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  • richardmitnick 10:34 am on October 9, 2021 Permalink | Reply
    Tags: "Oregon State microbiology research furthers understanding of ocean’s role in carbon cycling", A novel approach to track which microbes are consuming different types of organic carbon produced by common phytoplankton species, , Carbon cycling in the ocean, Microbes form the basis of the food web and biological carbon pump., Microbiology, Phytoplankton are microscopic organisms at the base of the ocean’s food chain and a key component of a critical biological carbon pump., Phytoplankton use the CO2 and sunlight for photosynthesis: they convert them into sugars and other compounds the cells can use for energy producing oxygen in the process., Scientists are studying the consumers–the heterotrophic microbes–of the organic material made by the primary producers-the microbial phytoplankton., The collective respiratory activity of the heterotrophic microbial consumers is the main way that fixed dissolved organic carbon from phytoplankton is returned to the atmosphere as CO2., , The scientists used stable isotope labeling to track carbon., The surface ocean stores nearly as much carbon as exists in the atmosphere., Tiny autotrophic plants–they make their own food–have a big effect on the levels of carbon dioxide in the atmosphere by sucking it up during photosynthesis.   

    From The Oregon State University (US): “Oregon State microbiology research furthers understanding of ocean’s role in carbon cycling” 

    From The Oregon State University (US)

    October 07, 2021

    Story By:
    Steve Lundeberg

    Ryan Mueller


    Microbiology researchers at The Oregon State University (US) have shed new light on the mechanisms of carbon cycling in the ocean, using a novel approach to track which microbes are consuming different types of organic carbon produced by common phytoplankton species.

    The research is an important step toward forecasting how much carbon will leave the ocean for the atmosphere as greenhouse gas carbon dioxide and how much will end up entombed in marine sediments, said Ryan Mueller, associate professor in The Oregon State University’s Department of Microbiology and the leader of the study.

    Findings were published today in the PNAS.

    “Our research shows that different species of microbes in the ocean are very particular yet predictable in the food sources they prefer to eat,” said first author Brandon Kieft, a recent Oregon State Ph.D. graduate who is now a postdoctoral researcher at The University of British Columbia (CA). “As global climate change continues to alter oceanic environments at a rapid pace, the availability of food sources for microbes will also change, ultimately favoring certain types over others.”

    Phytoplankton are microscopic organisms at the base of the ocean’s food chain and a key component of a critical biological carbon pump. Most float in the upper part of the ocean, where sunlight can easily reach them.

    The tiny autotrophic plants–they make their own food–have a big effect on the levels of carbon dioxide in the atmosphere by sucking it up during photosynthesis. It’s a natural sink and one of the primary ways that CO2, the most abundant greenhouse gas, is scrubbed from the atmosphere; atmospheric carbon dioxide has increased 40% since the dawn of the industrial age, contributing heavily to a warming planet.

    “We’re studying the consumers–the heterotrophic microbes–of the organic material made by the primary producers-the microbial phytoplankton,” Mueller said. “Both groups are microbes, the former primarily consumes organic carbon as a food source, while the latter ‘fix’ their own organic carbon. Microbes form the basis of the food web and biological carbon pump, and our work is primarily focused on exploring what the consumers are doing in this system.”

    The surface ocean stores nearly as much carbon as exists in the atmosphere. As the ocean pulls in atmospheric carbon dioxide, phytoplankton use the CO2 and sunlight for photosynthesis: They convert them into sugars and other compounds the cells can use for energy producing oxygen in the process.

    This so-called fixed carbon makes up the diet of heterotrophic microbes and higher organisms of the marine food web such as fish and mammals, which ultimately convert the carbon back to atmospheric CO2 through respiration or contribute to the carbon stock at the bottom of the ocean when they die and sink.

    The collective respiratory activity of the heterotrophic microbial consumers is the main way that fixed dissolved organic carbon from phytoplankton is returned to the atmosphere as CO2.

    Mueller, Kieft and collaborators at the DOE’s Oak Ridge National Laboratory (US) and DOE’s Lawrence Livermore National Laboratory (US) and The University of Tennessee (US), The University of Washington (US) and The University of Oklahoma(US) used stable isotope labeling to track carbon as it made its way into the organic matter produced by the phytoplankton and, ultimately, the heterotrophic microbes that consume it.

    The scientists used those isotopes to tell which organisms were eating diatoms and which were consuming cyanobacteria, two species of phytoplankton that combine to produce a majority of the ocean’s fixed carbon. The researchers could also tell when the consumption was happening – for example, at times the phytoplankton cells were producing substances known as lysates during their death phase or exudates during their growth phase.

    “Our findings have important implications for understanding how marine microbes and photosynthetic algae function together to impact global carbon cycling and how this oceanic food web may respond to continued environmental change,” Kieft said. “This will help us predict how much carbon will go back into the atmosphere and how much will be buried in marine sediments for centuries.”

    The research was funded by the Gordon and Betty Moore Foundation Marine Microbiology Initiative and the U.S. Department of Energy.

    See the full article here.


    Please help promote STEM in your local schools.

    Stem Education Coalition

    The Oregon State University(US) is a public land-grant research university in Corvallis, Oregon. The university currently offers more than 200 undergraduate-degree programs along with a variety of graduate and doctoral degrees. Student enrollment averages near 32,000, making it the state’s largest university. Since its founding over 230,000 students have graduated from OSU. It is classified among “R1: Doctoral Universities – Very high research activity” with an additional, optional designation as a “Community Engagement” university.

    The Oregon State University a land-grant university and it also participates in the sea-grant, space-grant and sun-grant research consortia; it is one of only four such universities in the country (The University of Hawaii at Manoa (US), Cornell University (US) and The Pennsylvania State University (US) are the only others with similar designations). OSU consistently ranks as the state’s top earner in research funding.


    Research has played a central role in the university’s overall operations for much of its history. Most of The Oregon State University’s research continues at the Corvallis campus, but an increasing number of endeavors are underway at various locations throughout the state and abroad. Research facilities beyond the campus include the John L. Fryer Aquatic Animal Health Laboratory in Corvallis, the Seafood Laboratory in Astoria and the Food Innovation Laboratory in Portland.

    The university’s College of Earth, Ocean and Atmospheric Sciences (CEOAS) operates several laboratories, including the Hatfield Marine Science Center and multiple oceanographic research vessels based in Newport. CEOAS is now co-leading the largest ocean science project in U.S. history, the Ocean Observatories Initiative (OOI). The OOI features a fleet of undersea gliders at six sites in the Pacific and Atlantic Oceans with multiple observation platforms. CEOAS is also leading the design and construction of the next class of ocean-faring research vessels for The National Science Foundation (US), which will be the largest grant or contract ever received by any Oregon university. The Oregon State University also manages nearly 11,250 acres (4,550 ha) of forest land, including the McDonald-Dunn Research Forest.

    The 2005 Carnegie Classification of Institutions of Higher Education recognized The Oregon State University as a “comprehensive doctoral with medical/veterinary” university. It is one of three such universities in the Pacific Northwest to be classified in this category. In 2006, Carnegie also recognized The Oregon State University as having “very high research activity,” making it the only university in Oregon to attain these combined classifications.

    The National Sea Grant College Program was founded in the 1960s. The Oregon State University is one of the original four Sea Grant Colleges selected in 1971.

    In 1967 the Radiation Center was constructed at the edge of campus, housing a 1.1 MW TRIGA Mark II Research Reactor. The reactor is equipped to utilize Highly Enriched Uranium (HEU) for fuel. U.S. News & World Report’s 2008 rankings placed The Oregon State University eighth in the nation in graduate nuclear engineering.

    The Oregon State University was one of the early members of the federal Space Grant program. Designated in 1991, the additional grant program made The Oregon State University one of only 13 schools in the United States to serve as a combined Land Grant, Sea Grant and Space Grant university. Most recently, The Oregon State University was designated as a federal Sun Grant institution. The designation, made in 2003, makes The Oregon State University one of only three such universities (the others being Cornell University (US) and The Pennsylvania State University (US)) and the first of two public institutions with all four designations (the other being Penn State).

    In 2001, The Oregon State University’s Wave Research Laboratory was designated by The National Science Foundation (US) as a site for tsunami research under the Network for Earthquake Engineering Simulation. The O. H. Hinsdale Wave Research Laboratory is on the edge of the campus and is one of the world’s largest and most sophisticated laboratories for education, research and testing in coastal, ocean and related areas.

    The National Institute of Environmental Health Sciences funds two research centers at The Oregon State University. The Environmental Health Sciences Center has been funded since 1969 and the Superfund Research Center has been funded since 2009.

    The Oregon State University administers the H.J. Andrews Experimental Forest, a United States Forest Service facility dedicated to forestry and ecology research. The Andrews Forest is a UNESCO International Biosphere Reserve.

    The Oregon State University’s Open Source Lab is a nonprofit founded in 2003 and funded in part by corporate sponsors that include Facebook, Google, and IBM. The organization’s goal is to advance open source technology, and it hires and trains The Oregon State University students in software development and operations for large-scale IT projects. The lab hosts a number of projects, including a contract with the Linux Foundation.

  • richardmitnick 11:02 am on September 8, 2021 Permalink | Reply
    Tags: "Researchers evaluate SURF extremophiles in effort to trap carbon dioxide deep underground", Acceleration of carbon mineralization with extremophiles found at SURF., “Thermophiles”: a type of extremophile that can survive temperatures from 54 to 70 degrees Celsius (130 – 158 degrees Fahrenheit)., Currently the two major inquiries—understanding the extremophiles and pinpointing carbon mineralization rates—are being done in parallel., Microbiology, , Scientists have identified certain microbes that at the surface produce enzymes that can greatly accelerate carbon mineralization.   

    From Sanford Underground Research Facility-SURF: “Researchers evaluate SURF extremophiles in effort to trap carbon dioxide deep underground” 

    SURF-Sanford Underground Research Facility, Lead, South Dakota, USA.

    From Sanford Underground Research Facility-SURF

    Homestake Mining, Lead, South Dakota, USA.

    Homestake Mining Company

    September 7, 2021
    Erin Lorraine Broberg

    South Dakota Mines researchers study microbial acceleration of carbon mineralization with extremophiles found at SURF.

    Core samples, drilled from the drifts of SURF, contain colonies of microscopic life. Photo by Adam Gomez.

    When first learning about the Sanford Underground Research Facility (SURF), it can help to imagine it as a vast, inverted apartment complex. Experiments move into the large, underground caverns. And SURF provides the usual amenities: electricity, running water, elevator maintenance, radon mitigation, liquid nitrogen deliveries and, of course, shielding from cosmic rays.

    But amidst the facility’s 370 miles of tunnels, shafts and drifts, there is one group of tenants who pay no rent at all. At SURF, billions of microorganisms—known to biologists as “extremophiles” for their ability to carve out a living far from sunlight and with limited oxygen—live deep underground.

    This summer, a research group from South Dakota Mines (Mines) retrieved a core sample—a smooth cylinder of grey rock—from 4,100 feet below of the surface of SURF. Under a microscope, it wriggled with SURF’s hardiest inhabitants.

    From this sample, the research group hopes to find a microbe with a distinct set of characteristics that could help store excess greenhouse gases deep underground.

    Locking away carbon dioxide

    While extremophiles have slowly evolved to withstand their adverse habitat, scientists are on a mission to keep the Earth’s atmosphere as hospitable as possible. And so, a global effort is underway to store carbon dioxide (CO2) emissions in deep underground reservoirs. One promising method to keep it locked in place is called “carbon mineralization.”

    “Carbon dioxide gas is captured from the atmosphere, then pumped in liquid form deep into underground rock formations,” said Bret Lingwall, a geotechnical, bio-geotechnical and earthquake engineering researcher, who leads the Mines research group. Deep underground, a chemical reaction transforms the CO2 into a stable, solid carbonate mineral—effectively trapping it for millennia.

    But this process has a severe limitation: speed.

    The crippling pace of the method’s chemical reaction is measured—not in weeks or months—but in years. Currently, the largest carbon mineralization project on Earth can sequester 10,000 tons of CO2 each year—barely a drop in the bucket when climatologists measure carbon emissions by the gigaton (one billion tons).

    Meanwhile, Earth is in a bit of a rush.

    For carbon mineralization to have an effect, the process desperately needs some added speed.

    “What we are trying to do is to accelerate that timescale from a couple of years to a couple of weeks,” Lingwall said. “How we propose to do that is through microbial acceleration.”

    Scientists have identified certain microbes that at the surface produce enzymes that can greatly accelerate carbon mineralization. “However, these microbes can’t stand the temperatures, pressures and acidic pH of the deep subsurface,” Lingwall said.

    At depths of 4 to 8 kilometers deep, pressures are intense and temperatures climb to 60-90 degrees Celsius (140-194 degrees Fahrenheit). While these conditions are ideal for carbon storage, they aren’t hospitable to most microbes.

    But most microbes weren’t born on the 4100 Level of SURF.

    Enter: Extremophiles

    Rajesh Sani, a microbiologist with the Mines research group, has studied various SURF extremophiles for 15 years. In that time, he’s worked with “thermophiles” a type of extremophile that can survive temperatures from 54 to 70 degrees Celsius (130 – 158 degrees Fahrenheit).

    Sani will examine the gene expressions of microbes found in the core sample. “This process will give us an idea of how these microorganisms function, what are they eating, how they are breathing, how they are producing biomass, and how they are interacting with rock samples underground,” Sani said.

    It will also help researchers determine if SURF’s extremophiles can produce the sought-after enzyme that hastens carbon mineralization.

    Magan Vaughn, a chemical and biological engineering masters student at South Dakota Mines, crushes a core sample from 4100 Level of Sanford Underground Research Facility, preparing the sample for DNA extraction. Photo by Tanvi Govil.

    “Our project will sample and survey extremophiles from SURF, looking at their enzymatic genes to determine if any of them have the right profile to both survive deep underground and accelerate carbon mineralization,” Lingwall said.

    Determining the rate

    While the team’s microbiologists are sifting through microbial samples, other researchers are trying to establish just how quickly carbon mineralization takes place without extremophiles.

