, an assistant professor of Earth system science at Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth). “This is the first time we’ve actually linked some part of a lipid to an environmental condition in archaea.”

    Rare chemistry

    The hot springs where S. acidocaldarius is found, such as those in Yellowstone National Park that are over 200 degrees Fahrenheit, can experience fluctuating acidity. This organism is also found in volcanic craters, deep-sea hydrothermal vents and other acidic environments with both moderate and cold temperatures.

    Welander became interested in studying this microbe because of its rare chemistry, including its unusual lipid membranes. Unlike plants and fungi, archaeal organisms do not produce protective outer walls of cellulose and their membranes do not contain the same chemicals as bacteria. Scientists had explored how the species produced its unusual membrane for about 10 years before experimentation stopped in 2006, she said.

    “I think we forget that some things just haven’t been done yet – I’ve been finding that a lot ever since I stepped into the geobiology world,” Welander said. “There are so many questions out there that we just need the basic knowledge of, such as, ‘What is the protein that’s doing this? Does this membrane structure really do what we’re saying it does?’”

    From previous research in archaea, Welander and her team knew that the organisms produce a membrane containing a ringed molecule called a calditol. The group thought this molecule might underlie the species’ ability to withstand environments where other organisms perish.

    To find out, they first went through the genome of S. acidocaldarius and identified three genes likely to be involved in making a calditol. They then mutated those genes one-by-one, eliminating any proteins the genes made. The experiments revealed one gene that, when mutated, produced S. acidocaldarius that lacked calditol in the membrane. That mutated organism was able to grow at high temperatures but withered in a highly acidic environment, suggesting that the protein is necessary to both make the unusual membrane and withstand acidity.

    The work was particularly challenging because Welander’s lab had to replicate those high temperature, acidic conditions in which the microbes thrive. Most of the incubators in her lab could only reach body temperature, so lead author Zhirui Zeng, a postdoctoral researcher in Welander’s lab, figured out how to imitate the organism’s home using a special small oven, she said.

    “That was really cool,” Welander said. “We did a lot of experimenting to try to figure out the chemistry.”

    Third domain of life

    This work is about more than just finding one protein, Welander said. Her research explores lipids found in present-day microbes with the goal of understanding Earth’s history, including ancient climatic events, mass extinctions and evolutionary transitions. But before scientists can interpret evolutionary characteristics, they need to understand the basics, like how novel lipids are created.

    Archaea are sometimes called the “third domain of life,” with one domain being bacteria and the other being a group that includes plants and animals – collectively known as eukaryotes. Archaea includes some of the oldest, most abundant lifeforms on the planet, without which the ecosystem would collapse. Archaea are particularly anomalous microbes, confused with bacteria one day and likened to plants or animals the next because of their unique molecular structures.

    The research is particularly interesting because the classification for archaea is still debated by taxonomists. They were only separated from the bacteria and eukaryote domains in the past two decades, following the development of genetic sequencing in the 1970s.

    “There are certain things about archaea that are different, like the lipids,” Welander said. “Archaea are a big area of research now because they are this different domain that we want to study, and understand – and they’re really cool.”

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Stanford University campus. No image credit

    Stanford University

    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

    Stanford University Seal

  • richardmitnick 11:30 am on November 16, 2018 Permalink | Reply
    Tags: , Biology, , Shedding new light on photosynthesis, , University of Michigan researchers have developed a powerful microscope that can map how light energy migrates in photosynthetic bacteria on timescales of one-quadrillionth of a second.   

    From University of Michigan: “Shedding new light on photosynthesis” 

    U Michigan bloc

    From University of Michigan

    October 11, 2018
    Morgan Sherburne

    Employing a series of ultrashort laser pulses, a new microscope reveals intricate details that govern photosynthetic processes in purple bacteria. Image credit: Vivek Tiwari, Yassel Acosta and Jennifer Ogilvie

    University of Michigan researchers have developed a powerful microscope that can map how light energy migrates in photosynthetic bacteria on timescales of one-quadrillionth of a second.

    The microscope could help researchers develop more efficient organic photovoltaic materials, a type of solar cell that could provide cheaper energy than silicon-based solar cells.

    In photosynthetic plants and bacteria, light hits the leaf or bacteria and a system of tiny light-harvesting antenna shuttle it along through proteins to what’s called a reaction center. Here, light is “trapped” and turned into metabolic energy for the organisms.

    Jennifer Ogilvie, U-M professor of physics and biophysics, and her team want to capture the movement of this light energy through proteins in a cell, and the team has taken one step toward that goal in developing this microscope. Their study has been published in Nature Communications.

    Ogilvie, graduate student Yassel Acosta and postdoctoral fellow Vivek Tiwari worked together to develop the microscope, which uses a method called two-dimensional electronic spectroscopy to generate images of energy migration within proteins during photosynthesis. The microscope images an area the size of one-fifth of a human blood cell and can capture events that take a period of one-quadrillionth of a second.

    Two-dimensional spectroscopy works by reading the energy levels within a system in two ways. First, it reads the wavelength of light that’s absorbed in a photosynthetic system. Then, it reads the wavelength of light detected within the system, allowing energy to be tracked as it flows through the organism.