    “Currently these types of experiments were replicated in the field, but not in laboratory environment. When you are conducting large scale investigations in the field, you are limited to the conditions (composition, pressure temperature, biological activity) that field site can offer,” said Gokce Ustunisik, a petrologist and high-temperature geochemist at Mines. “The beauty of experimental work is that you are the one—not Mother Nature—putting the controls on the system. You systematically change parameters, so that you can right away see the contribution of each parameter in a multi-component system.”

    When her biology and engineering colleagues first described the temperatures and pressures needed for this research, Ustunisik thought, “High temperatures and pressures? Those are low temperatures and pressures!”

    For Ustunisik, who studies the formation and evolution of the Moon, Mars and Earth, those parameters are quite low. In her experimental petrology lab, Ustunisik can easily replicate conditions comparable to the Earth’s lower crust and upper mantle, where temperatures begin at 1,400 degrees Celsius (2,552 degrees Fahrenheit).

    But for this research, both the microbes and the deep subsurface create strict limitations for each other. The extremophiles must be hardy enough to survive the upper limits of life, while the rock formations must be deep and vast enough to store gigatons of carbon, without killing the extremophiles.

    The key is finding an overlap.

    Earlier this summer, RESPEC researcher Brian Bormes and Gokce Ustunisik took initial observations of the core sample on the 4100 Level of Sanford Underground Research Facility. Photo courtesy Gokce Ustunisik.

    Layers of expertise

    Currently the two major inquiries—understanding the extremophiles and pinpointing carbon mineralization rates—are being done in parallel. In 2022, the group will introduce the microbes to the carbon mineralization process to see if the rate ticks up.

    Many questions will guide the next phase of the research: Can SURF extremophiles accelerate the carbon mineralization process? If so, by how much? Can they adapt to different rock environments? Or are they limited to their native rock formations?

    The effort, funded by an Eager Award from the National Science Foundation, brings together experts in geology, engineering, chemistry, petrology and microbiology.

    “The novelty of this project is not necessarily the microbial acceleration of carbon mineralization. The real innovation is the bringing together of a team of different backgrounds to study this new, interesting, complex problem in a different way,” Lingwall said.

    The current NSF grant supports two years of initial research. If, by the end of that period, the experiment’s results are promising, a larger experiment will be undertaken.

    And, perhaps, these extremophiles might be worth their back rent after all.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    About us: The Sanford Underground Research Facility-SURF 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.

    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 The U Washington MAJORANA Neutrinoless Double-beta Decay Experiment Demonstrator experiment (US), 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.

    The LUX Xenon dark matter detector | Sanford Underground Research Facility 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 National Accelerator Laboratory(US) 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.

    FNAL DUNE LBNF (US) from FNAL to SURF, Lead, South Dakota, USA

    FNAL DUNE LBNF (US) Caverns at Sanford Lab.

    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 Germanium Detector Array (or GERDA) experiment is searching for neutrinoless double beta decay (0νββ) in Ge-76 at the underground Laboratori Nazionali del Gran Sasso (LNGS) for a future tonne-scale 76Ge 0νββ search.

    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 9:11 am on September 8, 2021 Permalink | Reply
    Tags: "Geobacter pili", "Hidden bacterial hairs power nature’s ‘electric grid’", , , , Microbiology,   

    From Yale University (US) : “Hidden bacterial hairs power nature’s ‘electric grid’” 

    From Yale University (US)

    September 1, 2021

    Media Contact
    Bess Connolly

    By Bill Hathaway

    Bacterial hairs power nature’s electric grid. Credit: Ella Maru Studio.

    A hair-like protein hidden inside bacteria serves as a sort of on-off switch for nature’s “electric grid,” a global web of bacteria-generated nanowires that permeates all oxygen-less soil and deep ocean beds, Yale researchers report in the journal Nature.

    “The ground beneath our feet, the entire globe, is electrically wired,” said Nikhil Malvankar, assistant professor of molecular biophysics and biochemistry at the Microbial Science Institute at Yale’s West Campus and senior author of the paper. “These previously hidden bacterial hairs are the molecular switch controlling the release of nanowires that make up nature’s electrical grid.”

    Almost all living things breathe oxygen to get rid of excess electrons when converting nutrients into energy. Without access to oxygen, however, soil bacteria living deep under oceans or buried underground over billions of years have developed a way to respire by “breathing minerals,” like snorkeling, through tiny protein filaments called nanowires.

    Just how these soil bacteria use nanowires to exhale electricity, however, has remained a mystery. Since 2005, scientists had thought that the nanowires are made up of a protein called “pili” (“hair” in Latin) that many bacteria show on their surface. However, in research published 2019 [Cell] and 2020 [Nature Chemical Biology], a team led by Malvankar showed that nanowires are made of entirely different proteins. “This was a surprise to everyone in the field, calling into question thousands of publications about pili,” Malvankar said.

    For the new study, graduate students Yangqi Gu and Vishok Srikanth used cryo-electron microscopy to reveal that this pili structure is made up of two proteins And instead of serving as nanowires themselves, pili remain hidden inside the bacteria and act like pistons, thrusting the nanowires into the environment. Previously nobody had suspected such a structure.

    Hidden bacterial hairs power nature’s ‘electric grid’.

    Understanding how bacteria create nanowires will allow scientists to tailor bacteria to perform a host of functions — from combatting pathogenic infections or biohazard waste to creating living electrical circuits, the authors say. It will also assist scientists seeking to use bacteria to generate electricity, create biofuels, and even develop self-repairing electronics.

    Other authors are Aldo Salazar-Morales, Ruchi Jain, Patrick O’Brien, Sophia Yi, Fadel A. Samatey, and Sibel Ebru Yalcin, all from Yale, as well as Rajesh Soni from Columbia University (US).

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    Yale University (US) is a private Ivy League research university in New Haven, Connecticut. Founded in 1701 as the Collegiate School, it is the third-oldest institution of higher education in the United States and one of the nine Colonial Colleges chartered before the American Revolution. The Collegiate School was renamed Yale College in 1718 to honor the school’s largest private benefactor for the first century of its existence, Elihu Yale. Yale University is consistently ranked as one of the top universities and is considered one of the most prestigious in the nation.

    Chartered by Connecticut Colony, the Collegiate School was established in 1701 by clergy to educate Congregational ministers before moving to New Haven in 1716. Originally restricted to theology and sacred languages, the curriculum began to incorporate humanities and sciences by the time of the American Revolution. In the 19th century, the college expanded into graduate and professional instruction, awarding the first PhD in the United States in 1861 and organizing as a university in 1887. Yale’s faculty and student populations grew after 1890 with rapid expansion of the physical campus and scientific research.

    Yale is organized into fourteen constituent schools: the original undergraduate college, the Yale Graduate School of Arts and Sciences and twelve professional schools. While the university is governed by the Yale Corporation, each school’s faculty oversees its curriculum and degree programs. In addition to a central campus in downtown New Haven, the university owns athletic facilities in western New Haven, a campus in West Haven, Connecticut, and forests and nature preserves throughout New England. As of June 2020, the university’s endowment was valued at $31.1 billion, the second largest of any educational institution. The Yale University Library, serving all constituent schools, holds more than 15 million volumes and is the third-largest academic library in the United States. Students compete in intercollegiate sports as the Yale Bulldogs in the NCAA Division I – Ivy League.

    As of October 2020, 65 Nobel laureates, five Fields Medalists, four Abel Prize laureates, and three Turing award winners have been affiliated with Yale University. In addition, Yale has graduated many notable alumni, including five U.S. Presidents, 19 U.S. Supreme Court Justices, 31 living billionaires, and many heads of state. Hundreds of members of Congress and many U.S. diplomats, 78 MacArthur Fellows, 252 Rhodes Scholars, 123 Marshall Scholars, and nine Mitchell Scholars have been affiliated with the university.


    Yale is a member of the Association of American Universities (AAU) (US) and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation (US), Yale spent $990 million on research and development in 2018, ranking it 15th in the nation.

    Yale’s faculty include 61 members of the National Academy of Sciences (US), 7 members of the National Academy of Engineering (US) and 49 members of the American Academy of Arts and Sciences (US). The college is, after normalization for institution size, the tenth-largest baccalaureate source of doctoral degree recipients in the United States, and the largest such source within the Ivy League.

    Yale’s English and Comparative Literature departments were part of the New Criticism movement. Of the New Critics, Robert Penn Warren, W.K. Wimsatt, and Cleanth Brooks were all Yale faculty. Later, the Yale Comparative literature department became a center of American deconstruction. Jacques Derrida, the father of deconstruction, taught at the Department of Comparative Literature from the late seventies to mid-1980s. Several other Yale faculty members were also associated with deconstruction, forming the so-called “Yale School”. These included Paul de Man who taught in the Departments of Comparative Literature and French, J. Hillis Miller, Geoffrey Hartman (both taught in the Departments of English and Comparative Literature), and Harold Bloom (English), whose theoretical position was always somewhat specific, and who ultimately took a very different path from the rest of this group. Yale’s history department has also originated important intellectual trends. Historians C. Vann Woodward and David Brion Davis are credited with beginning in the 1960s and 1970s an important stream of southern historians; likewise, David Montgomery, a labor historian, advised many of the current generation of labor historians in the country. Yale’s Music School and Department fostered the growth of Music Theory in the latter half of the 20th century. The Journal of Music Theory was founded there in 1957; Allen Forte and David Lewin were influential teachers and scholars.

    In addition to eminent faculty members, Yale research relies heavily on the presence of roughly 1200 Postdocs from various national and international origin working in the multiple laboratories in the sciences, social sciences, humanities, and professional schools of the university. The university progressively recognized this working force with the recent creation of the Office for Postdoctoral Affairs and the Yale Postdoctoral Association.

    Notable alumni

    Over its history, Yale has produced many distinguished alumni in a variety of fields, ranging from the public to private sector. According to 2020 data, around 71% of undergraduates join the workforce, while the next largest majority of 16.6% go on to attend graduate or professional schools. Yale graduates have been recipients of 252 Rhodes Scholarships, 123 Marshall Scholarships, 67 Truman Scholarships, 21 Churchill Scholarships, and 9 Mitchell Scholarships. The university is also the second largest producer of Fulbright Scholars, with a total of 1,199 in its history and has produced 89 MacArthur Fellows. The U.S. Department of State Bureau of Educational and Cultural Affairs ranked Yale fifth among research institutions producing the most 2020–2021 Fulbright Scholars. Additionally, 31 living billionaires are Yale alumni.

    At Yale, one of the most popular undergraduate majors among Juniors and Seniors is political science, with many students going on to serve careers in government and politics. Former presidents who attended Yale for undergrad include William Howard Taft, George H. W. Bush, and George W. Bush while former presidents Gerald Ford and Bill Clinton attended Yale Law School. Former vice-president and influential antebellum era politician John C. Calhoun also graduated from Yale. Former world leaders include Italian prime minister Mario Monti, Turkish prime minister Tansu Çiller, Mexican president Ernesto Zedillo, German president Karl Carstens, Philippine president José Paciano Laurel, Latvian president Valdis Zatlers, Taiwanese premier Jiang Yi-huah, and Malawian president Peter Mutharika, among others. Prominent royals who graduated are Crown Princess Victoria of Sweden, and Olympia Bonaparte, Princess Napoléon.

    Yale alumni have had considerable presence in U.S. government in all three branches. On the U.S. Supreme Court, 19 justices have been Yale alumni, including current Associate Justices Sonia Sotomayor, Samuel Alito, Clarence Thomas, and Brett Kavanaugh. Numerous Yale alumni have been U.S. Senators, including current Senators Michael Bennet, Richard Blumenthal, Cory Booker, Sherrod Brown, Chris Coons, Amy Klobuchar, Ben Sasse, and Sheldon Whitehouse. Current and former cabinet members include Secretaries of State John Kerry, Hillary Clinton, Cyrus Vance, and Dean Acheson; U.S. Secretaries of the Treasury Oliver Wolcott, Robert Rubin, Nicholas F. Brady, Steven Mnuchin, and Janet Yellen; U.S. Attorneys General Nicholas Katzenbach, John Ashcroft, and Edward H. Levi; and many others. Peace Corps founder and American diplomat Sargent Shriver and public official and urban planner Robert Moses are Yale alumni.

    Yale has produced numerous award-winning authors and influential writers, like Nobel Prize in Literature laureate Sinclair Lewis and Pulitzer Prize winners Stephen Vincent Benét, Thornton Wilder, Doug Wright, and David McCullough. Academy Award winning actors, actresses, and directors include Jodie Foster, Paul Newman, Meryl Streep, Elia Kazan, George Roy Hill, Lupita Nyong’o, Oliver Stone, and Frances McDormand. Alumni from Yale have also made notable contributions to both music and the arts. Leading American composer from the 20th century Charles Ives, Broadway composer Cole Porter, Grammy award winner David Lang, and award-winning jazz pianist and composer Vijay Iyer all hail from Yale. Hugo Boss Prize winner Matthew Barney, famed American sculptor Richard Serra, President Barack Obama presidential portrait painter Kehinde Wiley, MacArthur Fellow and contemporary artist Sarah Sze, Pulitzer Prize winning cartoonist Garry Trudeau, and National Medal of Arts photorealist painter Chuck Close all graduated from Yale. Additional alumni include architect and Presidential Medal of Freedom winner Maya Lin, Pritzker Prize winner Norman Foster, and Gateway Arch designer Eero Saarinen. Journalists and pundits include Dick Cavett, Chris Cuomo, Anderson Cooper, William F. Buckley, Jr., and Fareed Zakaria.

    In business, Yale has had numerous alumni and former students go on to become founders of influential business, like William Boeing (Boeing, United Airlines), Briton Hadden and Henry Luce (Time Magazine), Stephen A. Schwarzman (Blackstone Group), Frederick W. Smith (FedEx), Juan Trippe (Pan Am), Harold Stanley (Morgan Stanley), Bing Gordon (Electronic Arts), and Ben Silbermann (Pinterest). Other business people from Yale include former chairman and CEO of Sears Holdings Edward Lampert, former Time Warner president Jeffrey Bewkes, former PepsiCo chairperson and CEO Indra Nooyi, sports agent Donald Dell, and investor/philanthropist Sir John Templeton,

    Yale alumni distinguished in academia include literary critic and historian Henry Louis Gates, economists Irving Fischer, Mahbub ul Haq, and Nobel Prize laureate Paul Krugman; Nobel Prize in Physics laureates Ernest Lawrence and Murray Gell-Mann; Fields Medalist John G. Thompson; Human Genome Project leader and National Institutes of Health (US) director Francis S. Collins; brain surgery pioneer Harvey Cushing; pioneering computer scientist Grace Hopper; influential mathematician and chemist Josiah Willard Gibbs; National Women’s Hall of Fame inductee and biochemist Florence B. Seibert; Turing Award recipient Ron Rivest; inventors Samuel F.B. Morse and Eli Whitney; Nobel Prize in Chemistry laureate John B. Goodenough; lexicographer Noah Webster; and theologians Jonathan Edwards and Reinhold Niebuhr.

    In the sporting arena, Yale alumni include baseball players Ron Darling and Craig Breslow and baseball executives Theo Epstein and George Weiss; football players Calvin Hill, Gary Fenick, Amos Alonzo Stagg, and “the Father of American Football” Walter Camp; ice hockey players Chris Higgins and Olympian Helen Resor; Olympic figure skaters Sarah Hughes and Nathan Chen; nine-time U.S. Squash men’s champion Julian Illingworth; Olympic swimmer Don Schollander; Olympic rowers Josh West and Rusty Wailes; Olympic sailor Stuart McNay; Olympic runner Frank Shorter; and others.

  • richardmitnick 9:05 am on September 4, 2021 Permalink | Reply
    Tags: "Building a better chemical factory—out of microbes", , , , Bioprocess engineering, , , , , , Glucaric acid, Metabolic engineering, Metabolite valve, Microbiology, MIT Technology Review (US), ,   

    From MIT Technology Review (US) : “Building a better chemical factory—out of microbes” 

    From MIT Technology Review (US)

    August 24, 2021
    Leigh Buchanan

    Credit: Sasha Israel.

    Professor Kristala Jones Prather ’94 has made it practical to turn microbes into efficient producers of desired chemicals. She’s also working to reduce our dependence on petroleum.

    Metabolic engineers have a problem: cells are selfish. The scientists want to use microbes to produce chemical compounds for industrial applications. The microbes prefer to concentrate on their own growth.

    Kristala L. Jones Prather ’94 has devised a tool that satisfies both conflicting objectives. Her metabolite valve acts like a train switch: it senses when a cell culture has reproduced enough to sustain itself and then redirects metabolic flux—the movement of molecules in a pathway—down the track that synthesizes the desired compound. The results: greater yield of the product and sufficient cell growth to keep the culture healthy and productive.

    William E. Bentley, a professor of bioengineering at The University of Maryland (US), has been following Prather’s work for more than two decades. He calls the valves “a new principle in engineering” that he anticipates will be highly valued in the research community. Their ability to eliminate bottlenecks can prove so essential to those attempting to synthesize a particular molecule in useful quantities that “in many cases it might decide whether it is a successful endeavor or not,” says Bentley.

    Prather, The Massachusetts Institute of Technology (US)’s Arthur D. Little Professor of Chemical Engineering, labors in the intersecting fields of synthetic biology and metabolic engineering: a place where science, rather than art, imitates life. The valves play a major role in her larger goal of programming microbes—chiefly E. coli—to produce chemicals that can be used in a wide range of fields, including energy and medicine. She does that by observing what nature can do. Then she hypothesizes what it should be able to do with an assist from strategically inserted DNA.

    “We are increasing the synthetic capacity of biological systems,” says Prather, who made MIT Technology Review’s TR35 list in 2007. “We need to push beyond what biology can naturally do and start getting it to make compounds that it doesn’t normally make.”

    Prather describes her work as creating a new kind of chemical factory inside microbial cells—one that makes ultra-pure compounds efficiently at scale. Coaxing microbes into producing desired compounds is safer and more environmentally friendly than relying on traditional chemical synthesis, which typically involves high temperatures, high pressures, and complicated instrumentation—and, often, toxic by-products. She didn’t originate the idea of turning microbes into chemical factories, but her lab is known for developing tools and fine-tuning processes that make it efficient and practical.

    That’s the approach she has taken with glucaric acid, which has multiple commercial applications, some of them green. Water treatment plants, for example, have long relied on phosphates to prevent corrosion in pipes and to bind with metals like lead and copper so they don’t leach into the water supply. But phosphates also feed algae blooms in lakes and oceans. Glucaric acid does the same work as phosphates without feeding those toxic blooms.

    Producing glucaric acid the usual way—through chemical oxidation of glucose—is expensive, often yields product that isn’t very pure, and creates a lot of hazardous waste. Prather’s microbial factories produce it with high levels of purity and without the toxic by-products, at a reasonable cost. She cofounded the startup Kalion in 2011 to put her microbial-factory approach into practice. (Prather is Kalion’s chief science officer. Her husband, Darcy Prather ’91, is its president.)

    The company, which is lining up large-scale production in Slovakia, has several prospective customers. Although the largest of these are in oil services, “it also turns out, in the wonderful, wacky way chemistry works, that the same compound is used in pharmaceutical manufacturing,” Prather says. It’s required, for example, in production of the ADHD drug Adderall. And it can be used to make textiles stronger, which could lead to more effective recycling of cotton and other natural materials.

    Kalion’s first target is phosphates, because of their immediate commercial applications. But in her wider research, Prather has also drawn a great big bull’s-eye on petroleum. Eager to produce greener alternatives to gasoline and plastics, she and her research group at MIT are using bacteria to synthesize molecules that would normally be derived from petroleum. “Big picture, if we are successful,” Prather says, “what we are doing is moving things one by one off the shelf to say, ‘That no longer is made from petroleum. That now is made from biomass.’”

    From East Texas to MIT

    Born in Cincinnati, Prather grew up in Longview, Texas, against a backdrop of oilfield pumps and derricks. Her father died before she turned two. Her mother worked at Wylie College, a small, historically Black school—and earned a bachelor’s degree there herself in 2004, Prather is quick to add.

    Her high school’s first valedictorian of color, Prather had only vague ideas about academic and professional opportunities outside her state. With college brochures flooding the family’s mailbox in her junior year, she sought advice from a history teacher. “Math was my favorite subject in high school, and I was enjoying chemistry,” says Prather. The teacher told her that math plus chemistry equaled chemical engineering, and that if she wanted to be an engineer she should go to The Massachusetts Institute of Technology (US). “What’s MIT?” asked Prather.

    Others in the community were no better informed. What was then the DeVry Institute of Technology, a for-profit school with a less-than-stellar academic reputation and campuses around the country, was advertising heavily on television. When she told people she was going to MIT, they assumed it was a DeVry branch in Massachusetts. “They were disappointed, because they thought I was going to do great things,” says Prather. “But here I was going to this trade school to be a plumber’s assistant.”

    In June 1990 Prather arrived on campus to participate in Interphase, a program offered through MIT’s Office of Minority Education. Designed to ease the transition for incoming students, Interphase “was a game-changer,” says Prather. The program introduced her to an enduring group of friends and familiarized her with the campus. Most important, it instilled confidence. Coming from a school without AP classes, Prather had worried about starting off behind the curve. When she found she knew the material in her Interphase math class, it came as a relief. “When I was bored, I thought, ‘I belong here,’” she says.

    As an undergraduate Prather was exposed to bioprocess engineering, which uses living cells to induce desired chemical or physical changes in a material. At that time scientists treated the cells from which the process starts as something fixed. Prather became intrigued by the idea that you could engineer not only the process but also the biology of the cell itself. “The way you could copy and cut and paste DNA appealed to the part of me that liked math,” she says.

    After graduating in 1994, Prather got her PhD at The University of California-Berkeley (US), where her advisor was Jay Keasling, a professor of chemical and biomolecular engineering who was at the forefront of the new field of synthetic biology. At Berkeley, Prather sought ways to move DNA in and out of cells to optimize the creation of desirable proteins.

    The practice at that time was to bulk up cells with lots of DNA, which would in turn produce lots of protein, which would generate lots of the desired chemical compound. But there was a problem, which Prather—who lives near a scenic state park—explains with a local analogy. “I can go for a light hike in the Blue Hills Reservation,” she says, “but not if you put a 50-pound pack on my back.” Similarly, an overloaded cell “can sometimes respond by saying, ‘I am too tired.’” Prather’s doctoral thesis explored systems that efficiently produce a lot of a desired chemical using less DNA.

    In her fourth year at Berkeley, Prather received a fellowship from DuPont and traveled to Delaware for her first full-length presentation. Following standard conference practice, she laid out for her audience the three motivations underlying her research. Afterward, one of the company’s scientists politely explained to her why all three were misguided. “He said, ‘What you are doing is interesting and important, but you are motivated by what you think is important in industry,’” says Prather. “‘And we just don’t care about any of that stuff.’”

    Humbled, Prather decided a sojourn in the corporate world would reduce the risk that her academic career would be consigned to real-world irrelevance. She spent the next four years at Merck, in a group developing processes to make things like therapeutic proteins and vaccines. There she learned about the kinds of projects and problems that matter most to practitioners like her DuPont critic.

    Merck employed hordes of chemists to produce large quantities of chemical compounds for use in new drugs. When part of that process seemed better suited to biology than to chemistry, they would hand it off to the department Prather worked in, which used enzymes to perform the next step. “They were typically not very complicated reactions,” says Prather. “A single step converting A to B.”

    Prather was intrigued by the possibility of performing not just individual steps but the entire chemical synthesis within cells, using chains of reactions called metabolic pathways. That work inspired what would become some of her most acclaimed research at MIT, where she joined the faculty in 2004.

    Finding the production switch

    It wasn’t long after returning to MIT that this young woman from the Texas oil patch took aim at fossil fuels and their by-­products. Many of her lab’s projects focus on replacing petroleum as a feedstock. In one—a collaboration with MIT colleagues Brad Olsen ’03, a chemical engineer, and Desiree Plata, PhD ’09, a civil and environmental engineer—Prather is using biomass to create renewable polymers that could lead to a greener kind of plastic. Her lab is figuring out how to induce microbes to convert sugar from plants into monomers that can then be chemically converted into polymers to create plastic. At the end of the plastic’s usable life, it biodegrades and turns back into nutrients. Those nutrients “will give you more plants from which you can extract more sugar that you can turn into new chemicals to go into new plastics,” says Prather. “It’s the circle of life there.”

    These days she is drawing the most attention for her research in optimizing metabolic pathways—research that she and other scientists can then use to maximize the yield of a desired product.

    The challenge is that cells prioritize the use of nutrients, such as glucose, to grow rather than to manufacture these desirable compounds. More growth for the cell means less product for the scientist. “So you run into a competition problem,” says Prather.

    Take glucaric acid, the chemical produced by Prather’s company—and one that Keasling says is extremely important to industry. (“These molecules are not trivial to produce, particularly at the levels that are needed industrially,” he says.) Prather and her lab had been adding three genes—drawn from mice, yeast, and a bacterium—to E. coli, enabling the bacteria to transform a type of simple sugar into glucaric acid. But the bacteria also needed that sugar for a metabolic pathway that breaks down glucose to feed its own growth and reproduction.

    Prather’s team wanted to shut down the pathway nourishing growth and divert the sugar into a pathway producing glucaric acid—but only after the bacterial culture had grown enough to sustain itself as a productive chemical factory. To do so they used quorum sensing, a kind of communication through which bacteria share information about changes in the number of cells in their colony, which allows them to coordinate colony-wide functions such as gene regulation. The team engineered each cell to produce a protein that then creates a molecule called AHL. When quorum sensing detects a certain amount of AHL—the amount produced in the time it takes for the culture to reach a sustainable size—it activates a switch that turns off production of an enzyme that is part of the glucose breakdown process. The glucose shifts to the chemical-synthesis pathway, greatly increasing the amount of glucaric acid produced.

    Prather’s switches, called metabolite valves, are now used in processes that harness microbes to produce a wide range of desired chemicals. The valves open or close in response to changes in the density of particular molecules in a pathway. These switches can be fine-tuned to optimize production without compromising the health of the bacteria, dramatically increasing output. The researchers’ flagship paper, which was published in Nature Biology in 2017, has been cited almost 200 times. The goal at this point is to step up the scale.

    Like many of the mechanisms Prather uses in her research, such switches already exist in biology. Cells whose resources are threatened by neighboring foreign cells will switch from growth mode to producing antibiotics to kill off their competitors, for example. “Cells that make things like antibiotics have a natural way of first making more of themselves, then putting their resources into making product,” she says. “We developed a synthetic way of mimicking nature.”

    Prather’s Berkeley advisor, Keasling, has been using a derivative of the switch inspired by her research. “The tool for channeling metabolic flux—the flow of material through a metabolic pathway—is super-important work that I think will be widely used in the future by metabolic engineers,” he says. “When Kristala publishes something, you know it is going to work.”

    Mentoring young scientists

    Prather receives at least as much recognition for teaching and mentoring as for her research. “She cares deeply about education and is invested in her students in a way that really stands out,” says Keasling. Students describe her optimism and supportiveness, saying that she motivates without commanding. “She created an environment where I was free to make my own mistakes and learn and grow,” says Kevin V. Solomon, SM ’08, PhD ’12, who studied with Prather between 2007 and 2012 and is now an assistant professor of chemical and biomedical engineering at The University of Delaware (US). In some other labs, he notes, “you have hard deadlines, and you perform or you freak out.”

    It was at Merck that Prather realized how much she loves working with young scientists—and it was also where she assembled the management arsenal she uses to run her lab. So, for example, she makes sure to get to know each student’s preferences about communication style, because “treating everyone fairly is not the same as treating everyone the same,” she says. One-on-one meetings commence with a few minutes of chat about general topics, so Prather can suss out students’ states of mind and make sure they are okay. She sets clear standards, intent on avoiding the uncertainty about expectations that is common in academic labs. And when students do raise concerns, “it is important to document and confirm that they have been heard,” she says.