    The instrument combines this method with a microscope to measure a signal from nearly a million times smaller volumes than before. Previous measurements imaged samples averaged over sections that were a million times larger. Averaging over large sections obscures the different ways energy might be moving within the same system.

    “We’ve now combined both of those techniques so we can get at really fast processes as well as really detailed information about how these molecules are interacting,” Ogilvie said. “If I look at one nanoscopic region of my sample versus another, the spectroscopy can look very different. Previously, I didn’t know that, because I only got the average measurement. I couldn’t learn about the differences, which can be important for understanding how the system works.”

    In developing the microscope, Ogilvie and her team studied colonies of photosynthetic purple bacterial cells. Previously, scientists have mainly looked at purified parts of these types of cells. By looking at an intact cell system, Ogilvie and her team were able to observe how a complete system’s different components interacted.

    The team also studied bacteria that had been grown in high light conditions, low light conditions and a mixture of both. By tracking light emitted from the bacteria, the microscope enabled them to view how the energy level structure and flow of energy through the system changed depending on the bacteria’s light conditions.

    Similarly, this microscope can help scientists understand how organic photovoltaic materials work, Ogilvie says. Instead of the light-harvesting antennae complexes found in plants and bacteria, organic photovoltaic materials have what are called “donor” molecules and “acceptor” molecules. When light travels through these materials, the donor molecule sends electrons to acceptor molecules, generating electricity.

    “We might find there are regions where the excitation doesn’t produce a charge that can be harvested, and then we might find regions where it works really well,” Ogilvie said. “If we look at the interactions between these components, we might be able to correlate the material’s morphology with what’s working well and what isn’t.”

    In organisms, these zones occur because one area of the organism might not be receiving as much light as another area, and therefore is packed with light-harvesting antennae and few reaction centers. Other areas might be flooded with light, and bacteria may have fewer antennae—but more reaction centers. In photovoltaic material, the distribution of donor and receptor molecules may change depending on the material’s morphology. This could affect the material’s efficiency in converting light into electricity.

    “All of these materials have to have different components that do different things—components that will absorb the light, components that will take that the energy from the light and convert it to something that can be used, like electricity,” Ogilvie said. “It’s a holy grail to be able to map in space and time the exact flow of energy through these systems.”

    See the full article here .



    Stem Education Coalition

    U MIchigan Campus

    The University of Michigan (U-M, UM, UMich, or U of M), frequently referred to simply as Michigan, is a public research university located in Ann Arbor, Michigan, United States. Originally, founded in 1817 in Detroit as the Catholepistemiad, or University of Michigania, 20 years before the Michigan Territory officially became a state, the University of Michigan is the state’s oldest university. The university moved to Ann Arbor in 1837 onto 40 acres (16 ha) of what is now known as Central Campus. Since its establishment in Ann Arbor, the university campus has expanded to include more than 584 major buildings with a combined area of more than 34 million gross square feet (781 acres or 3.16 km²), and has two satellite campuses located in Flint and Dearborn. The University was one of the founding members of the Association of American Universities.

    Considered one of the foremost research universities in the United States,[7] the university has very high research activity and its comprehensive graduate program offers doctoral degrees in the humanities, social sciences, and STEM fields (Science, Technology, Engineering and Mathematics) as well as professional degrees in business, medicine, law, pharmacy, nursing, social work and dentistry. Michigan’s body of living alumni (as of 2012) comprises more than 500,000. Besides academic life, Michigan’s athletic teams compete in Division I of the NCAA and are collectively known as the Wolverines. They are members of the Big Ten Conference.

  • richardmitnick 10:54 am on November 15, 2018 Permalink | Reply
    Tags: "Searching for ocean microbes", , Bermuda Atlantic Time Series, Biology, 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,   

    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.

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  • richardmitnick 7:22 pm on November 9, 2018 Permalink | Reply
    Tags: , , , , , Biology, , , , , , , , , Understanding our own backyard will be key in interpreting data from far-flung exoplanets   

    From COSMOS Magazine: “The tech we’re going to need to detect ET” 

    Cosmos Magazine bloc

    From COSMOS Magazine

    09 November 2018
    Lauren Fuge

    Searching for biosignatures rather than examples of life itself is considered a prime strategy in the hunt for ET. smartboy10/Getty Images

    Move over Mars rovers, new technologies to detect alien life are on the horizon.

    A group of scientists from around the world, led by astrochemistry expert Chaitanya Giri from the Tokyo Institute of Technology in Japan, have put their heads together to plan the next 20 years’ worth of life-detection technologies. The study is currently awaiting peer review, but is freely available on the pre-print site, ArXiv.

    For decades, astrobiologists have scoured the skies and the sands of other planets for hints of extraterrestrial life. Not only are these researchers trying to find ET, but they’re also aiming to learn about the origin and evolution of life on Earth, the chemical composition of organic extraterrestrial objects, what makes a planet or satellite habitable, and more.

    But the answers to such questions are preceded by long years of planning, development, problem-solving and strategising.

    Late in 2017, 20 scientists from Japan, India, France, Germany and the USA – each with a special area of expertise – came together at a workshop run by the Earth-Life Science Institute (ELSI) at Giri’s Tokyo campus. There, they discussed the current progress and enticing possibilities of life-detection technologies.

    In particular, the boffins debated which ones should be a priority for research and development for missions within the local solar system – in other words, which instruments will be most feasible to out onto a space probe and send off to Mars or Enceladus during the next couple of decades.

    Of course, the planets and moons in the solar system are an extremely limited sample of the number of potentially habitable worlds in the universe, but understanding our own backyard will be key in interpreting data from far-flung exoplanets.

    So, according to these astrobiology experts, what’s the future plan for alien detection?

    The first step of any space mission is to study the planet or satellite from afar to determine whether it is habitable. Luckily, an array of next-generation telescopes is currently being built, from the ultra-sensitive James Webb Space Telescope, slated for launch in 2021, to the gargantuan Extremely Large Telescope in Chile, which will turn its 39-metre eye to the sky in 2024. The authors point out that observatories such as these will vastly expand our theoretical knowledge of planet habitability.

    NASA/ESA/CSA Webb Telescope annotated

    ESO/E-ELT,to be on top of Cerro Armazones in the Atacama Desert of northern Chile. located at the summit of the mountain at an altitude of 3,060 metres (10,040 ft).

    Just because a world is deemed habitable doesn’t mean life will be found all over it, though. It may exist only in limited geographical niches. To reach these inaccessible sites, the paper argues that we will require “agile robotic probes that are robust, able to seamlessly communicate with orbiters and deep space communications networks, be operationally semi-autonomous, have high-performance energy supplies, and are sterilisable to avoid forward contamination”.

    But according to Elizabeth Tasker, associate professor at the Japan Aerospace Exploration Agency (JAXA), who was not involved in the study, getting there is only half the struggle.

    “In fact, it’s the most tractable half because we can picture the problems we will face,” she says.

    The second, more pressing issue is how to recognise life unlike anything we know on Earth.

    As Tasker explains: “We only have Earth life to compare to and this is the result of huge evolutionary history on a planet whose complex past is unlikely to be replicated closely. That’s a lot of baggage to separate out.”

    According to the paper, the way forward is to equip missions with a suite of life-detection instruments that don’t look for life as we know it, but are instead able to identify the kinds of features that make organisms function.

    The authors outline a huge variety of exciting technologies that could be used for this purpose, including spectroscopy techniques (to analyse potential biological materials), quantum tunnelling [Nature Nanotechnology
    ] (to find DNA, RNA, peptides, and other small molecules), and fluorescence microscopy [ https://www.hou.usra.edu/meetings/lpsc2014/pdf/2744.pdf ](to identify the presence of cell membranes).

    They also nominate different forms of gas chromatography (to spot amino acids and sugars formed by living organisms, plus checking to see if molecules are “homochiral” [Space Science Reviews] (a suspected biosignature) using microfluidic devices and microscopes.

    High-resolution, miniaturised mass spectrometers would also be helpful, characterising biopolymers, which are created by living organisms, and measuring the elemental composition of objects to aid isotopic dating.

    Giri and colleagues also stress that exciting developments in machine learning, artificial intelligence, and pattern recognition will be useful in determining whether chemical samples are biological in origin.

    Interestingly, researchers are also developing technologies that may allow the detection of life in more unconventional places. On Earth, for example, cryotubes were recently used [International Journal of Systematic and Evolutionary Microbiology] to discover several new species of bacteria in the upper atmosphere.

    The scientists also discuss how certain technologies – such as high-powered synchrotron radiation and magnetic field facilities – are not yet compact enough to fly to other planets, and so samples must continue to be brought back for analysis.

    Several sample-and-return missions are currently underway, including JAXA’s Martian Moons exploration mission to Phobos, Hayabusa-2 to asteroid Ryugu, and NASA’s OSIRIS-rex to asteroid Bennu. What we learn from handling the organic-rich extraterrestrial materials brought back from these trips will be invaluable.

    JAXA MMX spacecraft

    JAXA/Hayabusa 2 Credit: JAXA/Akihiro Ikeshita

    NASA OSIRIS-REx Spacecraft

    What we learn from handling the organic-rich extraterrestrial materials brought back from these trips will be invaluable.

    The predictions and recommendations put forward by Giri and colleagues are the first steps in getting these technologies discussed in panel reviews, included in decadal surveys, and eventually funded.

    They complement several similar efforts, including a report prepared by US National Academies of Science, Engineering and Medicine (NASEM), calling for an expansion of the range of possible ET indicators, and a US-led exploration of how the next generation of radio telescopes will be utilised by SETI.

    Perhaps most importantly, these papers all highlight the need for collaborative work between scientists across disciplines.

    “A successful detection of life will need astrophysicists and geologists to examine possible environments on other planets, engineers and physicists to design the missions and instruments that can collect data, and chemists and biologists to determine how to classify life,” JAXA’s Tasker says.

    “But maybe that is appropriate: finding out what life really is and where it can flourish is the story of everyone on Earth. It should take all of us to unravel.”

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

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