    The most effective leaders model the behaviors they want to see in others. Prather, who received MIT’s Martin Luther King Leadership Award in 2017, expects commitment and high performance from her grad students and postdocs, but not at the cost of their physical or mental health. She discourages working on weekends—to the extent that is possible in biology—and insists that lab members take vacations. And from the beginning she has demonstrated that it is possible to simultaneously do first-class science and have a personal life.

    Prather’s two daughters were both campus kids. She was 31, with a two-month-old baby, when she joined the faculty, and she would nurse her daughter in her office before leaving her at the Institute’s new infant-care facility. Later, she set up a small table and chairs near her desk as a play area. The children have accompanied her on work trips—Prather and her husband took turns watching them when they were small—and frequently attend their mother’s evening and weekend events. Prather recalls turning up for a presentation in 32-123 with both children in tow and setting them up with snacks in the front row. “My daughter promptly dropped the marinara sauce to go with her mozzarella sticks on the floor,” she says. “I was on my hands and knees wiping up red sauce 15 minutes before giving a talk.”

    Prather does set boundaries. She turns down almost every invitation for Friday nights, which is family time. Trips are limited to two a month, and she won’t travel on any family member’s birthday or on her anniversary. But she also welcomes students into her home, where she hosts barbecues and Thanksgiving dinners for anyone without a place to go. “I bring them into my home and into my life,” she says.

    When Solomon was Prather’s student, she even hosted his parents. That hospitality continued after he graduated, when he and his mother ran into his former professor at a conference in Germany. “She graciously kept my mom occupied because she knew I was networking to further my career,” says Solomon.

    It was an act in keeping with Prather’s priorities. Beyond the innovations, beyond the discoveries, her overarching objective is to create independently successful scientists. “The most important thing we do as scientists is to train students and postdocs,” she says. “If your students are well trained and ready to advance knowledge—even if the thing we are working on goes nowhere—to me that is a win.”

    On being Black at MIT-Bearing witness to racism

    As a student at MIT, Kristala Jones Prather ’94 was never the target of racist behavior. But she says other Black students weren’t so lucky. Even though no one challenged her directly, “there was a general atmosphere on campus that questioned the validity of my existence,” she says. Articles in The Tech claimed that affirmative action was diluting the quality of the student pool.

    During her junior year, a group standing on the roof of a frat hurled racial slurs at Black students walking back to their dorm. In response, Prather and another student collaborated with Clarence G. Williams, HM ’09, special assistant to the president, to produce a documentary called It’s Intuitively Obvious about the experience of Black students at MIT.

    “I was involved in a lot of activism to create a climate where students didn’t have to be subjected to the notion that MIT was doing charity,” says Prather. Rather, “it was providing an opportunity for students who had demonstrated their capacity to represent the institution proudly.”

    Prather’s decision to return to MIT as a faculty member was difficult, in part because her Black former classmates, many of whom had experienced overt racism, were discouraging their own children from attending. She worried, too, that she wouldn’t be able to avoid personal attacks this time around. “I didn’t want all the positive feelings I had about MIT to be ruined,” she says.

    Those fears turned out to be unfounded. Prather says she has received tremendous support from her department head and colleagues, as well as abundant leadership opportunities. But she recognizes that not all her peers can say the same. She is guardedly optimistic about the Institute’s current diversity initiative. “We are making progress,” she says. “I am waiting to see if there’s a real commitment to creating an environment where students of color can feel like the Institute is a home for them.”

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    The mission of MIT Technology Review (US) is to equip its audiences with the intelligence to understand a world shaped by technology.

  • richardmitnick 3:29 pm on August 19, 2021 Permalink | Reply
    Tags: "Blue-green algae key to unlocking secrets of ancient past", , Around 2500 million years ago young Earth was unrecognisable. No ozone layer existed and there was no oxygen to breathe in the atmosphere., , , , Cyanobacteria are the only bacteria capable of oxygenic photosynthesis-the process also used by plants to convert carbon dioxide into oxygen using sunlight., Cyanobacteria began using antioxidants called superoxide dismutase enzymes (SODs) to manage reactive oxygen., Cyanobacteria worked out early in their evolution how to protect themselves against the side effects of oxygen., , Microbiology, The planet was dominated by microbes.,   

    From University of Bristol (UK) : “Blue-green algae key to unlocking secrets of ancient past” 

    From University of Bristol (UK)

    17 August 2021

    Oxygen-producing bacteria emerged a thousand millions years before the great oxygenation event approximately 2400 million years ago, scientists have found.

    The blue green algae, which is responsible for seeping oxygen into the Earth’s atmosphere, changing the planet forever, diversified from its relatives to cope with the rise of the gas.

    To understand how oxygen shaped early life, scientists at the University of Bristol have been investigating when cyanobacteria evolved and when they began using antioxidants called superoxide dismutase enzymes (SODs) to manage reactive oxygen.

    They devised a ‘molecular clock’ using geochemical records, cyanobacteria fossils and genetic information to create a timeline of events.

    Around 2500 million years ago young Earth was unrecognisable. No ozone layer existed and there was no oxygen to breathe in the atmosphere. Instead, the planet was dominated by microbes. Cyanobacteria are the only bacteria capable of oxygenic photosynthesis-the process also used by plants to convert carbon dioxide into oxygen using sunlight. Today, cyanobacteria are widespread throughout the ocean, but then they were mostly restricted to freshwater and land.

    Oxygen is highly reactive and toxic. Cyanobacteria uses SODs to protect against e these effects which all have different evolutionary origins – and use different trace metals.

    Group leader author of the paper Dr Patricia Sanchez-Baracaldo of Bristol’s School of Geographical Sciences said: “We studied the evolutionary history of four of these antioxidant enzymes: NiSOD, CuZnSOD and Fe- and Mn-utilising SODs. Such SODs are found in everything from animals to plants and bacteria, where they manage ROS by converting superoxide free radicals into hydrogen peroxide.

    PhD student, Joanne Boden said: “We discovered that cyanobacteria had acquired their SOD genes from other bacteria on several occasions throughout history. As a result, different strains used different antioxidant enzymes depending on their circumstances. For example, cyanobacteria which live planktonic lifestyles, floating in the ocean, often use NiSOD. Whereas most cyanobacteria, regardless of their habitat, use Mn- or Fe-SODs.

    “The evolutionary trajectory of a different SOD, using copper and zinc cofactors instead of nickel matched those of older, more ancestral cyanobacteria which diversified at least 2,700 million years ago. This suggests that oxygen-producing bacteria were equipped with mechanisms of managing ROS before the global atmosphere was flooded with oxygen.”

    This genomic record, which has been published in Nature Communications, contains vital information about ancient habitats and proves the existence of life on land and in the ocean at that time.

    Dr Sanchez-Baracaldo said: “Cyanobacteria worked out early in their evolution how to protect themselves against the side effects of oxygen.

    “Our analyses of metalloenzymes dealing with reactive oxygen species (ROS) show that marine geochemical records alone may not predict patterns of metal usage by living organisms found in other environments such as freshwater and terrestrial habitats.”

    The team now plan to investigate when other antioxidants evolved.

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    U Bristol (UK) is one of the most popular and successful universities in the UK and was ranked within the top 50 universities in the world in the QS World University Rankings 2018.

    The University of Bristol (UK) is at the cutting edge of global research. We have made innovations in areas ranging from cot death prevention to nanotechnology.

    The University has had a reputation for innovation since its founding in 1876. Our research tackles some of the world’s most pressing issues in areas as diverse as infection and immunity, human rights, climate change, and cryptography and information security.

    The University currently has 40 Fellows of the Royal Society and 15 of the British Academy – a remarkable achievement for a relatively small institution.

    We aim to bring together the best minds in individual fields, and encourage researchers from different disciplines and institutions to work together to find lasting solutions to society’s pressing problems.

    We are involved in numerous international research collaborations and integrate practical experience in our curriculum, so that students work on real-life projects in partnership with business, government and community sectors.

  • richardmitnick 10:10 am on August 19, 2021 Permalink | Reply
    Tags: "New Technique Surveys Microbial Spatial Gene Expression Patterns", , , , , Microbiology, par-seqFISH: parallel and sequential fluorescence in situ hybridization   

    From California Institute of Technology (US) : “New Technique Surveys Microbial Spatial Gene Expression Patterns” 

    Caltech Logo

    From California Institute of Technology (US)

    August 16, 2021
    Lori Dajose
    (626) 395‑1217

    Left: A black-and-white image of a biofilm. Right: A closeup of a portion of this biofilm with individual cells circled and colors corresponding to the expression of particular genes. Credit: Courtesy of the Newman laboratory.

    What do you do at different times in the day? What do you eat? How do you interact with your neighbors? These are some of the questions that biologists would love to ask communities of microbes, from those that live in extreme environments deep in the ocean to those that cause chronic infections in humans. Now, a new technique developed at Caltech can answer these questions by surveying gene expression across a population of millions of bacterial cells while still preserving the cells’ positions relative to one another.

    The technique can be used to understand the wide variety of microbial communities on our planet, including the microbes that live within our gut and influence our health as well as those that colonize the roots of plants and contribute to soil health, to name a few.

    The technique was developed at Caltech by Daniel Dar, a former postdoctoral scholar in the laboratory of Dianne Newman, Gordon M. Binder/Amgen Professor of Biology and Geobiology and executive officer for biology and biological engineering, and by Dr. Nina Dar, a former senior research technician in the laboratory of Long Cai, professor of biology and biological engineering. Daniel Dar is now an assistant professor at the Weizmann Institute of Science (IL). A paper describing the research appears on August 12 in the journal Science.

    We cannot ask a bacterium what it is doing or how it is feeling, but we can look at the genes it is expressing. Gene expression is the basis of any behaviors or actions a microbe can take. For example, if there is a lack of food in a bacterium’s environment, the microbe can turn on a set of genes that will help it to conserve energy and dial back less necessary genes, such as those that are involved in reproduction. Though two bacteria in the same species can have the same genetic information, genes can be turned on and off in different situations, resulting in different behaviors at the individual bacterium level.

    “Traditional methods for measuring gene expression tend to minimize an entire population, in all of its complexity and three-dimensional organization, into a single number,” says Daniel Dar. “Imagine taking a tray of fruits with unique colors, flavors, and scents and having to blend them all together into a single smoothie. All identity is lost. The meaning of this technological limitation for microbiological research, both in medicine and environmental sciences, is that biological signatures that manifest at the microscale—the scale at which microorganisms make their living—remain mostly invisible. This was a major motivation for us along this collaborative study: building on the revolutionary technology first developed in the Cai lab to expose the complexity of microbial populations in a fundamentally new way.”

    The new technique, dubbed par-seqFISH (for parallel and sequential fluorescence in situ hybridization), can track these differences in gene expression with high precision. In this study, par-seqFISH was used to examine gene expression in populations of Pseudomonas aeruginosa, a pathogen that often causes infections (such as those found in the lungs of people with cystic fibrosis or within chronic skin wounds) and is studied extensively in the Newman laboratory. par-seqFISH can be used on virtually any species of bacteria whose genomes have been sequenced and on communities of microbes composed of different species.

    par-seqFISH is precise to the sub-micrometer level and is able to show differences in gene expression even within individual cells. For example, the team found that certain genes can be expressed more at the poles of a cell rather than near the center. The technique preserves the spatial organization of bacteria, or their positions relative to one another. Because of its level of precision, it revealed significant diversity in the gene expression and resulting activity of individual members of a population of the same species of bacteria.

    The method’s ability to image at this level of detail makes it a powerful technique for cellular biology research.

    “We saw patterns where certain genes were being expressed spatiotemporally—in space and in time—in ways that we would have never been able to predict, which suggested new ideas about how the population functions as a whole,” says Newman. “The heterogeneity of bacterial populations and communities at spatial scales on the order of a few micrometers is incredibly important and underappreciated. The profound thing that this technique hammers home is that context matters. Every cell is experiencing a slightly different microenvironment; for example, how much oxygen is around a given cell indicates what kind of metabolism that cell will engage in. Appreciating the full extent of such heterogeneities is necessary if we are to be able to manipulate these communities, such as being able to treat chronic bacterial infections. Understanding what all the members of the population are doing will help guide more effective therapeutic strategies.”

    seqFISH, the precursor technique to par-seqFISH, was pioneered in the Cai laboratory.

    “Every time we look at a biological system with both spatial context and genomics information, we find interesting new biology,” says Cai. “Microbial communities, with their rich diversity, show us again how beautiful and complex biology is when looked through the lens of spatial genomics.”

    Newman, who is the lead and faculty supervisor for the Ecology and Biosphere Engineering initiative at Caltech’s Resnick Sustainability Institute (RSI), envisions that the technology will be available to researchers across Caltech to utilize through RSI, assisting studies of microbes in diverse environments, from the soil around plant roots (called the rhizosphere) to deep-sea sediments.

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    The California Institute of Technology (US) is a private research university in Pasadena, California. The university is known for its strength in science and engineering, and is one among a small group of institutes of technology in the United States which is primarily devoted to the instruction of pure and applied sciences.

    Caltech was founded as a preparatory and vocational school by Amos G. Throop in 1891 and began attracting influential scientists such as George Ellery Hale, Arthur Amos Noyes, and Robert Andrews Millikan in the early 20th century. The vocational and preparatory schools were disbanded and spun off in 1910 and the college assumed its present name in 1920. In 1934, Caltech was elected to the Association of American Universities, and the antecedents of National Aeronautics and Space Administration (US)’s Jet Propulsion Laboratory, which Caltech continues to manage and operate, were established between 1936 and 1943 under Theodore von Kármán.

    Caltech has six academic divisions with strong emphasis on science and engineering. Its 124-acre (50 ha) primary campus is located approximately 11 mi (18 km) northeast of downtown Los Angeles. First-year students are required to live on campus, and 95% of undergraduates remain in the on-campus House System at Caltech. Although Caltech has a strong tradition of practical jokes and pranks, student life is governed by an honor code which allows faculty to assign take-home examinations. The Caltech Beavers compete in 13 intercollegiate sports in the NCAA Division III’s Southern California Intercollegiate Athletic Conference (SCIAC).

    As of October 2020, there are 76 Nobel laureates who have been affiliated with Caltech, including 40 alumni and faculty members (41 prizes, with chemist Linus Pauling being the only individual in history to win two unshared prizes). In addition, 4 Fields Medalists and 6 Turing Award winners have been affiliated with Caltech. There are 8 Crafoord Laureates and 56 non-emeritus faculty members (as well as many emeritus faculty members) who have been elected to one of the United States National Academies. Four Chief Scientists of the U.S. Air Force and 71 have won the United States National Medal of Science or Technology. Numerous faculty members are associated with the Howard Hughes Medical Institute(US) as well as National Aeronautics and Space Administration(US). According to a 2015 Pomona College(US) study, Caltech ranked number one in the U.S. for the percentage of its graduates who go on to earn a PhD.


    Caltech is classified among “R1: Doctoral Universities – Very High Research Activity”. Caltech was elected to the Association of American Universities in 1934 and remains a research university with “very high” research activity, primarily in STEM fields. The largest federal agencies contributing to research are National Aeronautics and Space Administration(US); National Science Foundation(US); Department of Health and Human Services(US); Department of Defense(US), and Department of Energy(US).

    In 2005, Caltech had 739,000 square feet (68,700 m^2) dedicated to research: 330,000 square feet (30,700 m^2) to physical sciences, 163,000 square feet (15,100 m^2) to engineering, and 160,000 square feet (14,900 m^2) to biological sciences.

    In addition to managing JPL, Caltech also operates the Caltech Palomar Observatory(US); the Owens Valley Radio Observatory(US);the Caltech Submillimeter Observatory(US); the W. M. Keck Observatory at the Mauna Kea Observatory(US); the Laser Interferometer Gravitational-Wave Observatory at Livingston, Louisiana and Richland, Washington; and Kerckhoff Marine Laboratory(US) in Corona del Mar, California. The Institute launched the Kavli Nanoscience Institute at Caltech in 2006; the Keck Institute for Space Studies in 2008; and is also the current home for the Einstein Papers Project. The Spitzer Science Center(US), part of the Infrared Processing and Analysis Center(US) located on the Caltech campus, is the data analysis and community support center for NASA’s Spitzer Infrared Space Telescope [no longer in service].

    Caltech partnered with University of California at Los Angeles(US) to establish a Joint Center for Translational Medicine (UCLA-Caltech JCTM), which conducts experimental research into clinical applications, including the diagnosis and treatment of diseases such as cancer.

    Caltech operates several Total Carbon Column Observing Network(US) stations as part of an international collaborative effort of measuring greenhouse gases globally. One station is on campus.

  • richardmitnick 9:35 am on August 19, 2021 Permalink | Reply
    Tags: "Stanford scientist recalls falling in love with microbes" Geomicrobiologist Paula Welander, , , Earth system science, Microbiology,   

    From Stanford University (US) : “Stanford scientist recalls falling in love with microbes” Geomicrobiologist Paula Welander 

    Stanford University Name

    From Stanford University (US)

    August 18, 2021
    Josie Garthwaite

    On an autumn day in 1997, Paula Welander watched an invasion in a Petri dish. Millions of rod-shaped Escherichia coli cells squiggled through jelly-like agar smeared on the plate, while predatory bacteria pursued and attacked the rapidly dividing cells.

    Paula Welander. Credit: Steve Castillo.

    Stanford’s Welander Lab discusses microbes, astrobiology, and searching for life on other planets.

    The high-speed transformation of the bacterial hordes under her microscope drew Welander, who is now an associate professor of Earth system science in Stanford’s School of Earth, Energy & Environmental Sciences (Stanford Earth), into a new world.

    “I just fell in love with microbes. I could put a drop in a culture tube and in a few hours have a complete population of these organisms,” she said. “And I had access to their genes and their proteins. Here was a system that would allow me in its simplicity to answer very complex questions. I could use microbes as a system to study life.”

    Welander is petite and quick to laugh. Listening to her describe her work in her sunny office on the Stanford campus, in a time before the coronavirus, microbes can begin to seem like both creative, scrappy beings and impressive machines. “Microbes have found different ways over billions of years of evolution to use their environment so they can just grow. We would never think to breathe arsenic; they breathe arsenic, or they’ll breathe iron and form rust as a byproduct. The only thing we can make is water and carbon dioxide.”

    Welander caught that first glimpse of the diversity of microbial life and the power of what she would later come to know as bench science as an undergraduate student at Occidental College-Los Angeles, California.

    The campus lies less than 30 miles from Welander’s childhood home, but her work in labs there helped her find a path that had been all but invisible in her upbringing. Her parents, who immigrated to Los Angeles from Mexico as teenagers in the early 1970s, had encouraged her to pursue medicine or law. “The idea of an academic career wasn’t something they had been exposed to,” Welander said.

    When a college professor and mentor encouraged Welander to pursue a career in bench science, Welander recalled, “I was like, wait, what does that even mean to be a scientist?” What it meant for Welander was starting out after graduation as a technician in a lab, where she studied the immune systems of mice dealing with herpes infections that go dormant and then suddenly reactivate.

    Working with mice made Welander realize something: She missed microbes.

    “Statistically, the number of mice we were looking at was just so low,” Welander said. “With microbes, for statistical significance, I could kill a million of them and then start a new culture the next day.”

    For Welander, who has begun most days since high school with an early morning run, the daily repetition demanded by laboratory research had hooked her from the start. “I fell in love with the ability to take a protocol and get a result, and if it doesn’t work, then you redo or rethink the experiment.”

    In grad school, at the The University of Illinois at Urbana-Champaign (US), Welander worked in a lab studying the only microbes that generate methane. The experience expanded her thinking from questions about how microbes affect human health and disease to how microbes exist with the Earth. “I realized that the reason the planet looks the way it does today is because of the life that’s on it,” she said. “The ecosystem would fall apart without microbes. That was true 100 million years ago, two billion years ago, even four and a half billion years ago when life was first starting to evolve.”

    After grad school, Welander worked as a postdoc with both a geologist and a geobiologist, and she began learning how to frame questions in a way that fed her curiosity about basic molecular biology while also enabling geologists to better interpret ecological records. She often found herself building intellectual and cultural bridges – familiar territory for a child of immigrants.

    “As a kid of immigrants, you’re bridging two worlds, because you’re at home and you’re speaking Spanish and you have these cultural norms, and then you’re shipped off to school where you’re then speaking English and you have these ambitions and goals and things that maybe don’t correlate well with what the goals are at home. You’re negotiating those two worlds,” Welander said. “I had to explain things to my parents and I had to explain things to my teachers and peers. It might have been why I was comfortable then making the leap from microbiology to studying molecular fossils.”

    Welander says that over time, she has grown more comfortable grappling with big questions about the early days of Earth and complex life. “I like systems that I can use to ask a very specific question and answer it in very fine detail, and then step back later to see if it has any implications for a bigger question,” she said.

    By examining fatty molecules made by marine bacteria, for example, Welander and colleagues have been able to show [PNAS] that a biomarker once thought to be produced only by flowering plants might also have been created by ancient bacteria – long before flowering plants evolved. And by deleting and mutating proteins in a type of microbe that thrives in extreme environments like Yellowstone’s highly acidic hot springs, she helped to prove a decades-old hypothesis about how the organism protects itself while simultaneously shedding light on its evolutionary origins.

    It’s the thrill of discovery at the smallest scales that still drives Welander’s work.

    “I’m uncovering biology that people have thought should happen but had no idea how it’s happening. A question will sit there for 40 years,” she said. “Then we find an answer by discovering new proteins, or a new fossil, or a new molecule made by some ancient organism. With microbes, you can always find new biology. We have just begun to scratch the surface of what’s there.”

    See the full article here .

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Stanford University campus
    Stanford University (US)

    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, officially Leland Stanford Junior University, is a private research university located in Stanford, California. Stanford was founded in 1885 by Leland and Jane Stanford in memory of their only child, Leland Stanford Jr., who had died of typhoid fever at age 15 the previous year. Stanford is consistently ranked as among the most prestigious and top universities in the world by major education publications. It is also one of the top fundraising institutions in the country, becoming the first school to raise more than a billion dollars in a year.

    Leland Stanford was a U.S. senator and former governor of California who made his fortune as a railroad tycoon. The school admitted its first students on October 1, 1891, as a coeducational and non-denominational institution. Stanford University struggled financially after the death of Leland Stanford in 1893 and again after much of the campus was damaged by the 1906 San Francisco earthquake. Following World War II, provost Frederick Terman supported faculty and graduates’ entrepreneurialism to build self-sufficient local industry in what would later be known as Silicon Valley.

    The university is organized around seven schools: three schools consisting of 40 academic departments at the undergraduate level as well as four professional schools that focus on graduate programs in law, medicine, education, and business. All schools are on the same campus. Students compete in 36 varsity sports, and the university is one of two private institutions in the Division I FBS Pac-12 Conference. It has gained 126 NCAA team championships, and Stanford has won the NACDA Directors’ Cup for 24 consecutive years, beginning in 1994–1995. In addition, Stanford students and alumni have won 270 Olympic medals including 139 gold medals.

    As of October 2020, 84 Nobel laureates, 28 Turing Award laureates, and eight Fields Medalists have been affiliated with Stanford as students, alumni, faculty, or staff. In addition, Stanford is particularly noted for its entrepreneurship and is one of the most successful universities in attracting funding for start-ups. Stanford alumni have founded numerous companies, which combined produce more than $2.7 trillion in annual revenue, roughly equivalent to the 7th largest economy in the world (as of 2020). Stanford is the alma mater of one president of the United States (Herbert Hoover), 74 living billionaires, and 17 astronauts. It is also one of the leading producers of Fulbright Scholars, Marshall Scholars, Rhodes Scholars, and members of the United States Congress.

    Stanford University was founded in 1885 by Leland and Jane Stanford, dedicated to Leland Stanford Jr, their only child. The institution opened in 1891 on Stanford’s previous Palo Alto farm.

    Jane and Leland Stanford modeled their university after the great eastern universities, most specifically Cornell University. Stanford opened being called the “Cornell of the West” in 1891 due to faculty being former Cornell affiliates (either professors, alumni, or both) including its first president, David Starr Jordan, and second president, John Casper Branner. Both Cornell and Stanford were among the first to have higher education be accessible, nonsectarian, and open to women as well as to men. Cornell is credited as one of the first American universities to adopt this radical departure from traditional education, and Stanford became an early adopter as well.

    Despite being impacted by earthquakes in both 1906 and 1989, the campus was rebuilt each time. In 1919, The Hoover Institution on War, Revolution and Peace was started by Herbert Hoover to preserve artifacts related to World War I. The Stanford Medical Center, completed in 1959, is a teaching hospital with over 800 beds. The DOE’s SLAC National Accelerator Laboratory(US)(originally named the Stanford Linear Accelerator Center), established in 1962, performs research in particle physics.


    Most of Stanford is on an 8,180-acre (12.8 sq mi; 33.1 km^2) campus, one of the largest in the United States. It is located on the San Francisco Peninsula, in the northwest part of the Santa Clara Valley (Silicon Valley) approximately 37 miles (60 km) southeast of San Francisco and approximately 20 miles (30 km) northwest of San Jose. In 2008, 60% of this land remained undeveloped.

    Stanford’s main campus includes a census-designated place within unincorporated Santa Clara County, although some of the university land (such as the Stanford Shopping Center and the Stanford Research Park) is within the city limits of Palo Alto. The campus also includes much land in unincorporated San Mateo County (including the SLAC National Accelerator Laboratory and the Jasper Ridge Biological Preserve), as well as in the city limits of Menlo Park (Stanford Hills neighborhood), Woodside, and Portola Valley.

    Non-central campus

    Stanford currently operates in various locations outside of its central campus.

    On the founding grant:

    Jasper Ridge Biological Preserve is a 1,200-acre (490 ha) natural reserve south of the central campus owned by the university and used by wildlife biologists for research.
    SLAC National Accelerator Laboratory is a facility west of the central campus operated by the university for the Department of Energy. It contains the longest linear particle accelerator in the world, 2 miles (3.2 km) on 426 acres (172 ha) of land.
    Golf course and a seasonal lake: The university also has its own golf course and a seasonal lake (Lake Lagunita, actually an irrigation reservoir), both home to the vulnerable California tiger salamander. As of 2012 Lake Lagunita was often dry and the university had no plans to artificially fill it.

    Off the founding grant:

    Hopkins Marine Station, in Pacific Grove, California, is a marine biology research center owned by the university since 1892.
    Study abroad locations: unlike typical study abroad programs, Stanford itself operates in several locations around the world; thus, each location has Stanford faculty-in-residence and staff in addition to students, creating a “mini-Stanford”.

    Redwood City campus for many of the university’s administrative offices located in Redwood City, California, a few miles north of the main campus. In 2005, the university purchased a small, 35-acre (14 ha) campus in Midpoint Technology Park intended for staff offices; development was delayed by The Great Recession. In 2015 the university announced a development plan and the Redwood City campus opened in March 2019.

    The Bass Center in Washington, DC provides a base, including housing, for the Stanford in Washington program for undergraduates. It includes a small art gallery open to the public.

    China: Stanford Center at Peking University, housed in the Lee Jung Sen Building, is a small center for researchers and students in collaboration with Beijing University [北京大学](CN) (Kavli Institute for Astronomy and Astrophysics at Peking University(CN) (KIAA-PKU).

    Administration and organization

    Stanford is a private, non-profit university that is administered as a corporate trust governed by a privately appointed board of trustees with a maximum membership of 38. Trustees serve five-year terms (not more than two consecutive terms) and meet five times annually.[83] A new trustee is chosen by the current trustees by ballot. The Stanford trustees also oversee the Stanford Research Park, the Stanford Shopping Center, the Cantor Center for Visual Arts, Stanford University Medical Center, and many associated medical facilities (including the Lucile Packard Children’s Hospital).

    The board appoints a president to serve as the chief executive officer of the university, to prescribe the duties of professors and course of study, to manage financial and business affairs, and to appoint nine vice presidents. The provost is the chief academic and budget officer, to whom the deans of each of the seven schools report. Persis Drell became the 13th provost in February 2017.

    As of 2018, the university was organized into seven academic schools. The schools of Humanities and Sciences (27 departments), Engineering (nine departments), and Earth, Energy & Environmental Sciences (four departments) have both graduate and undergraduate programs while the Schools of Law, Medicine, Education and Business have graduate programs only. The powers and authority of the faculty are vested in the Academic Council, which is made up of tenure and non-tenure line faculty, research faculty, senior fellows in some policy centers and institutes, the president of the university, and some other academic administrators, but most matters are handled by the Faculty Senate, made up of 55 elected representatives of the faculty.

    The Associated Students of Stanford University (ASSU) is the student government for Stanford and all registered students are members. Its elected leadership consists of the Undergraduate Senate elected by the undergraduate students, the Graduate Student Council elected by the graduate students, and the President and Vice President elected as a ticket by the entire student body.

    Stanford is the beneficiary of a special clause in the California Constitution, which explicitly exempts Stanford property from taxation so long as the property is used for educational purposes.

    Endowment and donations

    The university’s endowment, managed by the Stanford Management Company, was valued at $27.7 billion as of August 31, 2019. Payouts from the Stanford endowment covered approximately 21.8% of university expenses in the 2019 fiscal year. In the 2018 NACUBO-TIAA survey of colleges and universities in the United States and Canada, only Harvard University(US), the University of Texas System(US), and Yale University(US) had larger endowments than Stanford.

    In 2006, President John L. Hennessy launched a five-year campaign called the Stanford Challenge, which reached its $4.3 billion fundraising goal in 2009, two years ahead of time, but continued fundraising for the duration of the campaign. It concluded on December 31, 2011, having raised a total of $6.23 billion and breaking the previous campaign fundraising record of $3.88 billion held by Yale. Specifically, the campaign raised $253.7 million for undergraduate financial aid, as well as $2.33 billion for its initiative in “Seeking Solutions” to global problems, $1.61 billion for “Educating Leaders” by improving K-12 education, and $2.11 billion for “Foundation of Excellence” aimed at providing academic support for Stanford students and faculty. Funds supported 366 new fellowships for graduate students, 139 new endowed chairs for faculty, and 38 new or renovated buildings. The new funding also enabled the construction of a facility for stem cell research; a new campus for the business school; an expansion of the law school; a new Engineering Quad; a new art and art history building; an on-campus concert hall; a new art museum; and a planned expansion of the medical school, among other things. In 2012, the university raised $1.035 billion, becoming the first school to raise more than a billion dollars in a year.

    Research centers and institutes

    DOE’s SLAC National Accelerator Laboratory(US)
    Stanford Research Institute, a center of innovation to support economic development in the region.
    Hoover Institution, a conservative American public policy institution and research institution that promotes personal and economic liberty, free enterprise, and limited government.
    Hasso Plattner Institute of Design, a multidisciplinary design school in cooperation with the Hasso Plattner Institute of University of Potsdam [Universität Potsdam](DE) that integrates product design, engineering, and business management education).
    Martin Luther King Jr. Research and Education Institute, which grew out of and still contains the Martin Luther King Jr. Papers Project.
    John S. Knight Fellowship for Professional Journalists
    Center for Ocean Solutions
    Together with UC Berkeley(US) and UC San Francisco(US), Stanford is part of the Biohub, a new medical science research center founded in 2016 by a $600 million commitment from Facebook CEO and founder Mark Zuckerberg and pediatrician Priscilla Chan.

    Discoveries and innovation

    Natural sciences

    Biological synthesis of deoxyribonucleic acid (DNA) – Arthur Kornberg synthesized DNA material and won the Nobel Prize in Physiology or Medicine 1959 for his work at Stanford.
    First Transgenic organism – Stanley Cohen and Herbert Boyer were the first scientists to transplant genes from one living organism to another, a fundamental discovery for genetic engineering. Thousands of products have been developed on the basis of their work, including human growth hormone and hepatitis B vaccine.
    Laser – Arthur Leonard Schawlow shared the 1981 Nobel Prize in Physics with Nicolaas Bloembergen and Kai Siegbahn for his work on lasers.
    Nuclear magnetic resonance – Felix Bloch developed new methods for nuclear magnetic precision measurements, which are the underlying principles of the MRI.

    Computer and applied sciences

    ARPANETStanford Research Institute, formerly part of Stanford but on a separate campus, was the site of one of the four original ARPANET nodes.

    Internet—Stanford was the site where the original design of the Internet was undertaken. Vint Cerf led a research group to elaborate the design of the Transmission Control Protocol (TCP/IP) that he originally co-created with Robert E. Kahn (Bob Kahn) in 1973 and which formed the basis for the architecture of the Internet.

    Frequency modulation synthesis – John Chowning of the Music department invented the FM music synthesis algorithm in 1967, and Stanford later licensed it to Yamaha Corporation.

    Google – Google began in January 1996 as a research project by Larry Page and Sergey Brin when they were both PhD students at Stanford. They were working on the Stanford Digital Library Project (SDLP). The SDLP’s goal was “to develop the enabling technologies for a single, integrated and universal digital library” and it was funded through the National Science Foundation, among other federal agencies.

    Klystron tube – invented by the brothers Russell and Sigurd Varian at Stanford. Their prototype was completed and demonstrated successfully on August 30, 1937. Upon publication in 1939, news of the klystron immediately influenced the work of U.S. and UK researchers working on radar equipment.

    RISCARPA funded VLSI project of microprocessor design. Stanford and UC Berkeley are most associated with the popularization of this concept. The Stanford MIPS would go on to be commercialized as the successful MIPS architecture, while Berkeley RISC gave its name to the entire concept, commercialized as the SPARC. Another success from this era were IBM’s efforts that eventually led to the IBM POWER instruction set architecture, PowerPC, and Power ISA. As these projects matured, a wide variety of similar designs flourished in the late 1980s and especially the early 1990s, representing a major force in the Unix workstation market as well as embedded processors in laser printers, routers and similar products.
    SUN workstation – Andy Bechtolsheim designed the SUN workstation for the Stanford University Network communications project as a personal CAD workstation, which led to Sun Microsystems.

    Businesses and entrepreneurship

    Stanford is one of the most successful universities in creating companies and licensing its inventions to existing companies; it is often held up as a model for technology transfer. Stanford’s Office of Technology Licensing is responsible for commercializing university research, intellectual property, and university-developed projects.

    The university is described as having a strong venture culture in which students are encouraged, and often funded, to launch their own companies.

    Companies founded by Stanford alumni generate more than $2.7 trillion in annual revenue, equivalent to the 10th-largest economy in the world.

    Some companies closely associated with Stanford and their connections include:

    Hewlett-Packard, 1939, co-founders William R. Hewlett (B.S, PhD) and David Packard (M.S).
    Silicon Graphics, 1981, co-founders James H. Clark (Associate Professor) and several of his grad students.
    Sun Microsystems, 1982, co-founders Vinod Khosla (M.B.A), Andy Bechtolsheim (PhD) and Scott McNealy (M.B.A).
    Cisco, 1984, founders Leonard Bosack (M.S) and Sandy Lerner (M.S) who were in charge of Stanford Computer Science and Graduate School of Business computer operations groups respectively when the hardware was developed.[163]
    Yahoo!, 1994, co-founders Jerry Yang (B.S, M.S) and David Filo (M.S).
    Google, 1998, co-founders Larry Page (M.S) and Sergey Brin (M.S).
    LinkedIn, 2002, co-founders Reid Hoffman (B.S), Konstantin Guericke (B.S, M.S), Eric Lee (B.S), and Alan Liu (B.S).
    Instagram, 2010, co-founders Kevin Systrom (B.S) and Mike Krieger (B.S).
    Snapchat, 2011, co-founders Evan Spiegel and Bobby Murphy (B.S).
    Coursera, 2012, co-founders Andrew Ng (Associate Professor) and Daphne Koller (Professor, PhD).

    Student body

    Stanford enrolled 6,996 undergraduate and 10,253 graduate students as of the 2019–2020 school year. Women comprised 50.4% of undergraduates and 41.5% of graduate students. In the same academic year, the freshman retention rate was 99%.

    Stanford awarded 1,819 undergraduate degrees, 2,393 master’s degrees, 770 doctoral degrees, and 3270 professional degrees in the 2018–2019 school year. The four-year graduation rate for the class of 2017 cohort was 72.9%, and the six-year rate was 94.4%. The relatively low four-year graduation rate is a function of the university’s coterminal degree (or “coterm”) program, which allows students to earn a master’s degree as a 1-to-2-year extension of their undergraduate program.

    As of 2010, fifteen percent of undergraduates were first-generation students.


    As of 2016 Stanford had 16 male varsity sports and 20 female varsity sports, 19 club sports and about 27 intramural sports. In 1930, following a unanimous vote by the Executive Committee for the Associated Students, the athletic department adopted the mascot “Indian.” The Indian symbol and name were dropped by President Richard Lyman in 1972, after objections from Native American students and a vote by the student senate. The sports teams are now officially referred to as the “Stanford Cardinal,” referring to the deep red color, not the cardinal bird. Stanford is a member of the Pac-12 Conference in most sports, the Mountain Pacific Sports Federation in several other sports, and the America East Conference in field hockey with the participation in the inter-collegiate NCAA’s Division I FBS.

    Its traditional sports rival is the University of California, Berkeley, the neighbor to the north in the East Bay. The winner of the annual “Big Game” between the Cal and Cardinal football teams gains custody of the Stanford Axe.

    Stanford has had at least one NCAA team champion every year since the 1976–77 school year and has earned 126 NCAA national team titles since its establishment, the most among universities, and Stanford has won 522 individual national championships, the most by any university. Stanford has won the award for the top-ranked Division 1 athletic program—the NACDA Directors’ Cup, formerly known as the Sears Cup—annually for the past twenty-four straight years. Stanford athletes have won medals in every Olympic Games since 1912, winning 270 Olympic medals total, 139 of them gold. In the 2008 Summer Olympics, and 2016 Summer Olympics, Stanford won more Olympic medals than any other university in the United States. Stanford athletes won 16 medals at the 2012 Summer Olympics (12 gold, two silver and two bronze), and 27 medals at the 2016 Summer Olympics.


    The unofficial motto of Stanford, selected by President Jordan, is Die Luft der Freiheit weht. Translated from the German language, this quotation from Ulrich von Hutten means, “The wind of freedom blows.” The motto was controversial during World War I, when anything in German was suspect; at that time the university disavowed that this motto was official.
    Hail, Stanford, Hail! is the Stanford Hymn sometimes sung at ceremonies or adapted by the various University singing groups. It was written in 1892 by mechanical engineering professor Albert W. Smith and his wife, Mary Roberts Smith (in 1896 she earned the first Stanford doctorate in Economics and later became associate professor of Sociology), but was not officially adopted until after a performance on campus in March 1902 by the Mormon Tabernacle Choir.
    “Uncommon Man/Uncommon Woman”: Stanford does not award honorary degrees, but in 1953 the degree of “Uncommon Man/Uncommon Woman” was created to recognize individuals who give rare and extraordinary service to the University. Technically, this degree is awarded by the Stanford Associates, a voluntary group that is part of the university’s alumni association. As Stanford’s highest honor, it is not conferred at prescribed intervals, but only when appropriate to recognize extraordinary service. Recipients include Herbert Hoover, Bill Hewlett, Dave Packard, Lucile Packard, and John Gardner.
    Big Game events: The events in the week leading up to the Big Game vs. UC Berkeley, including Gaieties (a musical written, composed, produced, and performed by the students of Ram’s Head Theatrical Society).
    “Viennese Ball”: a formal ball with waltzes that was initially started in the 1970s by students returning from the now-closed Stanford in Vienna overseas program. It is now open to all students.
    “Full Moon on the Quad”: An annual event at Main Quad, where students gather to kiss one another starting at midnight. Typically organized by the Junior class cabinet, the festivities include live entertainment, such as music and dance performances.
    “Band Run”: An annual festivity at the beginning of the school year, where the band picks up freshmen from dorms across campus while stopping to perform at each location, culminating in a finale performance at Main Quad.
    “Mausoleum Party”: An annual Halloween Party at the Stanford Mausoleum, the final resting place of Leland Stanford Jr. and his parents. A 20-year tradition, the “Mausoleum Party” was on hiatus from 2002 to 2005 due to a lack of funding, but was revived in 2006. In 2008, it was hosted in Old Union rather than at the actual Mausoleum, because rain prohibited generators from being rented. In 2009, after fundraising efforts by the Junior Class Presidents and the ASSU Executive, the event was able to return to the Mausoleum despite facing budget cuts earlier in the year.
    Former campus traditions include the “Big Game bonfire” on Lake Lagunita (a seasonal lake usually dry in the fall), which was formally ended in 1997 because of the presence of endangered salamanders in the lake bed.

    Award laureates and scholars

    Stanford’s current community of scholars includes:

    19 Nobel Prize laureates (as of October 2020, 85 affiliates in total)
    171 members of the National Academy of Sciences
    109 members of National Academy of Engineering
    76 members of National Academy of Medicine
    288 members of the American Academy of Arts and Sciences
    19 recipients of the National Medal of Science
    1 recipient of the National Medal of Technology
    4 recipients of the National Humanities Medal
    49 members of American Philosophical Society
    56 fellows of the American Physics Society (since 1995)
    4 Pulitzer Prize winners
    31 MacArthur Fellows
    4 Wolf Foundation Prize winners
    2 ACL Lifetime Achievement Award winners
    14 AAAI fellows
    2 Presidential Medal of Freedom winners

    Stanford University Seal

  • richardmitnick 9:43 am on June 5, 2021 Permalink | Reply
    Tags: "Why Scientists Want to Solve an Underground Mystery about Where Microbes Live", , , , , Building a framework for forecasting the soil microbiome at sites across the US will improve the understanding of seasonal and interannual change., , It’s typical to see several hundred different types of fungi and bacteria in a single pinch of soil off the ground., Microbiology, phylogenetic scale-a system that classifies organisms based on evolutionary relatedness., , The more scientists learn the more they realize how important soil microbes are for agriculture; public health; and climate change., The soil under our feet is very much alive., Women in STEM-Jennifer Bhatnagar and Zoey Werbin   

    From Boston University (US) :Women in STEM-Jennifer Bhatnagar and Zoey Werbin “Why Scientists Want to Solve an Underground Mystery about Where Microbes Live” 

    From Boston University (US)

    May 7, 2021
    Jessica Colarossi

    Boston University researchers develop first-of-its-kind model to predict which species of soil organisms live in different environments, with huge implications for agriculture, climate change, and public health. Credit: Florian van Duyn on Unsplash.

    Though it might seem inanimate, the soil under our feet is very much alive. It’s filled with countless microorganisms actively breaking down organic matter, like fallen leaves and plants, and performing a host of other functions that maintain the natural balance of carbon and nutrients stored in the ground beneath us.

    “Soil is mostly microorganisms, both alive and dead,” says Jennifer Bhatnagar, soil microbiologist and Boston University College of Arts & Sciences assistant professor of biology. It’s typical to see several hundred different types of fungi and bacteria in a single pinch of soil off the ground, she says, making it one of the most diverse ecosystems that exist.

    Because there’s still so much unknown about soil organisms, until now scientists have not attempted to predict where certain species or groups of soil microbes live around the world. But having that knowledge about these organisms—too small to see with the naked eye—is key to better understanding the soil microbiome, which is made up of the communities of different microbes that live together.

    A team of BU biologists, including Bhatnagar, took on that challenge—and their research reveals, for the first time, that it is possible to accurately predict the abundance of different species of soil microbes in different parts of the world. The team recently published their findings in a new paper in Nature Ecology & Evolution.

    “If we know where organisms are on earth, and we know how they change through space and time due to different environmental forces, and something about what different species are doing, then we can much better predict how the function of these communities will change in terms of carbon and nutrient cycling,” Bhatnagar says. That kind of knowledge would have huge implications for agriculture, climate change, and public health.

    “The health of the soils is so tied to the soil microbes,” says Michael Dietze, senior author on the study and a BU College of Arts & Sciences professor of earth and environment. Dietze, Bhatnagar, and researchers from their labs joined forces to work on this project, which involved analyzing hundreds of soil samples collected by National Ecological Observatory Network (NEON) (US) research sites. Bhatnagar and her lab members brought to the team their soil expertise, while Dietze and his lab offered their unique ability to develop precise ecological forecasts and near-term environmental predictions.

    The team learned that microbe predictability increases as spatial area increases, so the bigger the piece of land their model makes forecasts about, the more likely the predictions about what types of microbes live there will be accurate.

    Dietze says the ability to accurately predict which microbes would likely be found in a given soil sample also increased as the researchers looked at organism groupings higher up on the phylogenetic scale, a system that classifies organisms based on evolutionary relatedness. On the smallest end of the scale, a “species” represents the finest level of classification; on the other end, a “phylum” makes up the largest and most diverse groupings of organisms. They were surprised to find that they were better able to predict the presence of a whole phylum, as opposed to individual species.

    After receiving the genomic data of the soil samples from NEON, the research team’s forecasting models take into account environmental factors specific to the place where the soil came from—what plants live there, the soil acidity (pH), temperature, climate, and many others. They found their model was best able to predict the presence of microorganisms based on their symbiotic relationship with local plant species. Mycorrhizal fungi, for example, is a very common soil microbe that about 90 percent of plant families associate with, including pines and oak trees in New England.

    In contrast, the team found it was more difficult to predict large groups of organisms based on their relationship with soil acidity. Despite knowing soil acidity levels, and what types of bacteria would typically like to live in that environment, their model couldn’t accurately predict the amount of bacteria that were actually present in the soil sample, Bhatnagar says. “That means there is something else beyond the relationship with [acidity], beyond the relationship with any other environmental factor that we typically measure in our ecosystems,” she says.

    Now, Dietze and Bhatnagar’s team are expanding their forecasts beyond predicting microbes based on only their location, to also include specific times of the year.

    “Building a framework for forecasting the soil microbiome at sites across the US will improve our understanding of seasonal and interannual change,” says Zoey Werbin, a PhD student working in Bhatnagar’s lab and an author on the paper. “This could help us anticipate how climate change could affect microbial processes like decomposition or nitrogen cycling.”

    With her dissertation project, Werbin hopes to answer fundamental questions about how and why the soil microbiome varies over time and space.

    “The more we learn the more we realize how important soil microbes are for agriculture; public health; and climate change. It’s really exciting to investigate how microscopic organisms can have such large-scale effects,” Werbin says. “We know certain factors, like temperature and moisture, affect microbial communities. But we don’t know how important those factors are compared to natural variability, or interactions between microbes. My PhD project will help identify the driving forces of the soil microbiome, as well as the biggest sources of uncertainty.”

    This work was funded by the National Science Foundation (US) and the Swiss National Science Foundation [Schweizerischer Nationalfonds zur Förderung der wissenschaftlichen Forschung] [Fonds national suisse de la recherche scientifique] (CH).

    See the full article here .


    Please help promote STEM in your local schools.

    Stem Education Coalition

    Boston University is a private research university in Boston, Massachusetts. The university is nonsectarian but has a historical affiliation with the United Methodist Church. It was founded in 1839 by Methodists with its original campus in Newbury, Vermont, before moving to Boston in 1867.

    The university now has more than 4,000 faculty members and nearly 34,000 students, and is one of Boston’s largest employers. It offers bachelor’s degrees, master’s degrees, doctorates, and medical, dental, business, and law degrees through 17 schools and colleges on three urban campuses. The main campus is situated along the Charles River in Boston’s Fenway-Kenmore and Allston neighborhoods, while the Boston University Medical Campus is located in Boston’s South End neighborhood. The Fenway campus houses the Wheelock College of Education and Human Development, formerly Wheelock College, which merged with BU in 2018.

    BU is a member of the Boston Consortium for Higher Education (US) and the Association of American Universities (US). It is classified among “R1: Doctoral Universities – Very High Research Activity”.

    Among its alumni and current or past faculty, the university counts eight Nobel Laureates, 23 Pulitzer Prize winners, 10 Rhodes Scholars, six Marshall Scholars, nine Academy Award winners, and several Emmy and Tony Award winners. BU also has MacArthur, Fulbright, and Truman Scholars, as well as American Academy of Arts and Sciences (US) and National Academy of Sciences (US) members, among its past and present graduates and faculty. In 1876, BU professor Alexander Graham Bell invented the telephone in a BU lab.

    The Boston University Terriers compete in the NCAA Division I. BU athletic teams compete in the Patriot League, and Hockey East conferences, and their mascot is Rhett the Boston Terrier. Boston University is well known for men’s hockey, in which it has won five national championships, most recently in 2009.


    In FY2016, the University reported in $368.9 million in sponsored research, comprising 1,896 awards to 722 faculty investigators. Funding sources included the National Science Foundation (US), the National Institutes of Health (US), the Department of Defense (US), the European Commission of the European Union, the Susan G. Komen Foundation (US), and the federal Health Resources and Services Administration (US). The University’s research enterprise encompasses dozens of fields, but its primary focus currently lies in seven areas: Data Science, Engineering Biology, Global Health, Infectious Diseases, Neuroscience, Photonics, and Urban Health.

    The University’s strategic plan calls for the removal of barriers between previously siloed departments, schools, and fields. The result has been an increasing emphasis by the University on interdisciplinary work and the creation of multidisciplinary centers such as the Rajen Kilachand Center for Integrated Life Sciences & Engineering, a $140 million, nine-story research facility that has brought together life scientists, engineers, and physicians from the Medical and Charles River Campuses; the Institute for Health Systems Innovation & Policy, a cross-campus initiative combining business, health law, medicine, and public policy; a neurophotonics center that combines photonics and neuroscience to study the brain; and the Software and Application Innovation Lab, where technologists work with colleagues in the arts and humanities and together develop digital research tools. The University also made a large investment in an emerging field, when it created a new university-wide academic unit called the Faculty of Computing & Data Sciences in 2019 and began construction of the nineteen-story Center for Computing & Data Sciences, slated to open in 2022.

    In 2003, the National Institute of Allergy and Infectious Diseases awarded Boston University a grant to build one of two National Biocontainment Laboratories. The National Emerging Infectious Diseases Laboratories (NEIDL) was created to study emerging infectious diseases that pose a significant threat to public health. NEIDL has biosafety level 2, 3, and 4 (BSL-2, BSL-3, and BSL-4, respectively) labs that enable researchers to work safely with the pathogens. BSL-4 labs are the highest level of biosafety labs and work with diseases with a high risk of aerosol transmission.

    The strategic plan also encouraged research collaborations with industry and government partners. In 2016, as part of a broadbased effort to solve the critical problem of antibiotic resistance, the US Department of Health & Human Services selected the Boston University School of Law (LAW)—and Kevin Outterson, a BU professor of law—to lead a $350 million trans-Atlantic public-private partnership called CARB-X to foster the preclinical development of new antibiotics and antimicrobial rapid diagnostics and vaccines.

    That same year, BU researcher Avrum Spira joined forces with Janssen Research & Development and its Disease Interception Accelerator group. Spira—a professor of medicine, pathology and laboratory medicine, and bioinformatics—has spent his career at BU pursuing a better, and earlier, way to diagnose pulmonary disorders and cancers, primarily using biomarkers and genomic testing. In 2015, under a $13.7 million Defense Department grant, Spira’s efforts to identify which members of the military will develop lung cancer and COPD caught the attention of Janssen, part Johnson & Johnson. They are investing $10.1 million to collaborate with Spira’s lab with the hope that his discoveries—and potential therapies—could then apply to the population at large.

    In its effort to increase diversity and inclusion, Boston University appointed Ibram X. Kendi in July 2020 as a history professor and the director and founder of its newly established Center for Antiracist Research. The university also appointed alumna Andrea Taylor as its first senior diversity officer.

  • richardmitnick 10:43 am on May 16, 2021 Permalink | Reply
    Tags: "New clues to ancient life from billion-year-old lake fossils", , , , , In April 2021 scientists led by Paul Strother of Boston College reported on the discovery of new microfossils in ancient Scottish lake sediments ., Microbiology, Newly discovered microscopic “ball” fossils – found in ancient lake sediments in Scotland – suggest that evolution from single-celled to multicellular organisms might have occurred in lakes., , The one-billion-year-old multicellular microfossils "Bicellum brasieri"., There are gaps or missing links in life’s timeline as it’s known to science., These fossils appear as tiny microscopic balls., These fossils are extremely tiny-measuring only 0.001 inches (0.03 mm) in diameter., University of Sheffield (UK)   

    From Boston College (US) and From University of Sheffield (UK) via EarthSky : “New clues to ancient life from billion-year-old lake fossils” 

    From Boston College (US)


    From University of Sheffield (UK)




    May 16, 2021
    Paul Scott Anderson

    We think of earthly life as evolving from the sea. But newly discovered microscopic “ball” fossils – found in ancient lake sediments in Scotland – suggest that evolution from single-celled to multicellular organisms might have occurred in lakes.

    Loch Torridan in Scotland’s northwest highlands. Loch is the Scottish word for lake. The newly discovered microfossils – Bicellum brasieri – were found in ancient sediments of this lake. Image via University of Sheffield (UK).

    The beginnings of life on Earth billions of years ago, from simple single-celled organisms to more complex multicellular ones, is a widely accepted fact in science. But there are gaps or missing links in life’s timeline as it’s known to science. In April 2021 scientists led by Paul Strother of Boston College reported on the discovery of new microfossils in ancient Scottish lake sediments that could help fill in the gap between the earliest single-celled life and multicellular life. These scientists say these microscopic fossils could be the oldest example of complex multicellular life in the evolutionary lineage leading to animals. They say the fossils are also significant because they come – not from ocean sediments – but from sediments of an ancient freshwater lake.

    The peer-reviewed findings were published in the journal Current Biology on April 13, 2021.

    The one-billion-year-old multicellular microfossils – Bicellum brasieri – were found in sediments that used to be at the bottom of Loch Torridan in Scotland’s northwest highlands. Co-author Charles Wellman of the University of Sheffield in the U.K. commented in a statement:

    “The origins of complex multicellularity and the origin of animals are considered two of the most important events in the history of life on Earth.

    Our discovery sheds new light on both of these.”

    Image of the newly discovered ancient microfossil Bicellum brasieri, via Paul Strother/ University of Sheffield.

    A specimen of Bicellum brasieri. Image via Paul Strother/ University of Sheffield.

    Another view of a Bicellum brasieri specimen, showing the elongated sausage-shaped cells in the outer layer. Image via Paul Strother/ Live Science.

    About Bicellum brasieri. Bicellum means “two-celled,” and brasieri is used to honor the late paleontologist and study co-author, Martin Brasier.

    These fossils appear as tiny microscopic balls, each containing two different kinds of cells. The cells inside the ball are round and tightly-packed with thin cell walls. The outer layer or surface of the balls, however, are composed of longer, sausage-shaped cells that have thicker cell walls.

    These fossils are clearly of multicelled organisms, the scientists say, albeit simple ones. But there’s an interesting puzzle. The fossils were found in ancient lake sediments, but most scientists think that multicellular life first began to appear in Earth’s primordial oceans.

    The fossils were found in nodules of phosphate minerals. According to lead author Paul Strother, those nodules were:

    “…Like little black lenses in rock strata, about one centimeter [0.4 inches] in thickness. We take those and slice them with a diamond saw and make thin sections out of them.”

    Those very thin sections can then be studied under a microscope.

    The researchers found multiple clumps of the Bicellum brasieri fossils, which all showed the same structure and organization regardless of their stage of development.

    These fossils are extremely tiny-measuring only 0.001 inches (0.03 mm) in diameter. But when examined under powerful microscopes, the researchers noticed that the two kinds of cells in the balls differed both in shape and how and where they were positioned within the balls. Why is that significant? As Strother told LiveScience.com:

    “That’s something that doesn’t exist in normal unicellular organisms. That amount of structural complexity is something that we normally associate with complex multicellularity.”

    This raises more questions. What type of organism is Bicellum brasieri? The scientists still don’t know for sure, but they don’t think it is a kind of algae, since the round cells don’t have rigid walls. Bicellum brasieri might instead have been a type of Holozoa, which includes both multicellular animals and single-celled organisms. Holozoa can include animals and their closest single-celled relatives, but it excludes fungi.

    Due to constant geological processes on our active planet, there aren’t a lot of fossil records left from the very earliest life on Earth. The oldest known fossils of microbes are about 3.5 billion years old. That’s fossils of the microorganisms themselves; other fossils associated with microbes are known to be up to 3.7 billion years old. These include sediment ripples on an ancient seafloor in Greenland and hematite tubes in volcanic rock in Quebec, Canada.

    The locations in the Scottish Highlands where the fossils were found. Image via Paul K. Strother et al./ Current Biology (CC BY 4.0).

    Scientists have thought that the earliest microscopic life forms originated in the oceans because that is where most ancient fossils have been found, in marine sediments, as opposed to sediments in freshwater lakes. Strother explained:

    “There aren’t that many lake deposits of this antiquity, so there’s a bias in the rock record toward a marine fossil record rather than a freshwater record.”

    But the discovery of Bicellum brasieri now throws a wrench into that hypothesis. It shows that the transition from single-celled microbes to multicellular ones could also have occurred in lakes, despite the fact that lakes are more greatly affected by changes in temperature and alkalinity. According to the researchers, those factors may even have helped evolution to proceed more quickly in such freshwater habitats.

    The findings show that the emergence of multicellular organisms may have occurred in more than one kind of aquatic environment, not just oceans as previously thought. That may also be good news for the Perseverance and Curiosity rovers on Mars, both of which are currently exploring sediments and rocks that used to be at the bottom of lakes a few billion years ago. Perseverance in particular is specifically searching for evidence of ancient microbial life. If life on Earth evolved in both oceans and lakes, could the same thing have happened on Mars?

    Outcrop of the Diabaig Shale along the north shore of Loch Torridon at the town of Lower Diabaig in Scotland, showing the locality where the new fossil, Bicellum brasieri was first collected. Image via Paul Strother.

    See the full article here.


    Please help promote STEM in your local schools.

    Stem Education Coalition

    University of Sheffield (UK) is a public research university in Sheffield, South Yorkshire, England. It received its royal charter in 1905 as successor to the University College of Sheffield, which was established in 1897 by the merger of Sheffield Medical School (founded in 1828), Firth College (1879) and Sheffield Technical School (1884).

    Sheffield is a multi-campus university predominantly over two campus areas: the Western Bank and the St George’s. The university is organised into five academic faculties composed of multiple departments. It had 20,005 undergraduate and 8,710 postgraduate students in 2016/17. The annual income of the institution for 2016–17 was £623.6 million of which £155.9 million was from research grants and contracts, with an expenditure of £633.0 million. Sheffield ranks among the top 10 of UK universities for research grant funding.

    Sheffield was placed 75th worldwide according to QS World University Rankings and 104th worldwide according to Times Higher Education World University Rankings. It was ranked 12th in the UK amongst multi-faculty institutions for the quality (GPA) of its research and for its Research Power in the 2014 Research Excellence Framework. In 2011, Sheffield was named ‘University of the Year’ in the Times Higher Education awards. The Times Higher Education Student Experience Survey 2014 ranked the University of Sheffield 1st for student experience, social life, university facilities and accommodation, among other categories.

    It is one of the original red brick universities, a member of the Russell Group of research-intensive universities, the Worldwide Universities Network, the N8 Group of the eight most research intensive universities in Northern England and the White Rose University Consortium. There are eight Nobel laureates affiliated with Sheffield and six of them are the alumni or former long-term staffs of the university.

    Boston College (US) is a private, Jesuit research university in Chestnut Hill, Massachusetts. Founded in 1863, the university has more than 9,300 full-time undergraduates and nearly 5,000 graduate students. Although Boston College is classified as an R1 research university, it still uses the word “college” in its name to reflect its historical position as a small liberal arts college. Its main campus is a historic district and features some of the earliest examples of collegiate gothic architecture in North America.

    Boston College offers bachelor’s degrees, master’s degrees, and doctoral degrees through its eight colleges and schools: Morrissey College of Arts & Sciences, Carroll School of Management, Lynch School of Education and Human Development, Connell School of Nursing, Graduate School of Social Work, Boston College Law School, Boston College School of Theology and Ministry, Woods College of Advancing Studies.

    Boston College athletic teams are the Eagles. Their colors are maroon and gold and their and mascot is Baldwin the Eagle. The Eagles compete in NCAA Division I as members of the Atlantic Coast Conference in all sports offered by the ACC. The men’s and women’s ice hockey teams compete in Hockey East. Boston College’s men’s ice hockey team has won five national championships.

    Alumni and affiliates of the university include governors, ambassadors, members of Congress, scholars, writers, medical researchers, Hollywood actors, and professional athletes. Boston College has graduated several Rhodes, Fulbright, and Goldwater scholars. Other notable alumni include a U.S. Speaker of the House, a U.S. Secretary of State, and chief executives of Fortune 500 companies.

    Schools and colleges

    As a research university, Boston College is made up of a total of eight constituent colleges and schools:[48]

    Morrissey College of Arts & Sciences
    Carroll School of Management
    Lynch School of Education and Human Development
    Connell School of Nursing
    Boston College School of Social Work
    Boston College Law School
    Boston College School of Theology and Ministry
    Woods College of Advancing Studies

    Research centers and institutes

    Boisi Center for Religion and American Public Life
    Business Institute
    Center for Asset Management
    Center for Child, Family, and Community Partnerships (CCFCP)
    Center for Christian-Jewish Learning
    Center for Corporate Citizenship (CCC)
    Center for East Europe, Russia, and Asia
    Center for Human Rights and International Justice
    Center for Ignatian Spirituality
    Center for International Higher Education
    Center for Investment and Research Management
    Center for Irish Programs Dublin
    Center for Nursing Research
    Center for Retirement Research
    Center for the Study of Home and Community Life
    Center for Study of Testing, Evaluation, and Educational Policy (CSTEEP)
    Center for Work and Family (CWF)
    Center on Aging & Work – Workplace Flexibility
    Center on Wealth and Philanthropy (CWP, formerly SWRI)
    Church in the 21st Century Center
    Clough Center for the Study of Constitutional Democracy
    EagleEyes Project
    Institute for Medieval Philosophy and Theology
    Institute of Religious Education and Pastoral Ministry (IREPM)
    Institute for Administrators in Catholic Higher Education
    Institute for Scientific Research
    Institute for the Study and Promotion of Race and Culture (ISPRC)
    International Study Center
    Irish Institute
    Jesuit Institute
    Lifelong Learning Institute
    Lonergan Institute
    Mathematics Institute
    Media Research and Action Project
    Presidential Scholars Program
    Sloan Work and Family Research Network
    Small Business Development Center
    Urban Ecology Institute
    Weston Observatory
    Winston Center for Leadership and Ethics
    Women’s Resource Center

  • richardmitnick 9:39 am on April 12, 2021 Permalink | Reply
    Tags: A group of microbes which feed off chemical reactions triggered by radioactivity have been at an evolutionary standstill for millions of years., , , , , Microbiology, , The scientists hypothesize the standstill evolution they discovered is due to the microbe’s powerful protections against mutation., These microbes inhabit water-filled cavities inside rocks in a completely independent ecosystem free from reliance on sunlight or any other organisms.   

    From Bigelow Laboratory for Ocean Sciences (US): “Microbe in Evolutionary Stasis for Millions of Years”: 

    From Bigelow Laboratory for Ocean Sciences (US)

    April 8, 2021

    Equipment for subsurface sampling of microbes in Death Valley, California. New research led by Bigelow Laboratory for Ocean Sciences has revealed that a group of microbes, Candidatus Desulforudis audaxviator, have been at an evolutionary standstill for millions of years. Credit: Duane Moser, Desert Research Institute

    It’s like something out of science fiction. Research led by Bigelow Laboratory for Ocean Sciences has revealed that a group of microbes which feed off chemical reactions triggered by radioactivity have been at an evolutionary standstill for millions of years. The discovery could have significant implications for biotechnology applications and scientific understanding of microbial evolution.

    “This discovery shows that we must be careful when making assumptions about the speed of evolution and how we interpret the tree of life,” said Eric Becraft, the lead author on the paper. “It is possible that some organisms go into an evolutionary full-sprint, while others slow to a crawl, challenging the establishment of reliable molecular timelines.”

    Becraft, now an assistant professor of biology at the University of Northern Alabama, completed the research as part of his postdoctoral work at Bigelow Laboratory and recently published it in the Nature publishing group’s ISME Journal.

    The microbe, Candidatus Desulforudis audaxviator, was first discovered in 2008 by a team of scientists, led by Tullis Onstott, a co-author on the new study. Found in a South African gold mine almost two miles beneath the Earth’s surface, the microbes acquire the energy they need from chemical reactions caused by the natural radioactive decay in minerals. They inhabit water-filled cavities inside rocks in a completely independent ecosystem free from reliance on sunlight or any other organisms.

    Because of their unique biology and isolation, the authors of the new study wanted to understand how the microbes evolved. They searched other environmental samples from deep underground and discovered Candidatus Desulforudis audaxviator in Siberia and California, as well as in several additional mines in South Africa. Since each environment was chemically different, these discoveries gave the researchers a unique opportunity to look for differences that have emerged between the populations over their millions of years of evolution.

    “We wanted to use that information to understand how they evolved and what kind of environmental conditions lead to what kind of genetic adaptations,” said Bigelow Laboratory Senior Research Scientist Ramunas Stepanauskas, the corresponding author on the paper and Becraft’s postdoctoral advisor. “We thought of the microbes as though they were inhabitants of isolated islands, like the finches that Darwin studied in the Galapagos.”

    Using advanced tools that allow scientists to read the genetic blueprints of individual cells, the researchers examined the genomes of 126 microbes obtained from three continents. Surprisingly, they all turned out to be almost identical.

    “It was shocking,” Stepanauskas said. “They had the same makeup, and so we started scratching our heads.”

    Scientists found no evidence that the microbes can travel long distances, survive on the surface, or live long in the presence of oxygen. So, once researchers determined that there was no possibility the samples were cross-contaminated during research, plausible explanations dwindled.

    “The best explanation we have at the moment is that these microbes did not change much since their physical locations separated during the breakup of supercontinent Pangaea, about 175 million years ago,” Stepanauskas said. “They appear to be living fossils from those days. That sounds quite crazy and goes against the contemporary understanding of microbial evolution.”

    What this means for the pace of microbial evolution, which often happens at a much more accelerated rate, is surprising. Many well-studied bacteria, such as E. coli, have been found to evolve in only a few years in response to environmental changes, such as exposure to antibiotics.

    Stepanauskas and his colleagues hypothesize the standstill evolution they discovered is due to the microbe’s powerful protections against mutation, which have essentially locked their genetic code. If the researchers are correct, this would be a rare feature with potentially valuable benefits.

    Microbial enzymes that create copies of DNA molecules, called DNA polymerases, are widely used in biotechnology. Enzymes with high fidelity, or the ability to recreate themselves with little differences between the copy and the original, are especially valuable.

    “There’s a high demand for DNA polymerases that don’t make many mistakes,” Stepanauskas said. “Such enzymes may be useful for DNA sequencing, diagnostic tests, and gene therapy.”

    Beyond potential applications, the results of this study could have far-reaching implications and change the way scientists think about microbial genetics and the pace of their evolution.

    “These findings are a powerful reminder that the various microbial branches we observe on the tree of life may differ vastly in the time since their last common ancestor,” Becraft said. “Understanding this is critical to understanding the history of life on Earth.”

    See the full article here.


    Please help promote STEM in your local schools.

    Stem Education Coalition

    Bigelow Laboratory for Ocean Sciences (US), founded in 1974, is an independent, non-profit oceanography research institute. The Laboratory’s research ranges from microbial oceanography to the large-scale biogeochemical processes that drive ocean ecosystems and health of the entire planet.

    The institute’s LEED Platinum laboratory is located on its research and education campus in East Boothbay, Maine. Bigelow Laboratory supports the work of about 100 scientists and staff. The majority of the institute’s funding comes from federal and state grants and contracts, philanthropic support, and licenses and contracts with the private sector.


    The Laboratory was established by Charles and Clarice Yentsch in 1974 as a private, non-profit research institution named for the oceanographer Henry Bryant Bigelow, founding director of the Woods Hole Oceanographic Institution (US). Bigelow’s extensive investigations in the early part of the twentieth century are recognized as the foundation of modern oceanography. His multi-year expeditions in the Gulf of Maine, where he collected water samples and data on phytoplankton, fish populations, and hydrography, established a new paradigm of intensive, ecologically-based oceanographic research in the United States and made this region one of the most thoroughly studied bodies of water, for its size, in the world.

    Since its founding, the Laboratory has attracted federal grants for research projects by winning competitive, peer reviewed awards from all of the principal federal research granting agencies. The Laboratory’s total operating revenue (including philanthropy) has grown to more than $10 million dollars a year. Federal research grants have supported most of the Laboratory’s research operations. Education and outreach programs rely on other sources of support, primarily contributions from individuals and private philanthropic foundations.

    In February 2018, Deborah Bronk became the president and CEO of Bigelow Laboratory. Prior to joining the Laboratory, Bronk was the Moses D. Nunnally Distinguished Professor of Marine Sciences and department chair at Virginia Institute of Marine Sciences. She previously served as division director for the National Science Foundation’s (US) Division of Ocean Science and as president of the Association for the Sciences of Limnology and Oceanography.

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